##fileformat=VCFv4.2 ##FILTER= ##DRAGENCommandLine= ##DRAGENVersion= ##FILTER= 200.0"> ##FILTER= 60.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0"> ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##GATKCommandLine.CombineVariants= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##reference=file:///media/majdi/Transcend/Tools_Majdi/FASTA-data/ucsc.hg19/ucsc.hg19.fa ##bcftools_viewVersion=1.2+htslib-1.2.1 ##bcftools_viewCommand=view -c 1 -s sample_74.variant35 sample.vcf #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample_74.variant35 chr1 13550 . G A 180.97 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=1259;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:378,60:438:99:217,0,8305:148,230,20,40 chr1 14653 . C T 145.02 DRAGENHardSNP AC=1;AF=0.574;AN=2;DP=565;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:9,5:14:99:104,0,216:7,2,4,1 chr1 14677 . G A 30.39 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=183;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:16,5:21:60:60,0,349:11,5,4,1 chr1 14907 . A G 1497.24 PASS AC=1;AF=0.5;AN=2;DP=11127;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-filterInvariant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:127,177:304:99:6962,0,4459:59,68,91,86 chr1 14930 . A G 2107.21 PASS AC=1;AF=0.5;AN=2;DP=11281;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-filterInvariant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:123,192:315:99:7485,0,4242:54,69,90,102 chr1 14933 . G A 190.39 PASS AC=1;AF=0.5;AN=2;DP=3262;set=filterInvariant-filterInvariant9-filterInvariant11-variant16-filterInvariant20-variant22-filterInvariant23-filterInvariant26-filterInvariant30-variant35-filterInvariant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:224,92:316:99:1480,0,7314:99,125,43,49 chr1 14976 . G A 148.8 PASS AC=1;AF=0.5;AN=2;DP=2513;set=filterInvariant-filterInvariant8-filterInvariant9-filterInvariant11-filterInvariant16-filterInvariant20-variant22-variant23-variant26-variant30-variant35-filterInvariant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:159,68:227:99:1223,0,3906:59,100,27,41 chr1 15053 . C T 67.9 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=91;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:40,8:48:99:106,0,1114:6,34,0,8 chr1 17385 . G A 238.68 PASS AC=1;AF=0.5;AN=2;DP=1589;set=variant2-variant4-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant13-filterInvariant16-variant18-filterInvariant19-filterInvariant20-variant21-variant23-filterInvariant24-variant26-filterInvariant27-filterInvariant30-variant33-filterInvariant35-filterInvariant38-filterInvariant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:73,12:85:67:67,0,1844:51,22,9,3 chr1 69270 . A G 32.29 DRAGENHardSNP AC=2;AF=1;AN=2;DP=30;FS=0;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:114,12,0:0,0,4,0 chr1 69511 . A G 2855.59 PASS AC=2;AF=0.938;AN=2;DP=5515;set=variant-variant2-variant3-variant4-variant7-variant8-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant22-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,167:168:99:4592,465,0:1,0,90,77 chr1 129285 . G A 34.73 DRAGENHardSNP AC=2;AF=0.708;AN=2;DP=85;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:84,12,0:0,0,2,2 chr1 137825 . G A 202.81 DRAGENHardSNP AC=1;AF=0.548;AN=2;DP=674;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:22,14:36:99:245,0,426:11,11,8,6 chr1 138593 . G T 33.74 DRAGENHardSNP AC=1;AF=0.591;AN=2;DP=155;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:16,8:24:99:107,0,343:8,8,5,3 chr1 139213 . A G 725.1 DRAGENHardSNP AC=1;AF=0.537;AN=2;DP=2258;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:80,34:114:99:1108,0,3941:38,42,17,17 chr1 139233 . C A 758.87 DRAGENHardSNP AC=1;AF=0.537;AN=2;DP=2756;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:96,39:135:99:1167,0,4257:49,47,21,18 chr1 662029 . G A 125.14 DRAGENHardSNP AC=2;AF=0.966;AN=2;DP=158;FS=0;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:80,9,0:0,0,0,3 chr1 663097 . G C 715.42 DRAGENHardSNP AC=2;AF=0.925;AN=2;DP=656;FS=0;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:373,45,0:0,0,8,7 chr1 664468 . G T 343.75 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=3234;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:71,22:93:99:266,0,1474:36,35,11,11 chr1 752894 . T C 40.18 PASS AC=2;AF=0.895;AN=2;DP=268;FS=0;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:475,33,0:0,0,0,11 chr1 761957 . A AT 455.32 PASS AC=2;AF=0.86;AN=2;DP=1319;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1411,105,0:0,0,35,0 chr1 762273 . G A 1157.09 PASS AC=2;AF=0.841;AN=2;DP=5222;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,115:115:99:3971,344,0:0,0,30,85 chr1 762589 . G C 556.46 PASS AC=2;AF=0.852;AN=2;DP=1967;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1930,129,0:0,0,15,28 chr1 762592 . C G 556.46 PASS AC=2;AF=0.852;AN=2;DP=1906;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1930,129,0:0,0,15,28 chr1 762601 . T C 556.46 PASS AC=2;AF=0.852;AN=2;DP=1732;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1738,117,0:0,0,14,24 chr1 762632 . T A 137.73 PASS AC=2;AF=0.852;AN=2;DP=1189;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:789,78,0:0,0,9,17 chr1 792263 . A G 276.79 PASS AC=2;AF=0.898;AN=2;DP=1405;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-filterInvariant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:896,87,0:0,0,17,12 chr1 792480 . C T 3383.51 PASS AC=2;AF=0.966;AN=2;DP=4598;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,98:98:99:2901,294,0:0,0,48,50 chr1 804115 . G A 411.85 PASS AC=2;AF=0.953;AN=2;DP=417;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-filterInvariant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:326,30,0:0,0,2,8 chr1 808631 . G A 199.97 PASS AC=2;AF=0.793;AN=2;DP=1594;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1671,138,0:0,0,37,9 chr1 808922 . G A 4382.01 PASS AC=2;AF=1;AN=2;DP=9647;FS=0;MQRankSum=-0.551;ReadPosRankSum=0.13;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,238:238:99:10728,731,0:0,0,140,98 chr1 808928 . C T 1200.84 PASS AC=2;AF=0.793;AN=2;DP=9235;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,243:243:99:10753,734,0:0,0,141,102 chr1 861008 . G C 590.34 PASS AC=2;AF=0.943;AN=2;DP=890;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:1016,90,0:0,0,21,9 chr1 861630 . G A 311.67 PASS AC=2;AF=0.75;AN=2;DP=451;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:616,54,0:0,0,5,13 chr1 866319 . G A 719.26 PASS AC=2;AF=1;AN=2;DP=1547;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,31:31:93:971,93,0:0,0,22,9 chr1 866511 . C CCCCT 484.32 PASS AC=2;AF=0.763;AN=2;DP=1003;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:7,33:40:17:725,17,0:6,1,3,30 chr1 871334 . G T 646.63 PASS AC=2;AF=0.784;AN=2;DP=1157;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1201,99,0:0,0,8,25 chr1 874950 . T TCCCTGGAGGACC 1520.32 PASS AC=1;AF=0.711;AN=2;DP=2245;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,31:64:99:1181,0,2059:12,21,10,21 chr1 876499 . A G 1882.55 PASS AC=2;AF=0.955;AN=2;DP=2368;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:2219,215,0:0,0,38,34 chr1 877715 . C G 143.34 PASS AC=2;AF=0.932;AN=2;DP=898;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:857,72,0:0,0,11,13 chr1 877831 . T C 439.32 PASS AC=2;AF=1;AN=2;DP=1128;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:741,69,0:0,0,8,15 chr1 878314 . G C 1492.74 PASS AC=1;AF=0.571;AN=2;DP=1448;MQ=60;set=variant8-variant10-variant12-variant14-variant25-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:134,126:260:99:3013,0,3096:65,69,61,65 chr1 879676 . G A 1408.37 PASS AC=2;AF=0.943;AN=2;DP=1667;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1293,102,0:0,0,6,28 chr1 879687 . T C 1236.05 PASS AC=2;AF=0.955;AN=2;DP=1367;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,31:31:93:1168,93,0:0,0,6,25 chr1 880238 . A G 3393.3 PASS AC=2;AF=0.955;AN=2;DP=4666;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,93:93:99:2916,278,0:0,0,45,48 chr1 881627 . G A 2994.94 PASS AC=2;AF=0.7;AN=2;DP=3979;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,115:116:99:3784,310,0:1,0,74,41 chr1 883625 . A G 4609.89 PASS AC=2;AF=1;AN=2;DP=6659;FS=0;MQRankSum=1.015;ReadPosRankSum=0.954;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,197:197:99:5774,590,0:0,0,95,102 chr1 884091 . C G,CACCCTGGTCCCCCTGGTCCCTTTGGCCCTGCACCTGGCTGG 5001.48 PASS AC=0,2;AF=0.019,0.923;AN=2;DP=3879;set=variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 2/2:146:99:1,0,43,102 chr1 886788 . G A 2211.72 PASS AC=2;AF=0.872;AN=2;DP=3233;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:2322,194,0:0,0,13,52 chr1 886817 . C T,CATTTT 2829.07 PASS AC=2,0;AF=0.852,0.102;AN=2;DP=2251;MQ=60;set=Intersection GT:DP:GQ:SB 1/1:45:99:0,0,9,36 chr1 887560 . A C 1452.03 PASS AC=2;AF=0.955;AN=2;DP=6243;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,169:169:99:5171,506,0:0,0,92,77 chr1 887801 . A G 4434.03 PASS AC=2;AF=0.966;AN=2;DP=8622;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,229:229:99:7559,686,0:0,0,138,91 chr1 888639 . T C 4516.36 PASS AC=2;AF=0.966;AN=2;DP=12259;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,340:340:99:14851,1050,0:0,0,175,165 chr1 888659 . T C 4816.6 PASS AC=2;AF=0.966;AN=2;DP=12310;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,334:334:99:14304,998,0:0,0,160,174 chr1 889158 . G C 373.04 PASS AC=2;AF=0.955;AN=2;DP=1550;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1625,111,0:0,0,28,9 chr1 889159 . A C 373.04 PASS AC=2;AF=0.955;AN=2;DP=1561;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1625,111,0:0,0,28,9 chr1 889638 . G C 595.76 PASS AC=2;AF=0.943;AN=2;DP=1606;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1685,135,0:0,0,7,38 chr1 892745 . G A 1918.45 PASS AC=2;AF=0.966;AN=2;DP=3748;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,96:96:99:2703,286,0:0,0,40,56 chr1 894573 . G A 2989.22 PASS AC=2;AF=0.86;AN=2;DP=10960;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,293:293:99:9021,876,0:0,0,119,174 chr1 897325 . G C 2862.26 PASS AC=2;AF=0.92;AN=2;DP=14802;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,398:398:99:11417,1191,0:0,0,174,224 chr1 897564 . T C 2909.93 PASS AC=2;AF=0.932;AN=2;DP=11047;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,308:308:99:10127,920,0:0,0,147,161 chr1 898153 . C A 1942.89 PASS AC=1;AF=0.5;AN=2;DP=156;FS=7.109;FractionInformativeReads=1;MQ=60;MQRankSum=-0.446;QD=12.45;ReadPosRankSum=1.584;SOR=0.355;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:72,84:156:99:1971,0,1857:47,25,46,38 chr1 898323 . T C 4219.65 PASS AC=2;AF=0.977;AN=2;DP=5091;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,162:162:99:5406,485,0:0,0,81,81 chr1 900285 . C T 474.01 PASS AC=2;AF=0.92;AN=2;DP=2618;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,67:67:99:3018,208,0:0,0,48,19 chr1 900286 . A G 1388.37 PASS AC=2;AF=0.955;AN=2;DP=2675;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,69:69:99:3018,208,0:0,0,48,21 chr1 900717 . CTTAT C 1579.23 PASS AC=2;AF=0.706;AN=2;DP=914;MQ=60;set=variant2-variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,31:31:97:1412,97,0:0,0,9,22 chr1 900730 . G A 310.68 PASS AC=2;AF=0.86;AN=2;DP=1053;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,32:32:99:1481,102,0:0,0,10,22 chr1 900972 . T G 2315.01 PASS AC=2;AF=0.955;AN=2;DP=3339;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:2307,231,0:0,0,40,37 chr1 901023 . T C 1702.94 PASS AC=2;AF=0.943;AN=2;DP=2741;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:2150,216,0:0,0,33,39 chr1 909073 . C T 423.71 PASS AC=2;AF=0.65;AN=2;DP=1238;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant22-variant25-variant26-variant28-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1491,120,0:0,0,7,33 chr1 909238 . G C 62.99 PASS AC=2;AF=0.782;AN=2;DP=1350;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1116,114,0:0,0,23,15 chr1 909768 . A G 6433.3 PASS AC=2;AF=1;AN=2;DP=9051;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,234:234:99:7082,699,0:0,0,109,125 chr1 910438 . A G 1028.88 PASS AC=2;AF=0.932;AN=2;DP=2341;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:2012,180,0:0,0,21,39 chr1 910903 . T C 1448.49 PASS AC=2;AF=0.953;AN=2;DP=2492;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:2380,204,0:0,0,35,33 chr1 911595 . A G 1888.2 PASS AC=2;AF=0.782;AN=2;DP=6986;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,189:189:99:5884,567,0:0,0,87,102 chr1 912049 . T C 213.23 PASS AC=2;AF=0.71;AN=2;DP=1203;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1208,108,0:0,0,9,27 chr1 914192 . G C 783.75 PASS AC=2;AF=0.953;AN=2;DP=2098;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,64:64:99:2108,192,0:0,0,42,22 chr1 914250 . A C 1142.99 PASS AC=1;AF=0.5;AN=2;DP=105;FS=3.739;FractionInformativeReads=1;MQ=60;MQRankSum=0.927;QD=10.89;ReadPosRankSum=-0.061;SOR=1.075;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:59,46:105:99:1171,0,1499:35,24,31,15 chr1 914333 . C G 1672.94 PASS AC=2;AF=0.712;AN=2;DP=4428;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,205:205:99:6135,614,0:0,0,118,87 chr1 914852 . G C 2797.3 PASS AC=2;AF=0.712;AN=2;DP=6985;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,248:248:99:10985,755,0:0,0,132,116 chr1 914876 . T C 8511.63 PASS AC=2;AF=0.953;AN=2;DP=10722;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,291:291:99:12295,881,0:0,0,154,137 chr1 914940 . T C 3310.69 PASS AC=2;AF=0.712;AN=2;DP=9728;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,349:349:99:10380,1046,0:0,0,181,168 chr1 915227 . A G 2530.8 PASS AC=2;AF=0.953;AN=2;DP=6830;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,182:182:99:5821,545,0:0,0,104,78 chr1 916549 . A G 815.56 PASS AC=2;AF=0.817;AN=2;DP=3721;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,86:86:99:2824,258,0:0,0,33,53 chr1 935222 . C A 762.28 PASS AC=2;AF=0.682;AN=2;DP=2685;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant25-variant26-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,99:99:99:3011,292,0:0,0,33,66 chr1 935459 . A G 693.98 PASS AC=2;AF=0.738;AN=2;DP=1591;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,61:61:99:1803,183,0:0,0,33,28 chr1 935492 . G T 799.7 PASS AC=2;AF=0.738;AN=2;DP=1755;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:2036,214,0:0,0,39,33 chr1 948692 . G A 732.73 PASS AC=2;AF=0.929;AN=2;DP=881;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:634,51,0:0,0,13,4 chr1 948846 . T TA 4513.25 PASS AC=2;AF=0.93;AN=2;DP=4122;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,90:90:99:4089,277,0:0,0,53,37 chr1 948870 . C G 4658.54 PASS AC=2;AF=0.94;AN=2;DP=4725;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,113:113:99:4680,339,0:0,0,64,49 chr1 948921 . T C 4151.07 PASS AC=2;AF=0.94;AN=2;DP=5417;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,142:142:99:4272,423,0:0,0,72,70 chr1 949654 . A G 6919.18 PASS AC=2;AF=0.929;AN=2;DP=12519;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,348:349:99:10917,1035,0:1,0,171,177 chr1 949925 . C T 1683.14 PASS AC=2;AF=0.94;AN=2;DP=1781;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:1572,143,0:0,0,15,33 chr1 976514 . C A 552.42 PASS AC=2;AF=0.908;AN=2;DP=834;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,19:19:56:647,56,0:0,0,18,1 chr1 977330 . T C 1812.74 PASS AC=2;AF=0.907;AN=2;DP=3375;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,109:109:99:3393,327,0:0,0,66,43 chr1 977570 . G A 3452 PASS AC=2;AF=0.872;AN=2;DP=3594;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,95:95:99:2966,284,0:0,0,34,61 chr1 978603 . CCT C 1953.61 PASS AC=2;AF=0.625;AN=2;DP=5268;MQ=60;set=variant-variant2-variant5-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:2,196:198:99:8594,495,0:2,0,133,63 chr1 980460 . G A 1079.07 PASS AC=2;AF=0.919;AN=2;DP=1636;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1016,102,0:0,0,20,14 chr1 981087 . A G 10819.3 PASS AC=2;AF=0.895;AN=2;DP=16227;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,421:421:99:13093,1261,0:0,0,214,207 chr1 981931 . A G 3749.51 PASS AC=2;AF=0.869;AN=2;DP=5620;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,142:142:99:5328,426,0:0,0,73,69 chr1 982941 . T C 7668.35 PASS AC=2;AF=0.86;AN=2;DP=11826;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,324:324:99:9771,969,0:0,0,170,154 chr1 982994 . T C 7388.93 PASS AC=2;AF=0.86;AN=2;DP=11974;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,293:293:99:9378,877,0:0,0,136,157 chr1 984147 . CAAAAAAAAAAA C,CAAAAAAAAAA,CAAAAAA 457.58 PASS AC=2,0,0;AF=0.554,0.041,0.014;AN=2;DP=769;MQ=60;set=variant-variant2-filterInvariant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:35:99:0,0,18,17 chr1 984171 . CAG C 496.56 PASS AC=2;AF=0.618;AN=2;DP=874;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1725,118,0:0,0,22,17 chr1 984302 . T C 572.85 PASS AC=2;AF=0.614;AN=2;DP=1379;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1288,132,0:0,0,23,21 chr1 985266 . C T 1809.38 PASS AC=2;AF=0.6;AN=2;DP=7784;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,265:265:99:7827,792,0:0,0,148,117 chr1 985446 . G T 777.49 PASS AC=2;AF=0.611;AN=2;DP=699;MQ=60;set=variant3-variant5-variant9-variant11-variant12-variant13-variant15-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:2,41:43:65:1465,65,0:0,2,11,30 chr1 985449 . G A 473.22 PASS AC=2;AF=0.672;AN=2;DP=707;MQ=60;set=variant3-variant5-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:2,37:39:62:1429,62,0:0,2,12,25 chr1 986443 . C T 2871.26 PASS AC=2;AF=0.857;AN=2;DP=5823;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,155:155:99:4898,463,0:0,0,73,82 chr1 987200 . C T 3285.53 PASS AC=2;AF=0.857;AN=2;DP=4407;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,108:108:99:3866,323,0:0,0,63,45 chr1 988932 . G C 2443.4 PASS AC=2;AF=0.857;AN=2;DP=2819;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:2301,225,0:0,0,28,47 chr1 990280 . C T 868.79 PASS AC=2;AF=0.671;AN=2;DP=2088;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:2253,230,0:0,0,43,34 chr1 990517 . C T 4780.66 PASS AC=2;AF=0.919;AN=2;DP=6138;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,174:174:99:5071,520,0:0,0,85,89 chr1 990773 . C T 2732.49 PASS AC=2;AF=0.905;AN=2;DP=4033;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,103:103:99:3047,307,0:0,0,52,51 chr1 990806 . G A 2966.61 PASS AC=2;AF=0.905;AN=2;DP=4009;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,111:111:99:3458,332,0:0,0,55,56 chr1 990984 . G A 4622.06 PASS AC=2;AF=0.919;AN=2;DP=6560;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,175:175:99:5072,523,0:0,0,82,93 chr1 1007203 . A G 1905.14 PASS AC=2;AF=0.841;AN=2;DP=1876;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1802,138,0:0,0,40,6 chr1 1007432 . G A 2492.6 PASS AC=2;AF=0.635;AN=2;DP=8614;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,278:279:99:8182,805,0:1,0,131,147 chr1 1017170 . C G 247.35 PASS AC=2;AF=0.657;AN=2;DP=1093;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1564,159,0:0,0,30,23 chr1 1017197 . C T 440.11 PASS AC=2;AF=0.643;AN=2;DP=1551;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:2172,228,0:0,0,43,33 chr1 1017341 . G T 3132.43 PASS AC=2;AF=0.838;AN=2;DP=3788;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,108:108:99:3087,323,0:0,0,55,53 chr1 1018021 . G A 2542.65 PASS AC=1;AF=0.5;AN=2;DP=549;FractionInformativeReads=1;MQ=60;set=variant12-variant35 GT:AD:DP:GQ:PL:SB 0/1:180,128:308:99:2966,0,4375:99,81,70,58 chr1 1018144 . T C 3254.98 PASS AC=2;AF=0.643;AN=2;DP=9092;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,294:294:99:8945,880,0:0,0,136,158 chr1 1019175 . C G 2185.37 PASS AC=2;AF=0.838;AN=2;DP=2769;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:3237,217,0:0,0,46,26 chr1 1019180 . T C 703.91 PASS AC=2;AF=0.622;AN=2;DP=2623;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,74:74:99:3352,226,0:0,0,49,25 chr1 1020406 . T C 296.28 PASS AC=2;AF=0.875;AN=2;DP=688;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:564,45,0:0,0,12,3 chr1 1021415 . A G 1461.02 PASS AC=2;AF=0.885;AN=2;DP=2498;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,97:97:99:3064,291,0:0,0,31,66 chr1 1023114 . G A 802.91 PASS AC=1;AF=0.5;AN=2;DP=189;MQ=60;set=variant12-variant35 GT:AD:DP:GQ:PL:SB 0/1:54,59:113:99:1453,0,1218:22,32,23,36 chr1 1026707 . C A 1062.94 PASS AC=1;AF=0.645;AN=2;DP=4380;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:79,88:167:99:1989,0,1773:44,35,55,33 chr1 1026801 . T A 2434.16 PASS AC=1;AF=0.686;AN=2;DP=6007;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:100,116:216:99:2812,0,2391:45,55,56,60 chr1 1158631 . A G 3973.15 PASS AC=2;AF=0.869;AN=2;DP=5952;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,207:207:99:6108,617,0:0,0,118,89 chr1 1190956 . C T 717.38 PASS AC=1;AF=0.5;AN=2;DP=37;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.541;QD=19.39;ReadPosRankSum=-0.201;SOR=0.616;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:15,22:37:99:746,0,453:3,12,5,17 chr1 1196863 . T C 680.56 PASS AC=2;AF=1;AN=2;DP=1591;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1392,126,0:0,0,12,30 chr1 1217362 . G A 206.73 PASS AC=1;AF=0.5;AN=2;DP=15;FS=2.363;FractionInformativeReads=1;MQ=60;MQRankSum=0.766;QD=13.78;ReadPosRankSum=1.591;SOR=0.148;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:6,9:15:99:235,0,181:5,1,5,4 chr1 1222690 . C T 1228.62 PASS AC=1;AF=0.5;AN=2;DP=479;MQ=60;set=variant5-variant14-variant21-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:64,74:138:99:2152,0,1764:24,40,25,49 chr1 1229111 . A ACGCCCCTGCCCTGGAGGCCC,ACGACCCTGCCCTGGAGGCCC 596.42 PASS AC=2,0;AF=0.929,0.014;AN=2;DP=1886;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant43 GT:DP:GQ:SB 1/1:16:59:0,0,7,9 chr1 1229680 . G T 6334.85 PASS AC=2;AF=0.977;AN=2;DP=8725;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,266:267:99:8139,785,0:0,1,123,143 chr1 1233254 . T C 1438.24 PASS AC=1;AF=0.5;AN=2;DP=161;FS=0.618;FractionInformativeReads=1;MQ=60;MQRankSum=0.338;QD=8.93;ReadPosRankSum=-1.448;SOR=0.761;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:104,57:161:99:1466,0,2832:62,42,35,22 chr1 1237604 . T C 106.77 PASS AC=2;AF=0.977;AN=2;DP=522;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:417,30,0:0,0,4,6 chr1 1239339 . T G 3655.98 PASS AC=2;AF=0.932;AN=2;DP=4131;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,135:135:99:4900,405,0:0,0,107,28 chr1 1242707 . A G 1082.04 PASS AC=2;AF=0.886;AN=2;DP=3710;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,66:66:99:2174,196,0:0,0,21,45 chr1 1243896 . C T 151.77 PASS AC=2;AF=0.9;AN=2;DP=334;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:74:873,74,0:0,0,22,3 chr1 1243929 . G T 139.03 PASS AC=1;AF=0.868;AN=2;DP=385;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,14:19:32:529,0,32:3,2,13,1 chr1 1245368 . G A 1846.94 PASS AC=2;AF=0.814;AN=2;DP=2804;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,63:63:99:2239,188,0:0,0,12,51 chr1 1246004 . A G 4796.48 PASS AC=2;AF=1;AN=2;DP=6127;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,159:159:99:5083,476,0:0,0,92,67 chr1 1246256 . CGGCTCTGGGTCACAGGT C 2668.53 PASS AC=1;AF=0.5;AN=2;DP=1127;set=variant5-variant14-variant21-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:104,96:200:99:2394,0,5883:49,55,45,51 chr1 1247494 . T C 1685.79 PASS AC=2;AF=0.837;AN=2;DP=3035;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,69:69:99:2318,207,0:0,0,29,40 chr1 1247578 . T TGGGGGGGGGG,TGGGGG,TGGGG,TGG,TGGGGGGGGG 263.17 PASS AC=0,0,2,0,0;AF=0.032,0.21,0.403,0.161,0.016;AN=2;DP=690;set=variant-variant4-variant5-variant6-variant7-variant9-variant10-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 3/3:10:29:0,0,10,0 chr1 1249187 . G A 9794.83 PASS AC=2;AF=0.814;AN=2;DP=15887;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,422:422:99:12960,1264,0:0,0,199,223 chr1 1254136 . G A 1474.25 PASS AC=2;AF=0.92;AN=2;DP=2435;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,31:31:93:1098,93,0:0,0,25,6 chr1 1254436 . A G 6032.9 PASS AC=2;AF=1;AN=2;DP=7323;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,200:200:99:8952,611,0:0,0,98,102 chr1 1254443 . G A 6097.61 PASS AC=2;AF=0.909;AN=2;DP=7517;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,203:203:99:9004,617,0:0,0,101,102 chr1 1254841 . C G 3017.72 PASS AC=2;AF=0.909;AN=2;DP=6951;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,160:160:99:5070,480,0:0,0,72,88 chr1 1257282 . A C 1386.68 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=13223;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:229,105:334:99:2558,0,4403:35,194,103,2 chr1 1257286 . A C 934.06 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=12942;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:231,112:343:99:1960,0,3943:38,193,103,9 chr1 1257289 . T C 1012.93 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=12171;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:253,84:337:99:1969,0,7498:46,207,83,1 chr1 1257295 . T C 345.53 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=3544;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:279,59:338:99:188,0,10580:59,220,59,0 chr1 1260168 . C A 419.87 PASS AC=2;AF=0.919;AN=2;DP=754;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:35:264,35,0:0,0,9,4 chr1 1262591 . C T 5793.43 PASS AC=2;AF=0.92;AN=2;DP=11197;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,321:321:99:9039,957,0:0,0,189,132 chr1 1262966 . C T 5368.34 PASS AC=2;AF=0.92;AN=2;DP=8392;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,270:270:99:8153,805,0:0,0,149,121 chr1 1263144 . G A 5057.15 PASS AC=2;AF=0.943;AN=2;DP=8619;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,214:214:99:6225,635,0:0,0,98,116 chr1 1263362 . G A 5152.24 PASS AC=2;AF=0.919;AN=2;DP=7147;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,199:199:99:6155,593,0:0,0,106,93 chr1 1263457 . T C 6336.73 PASS AC=2;AF=1;AN=2;DP=8452;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,249:249:99:7617,746,0:0,0,126,123 chr1 1263998 . C G 750.3 PASS AC=1;AF=0.5;AN=2;DP=92;FS=0.804;FractionInformativeReads=1;MQ=60;MQRankSum=0.412;QD=8.16;ReadPosRankSum=-0.188;SOR=0.745;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:56,36:92:99:779,0,1561:29,27,17,19 chr1 1268847 . T G 6254.9 PASS AC=2;AF=1;AN=2;DP=13507;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,314:314:99:9612,940,0:0,0,156,158 chr1 1269554 . T C 7467.9 PASS AC=2;AF=1;AN=2;DP=11872;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,305:305:99:9531,913,0:0,0,167,138 chr1 1270329 . A G 3230.16 PASS AC=2;AF=1;AN=2;DP=3749;FS=0;MQ=60;MQRankSum=1.347;ReadPosRankSum=1.572;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,110:110:99:3567,330,0:0,0,65,45 chr1 1270359 . T C 3083.73 PASS AC=2;AF=1;AN=2;DP=3908;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,113:113:99:3775,338,0:0,0,73,40 chr1 1271175 . A G 1988.59 PASS AC=2;AF=1;AN=2;DP=2459;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,66:66:99:2021,198,0:0,0,30,36 chr1 1273116 . A G 5293.62 PASS AC=2;AF=0.932;AN=2;DP=8387;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,265:265:99:7398,792,0:0,0,122,143 chr1 1273278 . A G 827.3 PASS AC=2;AF=0.875;AN=2;DP=1356;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:1288,96,0:0,0,23,9 chr1 1273614 . T C 326.52 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=1188;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:58,26:84:99:472,0,5728:8,50,26,0 chr1 1273622 . G C 292.2 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=1946;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:56,25:81:99:465,0,6194:9,47,25,0 chr1 1273625 . CTGAAG C 261.13 PASS AC=1;AF=0.5;AN=2;DP=1435;MQ=60;set=variant2-variant3-variant4-variant12-filterInvariant14-variant16-variant17-filterInvariant21-variant25-variant29-variant35-variant36-variant38-variant39-filterInvariant41 GT:AD:DP:GQ:PL:SB 0/1:64,25:89:99:437,0,6813:14,50,25,0 chr1 1275252 . G A 1518.99 PASS AC=1;AF=0.5;AN=2;DP=108;FS=3.976;FractionInformativeReads=0.981;MQ=59.98;MQRankSum=-1.457;QD=14.06;ReadPosRankSum=2.685;SOR=1.182;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:61,45:106:99:1547,0,2114:22,39,12,33 chr1 1275264 . A G,ACAGCCGCATGTCCCCCAGCAGCCCCCACAGACCCACCCG 2324.29 PASS AC=1,1;AF=0.056,0.833;AN=2;DP=501;set=variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/2:53:99:0,0,9,44 chr1 1276973 . G GACAC 1592.74 PASS AC=2;AF=1;AN=2;DP=5299;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,126:126:99:5839,396,0:0,0,83,43 chr1 1277533 . T C 3970.84 PASS AC=2;AF=1;AN=2;DP=5089;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,130:130:99:3968,389,0:0,0,52,78 chr1 1278237 . T C 1888.86 PASS AC=2;AF=1;AN=2;DP=2884;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:2498,225,0:0,0,23,52 chr1 1284490 . G A 2303.77 PASS AC=2;AF=0.943;AN=2;DP=3211;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,93:93:99:2870,277,0:0,0,26,67 chr1 1288345 . A G 2145.3 PASS AC=2;AF=1;AN=2;DP=2832;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:2316,228,0:0,0,39,37 chr1 1288471 . C T 4023.57 PASS AC=2;AF=0.932;AN=2;DP=5852;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,121:122:99:3635,353,0:0,1,71,50 chr1 1288583 . C G 5048.79 PASS AC=2;AF=0.955;AN=2;DP=8846;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,232:232:99:7098,693,0:0,0,133,99 chr1 1288823 . A G 1872.67 PASS AC=2;AF=0.943;AN=2;DP=2808;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2275,209,0:0,0,29,41 chr1 1289367 . CTG C 5486.53 PASS AC=2;AF=0.955;AN=2;DP=6386;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,130:130:99:5850,391,0:0,0,67,63 chr1 1289911 . G A 3232.35 PASS AC=2;AF=0.955;AN=2;DP=4335;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,106:107:99:3364,306,0:0,1,23,83 chr1 1291159 . GA G 367.86 PASS AC=2;AF=1;AN=2;DP=368;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:289,24,0:0,0,4,4 chr1 1293764 . G C 3070.36 PASS AC=2;AF=0.849;AN=2;DP=3582;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,105:105:99:3108,314,0:0,0,61,44 chr1 1296691 . C G 4222.45 PASS AC=2;AF=1;AN=2;DP=9751;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,310:310:99:9206,929,0:0,0,149,161 chr1 1296818 . C G 5665.68 PASS AC=2;AF=1;AN=2;DP=7155;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,218:218:99:6669,652,0:0,0,116,102 chr1 1297059 . G A 2773.48 PASS AC=2;AF=0.886;AN=2;DP=4188;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,101:102:99:3090,295,0:0,1,47,54 chr1 1297213 . G C 1020.73 PASS AC=2;AF=0.953;AN=2;DP=1278;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,31:31:93:1375,93,0:0,0,7,24 chr1 1297216 . A G 1020.73 PASS AC=2;AF=0.977;AN=2;DP=1229;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,30:30:93:1375,93,0:0,0,6,24 chr1 1308982 . A G 419.64 PASS AC=2;AF=1;AN=2;DP=754;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:763,60,0:0,0,15,5 chr1 1310074 . C G 4492.16 PASS AC=2;AF=0.953;AN=2;DP=7252;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,196:196:99:5913,588,0:0,0,97,99 chr1 1310668 . A C 4234.61 PASS AC=2;AF=0.953;AN=2;DP=6175;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,147:147:99:4782,441,0:0,0,82,65 chr1 1310924 . T C 1241.86 PASS AC=2;AF=1;AN=2;DP=1794;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1830,153,0:0,0,9,42 chr1 1310975 . C T 481.88 PASS AC=2;AF=0.953;AN=2;DP=650;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:763,57,0:0,0,1,18 chr1 1323078 . A G 1444.77 PASS AC=2;AF=0.849;AN=2;DP=2565;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,67:68:99:2123,163,0:1,0,30,37 chr1 1323143 . CCT C 1128.68 PASS AC=2;AF=0.849;AN=2;DP=1925;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:2465,166,0:0,0,28,27 chr1 1323945 . GTC G,GTCTC 536.31 PASS AC=2,0;AF=0.795,0.045;AN=2;DP=2179;MQ=60;set=Intersection GT:DP:GQ:SB 1/1:27:80:0,0,12,15 chr1 1323963 . C A 333.76 PASS AC=1;AF=0.5;AN=2;DP=171;MQ=60;set=variant2-variant20-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:15,13:28:99:257,0,352:6,9,7,6 chr1 1325493 . CAAA CAA,CA,CAAAA,C 36.64 PASS AC=2,0,0,0;AF=0.2,0.25,0.05,0.05;AN=2;DP=95;MQ=60;set=variant2-variant7-variant9-variant12-variant13-variant22-variant34-variant35-variant42-variant44 GT:DP:GQ:SB 1/1:11:11:1,0,9,1 chr1 1334475 . G C 3282.78 PASS AC=1;AF=0.5;AN=2;DP=1378;MQ=60;set=variant2-variant13-variant20-variant26-variant30-variant35 GT:AD:DP:GQ:PL:SB 0/1:145,126:271:99:3041,0,3515:77,68,70,56 chr1 1342612 . G C 2414.7 PASS AC=1;AF=0.5;AN=2;DP=2560;MQ=60;set=variant5-variant14-variant15-variant21-variant23-variant25-variant27-variant28-variant33-variant34-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:96,97:193:99:2447,0,2412:42,54,37,60 chr1 1387667 . C G 14727.4 PASS AC=2;AF=1;AN=2;DP=24153;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,682:682:99:20030,2042,0:0,0,350,332 chr1 1395449 . ATTT ATT,AT,ATTTT,A 36.35 PASS AC=1,0,0,0;AF=0.379,0.061,0.045,0.03;AN=2;DP=1249;set=filterInvariant-variant2-filterInvariant3-variant5-variant7-variant8-filterInvariant9-variant10-variant11-filterInvariant12-variant13-variant14-filterInvariant15-variant16-variant19-filterInvariant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant32-variant33-variant34-filterInvariant35-variant36-variant39-variant40-variant41-variant42-variant44 GT:DP:GQ:SB 0/1:30:69:6,15,4,5 chr1 1417696 . C G 195.72 PASS AC=2;AF=0.756;AN=2;DP=3051;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,90:90:99:3165,270,0:0,0,48,42 chr1 1420637 . C T 1730.46 PASS AC=1;AF=0.5;AN=2;DP=1184;set=variant5-variant14-variant21-variant35-variant37-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:92,95:187:99:2217,0,2206:37,55,39,56 chr1 1420704 . C T 1016.06 PASS AC=1;AF=0.5;AN=2;DP=292;FractionInformativeReads=1;set=variant20-variant26-variant30-variant35 GT:AD:DP:GQ:PL:SB 0/1:45,39:84:99:1050,0,1212:13,32,9,30 chr1 1451208 . G A 1513.79 PASS AC=1;AF=0.5;AN=2;DP=825;set=variant2-variant20-variant26-variant30-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:61,75:136:99:2329,0,1783:49,12,64,11 chr1 1460793 . CTT CT,CTTT,C 116.63 PASS AC=1,0,0;AF=0.37,0.111,0.019;AN=2;DP=1659;set=filterInvariant-variant3-variant4-variant5-filterInvariant6-variant7-variant8-variant13-variant15-filterInvariant17-variant18-variant19-filterInvariant21-variant22-filterInvariant23-variant24-filterInvariant25-filterInvariant31-filterInvariant33-filterInvariant35-variant36-variant37-filterInvariant39-filterInvariant40-variant42-variant43-filterInvariant44 GT:DP:GQ:SB 0/1:37:99:7,18,2,10 chr1 1469546 . G A 786.13 PASS AC=2;AF=0.767;AN=2;DP=5039;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,203:203:99:6302,601,0:0,0,117,86 chr1 1470120 . G A 697.09 PASS AC=1;AF=0.5;AN=2;DP=60;FS=1.028;FractionInformativeReads=1;MQ=60;MQRankSum=1.338;QD=11.62;ReadPosRankSum=-2.269;SOR=0.996;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:30,30:60:99:725,0,673:12,18,10,20 chr1 1477244 . T C 1477.82 PASS AC=1;AF=0.577;AN=2;DP=2180;MQ=60;set=variant4-variant6-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant33-variant34-variant35-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,47:92:99:1269,0,1172:25,20,30,17 chr1 1479333 . A G 808.99 PASS AC=1;AF=0.577;AN=2;DP=2175;MQ=60;set=variant4-variant6-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant33-variant34-variant35-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,45:97:99:996,0,1229:26,26,23,22 chr1 1480653 . G C 32.02 PASS AC=1;AF=0.5;AN=2;DP=1448;MQ=60;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant12-filterInvariant16-variant18-filterInvariant22-filterInvariant31-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant39-filterInvariant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,29:90:99:504,0,4555:7,54,29,0 chr1 1480659 . G C 425.12 PASS AC=1;AF=0.5;AN=2;DP=1581;MQ=60;set=filterInvariant2-filterInvariant3-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant12-filterInvariant15-filterInvariant16-variant18-filterInvariant22-filterInvariant27-filterInvariant31-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant39-filterInvariant42-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:62,28:90:99:498,0,4656:8,54,28,0 chr1 1480663 . A C 427.18 PASS AC=1;AF=0.5;AN=2;DP=1007;MQ=60;set=filterInvariant2-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant9-filterInvariant12-filterInvariant16-variant18-filterInvariant22-filterInvariant35-variant36-filterInvariant39-filterInvariant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,21:86:99:466,0,4764:10,55,21,0 chr1 1480664 . G C 89.73 PASS AC=1;AF=0.5;AN=2;DP=539;MQ=60;set=filterInvariant5-filterInvariant7-variant9-variant18-filterInvariant22-filterInvariant35-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,15:82:99:466,0,4764:11,56,15,0 chr1 1481175 . C A 448.33 PASS AC=1;AF=0.591;AN=2;DP=513;FractionInformativeReads=1;set=variant4-variant6-variant8-variant10-variant11-variant14-variant15-variant17-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant34-variant35-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,8:27:99:180,0,550:13,6,6,2 chr1 1481348 . T C 356.04 PASS AC=1;AF=0.523;AN=2;DP=1033;MQ=60;set=variant4-variant5-variant6-variant8-variant10-variant11-variant14-variant15-variant17-variant18-variant23-variant24-variant25-variant28-variant29-variant30-variant35-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,31:74:99:746,0,1182:16,27,15,16 chr1 1497641 . TTTTC T 109.68 PASS AC=1;AF=0.583;AN=2;DP=324;MQ=60;set=variant4-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant33-variant34-variant35-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,9:13:99:366,0,209:2,2,6,3 chr1 1499298 . A G 363.97 PASS AC=1;AF=0.593;AN=2;DP=807;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant6-variant8-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant33-variant34-variant35-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,8:21:99:254,0,305:8,5,5,3 chr1 1509825 . A G 2603.23 PASS AC=1;AF=0.596;AN=2;DP=4730;MQ=60;set=variant5-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant33-variant34-variant35-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:101,122:223:99:2991,0,2392:54,47,73,49 chr1 1510035 . GGC G 1281.93 PASS AC=1;AF=0.596;AN=2;DP=1836;MQ=60;set=variant5-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant33-variant34-variant35-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,45:90:99:1703,0,1774:18,27,14,31 chr1 1510801 . C T 163.81 PASS AC=1;AF=0.596;AN=2;DP=476;MQ=60;set=variant5-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant33-variant34-variant35-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,9:20:99:272,0,383:1,10,1,8 chr1 1534614 . T C 3678.6 PASS AC=2;AF=0.618;AN=2;DP=3440;MQ=60;set=variant3-variant4-variant6-variant7-variant8-variant11-variant15-variant18-variant19-variant23-variant25-variant26-variant32-variant34-variant35-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,204:204:99:6037,608,0:0,0,104,100 chr1 1558792 . T C 2624.05 PASS AC=2;AF=0.966;AN=2;DP=4846;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,148:149:99:4495,392,0:0,1,82,66 chr1 1559971 . C T 304.44 PASS AC=2;AF=0.966;AN=2;DP=671;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:577,39,0:0,0,13,0 chr1 1560103 . C T 1734.02 PASS AC=1;AF=0.536;AN=2;DP=1828;MQ=60;set=variant3-variant6-variant7-variant8-variant15-variant19-variant23-variant25-variant26-variant32-variant33-variant34-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:63,76:139:99:1925,0,1355:36,27,46,30 chr1 1562437 . C G 2896.53 PASS AC=2;AF=0.625;AN=2;DP=3221;MQ=60;set=variant3-variant4-variant6-variant7-variant8-variant11-variant13-variant15-variant18-variant19-variant23-variant25-variant26-variant32-variant34-variant35-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,169:169:99:5682,507,0:0,0,66,103 chr1 1566065 . A AG 374.15 PASS AC=1;AF=0.553;AN=2;DP=857;set=variant3-variant4-filterInvariant6-variant7-variant8-variant11-variant12-variant15-variant18-variant19-variant24-filterInvariant26-variant32-variant34-variant35-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,19:27:99:448,0,130:1,7,3,16 chr1 1566068 . A G 791.3 PASS AC=2;AF=0.841;AN=2;DP=1734;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1481,114,0:0,0,7,31 chr1 1574019 . A G 232.83 PASS AC=1;AF=0.515;AN=2;DP=2036;set=variant-variant2-variant3-variant5-filterInvariant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant30-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,30:52:99:650,0,434:6,16,12,18 chr1 1574076 . G A 206.69 PASS AC=1;AF=0.515;AN=2;DP=1379;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant30-variant32-filterInvariant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,21:34:99:558,0,355:1,12,5,16 chr1 1575616 . T C 1989.91 PASS AC=2;AF=0.977;AN=2;DP=2881;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant13-filterInvariant14-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant26-variant27-variant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant38-filterInvariant39-filterInvariant40-filterInvariant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:2252,231,0:0,0,59,18 chr1 1575836 . C G 2109.87 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=11550;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:241,162:403:99:2785,0,5364:93,148,82,80 chr1 1580738 . T A 148 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=8719;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:112,117:229:99:2356,0,2306:42,70,45,72 chr1 1581558 . C T 543.7 PASS AC=2;AF=0.964;AN=2;DP=471;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-filterInvariant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-filterInvariant35-variant36-variant37-variant38-filterInvariant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:362,33,0:0,0,2,9 chr1 1581586 . T C 455.93 PASS AC=2;AF=0.988;AN=2;DP=360;FS=0;MQRankSum=-2.857;ReadPosRankSum=-0.328;set=variant-filterInvariant2-variant3-variant4-variant5-filterInvariant6-variant7-filterInvariant8-filterInvariant9-variant10-variant11-variant12-variant13-filterInvariant14-variant15-filterInvariant16-filterInvariant17-filterInvariant18-variant19-filterInvariant20-variant21-variant22-variant23-variant24-filterInvariant25-variant26-variant27-variant29-variant30-variant31-variant32-filterInvariant33-variant34-variant35-variant36-filterInvariant37-filterInvariant38-variant39-variant40-variant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:271,24,0:0,0,3,5 chr1 1581713 . A C,G 818.77 PASS AC=0,1;AF=0.589,0.071;AN=2;DP=1616;set=variant-variant2-variant3-variant5-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant25-variant26-filterInvariant27-variant29-variant30-variant31-variant33-filterInvariant35-variant36-variant37-variant38-variant39-variant42-variant44 GT:DP:GQ:SB 0/2:57:63:36,14,7,0 chr1 1581759 . G A 83.67 PASS AC=1;AF=0.5;AN=2;DP=4743;set=filterInvariant-variant2-variant3-variant4-variant5-variant7-filterInvariant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-filterInvariant28-filterInvariant29-variant30-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:75,36:111:99:795,0,1939:45,30,26,10 chr1 1581926 . G T 361.78 PASS AC=1;AF=0.5;AN=2;DP=3853;set=variant-variant2-variant3-variant4-variant5-filterInvariant6-variant7-filterInvariant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-filterInvariant31-variant32-variant33-filterInvariant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,37:89:99:856,0,1521:18,34,13,24 chr1 1582106 . T C 2887.64 PASS AC=2;AF=0.977;AN=2;DP=5193;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,136:136:99:3915,408,0:0,0,83,53 chr1 1582202 . C T 940.35 PASS AC=1;AF=0.5;AN=2;DP=9587;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:127,131:258:99:2818,0,2775:61,66,66,65 chr1 1582794 . C A 171.06 PASS AC=2;AF=0.955;AN=2;DP=669;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:782,72,0:0,0,17,7 chr1 1582841 . A G 379.63 PASS AC=1;AF=0.5;AN=2;DP=613;FractionInformativeReads=1;set=variant2-variant3-variant4-variant5-variant6-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,8:19:99:303,0,438:6,5,4,4 chr1 1582844 . G T 379.63 PASS AC=1;AF=0.5;AN=2;DP=611;FractionInformativeReads=1;set=variant2-variant3-variant4-variant5-variant6-filterInvariant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,8:19:99:303,0,438:6,5,4,4 chr1 1582880 . G C 38.35 PASS AC=1;AF=0.5;AN=2;DP=2018;set=filterInvariant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-filterInvariant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-filterInvariant30-variant31-filterInvariant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,33:67:99:733,0,835:19,15,20,13 chr1 1582961 . G C 552.78 PASS AC=1;AF=0.513;AN=2;DP=5742;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:73,98:171:99:2387,0,1328:33,40,53,45 chr1 1583003 . C T 36.46 PASS AC=1;AF=0.5;AN=2;DP=6943;set=filterInvariant-variant2-variant3-variant4-variant5-variant6-variant7-filterInvariant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-filterInvariant28-variant29-variant30-variant31-variant32-variant33-filterInvariant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:120,60:180:99:1009,0,2707:61,59,27,33 chr1 1583669 . C CT 1119.03 PASS AC=2;AF=0.965;AN=2;DP=1469;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1512,114,0:0,0,6,32 chr1 1585597 . A G 1221.47 PASS AC=2;AF=0.75;AN=2;DP=3841;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,90:90:99:2731,270,0:0,0,52,38 chr1 1585642 . G T 1183.17 PASS AC=2;AF=0.75;AN=2;DP=4536;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,112:112:99:3351,336,0:0,0,57,55 chr1 1586752 . T C 2340.97 PASS AC=2;AF=0.989;AN=2;DP=3123;MQRankSum=1.009;ReadPosRankSum=1.492;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,83:83:99:2631,248,0:0,0,53,30 chr1 1588670 . G A 98.08 PASS AC=1;AF=0.5;AN=2;DP=3214;set=filterInvariant-variant2-variant3-variant4-variant5-variant6-variant7-filterInvariant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-filterInvariant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,18:75:99:333,0,1635:41,16,12,6 chr1 1588717 . G A 59.09 PASS AC=1;AF=0.5;AN=2;DP=4516;set=filterInvariant-variant2-variant3-variant4-variant5-filterInvariant6-variant7-variant9-filterInvariant11-variant12-variant13-variant14-variant15-variant16-variant17-filterInvariant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-filterInvariant28-filterInvariant29-variant30-variant32-variant33-filterInvariant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:87,21:108:99:247,0,2425:57,30,12,9 chr1 1588737 . C T 282.57 PASS AC=1;AF=0.5;AN=2;DP=5037;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-filterInvariant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:103,21:124:99:543,0,4457:64,39,12,9 chr1 1588743 . A T 276.52 PASS AC=1;AF=0.5;AN=2;DP=5130;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-filterInvariant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:107,21:128:99:549,0,4560:65,42,11,10 chr1 1588744 . AGCG A 261.54 PASS AC=1;AF=0.5;AN=2;DP=5231;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-filterInvariant29-variant30-variant32-variant33-filterInvariant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:108,21:129:99:543,0,4615:65,43,11,10 chr1 1595867 . C A 1455.21 PASS AC=2;AF=1;AN=2;DP=4128;FS=0;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,132:132:99:3787,395,0:0,0,74,58 chr1 1596304 . G A 88.71 PASS AC=2;AF=0.794;AN=2;DP=222;FS=0;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant22-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:222,15,0:0,0,5,0 chr1 1596974 . C T 3788.7 PASS AC=2;AF=0.989;AN=2;DP=5315;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,139:139:99:4284,415,0:0,0,64,75 chr1 1599812 . C T 495.65 PASS AC=1;AF=0.524;AN=2;DP=1730;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-filterInvariant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,25:56:99:827,0,634:19,12,25,0 chr1 1599888 . A G 2767.6 PASS AC=1;AF=0.568;AN=2;DP=5891;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:67,143:210:99:3804,0,1009:34,33,93,50 chr1 1599940 . C T 165.78 PASS AC=1;AF=0.5;AN=2;DP=1733;set=filterInvariant11-variant14-filterInvariant15-filterInvariant17-variant20-filterInvariant27-filterInvariant31-filterInvariant33-filterInvariant34-filterInvariant35 GT:AD:DP:GQ:PL:SB 0/1:178,36:214:99:305,0,4395:93,85,15,21 chr1 1599974 . A C 172.99 PASS AC=1;AF=0.5;AN=2;DP=2002;set=filterInvariant11-variant14-variant15-filterInvariant17-filterInvariant18-variant20-filterInvariant27-filterInvariant31-filterInvariant33-filterInvariant34-filterInvariant35-filterInvariant38 GT:AD:DP:GQ:PL:SB 0/1:169,38:207:99:366,0,4177:70,99,16,22 chr1 1602787 . G T 1213.76 PASS AC=2;AF=1;AN=2;DP=1683;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:1829,185,0:0,0,35,27 chr1 1608229 . C T 205.22 PASS AC=1;AF=0.765;AN=2;DP=160;FS=0;FractionInformativeReads=1;set=filterInvariant2-filterInvariant3-filterInvariant6-filterInvariant10-filterInvariant13-filterInvariant15-variant16-filterInvariant17-filterInvariant19-filterInvariant21-filterInvariant25-filterInvariant31-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant38-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:9,5:14:92:92,0,192:5,4,3,2 chr1 1633003 . C CCG,CCGG 189.89 PASS AC=2,0;AF=0.714,0.143;AN=2;DP=44;set=variant3-variant6-variant10-variant15-variant32-variant35-variant41 GT:DP:GQ:SB 1/1:3:9:0,0,3,0 chr1 1635004 . T C 1839.55 PASS AC=2;AF=0.757;AN=2;DP=5897;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant30-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,150:150:99:4456,449,0:0,0,84,66 chr1 1635619 . T C 6367.38 PASS AC=2;AF=0.75;AN=2;DP=7889;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant30-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,269:270:99:7787,794,0:0,1,138,131 chr1 1635749 . C A 2329.6 PASS AC=2;AF=0.7;AN=2;DP=6100;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant30-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,191:193:99:5901,523,0:1,1,91,100 chr1 1636044 . G A 5047.46 PASS AC=2;AF=0.75;AN=2;DP=12609;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-filterInvariant28-variant30-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,360:361:99:11503,1071,0:0,1,150,210 chr1 1636274 . C T 2177.68 PASS AC=2;AF=0.691;AN=2;DP=3908;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant30-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,145:145:99:4564,433,0:0,0,84,61 chr1 1637295 . G A 46.52 PASS AC=2;AF=1;AN=2;DP=2;FS=0;FractionInformativeReads=1;MQ=39.53;QD=23.26;SOR=2.303;set=variant35 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:75,6,0:0,0,2,0 chr1 1637306 . T C 46.52 PASS AC=2;AF=1;AN=2;DP=2;FS=0;FractionInformativeReads=1;MQ=39.53;QD=23.26;SOR=2.303;set=variant35 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:75,6,0:0,0,2,0 chr1 1639046 . C G 793.85 PASS AC=2;AF=1;AN=2;DP=441;FS=0;FractionInformativeReads=1;set=variant-variant2-variant6-variant8-variant11-variant12-variant14-variant15-variant17-variant18-variant20-variant23-variant32-variant34-variant35-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:927,81,0:0,0,0,27 chr1 1639062 . T C 466.7 PASS AC=2;AF=0.941;AN=2;DP=157;FS=0;FractionInformativeReads=1;set=filterInvariant-filterInvariant2-filterInvariant6-filterInvariant8-filterInvariant11-variant12-filterInvariant14-filterInvariant15-filterInvariant17-filterInvariant18-filterInvariant20-filterInvariant23-filterInvariant32-filterInvariant34-filterInvariant35-filterInvariant42-filterInvariant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:459,42,0:0,0,0,14 chr1 1639801 . T C 132.2 PASS AC=2;AF=0.875;AN=2;DP=80;FractionInformativeReads=1;set=filterInvariant2-filterInvariant11-filterInvariant14-filterInvariant15-filterInvariant17-filterInvariant18-variant23-variant24-variant27-filterInvariant32-filterInvariant35-filterInvariant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:134,15,0:0,0,2,3 chr1 1644908 . C T 422.34 PASS AC=2;AF=0.955;AN=2;DP=966;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:558,51,0:0,0,5,12 chr1 1645050 . C T 248.72 PASS AC=2;AF=0.974;AN=2;DP=412;FS=0;FractionInformativeReads=1;set=variant2-variant3-variant4-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant11-variant12-filterInvariant13-variant14-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant18-variant19-filterInvariant20-filterInvariant21-variant22-variant23-filterInvariant24-filterInvariant25-filterInvariant26-variant27-variant30-variant31-filterInvariant32-filterInvariant33-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant38-filterInvariant39-filterInvariant40-filterInvariant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:687,78,0:0,0,12,14 chr1 1646074 . A G 151.77 PASS AC=1;AF=0.825;AN=2;DP=79;FS=0;FractionInformativeReads=1;set=variant4-filterInvariant6-variant7-filterInvariant9-filterInvariant14-variant15-filterInvariant16-filterInvariant18-filterInvariant19-filterInvariant22-variant24-filterInvariant25-variant30-variant32-variant33-filterInvariant35-variant39-variant40-variant41-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:2,4:6:66:162,0,66:1,1,2,2 chr1 1646077 . G T 151.77 PASS AC=1;AF=0.825;AN=2;DP=82;FS=0;FractionInformativeReads=1;set=variant4-filterInvariant6-variant7-filterInvariant9-filterInvariant14-variant15-filterInvariant16-filterInvariant18-filterInvariant19-filterInvariant22-variant24-filterInvariant25-variant30-variant32-variant33-variant35-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,5:7:63:195,0,63:1,1,3,2 chr1 1646113 . G C 102.81 PASS AC=1;AF=0.852;AN=2;DP=118;FractionInformativeReads=1;set=variant3-variant4-variant7-filterInvariant9-variant13-filterInvariant14-filterInvariant15-filterInvariant16-filterInvariant18-filterInvariant19-variant20-variant21-filterInvariant22-variant24-variant27-variant29-variant30-variant31-filterInvariant32-variant33-variant35-variant36-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,6:8:25:153,0,25:1,1,4,2 chr1 1646231 . T C 40.54 PASS AC=2;AF=0.952;AN=2;DP=575;set=filterInvariant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-filterInvariant20-variant21-variant22-filterInvariant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-filterInvariant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:45:667,45,0:0,0,14,0 chr1 1646236 . C T 40.54 PASS AC=2;AF=0.942;AN=2;DP=702;set=filterInvariant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-filterInvariant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:667,45,0:0,0,15,0 chr1 1646371 . G T 100.99 PASS AC=2;AF=0.714;AN=2;DP=1304;FractionInformativeReads=1;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant30-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:1391,141,0:0,0,18,29 chr1 1646427 . T G 395.83 PASS AC=2;AF=0.964;AN=2;DP=723;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:728,51,0:0,0,0,17 chr1 1646450 . G A 168.83 PASS AC=2;AF=0.976;AN=2;DP=411;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:381,27,0:0,0,0,9 chr1 1646657 . T C 198.68 PASS AC=2;AF=0.985;AN=2;DP=155;FS=0;set=variant3-filterInvariant4-variant5-variant7-variant8-variant9-variant11-variant12-filterInvariant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-filterInvariant23-variant24-variant25-variant27-variant29-variant30-filterInvariant31-variant32-variant33-variant35-variant36-variant38-filterInvariant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:136,12,0:0,0,4,0 chr1 1646789 . T C 429.52 PASS AC=2;AF=0.953;AN=2;DP=1616;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1070,102,0:0,0,23,11 chr1 1647722 . G T 1078.09 PASS AC=1;AF=0.511;AN=2;DP=2553;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:39,21:60:99:791,0,1781:29,10,15,6 chr1 1647725 . G A 1063.04 PASS AC=1;AF=0.511;AN=2;DP=2745;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:45,23:68:99:911,0,1856:34,11,17,6 chr1 1647726 . T G 1051 PASS AC=1;AF=0.511;AN=2;DP=2799;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:46,24:70:99:995,0,1850:35,11,17,7 chr1 1647729 . C T 1090 PASS AC=1;AF=0.511;AN=2;DP=2995;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:46,27:73:99:1079,0,1844:35,11,18,9 chr1 1647730 . A G 1090 PASS AC=1;AF=0.511;AN=2;DP=3071;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:46,27:73:99:1079,0,1844:35,11,18,9 chr1 1647745 . G A 1900.84 PASS AC=1;AF=0.511;AN=2;DP=4407;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:61,42:103:99:1706,0,2426:46,15,26,16 chr1 1647753 . C T 2022.4 PASS AC=1;AF=0.511;AN=2;DP=5070;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:68,49:117:99:1893,0,2744:51,17,29,20 chr1 1647778 . C G 2535.07 PASS AC=1;AF=0.511;AN=2;DP=7411;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:94,73:167:99:2488,0,3282:59,35,45,28 chr1 1647814 . T C 3796.76 PASS AC=1;AF=0.511;AN=2;DP=10746;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:132,131:263:99:3246,0,3249:74,58,74,57 chr1 1647871 . T C 4237.5 PASS AC=1;AF=0.511;AN=2;DP=13363;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:172,175:347:99:4035,0,4019:82,90,81,94 chr1 1647893 . C CTTTCTT 6300.47 PASS AC=1;AF=0.511;AN=2;DP=12051;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:149,145:294:99:5613,0,5746:64,85,63,82 chr1 1647968 . C CAT 2494.68 PASS AC=1;AF=0.511;AN=2;DP=5490;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:72,52:124:99:1938,0,2816:21,51,11,41 chr1 1647971 . G A 2343.37 PASS AC=1;AF=0.511;AN=2;DP=4943;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:68,47:115:99:1883,0,2821:20,48,9,38 chr1 1647983 . T A 1606.07 PASS AC=1;AF=0.511;AN=2;DP=3799;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:57,40:97:99:1346,0,2081:15,42,8,32 chr1 1647990 . C T 1302.97 PASS AC=1;AF=0.511;AN=2;DP=3225;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:49,28:77:99:1066,0,1985:9,40,3,25 chr1 1648002 . C T 1117.93 PASS AC=1;AF=0.511;AN=2;DP=2554;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:40,18:58:99:514,0,1431:4,36,2,16 chr1 1648018 . C T 652.33 PASS AC=1;AF=0.511;AN=2;DP=1789;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:29,12:41:99:376,0,1011:1,28,0,12 chr1 1648027 . T C 966.69 PASS AC=2;AF=0.955;AN=2;DP=1376;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,28:28:87:1267,87,0:0,0,0,28 chr1 1650787 . T C 1683.71 PASS AC=1;AF=0.511;AN=2;DP=3813;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:64,30:94:99:1109,0,2594:41,23,19,11 chr1 1650797 . A G 1999.66 PASS AC=1;AF=0.511;AN=2;DP=4140;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:70,36:106:99:1329,0,2912:45,25,23,13 chr1 1650801 . T C 2015.38 PASS AC=1;AF=0.511;AN=2;DP=4267;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:73,38:111:99:1391,0,2948:45,28,25,13 chr1 1650807 . T C 347.47 PASS AC=1;AF=0.5;AN=2;DP=4385;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,73:114:99:1803,0,1452:26,15,44,29 chr1 1650832 . A G 1512.51 PASS AC=1;AF=0.511;AN=2;DP=5041;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:80,61:141:99:1469,0,1958:46,34,39,22 chr1 1650845 . G A 397.67 PASS AC=1;AF=0.5;AN=2;DP=5241;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:63,87:150:99:2128,0,1465:37,26,51,36 chr1 1650920 . G A 472.1 PASS AC=1;AF=0.513;AN=2;DP=4605;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-filterInvariant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-filterInvariant36-variant37-variant38-variant39-variant40-variant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:78,67:145:99:2430,0,2986:34,44,32,35 chr1 1650938 . CGG C 1725.69 PASS AC=1;AF=0.511;AN=2;DP=4528;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:75,57:132:99:2207,0,3027:30,45,25,32 chr1 1650942 . A AAG 1722.69 PASS AC=1;AF=0.511;AN=2;DP=4383;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:74,53:127:99:2126,0,2991:29,45,23,30 chr1 1650960 . G A 1134.99 PASS AC=1;AF=0.511;AN=2;DP=3573;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:58,40:98:99:1580,0,2445:21,37,15,25 chr1 1650967 . T C 934.07 PASS AC=1;AF=0.511;AN=2;DP=3282;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:53,35:88:99:1394,0,2124:19,34,13,22 chr1 1650996 . T C 568.79 PASS AC=1;AF=0.511;AN=2;DP=2222;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:40,25:65:99:877,0,1573:11,29,8,17 chr1 1651003 . G A 511.31 PASS AC=1;AF=0.511;AN=2;DP=1956;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:34,22:56:99:809,0,1489:11,23,6,16 chr1 1651054 . CTT CT,C 92.06 PASS AC=2,0;AF=0.5,0.2;AN=2;DP=150;FS=0;set=variant-variant2-variant7-variant11-variant19-variant24-variant25-variant33-variant34-variant35 GT:DP:GQ:SB 1/1:8:23:0,0,2,6 chr1 1651077 . C CTCGCTCTGTCACCCAGGCT 134.21 PASS AC=2;AF=0.896;AN=2;DP=180;FS=0;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant22-variant24-variant25-variant27-variant33-variant34-variant35-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:36:492,36,0:0,0,1,6 chr1 1653004 . T C 1033.93 PASS AC=2;AF=0.953;AN=2;DP=4626;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,117:117:99:5265,370,0:0,0,65,52 chr1 1653028 . C T 1345.1 PASS AC=2;AF=0.953;AN=2;DP=5736;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,151:151:99:6210,460,0:0,0,81,70 chr1 1654013 . C G 92.75 PASS AC=2;AF=0.971;AN=2;DP=60;FS=0;FractionInformativeReads=1;MQRankSum=-0.731;ReadPosRankSum=-0.731;set=filterInvariant5-variant6-filterInvariant7-filterInvariant8-variant9-variant12-variant14-filterInvariant16-filterInvariant19-variant22-variant23-variant25-variant30-variant31-variant35-variant38-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:144,12,0:0,0,4,0 chr1 1654038 . G A 370.86 PASS AC=2;AF=0.95;AN=2;DP=505;FractionInformativeReads=1;set=variant2-variant3-variant4-variant5-variant6-variant7-filterInvariant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:547,48,0:0,0,14,2 chr1 1654058 . C T 202.23 PASS AC=2;AF=0.919;AN=2;DP=986;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:81:1215,81,0:0,0,19,5 chr1 1654064 . A T 238.14 PASS AC=2;AF=0.919;AN=2;DP=1096;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:1305,87,0:0,0,23,6 chr1 1654065 . AGCG A 220.16 PASS AC=2;AF=0.919;AN=2;DP=1137;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:1305,87,0:0,0,23,6 chr1 1657021 . T C 241.7 DRAGENHardSNP AC=2;AF=0.879;AN=2;DP=291;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:230,24,0:0,0,2,6 chr1 1661844 . G C 1130.11 PASS AC=2;AF=0.591;AN=2;DP=8095;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,172:172:99:4914,515,0:0,0,77,95 chr1 1663605 . A G 283.53 PASS AC=2;AF=0.938;AN=2;DP=221;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:274,21,0:0,0,6,1 chr1 1663831 . C T 1396.96 PASS AC=2;AF=0.682;AN=2;DP=4731;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,160:160:99:4801,477,0:0,0,90,70 chr1 1664019 . T C 883.8 PASS AC=2;AF=0.929;AN=2;DP=4278;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,121:121:99:3717,362,0:0,0,52,69 chr1 1664124 . T C 330.96 PASS AC=2;AF=0.915;AN=2;DP=2013;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,73:73:99:2210,219,0:0,0,27,46 chr1 1666175 . C T 286.66 PASS AC=2;AF=0.547;AN=2;DP=894;set=variant2-variant3-filterInvariant6-variant9-filterInvariant10-filterInvariant11-variant12-filterInvariant14-filterInvariant15-variant16-filterInvariant17-variant18-filterInvariant19-filterInvariant20-variant21-filterInvariant22-filterInvariant23-filterInvariant25-filterInvariant26-variant29-variant30-filterInvariant31-filterInvariant33-variant34-filterInvariant35-filterInvariant36-variant37-filterInvariant38-filterInvariant39-variant40-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,9:10:2:202,2,0:1,0,5,4 chr1 1666338 . G A 215.07 PASS AC=2;AF=0.878;AN=2;DP=3058;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:1429,96,0:0,0,18,14 chr1 1666342 . A G 218.08 PASS AC=2;AF=0.667;AN=2;DP=1568;set=variant-filterInvariant2-filterInvariant3-variant6-variant8-filterInvariant9-variant13-variant14-variant15-variant17-filterInvariant18-variant19-variant20-filterInvariant21-variant22-filterInvariant24-filterInvariant25-variant26-variant27-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:1429,96,0:0,0,18,14 chr1 1669734 . G T 2187.53 PASS AC=2;AF=0.688;AN=2;DP=7298;set=variant-variant2-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,342:342:99:9759,1020,0:0,0,202,140 chr1 1670570 . T C 78.15 PASS AC=2;AF=0.742;AN=2;DP=262;FractionInformativeReads=1;set=variant-filterInvariant2-variant3-filterInvariant5-variant7-filterInvariant9-filterInvariant10-variant11-variant12-filterInvariant15-variant17-filterInvariant18-filterInvariant19-variant20-variant21-variant23-variant24-filterInvariant25-variant26-variant27-variant28-filterInvariant30-filterInvariant31-filterInvariant33-filterInvariant35-variant36-variant37-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:166,15,0:0,0,0,5 chr1 1683565 . G A 1632.12 PASS AC=1;AF=0.613;AN=2;DP=5385;set=variant-variant2-variant3-variant6-variant7-variant8-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:80,76:156:99:1991,0,2033:52,28,48,28 chr1 1683900 . G A 484.57 PASS AC=1;AF=0.613;AN=2;DP=1734;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,31:62:99:685,0,893:15,16,13,18 chr1 1684169 . C G 1098.83 PASS AC=1;AF=0.613;AN=2;DP=2187;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,40:84:99:932,0,1181:25,19,25,15 chr1 1684347 . C CCCT 3716.21 PASS AC=1;AF=0.606;AN=2;DP=7735;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:135,127:262:99:4820,0,5204:75,60,72,55 chr1 1684472 . C T 1918.31 PASS AC=1;AF=0.613;AN=2;DP=7300;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:132,132:264:99:3098,0,3149:47,85,47,85 chr1 1685213 . C G 169.68 PASS AC=2;AF=0.92;AN=2;DP=923;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:878,66,0:0,0,6,16 chr1 1685921 . TCCCTGGGACCGAAGTCGCCCCA T 1354.09 PASS AC=1;AF=0.613;AN=2;DP=2515;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,37:71:99:1421,0,7149:25,9,21,16 chr1 1686040 . G T 1804.46 PASS AC=1;AF=0.609;AN=2;DP=8264;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:119,144:263:99:3424,0,2973:69,50,81,63 chr1 1686943 . T C 936.39 PASS AC=1;AF=0.676;AN=2;DP=1279;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,9:22:99:319,0,707:4,9,3,6 chr1 1686962 . C T 822.19 PASS AC=1;AF=0.682;AN=2;DP=926;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,8:17:99:289,0,579:3,6,2,6 chr1 1687625 . T C 218.85 PASS AC=1;AF=0.606;AN=2;DP=949;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:18,13:31:99:445,0,541:13,5,11,2 chr1 1688192 . A G 653.81 PASS AC=2;AF=0.919;AN=2;DP=2704;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,64:64:99:2373,191,0:0,0,40,24 chr1 1688469 . C G 279.8 PASS AC=2;AF=0.93;AN=2;DP=474;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:518,39,0:0,0,2,11 chr1 1688513 . G T 112.25 PASS AC=1;AF=0.648;AN=2;DP=184;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant23-variant25-variant26-variant27-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:1,6:7:25:205,0,25:1,0,2,4 chr1 1689762 . T C 518.28 PASS AC=1;AF=0.614;AN=2;DP=1423;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:20,18:38:99:517,0,481:11,9,12,6 chr1 1690126 . A AAC 124.67 PASS AC=2;AF=0.92;AN=2;DP=685;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,17:17:52:755,52,0:0,0,3,14 chr1 1690793 . G A 308.26 PASS AC=1;AF=0.613;AN=2;DP=988;FractionInformativeReads=1;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,21:34:99:539,0,409:3,10,5,16 chr1 1693726 . A G 157.57 PASS AC=1;AF=0.629;AN=2;DP=401;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,7:13:99:183,0,222:0,6,3,4 chr1 1696659 . A G 116.32 PASS AC=2;AF=0.932;AN=2;DP=686;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:608,57,0:0,0,13,6 chr1 1710035 . C T 401 PASS AC=1;AF=0.743;AN=2;DP=412;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,3:12:58:58,0,274:7,2,1,2 chr1 1747483 . G A 500 PASS AC=1;AF=0.5;AN=2;DP=73;FractionInformativeReads=1;MQ=60;set=variant9-variant35 GT:AD:DP:GQ:PL:SB 0/1:23,13:36:99:383,0,744:5,18,2,11 chr1 1823524 . G C 541.37 PASS AC=1;AF=0.522;AN=2;DP=875;MQ=60;set=variant-variant4-variant5-variant6-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant27-variant33-variant35-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:23,24:47:99:758,0,632:12,11,15,9 chr1 1823922 . A G 318.22 PASS AC=2;AF=0.955;AN=2;DP=3831;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,81:81:99:2653,242,0:0,0,30,51 chr1 1846357 . G A 834.55 PASS AC=1;AF=0.617;AN=2;DP=2692;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,45:82:99:1061,0,955:17,20,20,25 chr1 1846582 . A G 824.25 PASS AC=1;AF=0.756;AN=2;DP=3632;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,53:121:99:1290,0,1737:35,33,24,29 chr1 1846765 . G A 1117.43 PASS AC=1;AF=0.617;AN=2;DP=2802;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,47:92:99:1197,0,1218:19,26,22,25 chr1 1847065 . A G 616.1 PASS AC=1;AF=0.5;AN=2;DP=51;FS=2.556;FractionInformativeReads=1;MQ=60;MQRankSum=0.763;QD=12.08;ReadPosRankSum=-1.479;SOR=0.38;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:26,25:51:99:644,0,715:19,7,16,9 chr1 1847856 . G T 1182.23 PASS AC=1;AF=0.597;AN=2;DP=5715;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:89,79:168:99:1729,0,2150:50,39,45,34 chr1 1848109 . G C 1593.98 PASS AC=1;AF=0.597;AN=2;DP=4964;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:73,96:169:99:2513,0,1789:34,39,46,50 chr1 1848734 . A G 430.67 PASS AC=2;AF=0.929;AN=2;DP=642;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:361,30,0:0,0,4,6 chr1 1849529 . A G 1409.97 PASS AC=1;AF=0.617;AN=2;DP=3479;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,68:121:99:2191,0,1509:27,26,33,35 chr1 1850428 . A G 2044.76 PASS AC=1;AF=0.611;AN=2;DP=2186;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,45:82:99:1025,0,1028:19,18,21,24 chr1 1850627 . CAGCGGCAGG C,CAGCGGCAGGAGCGGCAGG 356.51 PASS AC=1,0;AF=0.617,0.017;AN=2;DP=1360;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:DP:GQ:SB 0/1:27:99:2,13,4,8 chr1 1853615 . T TCTGA 367.6 PASS AC=2;AF=1;AN=2;DP=769;FS=0;MQ=60;MQRankSum=-0.742;ReadPosRankSum=-0.628;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,20:20:66:990,66,0:0,0,15,5 chr1 1854109 . A G 787.82 PASS AC=1;AF=0.597;AN=2;DP=3621;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,49:100:99:1251,0,1391:30,21,27,22 chr1 1854321 . A G 432.35 PASS AC=1;AF=0.738;AN=2;DP=1185;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,20:44:99:541,0,680:11,13,10,10 chr1 1854861 . G A 1314.78 PASS AC=1;AF=0.5;AN=2;DP=280;MQ=60;set=variant9-variant35 GT:AD:DP:GQ:PL:SB 0/1:91,80:171:99:1776,0,2020:50,41,45,35 chr1 1855450 . A G 93.15 PASS AC=1;AF=0.786;AN=2;DP=736;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,6:13:99:170,0,155:3,4,1,5 chr1 1856227 . C T 325.27 PASS AC=1;AF=0.625;AN=2;DP=569;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant9-variant10-variant11-variant12-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,16:27:99:434,0,307:7,4,9,7 chr1 1858309 . T C 2274.76 PASS AC=1;AF=0.592;AN=2;DP=10099;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:166,160:326:99:3740,0,4005:73,93,78,82 chr1 1859296 . T C 563.27 PASS AC=1;AF=0.617;AN=2;DP=1287;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,30:52:99:1012,0,796:1,21,5,25 chr1 1860087 . C T 393.19 PASS AC=1;AF=0.597;AN=2;DP=2230;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,31:75:99:709,0,1114:24,20,17,14 chr1 1861582 . C T 2127.02 PASS AC=1;AF=0.633;AN=2;DP=6291;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:133,86:219:99:1924,0,3125:78,55,55,31 chr1 1870210 . G A 186.75 PASS AC=1;AF=0.768;AN=2;DP=978;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,11:30:99:353,0,602:15,4,10,1 chr1 1871979 . G A 358.46 PASS AC=1;AF=0.611;AN=2;DP=2008;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,33:68:99:844,0,777:15,20,11,22 chr1 1873453 . G A 42.23 PASS AC=1;AF=0.611;AN=2;DP=742;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,19:42:99:511,0,540:15,8,13,6 chr1 1873514 . A G 206.4 PASS AC=1;AF=0.611;AN=2;DP=1435;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,37:70:99:842,0,806:19,14,22,15 chr1 1873525 . T C 191.38 PASS AC=1;AF=0.611;AN=2;DP=1535;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,39:73:99:877,0,823:20,14,24,15 chr1 1873697 . G A 466.65 PASS AC=1;AF=0.611;AN=2;DP=1486;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,38:69:99:1513,0,1727:13,18,18,20 chr1 1873699 . G C 466.65 PASS AC=1;AF=0.611;AN=2;DP=1466;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,39:70:99:1513,0,1727:13,18,18,21 chr1 1875858 . C G 1894.94 PASS AC=1;AF=0.633;AN=2;DP=3341;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:62,59:121:99:2303,0,3461:35,27,32,27 chr1 1875859 . A G 1894.94 PASS AC=1;AF=0.633;AN=2;DP=3358;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:63,60:123:99:2303,0,3461:36,27,33,27 chr1 1878628 . C T 317.23 PASS AC=1;AF=0.633;AN=2;DP=872;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,25:54:99:654,0,922:5,24,6,19 chr1 1891477 . A G 1680.81 PASS AC=1;AF=0.529;AN=2;DP=2452;MQ=60;set=variant-variant7-variant8-variant14-variant16-variant17-variant21-variant22-variant23-variant24-variant28-variant32-variant35-variant36-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:98,80:178:99:1903,0,2378:45,53,32,48 chr1 1900186 . T C 2404.33 PASS AC=2;AF=0.676;AN=2;DP=2846;MQ=60;set=variant3-variant4-variant6-variant9-variant11-variant12-variant16-variant17-variant24-variant25-variant26-variant27-variant30-variant32-variant33-variant35-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,164:164:99:4807,491,0:0,0,88,76 chr1 1900232 . T C 1328.25 PASS AC=2;AF=0.603;AN=2;DP=5110;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,162:162:99:5090,486,0:0,0,73,89 chr1 1903357 . G C 516.51 PASS AC=1;AF=0.611;AN=2;DP=599;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant9-variant11-variant12-variant15-variant16-variant17-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:10,21:31:99:624,0,314:6,4,15,6 chr1 1905790 . A G 348.68 PASS AC=2;AF=0.676;AN=2;DP=373;MQ=60;set=variant3-variant6-variant9-variant11-variant12-variant15-variant16-variant17-variant23-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant35 GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:767,69,0:0,0,7,16 chr1 1918191 . A G 54.14 PASS AC=2;AF=0.676;AN=2;DP=369;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:517,48,0:0,0,8,8 chr1 1918488 . A G 769.45 PASS AC=2;AF=0.653;AN=2;DP=4387;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,109:109:99:3514,327,0:0,0,47,62 chr1 1922303 . C T 647.24 PASS AC=1;AF=0.653;AN=2;DP=1917;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:30,17:47:99:485,0,708:18,12,10,7 chr1 1956362 . G A 1237.99 PASS AC=2;AF=0.86;AN=2;DP=9196;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,254:254:99:7209,757,0:0,0,142,112 chr1 1957037 . T C 3027.07 PASS AC=2;AF=0.72;AN=2;DP=17463;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,508:508:99:15288,1522,0:0,0,240,268 chr1 1960926 . T C 427.94 PASS AC=2;AF=0.884;AN=2;DP=1358;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1309,105,0:0,0,26,9 chr1 1981836 . C T 70.68 PASS AC=2;AF=0.889;AN=2;DP=291;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:157,15,0:0,0,2,3 chr1 1986736 . GA G 312.46 PASS AC=1;AF=0.536;AN=2;DP=310;MQ=60;set=variant5-variant11-variant14-variant16-variant17-variant18-variant20-variant25-variant27-variant29-variant35-variant36-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:16,15:31:99:446,0,501:15,1,13,2 chr1 1987993 . T C 1178.57 PASS AC=1;AF=0.63;AN=2;DP=3026;MQ=60;set=variant-variant4-variant5-variant7-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant20-variant25-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:76,62:138:99:1469,0,1923:40,36,32,30 chr1 1988044 . G C 1487.45 PASS AC=1;AF=0.545;AN=2;DP=1274;FractionInformativeReads=1;MQ=60;set=variant5-variant11-variant14-variant17-variant18-variant20-variant25-variant27-variant35-variant36-variant42 GT:AD:DP:GQ:PL:SB 0/1:69,60:129:99:1386,0,1682:32,37,29,31 chr1 1988168 . CT C,CTT,CTTT 87.53 PASS AC=1,0,0;AF=0.429,0.048,0.024;AN=2;DP=866;set=filterInvariant3-filterInvariant4-filterInvariant6-variant7-filterInvariant9-variant10-filterInvariant11-variant14-variant16-variant18-variant19-variant20-variant25-variant26-variant27-variant28-variant29-filterInvariant31-filterInvariant34-filterInvariant35-filterInvariant36 GT:DP:GQ:SB 0/1:27:74:3,17,1,6 chr1 1991162 . G A 671.85 PASS AC=1;AF=0.529;AN=2;DP=1196;MQ=60;set=variant5-variant11-variant14-variant16-variant17-variant18-variant20-variant25-variant27-variant29-variant30-variant34-variant35-variant36-variant37-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:37,44:81:99:1176,0,835:14,23,14,30 chr1 1991173 . A G 175.39 PASS AC=1;AF=0.63;AN=2;DP=1553;MQ=60;set=variant-variant4-variant5-variant7-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant20-variant25-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,33:64:99:1023,0,684:12,19,7,26 chr1 2004947 . T C 2000.7 PASS AC=1;AF=0.636;AN=2;DP=2791;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant11-variant14-variant16-variant17-variant18-variant20-variant25-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:86,86:172:99:1949,0,2108:48,38,44,42 chr1 2005740 . T C 1889.94 PASS AC=2;AF=0.932;AN=2;DP=2873;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,67:67:99:1926,199,0:0,0,27,40 chr1 2036263 . G A 2418.21 PASS AC=1;AF=0.744;AN=2;DP=3949;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,46:105:99:1128,0,1373:28,31,19,27 chr1 2075570 . T C 370.46 PASS AC=1;AF=0.6;AN=2;DP=965;MQ=60;set=variant3-variant4-variant5-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,25:43:99:787,0,392:12,6,20,5 chr1 2075814 . C T 439.77 PASS AC=1;AF=0.536;AN=2;DP=816;MQ=60;set=variant4-variant5-variant12-variant13-variant20-variant23-variant25-variant29-variant31-variant33-variant34-variant35-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,24:52:99:546,0,763:10,18,7,17 chr1 2082489 . G A 422.82 PASS AC=1;AF=0.6;AN=2;DP=578;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,7:9:51:285,0,51:0,2,1,6 chr1 2082505 . C T 518.75 PASS AC=2;AF=0.571;AN=2;DP=181;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant12-variant13-variant20-variant23-variant25-variant29-variant31-variant33-variant34-variant35-variant36-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:18:270,18,0:0,0,1,4 chr1 2087557 . T C 1121.96 PASS AC=1;AF=0.536;AN=2;DP=1431;MQ=60;set=variant4-variant5-variant12-variant13-variant20-variant23-variant25-variant29-variant31-variant33-variant34-variant35-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,39:78:99:1022,0,972:17,22,18,21 chr1 2101059 . C G 617.67 PASS AC=1;AF=0.536;AN=2;DP=667;MQ=60;set=variant4-variant5-variant12-variant13-variant20-variant23-variant25-variant29-variant31-variant33-variant34-variant35-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,26:63:99:565,0,1041:14,23,8,18 chr1 2106840 . T C 328.54 PASS AC=2;AF=1;AN=2;DP=627;FS=0;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:575,42,0:0,0,0,14 chr1 2106896 . T C 61.77 PASS AC=2;AF=1;AN=2;DP=186;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:263,18,0:0,0,0,6 chr1 2117558 . C T 1466.69 PASS AC=1;AF=0.536;AN=2;DP=1576;MQ=60;set=variant4-variant5-variant12-variant13-variant20-variant23-variant25-variant29-variant31-variant33-variant34-variant35-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:70,77:147:99:1826,0,1674:26,44,35,42 chr1 2118539 . T C 434.21 PASS AC=2;AF=0.75;AN=2;DP=1598;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1468,132,0:0,0,27,17 chr1 2118724 . CTTTT CTTTTT,C 140.17 PASS AC=1,0;AF=0.5,0.05;AN=2;DP=247;MQ=60;set=variant5-variant11-variant13-variant25-variant31-variant33-variant35-variant36-variant40-variant44 GT:DP:GQ:SB 0/1:22:99:1,9,2,10 chr1 2121118 . C T 2926.23 PASS AC=1;AF=0.757;AN=2;DP=7430;set=variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:90,111:201:99:2542,0,2333:54,36,63,48 chr1 2124927 . C T 1434.14 PASS AC=1;AF=0.5;AN=2;DP=95;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.293;QD=15.1;ReadPosRankSum=-1.45;SOR=0.594;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:45,50:95:99:1462,0,1352:36,9,39,11 chr1 2125172 . G A 2574.78 PASS AC=1;AF=0.536;AN=2;DP=2102;MQ=60;set=variant4-variant5-variant12-variant13-variant20-variant23-variant25-variant31-variant33-variant34-variant35-variant36-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:77,81:158:99:2084,0,2017:43,34,42,39 chr1 2126139 . C G 161.96 PASS AC=2;AF=1;AN=2;DP=505;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:292,33,0:0,0,5,6 chr1 2144788 . A G 4672.92 PASS AC=1;AF=0.554;AN=2;DP=5005;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant17-variant18-variant19-variant21-variant23-variant25-variant26-variant28-variant29-variant31-variant33-variant35-variant36-variant37-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:106,93:199:99:2497,0,3052:55,51,48,45 chr1 2144982 . G T 3444.13 PASS AC=2;AF=0.829;AN=2;DP=4014;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,109:110:99:3248,319,0:1,0,46,63 chr1 2234251 . A G 238.54 PASS AC=1;AF=0.821;AN=2;DP=632;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,12:19:99:421,0,264:7,0,11,1 chr1 2240006 . T C 7534.4 PASS AC=2;AF=0.826;AN=2;DP=9640;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,220:221:99:6750,616,0:1,0,128,92 chr1 2241376 . C CT,CTT 405.72 PASS AC=1,0;AF=0.577,0.244;AN=2;DP=562;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:18:59:2,2,9,5 chr1 2252626 . A T 486.46 PASS AC=1;AF=0.5;AN=2;DP=239;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant13-variant26-variant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:33,30:63:99:753,0,950:24,9,20,10 chr1 2252759 . A G 2072.78 PASS AC=1;AF=0.581;AN=2;DP=4216;MQ=60;set=variant-variant3-variant5-variant6-variant8-variant9-variant10-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:73,83:156:99:2221,0,1773:38,35,42,41 chr1 2286947 . A G 557.96 PASS AC=2;AF=0.881;AN=2;DP=2906;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,94:94:99:2848,282,0:0,0,39,55 chr1 2288852 . G A 1111.84 PASS AC=1;AF=0.5;AN=2;DP=877;MQ=60;set=variant8-variant9-variant21-variant22-variant23-variant26-variant27-variant31-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:56,47:103:99:1446,0,1743:29,27,27,20 chr1 2310470 . A T 764.87 PASS AC=1;AF=0.5;AN=2;DP=272;MQ=60;set=variant2-variant22-variant24-variant35 GT:AD:DP:GQ:PL:SB 0/1:26,29:55:99:729,0,744:16,10,12,17 chr1 2316583 . C T 751.45 PASS AC=1;AF=0.5;AN=2;DP=280;FractionInformativeReads=1;MQ=60;set=variant2-variant22-variant24-variant35 GT:AD:DP:GQ:PL:SB 0/1:41,31:72:99:764,0,1028:21,20,13,18 chr1 2323041 . T C 5410.81 PASS AC=1;AF=0.565;AN=2;DP=3406;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant9-variant10-variant13-variant14-variant15-variant16-variant18-variant20-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant35-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:70,70:140:99:1700,0,1643:34,36,36,34 chr1 2325760 . G A 1561.92 PASS AC=1;AF=0.5;AN=2;DP=287;FractionInformativeReads=1;MQ=60;set=variant22-variant35 GT:AD:DP:GQ:PL:SB 0/1:63,91:154:99:2345,0,1600:33,30,51,40 chr1 2326009 . G A 997.97 PASS AC=1;AF=0.586;AN=2;DP=2311;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant35-variant36-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,45:92:99:1103,0,1284:20,27,20,25 chr1 2326812 . A G 964.11 PASS AC=1;AF=0.603;AN=2;DP=1888;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant35-variant36-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,28:76:99:844,0,1234:22,26,14,14 chr1 2326960 . A C 659.56 PASS AC=1;AF=0.5;AN=2;DP=145;FractionInformativeReads=1;MQ=60;set=variant22-variant29-variant35 GT:AD:DP:GQ:PL:SB 0/1:36,22:58:99:547,0,933:15,21,10,12 chr1 2328714 . A G 2190.97 PASS AC=2;AF=0.955;AN=2;DP=2261;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,52:53:99:1824,147,0:0,1,11,41 chr1 2332391 . C T 1978.98 PASS AC=1;AF=0.621;AN=2;DP=3881;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant35-variant36-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:79,52:131:99:1258,0,2073:38,41,22,30 chr1 2337032 . C T 689.54 PASS AC=1;AF=0.643;AN=2;DP=1385;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:20,27:47:99:746,0,640:12,8,17,10 chr1 2337194 . C T 1420.47 PASS AC=1;AF=0.5;AN=2;DP=413;FractionInformativeReads=1;MQ=60;set=variant22-variant29-variant35 GT:AD:DP:GQ:PL:SB 0/1:87,75:162:99:1779,0,2058:43,44,39,36 chr1 2338126 . C A 1242.2 PASS AC=1;AF=0.635;AN=2;DP=4257;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant30-variant35-variant36-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:93,97:190:99:2331,0,2383:44,49,50,47 chr1 2338389 . C T 2000.78 PASS AC=1;AF=0.5;AN=2;DP=236;FS=1.611;FractionInformativeReads=1;MQ=60;MQRankSum=-1.464;QD=8.48;ReadPosRankSum=-2.198;SOR=0.835;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:140,96:236:99:2029,0,3677:66,74,42,54 chr1 2339573 . G T 42.97 PASS AC=1;AF=0.5;AN=2;DP=17;FS=0;FractionInformativeReads=1;MQ=60;set=variant22-variant29-variant35 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:76:76,0,84:1,2,2,1 chr1 2340173 . C T 2001.5 PASS AC=1;AF=0.5;AN=2;DP=366;MQ=60;set=variant-variant35 GT:AD:DP:GQ:PL:SB 0/1:109,106:215:99:2485,0,2683:67,42,59,47 chr1 2340200 . T C 4682.04 PASS AC=2;AF=0.89;AN=2;DP=9238;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,264:264:99:7768,791,0:0,0,146,118 chr1 2398864 . C G 402.1 PASS AC=1;AF=0.542;AN=2;DP=520;FractionInformativeReads=1;MQ=60;set=variant5-variant7-variant8-variant12-variant15-variant16-variant19-variant20-variant21-variant35-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,40:49:99:913,0,174:6,3,21,19 chr1 2398881 . GCCTTCCTCA G 623.8 PASS AC=1;AF=0.648;AN=2;DP=1205;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant13-variant14-variant17-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,12:59:99:352,0,1896:24,23,9,3 chr1 2399119 . A G 2255.79 PASS AC=2;AF=0.694;AN=2;DP=5468;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,170:170:99:7336,515,0:0,0,80,90 chr1 2399149 . A G 2060.83 PASS AC=2;AF=0.694;AN=2;DP=4808;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,154:154:99:6851,467,0:0,0,71,83 chr1 2409892 . A G 1373.09 PASS AC=1;AF=0.814;AN=2;DP=4422;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:74,68:142:99:1546,0,2029:43,31,36,32 chr1 2410789 . C T 1165.85 PASS AC=1;AF=0.809;AN=2;DP=2300;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,42:76:99:1157,0,846:13,21,16,26 chr1 2411451 . A G 2087.81 PASS AC=1;AF=0.824;AN=2;DP=4335;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:72,71:143:99:1767,0,2002:29,43,29,42 chr1 2418935 . C T 294.88 PASS AC=1;AF=0.794;AN=2;DP=812;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,19:37:99:685,0,624:13,5,15,4 chr1 2420590 . T C 652.97 PASS AC=1;AF=0.805;AN=2;DP=2233;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,21:53:99:537,0,977:23,9,13,8 chr1 2420913 . A G 74.46 PASS AC=1;AF=0.778;AN=2;DP=971;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,19:32:99:658,0,304:3,10,5,14 chr1 2422614 . G A 772.2 PASS AC=1;AF=0.798;AN=2;DP=3909;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,43:89:99:941,0,1161:26,20,25,18 chr1 2426766 . A G 211.39 PASS AC=1;AF=0.647;AN=2;DP=649;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,12:27:99:297,0,467:10,5,8,4 chr1 2428874 . T C 439.37 PASS AC=1;AF=0.833;AN=2;DP=3383;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,52:112:99:1356,0,978:36,24,45,7 chr1 2430617 . C T 2186.62 PASS AC=1;AF=0.633;AN=2;DP=8532;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant14-variant15-variant17-variant20-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:195,184:379:99:4029,0,4635:97,98,90,94 chr1 2433900 . C T 1513.56 PASS AC=1;AF=0.652;AN=2;DP=4398;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,75:129:99:1884,0,1202:25,29,41,34 chr1 2434744 . C T 1060.29 PASS AC=1;AF=0.556;AN=2;DP=2145;MQ=60;set=variant-variant3-variant5-variant7-variant9-variant11-variant16-variant18-variant21-variant26-variant28-variant33-variant34-variant35-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:74,59:133:99:1533,0,1788:41,33,28,31 chr1 2435349 . A C 335.87 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=3245;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:69,25:94:99:205,0,2591:5,64,24,1 chr1 2435352 . T C 314.56 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=2836;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:68,29:97:99:477,0,1132:4,64,27,2 chr1 2435357 . A C 553.33 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=1176;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:68,18:86:99:190,0,2542:5,63,17,1 chr1 2444414 . G A 1373.04 PASS AC=1;AF=0.705;AN=2;DP=2861;set=variant-variant2-variant4-variant6-variant9-variant14-variant15-variant16-variant17-variant18-variant20-variant23-variant27-variant29-variant32-variant35-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:81,76:157:99:1697,0,2029:41,40,39,37 chr1 2452569 . T C 950.93 PASS AC=1;AF=0.821;AN=2;DP=2170;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,26:64:99:733,0,1039:26,12,18,8 chr1 2487663 . C A 918.5 PASS AC=1;AF=0.703;AN=2;DP=4549;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant19-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:88,82:170:99:1968,0,2132:51,37,49,33 chr1 2487766 . T C 1438.44 PASS AC=1;AF=0.703;AN=2;DP=5104;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant19-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:93,99:192:99:2262,0,2310:37,56,42,57 chr1 2488153 . A G 634.98 PASS AC=1;AF=0.703;AN=2;DP=2462;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant19-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:52,44:96:99:1083,0,1348:16,36,18,26 chr1 2490898 . C A 1606.99 PASS AC=1;AF=0.703;AN=2;DP=7042;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant19-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:132,131:263:99:2945,0,3195:69,63,81,50 chr1 2490942 . C A 2833.18 PASS AC=1;AF=0.703;AN=2;DP=8428;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant19-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:160,157:317:99:3910,0,3886:82,78,82,75 chr1 2491205 . C T 2395.35 PASS AC=1;AF=0.703;AN=2;DP=6689;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant19-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:122,148:270:99:3872,0,3251:65,57,74,74 chr1 2494785 . G A 1226.27 PASS AC=1;AF=0.703;AN=2;DP=3451;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant19-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:51,64:115:99:1596,0,1378:27,24,29,35 chr1 2518186 . A G 667.58 PASS AC=2;AF=1;AN=2;DP=909;FS=0;MQ=60;MQRankSum=1.239;ReadPosRankSum=1.569;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:866,69,0:0,0,19,4 chr1 2520302 . T C 5864 PASS AC=1;AF=0.611;AN=2;DP=4363;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant16-variant19-variant20-variant21-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:102,87:189:99:2000,0,2541:56,46,49,38 chr1 2520500 . G A 3274.49 PASS AC=1;AF=0.611;AN=2;DP=1662;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant16-variant19-variant20-variant21-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:39,31:70:99:923,0,1157:10,29,8,23 chr1 2520527 . T C 2152.55 PASS AC=1;AF=0.611;AN=2;DP=1009;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant16-variant19-variant20-variant21-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:23,20:43:99:628,0,728:5,18,7,13 chr1 2522204 . G T 6578.55 PASS AC=1;AF=0.545;AN=2;DP=1822;MQ=60;set=variant3-variant5-variant7-variant8-variant9-variant16-variant21-variant28-variant34-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:87,104:191:99:2576,0,2041:46,41,56,48 chr1 2522392 . G A 2647.81 PASS AC=1;AF=0.7;AN=2;DP=5769;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant9-variant11-variant14-variant15-variant16-variant17-variant18-variant20-variant23-variant24-variant26-variant27-variant32-variant35-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:137,107:244:99:2617,0,3688:64,73,56,51 chr1 2523212 . G C 1286.29 PASS AC=1;AF=0.611;AN=2;DP=707;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant16-variant19-variant20-variant21-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:20,10:30:99:311,0,670:13,7,10,0 chr1 2524205 . C T 7252.87 PASS AC=1;AF=0.611;AN=2;DP=4910;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant16-variant19-variant20-variant21-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:102,94:196:99:2298,0,2460:58,44,56,38 chr1 2524457 . T C 2581.71 PASS AC=1;AF=0.611;AN=2;DP=1421;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant16-variant19-variant20-variant21-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:27,40:67:99:1218,0,772:5,22,9,31 chr1 2526571 . G A 1671.22 PASS AC=1;AF=0.545;AN=2;DP=551;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant7-variant8-variant9-variant16-variant21-variant28-variant34-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:26,36:62:99:1075,0,705:20,6,27,9 chr1 2526746 . A G 10768.2 PASS AC=1;AF=0.611;AN=2;DP=7578;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant16-variant19-variant20-variant21-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:136,157:293:99:3873,0,3201:69,67,78,79 chr1 2527678 . A G 509.75 PASS AC=1;AF=0.737;AN=2;DP=1352;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,24:45:99:696,0,601:3,18,7,17 chr1 2528133 . T C 5016.85 PASS AC=1;AF=0.724;AN=2;DP=9553;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:165,137:302:99:3086,0,4038:72,93,62,75 chr1 2530341 . A AG 811.16 PASS AC=1;AF=0.737;AN=2;DP=1145;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,13:34:99:384,0,669:7,14,3,10 chr1 2535613 . C A 4507.78 PASS AC=1;AF=0.611;AN=2;DP=3117;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant16-variant19-variant20-variant21-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:78,86:164:99:2345,0,2167:40,38,47,39 chr1 2535758 . A G 6090.62 PASS AC=1;AF=0.611;AN=2;DP=4922;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant16-variant19-variant20-variant21-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:129,117:246:99:2781,0,3090:59,70,51,66 chr1 2537095 . G A 5408.89 PASS AC=1;AF=0.611;AN=2;DP=3799;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant16-variant19-variant20-variant21-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:78,83:161:99:1920,0,1723:34,44,34,49 chr1 2537838 . C T 3749.54 PASS AC=1;AF=0.611;AN=2;DP=2192;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant16-variant19-variant20-variant21-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:53,33:86:99:739,0,1299:23,30,14,19 chr1 2538349 . G A 2103.88 PASS AC=1;AF=0.611;AN=2;DP=1365;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant16-variant19-variant20-variant21-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:34,30:64:99:827,0,1034:26,8,23,7 chr1 2541269 . A G 3158.02 PASS AC=1;AF=0.611;AN=2;DP=2485;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant16-variant19-variant20-variant21-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:50,61:111:99:1409,0,1195:21,29,28,33 chr1 2542653 . A G 5548.88 PASS AC=1;AF=0.611;AN=2;DP=4411;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant16-variant19-variant20-variant21-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:91,94:185:99:2441,0,2044:54,37,56,38 chr1 2560735 . A G 839.58 PASS AC=1;AF=0.724;AN=2;DP=1882;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,24:38:99:743,0,402:12,2,15,9 chr1 2560882 . G A 2668.7 PASS AC=1;AF=0.724;AN=2;DP=2881;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,47:89:99:1741,0,2001:18,24,21,26 chr1 2560903 . T G 2517.21 PASS AC=1;AF=0.724;AN=2;DP=2809;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,47:77:99:1792,0,1679:11,19,21,26 chr1 2564183 . T C 1038.18 PASS AC=1;AF=0.724;AN=2;DP=1927;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,30:47:99:966,0,503:9,8,16,14 chr1 2564465 . T C 1819.09 PASS AC=1;AF=0.724;AN=2;DP=1842;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,19:33:99:559,0,358:8,6,8,11 chr1 2573199 . A G 3678.94 PASS AC=1;AF=0.884;AN=2;DP=4829;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,69:125:99:1612,0,1256:25,31,31,38 chr1 2700117 . C G 1445.55 PASS AC=1;AF=0.7;AN=2;DP=1475;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant23-variant24-variant26-variant27-variant29-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,32:61:99:872,0,869:23,6,22,10 chr1 2704444 . C T 74.6 PASS AC=1;AF=0.5;AN=2;DP=49;FractionInformativeReads=1;MQ=60;set=variant-variant17-variant35 GT:AD:DP:GQ:PL:SB 0/1:10,10:20:99:250,0,220:4,6,4,6 chr1 2704471 . C T 401.14 PASS AC=1;AF=0.731;AN=2;DP=279;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant23-variant24-variant26-variant29-variant31-variant32-variant33-variant35-variant37-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,9:15:99:225,0,145:2,4,3,6 chr1 2717470 . G A 1658.91 PASS AC=1;AF=0.611;AN=2;DP=1066;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant16-variant19-variant20-variant21-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:15,28:43:99:739,0,284:7,8,8,20 chr1 2938989 . G A 1606.92 PASS AC=1;AF=0.6;AN=2;DP=3211;MQ=60;set=variant-variant3-variant5-variant8-variant11-variant12-variant13-variant17-variant18-variant19-variant22-variant23-variant24-variant25-variant31-variant32-variant34-variant35-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:85,87:172:99:2416,0,2272:36,49,36,51 chr1 2983963 . G A 6949.55 PASS AC=1;AF=0.645;AN=2;DP=7384;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant27-variant31-variant32-variant33-variant34-variant35-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:138,128:266:99:2737,0,3092:80,58,73,55 chr1 3154621 . C T 1271.83 PASS AC=1;AF=0.545;AN=2;DP=924;MQ=60;set=variant3-variant10-variant28-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:28,42:70:99:1010,0,609:14,14,23,19 chr1 3301721 . C T 2218.61 PASS AC=1;AF=0.63;AN=2;DP=3080;MQ=60;set=variant-variant2-variant3-variant9-variant10-variant11-variant15-variant16-variant17-variant19-variant20-variant21-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant35-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:53,76:129:99:2164,0,1343:37,16,53,23 chr1 3310928 . C CCG 228.73 PASS AC=2;AF=1;AN=2;DP=587;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:33:448,33,0:0,0,4,5 chr1 3311212 . C G 801.47 PASS AC=2;AF=0.795;AN=2;DP=1040;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:836,87,0:0,0,12,17 chr1 3311261 . C T 433.73 PASS AC=2;AF=0.75;AN=2;DP=499;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:606,60,0:0,0,8,12 chr1 3312914 . T G 4084.81 PASS AC=1;AF=0.63;AN=2;DP=3121;MQ=60;set=variant-variant2-variant9-variant10-variant11-variant15-variant16-variant17-variant19-variant20-variant21-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant35-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:72,67:139:99:1499,0,1698:30,42,37,30 chr1 3312963 . C T 1469.31 PASS AC=1;AF=0.607;AN=2;DP=1715;MQ=60;set=variant3-variant4-variant6-variant7-variant8-variant15-variant23-variant25-variant29-variant32-variant35-variant36-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:59,49:108:99:1250,0,1492:27,32,19,30 chr1 3319365 . G A 2946.43 PASS AC=1;AF=0.5;AN=2;DP=217;FS=1.682;FractionInformativeReads=1;MQ=60;MQRankSum=-2.216;QD=13.58;ReadPosRankSum=2.274;SOR=0.585;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:88,129:217:99:2975,0,2055:51,37,71,58 chr1 3322228 . G A 4806.6 PASS AC=1;AF=0.5;AN=2;DP=399;FS=2.123;FractionInformativeReads=0.997;MQ=60;MQRankSum=2.717;QD=12.05;ReadPosRankSum=6.467;SOR=0.584;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:182,216:398:99:4835,0,4253:79,103,100,116 chr1 3328358 . T C 1550.43 PASS AC=1;AF=0.817;AN=2;DP=8802;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:170,109:279:99:2588,0,4049:83,87,61,48 chr1 3328659 . C T 11882.7 PASS AC=1;AF=0.583;AN=2;DP=4494;MQ=60;set=variant7-variant8-variant15-variant25-variant27-variant29-variant32-variant35-variant36-variant37-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:218,181:399:99:4124,0,5319:106,112,89,92 chr1 3342109 . G T 288.69 PASS AC=1;AF=0.639;AN=2;DP=956;MQ=60;set=variant-variant7-variant8-variant11-variant14-variant15-variant17-variant18-variant28-variant29-variant30-variant32-variant33-variant35-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:34,34:68:99:755,0,875:20,14,20,14 chr1 3350134 . T TGGGATGGCCCGCCCTGCCCACGCGCTCACCTGCCTGTCTGGGATGGCCCGCCCTGCCCACGCGCTCACCTGCCTGTCC 224.46 PASS AC=1;AF=0.813;AN=2;DP=42;FS=0;set=variant5-variant10-variant15-filterInvariant18-filterInvariant34-variant35-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:16,0:16:99:240,0,334:13,3,0,0 chr1 3350173 . T TGGGATGGCCCGCCCTGCCCACGCGCTCACCTGCCTGTCCGGGATGGCCCGCCCTGCCCACGCGCTCACCTGCCTGTCC,TGGGATGGCCCGCCCTGCCCACGCGCTCACCTGCCTGTCC 859.75 PASS AC=0,1;AF=0.25,0.375;AN=2;DP=180;set=variant7-variant15-variant35-variant41 GT:DP:GQ:SB 0/2:44:99:29,14,1,0 chr1 3352227 . T C 2206.83 PASS AC=2;AF=0.965;AN=2;DP=2861;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:2302,216,0:0,0,42,30 chr1 3352347 . T C 4129.58 PASS AC=2;AF=0.965;AN=2;DP=7808;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,187:187:99:6080,559,0:0,0,126,61 chr1 3352503 . G C 7294.78 PASS AC=2;AF=0.965;AN=2;DP=12181;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,379:379:99:10946,1131,0:0,0,159,220 chr1 3352541 . T C 5234.77 PASS AC=2;AF=0.833;AN=2;DP=8531;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,273:273:99:8547,816,0:0,0,107,166 chr1 3352579 . T C 3752.35 PASS AC=2;AF=0.965;AN=2;DP=5733;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,186:186:99:6113,558,0:0,0,65,121 chr1 3352763 . CTT CT,C 3376.53 PASS AC=2,0;AF=0.953,0.012;AN=2;DP=2973;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:75:99:2,0,38,35 chr1 3352784 . A G 3981.18 PASS AC=2;AF=0.965;AN=2;DP=3084;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,74:74:99:3236,226,0:0,0,40,34 chr1 3353890 . A G 2087.8 PASS AC=2;AF=0.965;AN=2;DP=3842;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,105:105:99:3170,315,0:0,0,53,52 chr1 3353949 . A G 2356.88 PASS AC=2;AF=0.965;AN=2;DP=4109;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,108:108:99:3322,322,0:0,0,52,56 chr1 3354595 . T C 5468.96 PASS AC=2;AF=0.965;AN=2;DP=5000;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,126:126:99:5435,385,0:0,0,64,62 chr1 3354615 . T C 5568.17 PASS AC=2;AF=0.965;AN=2;DP=4971;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,119:119:99:5222,361,0:0,0,63,56 chr1 3354671 . A G 2194.08 PASS AC=1;AF=0.5;AN=2;DP=181;FS=2.62;FractionInformativeReads=1;MQ=60;MQRankSum=1.674;QD=12.12;ReadPosRankSum=1.461;SOR=0.915;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:97,84:181:99:2222,0,2519:54,43,51,33 chr1 3383038 . G A 426.45 PASS AC=1;AF=0.565;AN=2;DP=389;FractionInformativeReads=1;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant18-variant23-variant25-variant27-variant30-variant35-variant36-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,22:30:99:640,0,192:3,5,7,15 chr1 3383593 . G T 1354.59 PASS AC=2;AF=0.953;AN=2;DP=3314;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,83:83:99:2487,248,0:0,0,47,36 chr1 3383665 . G A 2730.25 PASS AC=2;AF=0.953;AN=2;DP=5880;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,142:142:99:4387,424,0:0,0,84,58 chr1 3383898 . A G 1913.72 PASS AC=2;AF=0.953;AN=2;DP=3186;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,91:91:99:2826,273,0:0,0,33,58 chr1 3385250 . C A 1361.15 PASS AC=1;AF=0.671;AN=2;DP=1625;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,25:54:99:684,0,1128:23,6,19,6 chr1 3385256 . A G 709.72 PASS AC=1;AF=0.583;AN=2;DP=1415;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant18-variant19-variant20-variant21-variant23-variant25-variant27-variant28-variant30-variant31-variant32-variant35-variant36-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:30,30:60:99:826,0,1075:22,8,22,8 chr1 3385330 . T C 3150.19 PASS AC=2;AF=1;AN=2;DP=5133;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,121:121:99:3780,362,0:0,0,68,53 chr1 3389727 . C T 1141.08 PASS AC=2;AF=0.952;AN=2;DP=4608;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,123:123:99:3506,367,0:0,0,63,60 chr1 3390238 . T A 3745.3 PASS AC=2;AF=1;AN=2;DP=5680;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,125:125:99:3870,373,0:0,0,41,84 chr1 3394456 . T C 1881.94 PASS AC=2;AF=1;AN=2;DP=3763;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,116:116:99:3926,347,0:0,0,63,53 chr1 3394640 . A G 3232.56 PASS AC=2;AF=0.988;AN=2;DP=5562;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,147:147:99:4354,439,0:0,0,57,90 chr1 3394674 . T C 1804.3 PASS AC=2;AF=1;AN=2;DP=3551;FS=0;MQ=60;MQRankSum=0.554;ReadPosRankSum=1.661;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,101:101:99:3484,302,0:0,0,27,74 chr1 3395039 . G A 6477.59 PASS AC=2;AF=0.94;AN=2;DP=12732;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,347:347:99:10000,1035,0:0,0,164,183 chr1 3395171 . C A 1092.93 PASS AC=1;AF=0.5;AN=2;DP=77;FS=3.875;FractionInformativeReads=1;MQ=60;MQRankSum=1.138;QD=14.19;ReadPosRankSum=0.577;SOR=0.293;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:36,41:77:99:1121,0,1121:6,30,11,30 chr1 3395229 . T C 716.23 PASS AC=2;AF=1;AN=2;DP=1143;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:1087,96,0:0,0,7,25 chr1 3395973 . ACC A 3390.47 PASS AC=2;AF=0.952;AN=2;DP=4570;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,140:140:99:6106,422,0:0,0,92,48 chr1 3396609 . C T 942.84 PASS AC=2;AF=0.952;AN=2;DP=1364;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1564,117,0:0,0,3,36 chr1 3397188 . T C 4270.55 PASS AC=2;AF=1;AN=2;DP=7570;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,177:177:99:6042,531,0:0,0,76,101 chr1 3397415 . C CCT 3504.79 PASS AC=2;AF=1;AN=2;DP=4067;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,100:100:99:4373,300,0:0,0,45,55 chr1 3397455 . G A 2015.75 PASS AC=2;AF=0.952;AN=2;DP=3070;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:2538,236,0:0,0,33,46 chr1 3397564 . C T 795.96 PASS AC=2;AF=0.952;AN=2;DP=1841;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,52:52:99:1502,156,0:0,0,24,28 chr1 3413868 . C G 1422.26 PASS AC=1;AF=0.717;AN=2;DP=2838;MQ=60;set=variant-variant2-variant5-variant7-variant9-variant10-variant11-variant13-variant14-variant17-variant18-variant20-variant22-variant25-variant29-variant31-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:74,82:156:99:2135,0,2073:37,37,42,40 chr1 3414105 . C T 1594.84 PASS AC=1;AF=0.722;AN=2;DP=4219;set=variant-variant3-variant4-variant6-variant7-variant8-variant11-variant12-variant15-variant16-variant17-variant19-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:86,86:172:99:1906,0,2112:39,47,42,44 chr1 3416449 . C A 2846.6 PASS AC=2;AF=0.845;AN=2;DP=3942;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,89:89:99:2747,267,0:0,0,37,52 chr1 3416758 . A G 62.99 PASS AC=2;AF=0.97;AN=2;DP=202;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant31-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:267,24,0:0,0,3,5 chr1 3417131 . A G 4143.91 PASS AC=2;AF=0.898;AN=2;DP=7206;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,215:215:99:6494,643,0:0,0,115,100 chr1 3417960 . G A 2286.88 PASS AC=2;AF=0.845;AN=2;DP=4198;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,133:133:99:3794,396,0:0,0,54,79 chr1 3418391 . C T 1657 PASS AC=1;AF=0.712;AN=2;DP=4326;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant9-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant20-variant22-variant25-variant28-variant29-variant34-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,92:148:99:2170,0,1266:32,24,47,45 chr1 3418565 . T C 1653.24 PASS AC=2;AF=0.961;AN=2;DP=2424;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,67:67:99:2148,201,0:0,0,31,36 chr1 3440647 . T C 1815.65 PASS AC=2;AF=0.92;AN=2;DP=3171;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:2395,231,0:0,0,51,26 chr1 3447914 . G C 151.87 PASS AC=1;AF=0.673;AN=2;DP=555;MQ=60;set=variant-variant3-variant4-variant6-variant8-variant12-variant15-variant16-variant17-variant19-variant21-variant23-variant24-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:11,12:23:99:265,0,290:4,7,6,6 chr1 3496328 . T C 1270.13 PASS AC=2;AF=0.943;AN=2;DP=1876;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:1579,144,0:0,0,34,14 chr1 3496479 . T C 3123.75 PASS AC=2;AF=0.955;AN=2;DP=5379;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,128:128:99:3887,382,0:0,0,59,69 chr1 3518857 . A C 271.38 PASS AC=2;AF=0.989;AN=2;DP=471;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:463,39,0:0,0,9,4 chr1 3518944 . T C 1579.37 PASS AC=1;AF=0.705;AN=2;DP=1947;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,22:56:99:485,0,900:22,12,15,7 chr1 3519179 . C T 1233.32 PASS AC=1;AF=0.586;AN=2;DP=2940;MQ=60;set=variant2-variant4-variant5-variant6-variant9-variant10-variant13-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:81,56:137:99:1360,0,2172:31,50,22,34 chr1 3527944 . C G 2126.01 PASS AC=2;AF=0.966;AN=2;DP=3145;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:2379,228,0:0,0,34,42 chr1 3528082 . T C 740.88 PASS AC=2;AF=0.989;AN=2;DP=1687;FS=0;MQ=60;MQRankSum=-0.905;ReadPosRankSum=0.358;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1455,150,0:0,0,20,30 chr1 3542106 . T TG 2245.69 PASS AC=1;AF=0.6;AN=2;DP=5824;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant11-variant12-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:113,94:207:99:2286,0,2882:45,68,47,47 chr1 3544235 . TA T 1986.71 PASS AC=1;AF=0.577;AN=2;DP=3963;MQ=60;set=variant-variant3-variant6-variant7-variant11-variant12-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant34-variant35-variant36-variant37-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:68,62:130:99:1821,0,2018:31,37,18,44 chr1 3545175 . GTTCTGGGAGCTCCTCCCCC G 2754.17 PASS AC=2;AF=0.857;AN=2;DP=4161;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,86:86:99:3765,266,0:0,0,39,47 chr1 3545612 . A G 599.57 PASS AC=1;AF=0.58;AN=2;DP=860;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant6-variant7-variant11-variant12-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant34-variant35-variant36-variant37-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,19:32:99:553,0,365:5,8,9,10 chr1 3546264 . CCGGG C 427.59 PASS AC=1;AF=0.621;AN=2;DP=440;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant22-variant23-variant25-variant27-variant28-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,8:23:99:291,0,829:9,6,7,1 chr1 3548136 . T C 1994.12 PASS AC=2;AF=0.845;AN=2;DP=3769;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,100:100:99:3347,300,0:0,0,42,58 chr1 3548342 . G A 72.21 PASS AC=1;AF=0.583;AN=2;DP=494;MQ=60;set=variant-variant6-variant7-variant11-variant12-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant34-variant35-variant36-variant37-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,9:17:99:244,0,248:3,5,2,7 chr1 3549852 . G A 1060.85 PASS AC=1;AF=0.596;AN=2;DP=1155;MQ=60;set=variant-variant5-variant6-variant7-variant11-variant12-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant34-variant35-variant36-variant37-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,22:31:99:654,0,178:6,3,17,5 chr1 3555428 . G T 634.31 PASS AC=1;AF=0.583;AN=2;DP=1405;MQ=60;set=variant-variant6-variant7-variant11-variant12-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant34-variant35-variant36-variant37-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:29,48:77:99:1218,0,757:10,19,21,27 chr1 3563512 . GC G 175.71 PASS AC=1;AF=0.689;AN=2;DP=877;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant22-variant23-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,16:35:99:525,0,661:5,14,4,12 chr1 3566625 . AGCAGGCTG A 2435.27 PASS AC=1;AF=0.603;AN=2;DP=3918;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant22-variant23-variant25-variant27-variant28-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:69,85:154:99:3335,0,2636:24,45,35,50 chr1 3566706 . G A 2038.47 PASS AC=2;AF=0.909;AN=2;DP=1846;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1538,136,0:0,0,11,35 chr1 3607520 . G A 2830.57 PASS AC=1;AF=0.64;AN=2;DP=5764;MQ=60;set=variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant17-variant19-variant21-variant22-variant23-variant24-variant26-variant30-variant31-variant32-variant35-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:148,108:256:99:2446,0,3727:77,71,52,56 chr1 3638674 . C T 4834.06 PASS AC=2;AF=0.932;AN=2;DP=11405;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,280:280:99:8211,835,0:0,0,125,155 chr1 3640085 . C G 357.88 PASS AC=2;AF=0.886;AN=2;DP=1275;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:842,69,0:0,0,6,17 chr1 3640134 . TCTGC T 232.97 PASS AC=2;AF=0.886;AN=2;DP=798;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:585,39,0:0,0,2,11 chr1 3644085 . G A 465.42 PASS AC=2;AF=0.667;AN=2;DP=856;MQ=60;set=variant-variant2-variant4-variant6-variant8-variant9-variant10-variant11-variant14-variant19-variant21-variant22-variant23-variant24-variant26-variant29-variant30-variant31-variant32-variant33-variant35-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:1732,141,0:0,0,36,11 chr1 3644349 . A G 2276.64 PASS AC=2;AF=0.852;AN=2;DP=3970;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,104:104:99:4055,312,0:0,0,35,69 chr1 3644374 . A G 1634.88 PASS AC=2;AF=0.852;AN=2;DP=2547;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:2917,202,0:0,0,18,44 chr1 3645835 . C A 390.74 PASS AC=2;AF=0.791;AN=2;DP=1106;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1738,120,0:0,0,25,13 chr1 3645844 . G A 390.74 PASS AC=2;AF=0.83;AN=2;DP=1295;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1909,138,0:0,0,28,18 chr1 3646137 . C T 4166.65 PASS AC=2;AF=0.791;AN=2;DP=6258;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,158:158:99:4458,469,0:0,0,73,85 chr1 3646192 . G A 5059.29 PASS AC=2;AF=0.83;AN=2;DP=5818;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,157:157:99:6742,475,0:0,0,66,91 chr1 3646214 . T C 5033.4 PASS AC=2;AF=0.852;AN=2;DP=5618;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,143:143:99:6296,439,0:0,0,62,81 chr1 3646291 . G A 2345.98 PASS AC=2;AF=0.83;AN=2;DP=4402;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,107:107:99:3265,321,0:0,0,50,57 chr1 3647962 . T C 1746.15 PASS AC=2;AF=0.83;AN=2;DP=2445;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:2085,186,0:0,0,40,22 chr1 3650483 . CT CTT,CTTT,C 86.31 PASS AC=1,0,0;AF=0.446,0.018,0.089;AN=2;DP=917;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant26-variant27-variant28-filterInvariant29-variant31-variant34-variant35-variant40-variant42 GT:DP:GQ:SB 0/1:19:24:2,3,6,8 chr1 3651098 . C T 1764.72 PASS AC=2;AF=0.791;AN=2;DP=3577;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,84:84:99:2684,252,0:0,0,43,41 chr1 3651126 . G T 1650.27 PASS AC=2;AF=0.791;AN=2;DP=3952;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,85:85:99:2646,254,0:0,0,49,36 chr1 3651318 . A G 2327.96 PASS AC=2;AF=0.83;AN=2;DP=4384;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,141:141:99:4435,422,0:0,0,70,71 chr1 3652822 . C G 341.9 PASS AC=2;AF=0.81;AN=2;DP=510;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:496,42,0:0,0,5,9 chr1 3683690 . A C 137.38 PASS AC=1;AF=0.671;AN=2;DP=1021;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,21:34:99:555,0,370:11,2,14,7 chr1 3691727 . A C 81.98 PASS AC=1;AF=0.563;AN=2;DP=342;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant10-variant16-variant18-variant20-variant21-variant24-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,6:17:99:179,0,290:9,2,5,1 chr1 3696890 . A C 1082.19 PASS AC=1;AF=0.671;AN=2;DP=4186;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:79,69:148:99:1869,0,1965:42,37,41,28 chr1 3697137 . G T 5124.2 PASS AC=1;AF=0.6;AN=2;DP=6706;MQ=60;set=variant-variant4-variant7-variant9-variant11-variant13-variant14-variant16-variant18-variant22-variant26-variant27-variant28-variant32-variant35-variant36-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:172,165:337:99:3877,0,4433:76,96,80,85 chr1 3697291 . C T 1017.77 PASS AC=1;AF=0.56;AN=2;DP=1456;MQ=60;set=variant-variant3-variant5-variant6-variant8-variant10-variant12-variant16-variant18-variant20-variant21-variant24-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,39:64:99:1214,0,699:3,22,8,31 chr1 3701491 . A G 64.2 PASS AC=1;AF=0.7;AN=2;DP=593;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,7:20:99:174,0,419:11,2,5,2 chr1 3703337 . G C 302.59 PASS AC=1;AF=0.731;AN=2;DP=1165;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,15:35:99:434,0,584:13,7,11,4 chr1 3703710 . G A 1838.9 PASS AC=1;AF=0.5;AN=2;DP=462;FractionInformativeReads=1;MQ=60;set=variant19-variant28-variant35 GT:AD:DP:GQ:PL:SB 0/1:105,83:188:99:2093,0,2735:53,52,45,38 chr1 3704041 . C T 194.88 PASS AC=1;AF=0.563;AN=2;DP=304;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant6-variant8-variant10-variant11-variant12-variant16-variant17-variant18-variant20-variant21-variant22-variant24-variant27-variant29-variant30-variant33-variant34-variant35-variant37-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:4,10:14:99:299,0,111:0,4,2,8 chr1 3729169 . C G 2334.27 PASS AC=1;AF=0.73;AN=2;DP=2485;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,46:82:99:1088,0,856:12,24,17,29 chr1 3729587 . A G 906.94 PASS AC=1;AF=0.645;AN=2;DP=1508;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,17:30:99:496,0,349:7,6,10,7 chr1 3730435 . T C 2496.48 PASS AC=1;AF=0.724;AN=2;DP=3103;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,35:90:99:1138,0,1739:44,11,33,2 chr1 3731654 . C CT 2162.82 PASS AC=1;AF=0.718;AN=2;DP=3093;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,44:80:99:1470,0,1200:16,20,25,19 chr1 3732103 . T C 7093.25 PASS AC=1;AF=0.724;AN=2;DP=9008;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:136,127:263:99:3122,0,3341:57,79,52,75 chr1 3732172 . C T 2919.41 PASS AC=1;AF=0.724;AN=2;DP=3837;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,63:124:99:1734,0,1583:20,41,18,45 chr1 3732596 . G T 1390.15 PASS AC=1;AF=0.73;AN=2;DP=1628;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,28:50:99:817,0,500:13,9,21,7 chr1 3732639 . T A 2161.46 PASS AC=1;AF=0.724;AN=2;DP=2929;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,44:82:99:1121,0,798:21,17,28,16 chr1 3732707 . T C 2879.57 PASS AC=1;AF=0.724;AN=2;DP=4495;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,70:122:99:1862,0,1183:27,25,36,34 chr1 3732782 . T C 3428.93 PASS AC=1;AF=0.718;AN=2;DP=4990;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:62,77:139:99:1984,0,1573:35,27,34,43 chr1 3743109 . A G 1678.54 PASS AC=1;AF=0.724;AN=2;DP=1794;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,28:52:99:1181,0,1711:22,2,22,6 chr1 3743132 . T C 2467.58 PASS AC=1;AF=0.736;AN=2;DP=2517;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,43:83:99:1521,0,2060:31,9,32,11 chr1 3743391 . C T 1763.56 PASS AC=1;AF=0.574;AN=2;DP=2865;MQ=60;set=variant3-variant5-variant6-variant8-variant10-variant11-variant12-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,53:109:99:1235,0,1373:22,34,19,34 chr1 3743433 . T TG 2718.13 PASS AC=2;AF=0.909;AN=2;DP=2689;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2465,210,0:0,0,21,49 chr1 3745721 . C T 523.97 PASS AC=1;AF=0.577;AN=2;DP=973;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant6-variant8-variant10-variant11-variant12-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant33-variant34-variant35-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,29:47:99:773,0,453:13,5,20,9 chr1 3745787 . T C 2025.52 PASS AC=1;AF=0.724;AN=2;DP=3458;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,45:100:99:1033,0,1317:33,22,26,19 chr1 3746254 . T C 900.02 PASS AC=2;AF=0.989;AN=2;DP=896;MQ=60;MQRankSum=-1.288;ReadPosRankSum=-1.111;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:605,57,0:0,0,13,6 chr1 3746583 . G T 1795.44 PASS AC=1;AF=0.611;AN=2;DP=1029;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant7-variant9-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:22,23:45:99:878,0,844:7,15,7,16 chr1 3746585 . T G 317.24 PASS AC=1;AF=0.577;AN=2;DP=966;MQ=60;set=variant3-variant5-variant6-variant8-variant10-variant11-variant12-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant33-variant34-variant35-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,21:43:99:813,0,883:7,15,7,14 chr1 3746589 . C G 1765.47 PASS AC=2;AF=0.989;AN=2;DP=1546;FractionInformativeReads=1;MQ=60;MQRankSum=1.168;ReadPosRankSum=0.526;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1924,129,0:0,0,14,29 chr1 3747580 . C T 343.46 PASS AC=1;AF=0.611;AN=2;DP=394;MQ=60;set=variant-variant4-variant5-variant7-variant9-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,12:21:99:374,0,342:8,1,10,2 chr1 3747603 . T C 885.15 PASS AC=2;AF=0.989;AN=2;DP=1043;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:1160,96,0:0,0,24,8 chr1 3752868 . CAAAA CAA,CA,C,CAAA 200.71 PASS AC=1,1,0,0;AF=0.357,0.381,0.012,0.024;AN=2;DP=491;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 2/1:17:99:0,1,13,3 chr1 3753032 . GTT GTTTT,GTTT,GTTTTT,GT,G,GTTTTTT 220.48 PASS AC=0,0,0,1,0,0;AF=0.104,0.313,0.021,0.063,0.021,0.021;AN=2;DP=1516;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant19-filterInvariant22-variant25-filterInvariant28-variant31-variant33-filterInvariant35-variant38-variant40-filterInvariant44 GT:DP:GQ:SB 0/4:40:99:12,12,7,9 chr1 3753136 . A T 1222.26 PASS AC=1;AF=0.611;AN=2;DP=2175;MQ=60;set=variant-variant4-variant5-variant7-variant9-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:57,33:90:99:829,0,1335:23,34,18,15 chr1 3755675 . T C 2416.4 PASS AC=2;AF=0.989;AN=2;DP=6954;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,175:175:99:5403,525,0:0,0,81,94 chr1 3756120 . A G 2938.76 PASS AC=1;AF=0.63;AN=2;DP=2119;MQ=60;set=variant-variant4-variant5-variant7-variant9-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:46,44:90:99:1120,0,1120:29,17,26,18 chr1 3759784 . A G 2690.8 PASS AC=2;AF=0.989;AN=2;DP=3906;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,83:83:99:2686,249,0:0,0,34,49 chr1 3759889 . TA TAA,T,TAAA 95.89 PASS AC=1,0,0;AF=0.524,0.024,0.024;AN=2;DP=389;MQ=60;set=variant-variant4-variant6-variant7-variant11-variant13-variant14-variant17-variant18-variant19-variant23-variant25-variant27-variant31-variant32-variant35-variant38-variant39-variant40-variant41-variant43 GT:DP:GQ:SB 0/1:15:99:3,5,1,6 chr1 3759937 . A G 33.26 PASS AC=1;AF=0.643;AN=2;DP=166;FractionInformativeReads=1;set=variant-variant4-variant5-variant9-variant13-variant14-variant16-variant17-variant19-variant25-variant26-variant27-variant28-variant31-variant32-variant35-variant36-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:3,7:10:99:219,0,107:0,3,2,5 chr1 3759940 . ATT ATTT,AT,A 44.53 PASS AC=1,0,0;AF=0.375,0.188,0.125;AN=2;DP=75;set=variant11-variant14-variant17-variant28-variant35-variant38-variant39-variant40 GT:DP:GQ:SB 0/1:9:99:0,3,2,4 chr1 3761273 . G GA 55.12 PASS AC=2;AF=0.8;AN=2;DP=97;FS=0;FractionInformativeReads=1;set=variant-variant4-variant14-variant17-variant18-variant23-variant25-variant27-variant28-variant31-variant32-variant35-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:122,12,0:0,0,3,1 chr1 3761479 . C T 2930.49 PASS AC=1;AF=0.611;AN=2;DP=2608;MQ=60;set=variant-variant4-variant5-variant7-variant9-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:58,67:125:99:1511,0,1310:29,29,35,32 chr1 3761650 . A G 1165.07 PASS AC=2;AF=0.989;AN=2;DP=1621;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:1181,96,0:0,0,9,23 chr1 3761772 . C T 828.1 PASS AC=1;AF=0.58;AN=2;DP=746;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant6-variant8-variant10-variant11-variant12-variant16-variant18-variant20-variant21-variant22-variant24-variant26-variant27-variant29-variant30-variant33-variant34-variant35-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,20:37:99:533,0,413:10,7,12,8 chr1 3764216 . C T 1218.03 PASS AC=1;AF=0.58;AN=2;DP=1999;set=variant3-variant5-variant6-variant8-variant10-variant11-variant12-variant16-variant18-variant20-variant21-variant22-variant24-variant26-variant27-variant29-variant30-variant33-variant34-variant35-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,43:69:99:1167,0,533:10,16,15,28 chr1 3765095 . CA CAAAA,C,CAA,CAAAAAAA,CAAAAAA,CAAAAA,CAAAAAAAAAA 207.8 PASS AC=0,0,0,0,1,0,0;AF=0.032,0.145,0.032,0.032,0.226,0.081,0.016;AN=2;DP=706;set=variant-filterInvariant2-filterInvariant3-variant4-variant7-filterInvariant10-variant12-variant13-filterInvariant15-variant16-variant17-variant19-filterInvariant22-variant23-filterInvariant24-variant25-variant26-variant28-variant29-variant31-variant32-filterInvariant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-filterInvariant42-variant43 GT:DP:GQ:SB 0/5:18:99:10,4,4,0 chr1 3773511 . G A 647.06 PASS AC=1;AF=0.583;AN=2;DP=862;MQ=60;set=variant3-variant5-variant6-variant8-variant10-variant11-variant12-variant16-variant18-variant20-variant21-variant22-variant24-variant26-variant29-variant30-variant33-variant34-variant35-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,31:46:99:755,0,320:6,9,16,15 chr1 3773588 . C G 1380.53 PASS AC=1;AF=0.615;AN=2;DP=1208;MQ=60;set=variant-variant4-variant7-variant9-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:28,19:47:99:517,0,679:14,14,13,6 chr1 3773718 . A G 2671.87 PASS AC=2;AF=0.989;AN=2;DP=4568;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,105:105:99:3245,314,0:0,0,58,47 chr1 3773815 . C G 1936.15 PASS AC=1;AF=0.604;AN=2;DP=2240;MQ=60;set=variant3-variant5-variant6-variant8-variant10-variant11-variant12-variant16-variant18-variant20-variant21-variant22-variant24-variant26-variant29-variant30-variant33-variant34-variant35-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,59:127:99:1365,0,1805:34,34,31,28 chr1 3775454 . C G 2696.93 PASS AC=2;AF=0.989;AN=2;DP=4562;MQ=60;MQRankSum=-0.24;ReadPosRankSum=-2.182;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,115:115:99:4031,345,0:0,0,31,84 chr1 3782115 . G A 552.51 PASS AC=1;AF=0.575;AN=2;DP=685;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant6-variant8-variant11-variant12-variant16-variant18-variant20-variant21-variant22-variant24-variant26-variant30-variant33-variant35-variant37-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,21:52:99:521,0,752:15,16,12,9 chr1 3782608 . C T 1645.17 PASS AC=2;AF=0.744;AN=2;DP=2338;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,63:63:99:1972,188,0:0,0,42,21 chr1 3784454 . T C 2893.14 PASS AC=1;AF=0.542;AN=2;DP=1542;FractionInformativeReads=1;MQ=60;set=variant5-variant10-variant11-variant12-variant20-variant26-variant33-variant34-variant35-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:60,80:140:99:3207,0,3444:39,21,52,28 chr1 3784464 . G A 3056.24 PASS AC=1;AF=0.5;AN=2;DP=1479;FractionInformativeReads=1;MQ=60;set=variant5-variant10-variant11-variant20-variant26-variant34-variant35-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:77,84:161:99:3259,0,3814:52,25,54,30 chr1 3786189 . G A 2788.78 PASS AC=1;AF=0.587;AN=2;DP=2273;MQ=60;set=variant-variant4-variant7-variant9-variant11-variant14-variant17-variant19-variant22-variant23-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:63,55:118:99:1365,0,1632:41,22,37,18 chr1 3786612 . C T 410.47 PASS AC=2;AF=0.74;AN=2;DP=220;MQ=60;set=variant4-variant7-variant13-variant14-variant15-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:226,21,0:0,0,1,6 chr1 3789194 . G GCGGCCC 1728.27 PASS AC=1;AF=0.672;AN=2;DP=2337;MQ=60;set=variant-variant2-variant4-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,29:81:99:1070,0,6538:19,33,11,18 chr1 3789195 . T TGTCCCTGCCGC,TGTCCCTGCCAC 1728.27 PASS AC=1,0;AF=0.656,0.016;AN=2;DP=2200;MQ=60;set=variant-variant2-variant4-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:79:99:19,33,9,18 chr1 3800242 . A G 4758.38 PASS AC=2;AF=0.731;AN=2;DP=6210;MQ=60;set=variant-variant4-variant7-variant9-variant11-variant14-variant17-variant19-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,293:293:99:8727,878,0:0,0,160,133 chr1 3800480 . G T 3380.95 PASS AC=2;AF=0.75;AN=2;DP=2729;MQ=60;set=variant-variant4-variant7-variant9-variant11-variant14-variant17-variant19-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,150:150:99:4804,450,0:0,0,48,102 chr1 3806264 . GAAAA GA,GAAA,G,GAA 55.73 PASS AC=1,0,0,0;AF=0.269,0.115,0.077,0.154;AN=2;DP=118;MQ=60;set=variant3-filterInvariant4-variant9-variant10-variant13-variant15-variant21-variant24-variant25-variant28-variant35-variant37-variant40 GT:DP:GQ:SB 0/1:5:68:1,2,2,0 chr1 3806358 . T C 489.85 PASS AC=1;AF=0.556;AN=2;DP=319;FractionInformativeReads=1;MQ=60;set=variant25-variant28-variant30-variant31-variant32-variant35-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,20:48:99:523,0,738:19,9,13,7 chr1 3806643 . T A 1367.65 PASS AC=1;AF=0.593;AN=2;DP=1869;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant13-variant15-variant18-variant20-variant21-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,32:77:99:844,0,1104:17,28,11,21 chr1 3807593 . G C 3277.02 PASS AC=2;AF=1;AN=2;DP=4492;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,123:123:99:3808,369,0:0,0,55,68 chr1 3809423 . G A 1652.85 PASS AC=1;AF=0.556;AN=2;DP=1381;FractionInformativeReads=1;MQ=60;set=variant25-variant28-variant30-variant31-variant32-variant35-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:89,86:175:99:1866,0,2164:38,51,43,43 chr1 3816508 . T C 300.13 PASS AC=1;AF=0.635;AN=2;DP=258;set=variant2-variant3-variant4-variant5-variant7-variant10-variant13-variant15-variant18-variant20-variant21-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,4:12:99:103,0,255:7,1,3,1 chr1 3816854 . G A 1625.89 PASS AC=1;AF=0.556;AN=2;DP=1104;MQ=60;set=variant25-variant28-variant30-variant31-variant32-variant35-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:63,87:150:99:2516,0,1773:42,21,53,34 chr1 3816892 . TCCCC TCC,TCCC,TC,T,TCCCCC,TTCCCCC,TTCCCCCCCCCCCCCC,TTCCCCCC 1597.52 PASS AC=2,0,0,0,0,0,0,0;AF=0.281,0.094,0.188,0.016,0.016,0.016,0.016,0.016;AN=2;DP=2708;MQ=60;set=variant-variant3-variant4-filterInvariant8-filterInvariant9-variant10-filterInvariant12-variant14-variant17-variant19-variant20-filterInvariant21-variant22-variant23-variant25-variant26-variant27-filterInvariant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:108:99:9,0,37,62 chr1 3816895 . C T 239.24 PASS AC=1;AF=0.5;AN=2;DP=1285;MQ=60;set=variant-filterInvariant20-variant22-filterInvariant23-filterInvariant26-variant30-variant31-variant32-variant35-variant36-variant38-filterInvariant39-filterInvariant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,44:64:99:693,0,151:9,11,11,33 chr1 4714995 . A G 2110.01 PASS AC=1;AF=0.675;AN=2;DP=1680;MQ=60;set=variant-filterInvariant2-variant3-variant4-variant5-variant6-variant8-variant14-variant15-variant16-variant19-variant20-variant22-variant23-variant27-variant28-variant34-variant35-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:74,32:106:99:607,0,1715:34,40,15,17 chr1 4772053 . T C 2461.02 PASS AC=1;AF=0.563;AN=2;DP=5271;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant12-variant14-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant33-variant34-variant35-variant36-variant37-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:143,143:286:99:3202,0,3140:66,77,71,72 chr1 4772717 . G A 1872.01 PASS AC=1;AF=0.763;AN=2;DP=3684;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,53:103:99:1411,0,1577:12,38,15,38 chr1 4834606 . T C 2311.08 PASS AC=1;AF=0.654;AN=2;DP=5301;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant28-variant30-variant32-variant35-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:117,122:239:99:3187,0,2894:47,70,46,76 chr1 4847595 . G A 1083.11 PASS AC=1;AF=0.5;AN=2;DP=103;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.848;QD=10.52;ReadPosRankSum=-0.834;SOR=0.695;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:58,45:103:99:1111,0,1704:36,22,28,17 chr1 4847845 . G A 3069.62 PASS AC=2;AF=0.762;AN=2;DP=13008;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,350:350:99:10644,1049,0:0,0,159,191 chr1 5623965 . C T 360.77 PASS AC=1;AF=0.62;AN=2;DP=1288;MQ=60;set=variant-variant2-variant7-variant8-variant9-variant10-variant14-variant16-variant18-variant20-variant21-variant23-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:22,30:52:99:835,0,619:14,8,19,11 chr1 5873771 . A G 121.45 PASS AC=1;AF=0.763;AN=2;DP=1037;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,13:29:99:340,0,467:7,9,8,5 chr1 5922697 . C T 506.18 PASS AC=1;AF=0.5;AN=2;DP=319;FractionInformativeReads=1;MQ=60;set=variant4-filterInvariant5-variant7-variant17-variant18-variant26-variant32-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:7,26:33:99:724,0,138:4,3,16,10 chr1 5923788 . T G 110.6 PASS AC=2;AF=0.7;AN=2;DP=583;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:441,36,0:0,0,10,2 chr1 5925371 . G A 387.48 PASS AC=2;AF=0.65;AN=2;DP=1130;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,45:46:99:1292,104,0:0,1,19,26 chr1 5926507 . T C 211.24 PASS AC=2;AF=0.645;AN=2;DP=2714;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,103:103:99:2939,308,0:0,0,44,59 chr1 5933530 . A G 121.92 PASS AC=1;AF=0.5;AN=2;DP=413;FractionInformativeReads=1;set=variant-variant4-variant5-variant7-variant11-variant17-variant18-variant26-variant32-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:23,20:43:99:595,0,700:8,15,4,16 chr1 5934236 . C T 87.97 PASS AC=2;AF=0.771;AN=2;DP=242;FractionInformativeReads=1;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant15-variant17-variant18-variant19-variant22-variant26-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:506,45,0:0,0,11,4 chr1 5934490 . A G 2104.42 PASS AC=2;AF=0.713;AN=2;DP=5956;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,121:121:99:5594,385,0:0,0,72,49 chr1 5934500 . T C 2113.91 PASS AC=2;AF=0.556;AN=2;DP=2839;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant11-variant14-variant16-variant17-variant18-variant19-variant26-variant30-variant32-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,135:135:99:5747,406,0:0,0,76,59 chr1 5934837 . C T 143.99 PASS AC=1;AF=0.649;AN=2;DP=1033;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,18:37:99:367,0,609:15,4,9,9 chr1 5935162 . A T 617.04 PASS AC=2;AF=0.774;AN=2;DP=4113;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,111:111:99:3282,332,0:0,0,52,59 chr1 5937091 . T C 1532.33 PASS AC=1;AF=0.943;AN=2;DP=3168;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:37,43:80:99:1174,0,949:23,14,28,15 chr1 5964991 . T C 549.75 PASS AC=1;AF=0.849;AN=2;DP=3065;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,52:93:99:1452,0,1196:7,34,12,40 chr1 6027167 . C A 563.35 PASS AC=1;AF=0.75;AN=2;DP=1476;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,19:38:99:436,0,460:10,9,13,6 chr1 6027252 . A G 1369.9 PASS AC=1;AF=0.737;AN=2;DP=3091;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,47:81:99:1209,0,863:21,13,27,20 chr1 6029086 . CAA CA,C,CAAA 233.73 PASS AC=1,0,0;AF=0.7,0.025,0.013;AN=2;DP=1570;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:26:99:11,4,9,2 chr1 6038583 . G C 559.42 PASS AC=2;AF=0.884;AN=2;DP=1845;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1604,132,0:0,0,10,34 chr1 6046432 . C G 325.75 PASS AC=1;AF=0.611;AN=2;DP=1024;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant14-variant18-variant19-variant22-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:16,26:42:99:654,0,429:6,10,9,17 chr1 6052571 . G A 1354.57 PASS AC=1;AF=0.5;AN=2;DP=886;FractionInformativeReads=1;MQ=60;set=variant5-variant6-variant22-variant26-variant32-variant34-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:53,61:114:99:1531,0,1353:31,22,32,29 chr1 6052581 . G A 974.21 PASS AC=2;AF=0.841;AN=2;DP=4648;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,116:116:99:4523,364,0:0,0,67,49 chr1 6094594 . T G 2883.24 PASS AC=2;AF=0.966;AN=2;DP=5351;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,164:164:99:4901,490,0:0,0,82,82 chr1 6094625 . C T 1101.1 PASS AC=1;AF=0.5;AN=2;DP=492;MQ=60;set=variant5-variant24-variant32-variant35 GT:AD:DP:GQ:PL:SB 0/1:61,71:132:99:1780,0,1521:27,34,38,33 chr1 6094800 . G A 1844.69 PASS AC=2;AF=0.606;AN=2;DP=2131;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:2267,213,0:0,0,32,39 chr1 6100458 . G A 1410.29 PASS AC=2;AF=0.615;AN=2;DP=912;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant25-variant32-variant33-variant35-variant36-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1564,126,0:0,0,32,10 chr1 6101773 . G A 1570.49 PASS AC=1;AF=0.5;AN=2;DP=365;FractionInformativeReads=1;MQ=60;set=variant5-variant32-variant35 GT:AD:DP:GQ:PL:SB 0/1:86,58:144:99:1217,0,2107:51,35,34,24 chr1 6145365 . A G 1924.69 PASS AC=1;AF=0.703;AN=2;DP=2324;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,33:75:99:1095,0,1310:7,35,4,29 chr1 6145379 . C T 644.19 PASS AC=1;AF=0.5;AN=2;DP=846;MQ=60;set=variant2-variant3-variant6-variant7-variant17-variant21-variant27-variant28-variant31-variant32-variant33-variant35-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,29:58:99:1001,0,960:4,25,3,26 chr1 6147341 . A C 94.76 PASS AC=1;AF=0.545;AN=2;DP=107;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant7-variant21-variant28-variant31-variant32-variant35-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,5:6:28:108,0,28:1,0,3,2 chr1 6149053 . C T 1053.29 PASS AC=1;AF=0.5;AN=2;DP=2031;MQ=60;set=variant2-variant3-variant6-variant7-variant21-variant27-variant28-variant31-variant32-variant33-variant35-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:93,59:152:99:1326,0,2209:45,48,27,32 chr1 6149122 . G A 484.36 PASS AC=1;AF=0.5;AN=2;DP=1185;MQ=60;set=variant2-variant3-variant6-variant7-variant21-variant27-variant28-variant31-variant32-variant33-variant35-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,38:93:99:843,0,1498:20,35,13,25 chr1 6150637 . C T 942.45 PASS AC=1;AF=0.645;AN=2;DP=1146;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,15:46:99:397,0,922:10,21,2,13 chr1 6154417 . C T 520.99 PASS AC=1;AF=0.523;AN=2;DP=959;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant14-variant21-variant24-variant25-variant27-variant28-variant31-variant32-variant33-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,25:49:99:571,0,669:17,7,14,11 chr1 6155332 . T C 367.85 PASS AC=2;AF=0.813;AN=2;DP=1183;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:785,75,0:0,0,16,9 chr1 6155530 . G C 1017 PASS AC=1;AF=0.5;AN=2;DP=1910;set=filterInvariant3-filterInvariant6-filterInvariant7-filterInvariant9-filterInvariant12-filterInvariant17-filterInvariant19-filterInvariant20-filterInvariant22-filterInvariant26-filterInvariant29-variant30-filterInvariant31-filterInvariant32-filterInvariant35-filterInvariant36-filterInvariant39-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:96,29:125:99:298,0,4979:35,61,29,0 chr1 6155535 . A C 1351.88 PASS AC=1;AF=0.5;AN=2;DP=2340;set=filterInvariant3-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant12-filterInvariant15-filterInvariant17-filterInvariant19-filterInvariant20-filterInvariant22-filterInvariant23-filterInvariant26-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant35-variant36-filterInvariant39-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:102,35:137:99:642,0,2082:40,62,33,2 chr1 6155540 . A C 36.82 PASS AC=1;AF=0.5;AN=2;DP=2554;set=filterInvariant-filterInvariant3-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant12-filterInvariant15-filterInvariant17-filterInvariant19-variant20-filterInvariant22-filterInvariant23-filterInvariant26-filterInvariant28-filterInvariant29-variant30-filterInvariant31-filterInvariant32-filterInvariant35-filterInvariant36-filterInvariant39-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:108,34:142:99:621,0,2206:44,64,34,0 chr1 6157282 . C T 898.55 PASS AC=1;AF=0.615;AN=2;DP=1424;MQ=60;set=variant-variant3-variant5-variant6-variant9-variant10-variant11-variant12-variant15-variant16-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant33-variant34-variant35-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,25:49:99:611,0,679:18,6,15,10 chr1 6157297 . T C 850.25 PASS AC=1;AF=0.531;AN=2;DP=1090;MQ=60;set=variant2-variant3-variant6-variant7-variant21-variant27-variant28-variant31-variant32-variant33-variant35-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,42:71:99:1017,0,702:18,11,27,15 chr1 6157434 . C T 5624.79 PASS AC=1;AF=0.655;AN=2;DP=7008;MQ=60;set=variant-variant3-variant5-variant6-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:133,157:290:99:3938,0,3135:71,62,98,59 chr1 6157993 . T C 2287.13 PASS AC=1;AF=0.596;AN=2;DP=2516;MQ=60;set=variant-variant3-variant5-variant6-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant22-variant23-variant24-variant25-variant27-variant30-variant33-variant34-variant35-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,51:95:99:1423,0,1073:22,22,30,21 chr1 6158147 . C T 491.09 PASS AC=1;AF=0.531;AN=2;DP=1290;MQ=60;set=variant2-variant3-variant6-variant7-variant21-variant27-variant28-variant31-variant32-variant33-variant35-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,47:91:99:1036,0,1162:15,29,20,27 chr1 6158562 . A G 5872.58 PASS AC=2;AF=0.771;AN=2;DP=6184;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,226:226:99:6968,677,0:0,0,114,112 chr1 6159032 . A G 3269.35 PASS AC=2;AF=0.8;AN=2;DP=4040;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,137:137:99:4328,410,0:0,0,75,62 chr1 6160563 . A G 4220.84 PASS AC=2;AF=0.817;AN=2;DP=5439;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,158:158:99:4844,473,0:0,0,83,75 chr1 6160692 . G GC 4464.14 PASS AC=2;AF=0.817;AN=2;DP=5522;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,154:155:99:6961,464,0:1,0,74,80 chr1 6160698 . A G 4546.86 PASS AC=2;AF=0.817;AN=2;DP=5443;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,161:162:99:7158,482,0:1,0,78,83 chr1 6160876 . A G 3566.83 PASS AC=2;AF=0.817;AN=2;DP=3829;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,105:105:99:3231,314,0:0,0,47,58 chr1 6160958 . A G 2786.05 PASS AC=2;AF=0.817;AN=2;DP=2605;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,74:75:99:2373,220,0:1,0,34,40 chr1 6161075 . T A 1882.89 PASS AC=2;AF=0.771;AN=2;DP=2120;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:2275,227,0:0,0,40,36 chr1 6161100 . T TA 1835.83 PASS AC=2;AF=0.771;AN=2;DP=2162;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:2390,216,0:0,0,37,34 chr1 6161977 . G A 2524.3 PASS AC=1;AF=0.5;AN=2;DP=201;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.446;QD=12.56;ReadPosRankSum=1.869;SOR=0.659;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:85,116:201:99:2553,0,1824:44,41,59,57 chr1 6162054 . T C 3897.04 PASS AC=1;AF=0.782;AN=2;DP=3708;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,49:106:99:1133,0,1729:22,35,22,27 chr1 6162583 . G A 2927.62 PASS AC=2;AF=0.797;AN=2;DP=5036;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,197:197:99:6024,585,0:0,0,95,102 chr1 6163135 . C T 2252.29 PASS AC=1;AF=0.596;AN=2;DP=2828;MQ=60;set=variant-variant3-variant5-variant6-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant22-variant23-variant24-variant25-variant27-variant30-variant33-variant34-variant35-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,61:112:99:2380,0,2958:25,26,37,24 chr1 6163141 . C T 2420.23 PASS AC=1;AF=0.596;AN=2;DP=2950;MQ=60;set=variant-variant3-variant5-variant6-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant22-variant23-variant24-variant25-variant27-variant30-variant33-variant34-variant35-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,64:118:99:2363,0,2937:26,28,38,26 chr1 6163584 . C T 3165.44 PASS AC=2;AF=0.742;AN=2;DP=4816;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,179:179:99:5250,532,0:0,0,90,89 chr1 6163925 . C T 2031 PASS AC=2;AF=0.795;AN=2;DP=1979;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1841,153,0:0,0,31,20 chr1 6164550 . A AGG 4096.8 PASS AC=2;AF=0.742;AN=2;DP=3221;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,106:106:99:4552,319,0:0,0,55,51 chr1 6164671 . A G 840.86 PASS AC=1;AF=0.523;AN=2;DP=1481;set=variant2-variant3-variant6-variant7-variant11-variant12-variant13-variant21-variant27-variant28-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,30:72:99:1041,0,1605:18,24,10,20 chr1 6164678 . GC GGCCCC,GGCCC,G,GCAC,GGCC,GGCCCCC 696.46 PASS AC=0,0,0,1,0,0;AF=0.079,0.184,0.132,0.079,0.026,0.026;AN=2;DP=1148;set=variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant20-variant21-variant25-variant26-variant29-variant31-filterInvariant35-variant36-variant41-variant42 GT:DP:GQ:SB 0/4:60:94:10,39,11,0 chr1 6164679 . C G 2131.37 PASS AC=1;AF=0.545;AN=2;DP=1983;set=variant2-variant3-variant4-variant5-variant6-filterInvariant7-filterInvariant8-variant11-variant12-variant13-variant14-variant17-variant18-variant21-variant24-variant25-variant26-variant27-variant28-filterInvariant29-filterInvariant31-filterInvariant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-filterInvariant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,20:61:99:368,0,1615:19,22,2,18 chr1 6164680 . C G,A 410.68 PASS AC=0,1;AF=0.233,0.3;AN=2;DP=854;MQ=60;set=variant4-variant5-variant9-filterInvariant10-variant12-variant17-variant20-variant21-variant22-variant25-variant26-variant35-variant36-variant41-variant44 GT:DP:GQ:SB 0/2:59:99:19,21,0,19 chr1 6164688 . CAG C 597.67 PASS AC=1;AF=0.5;AN=2;DP=1002;set=variant2-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-filterInvariant15-variant25-variant26-variant29-variant31-filterInvariant35-variant36-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:48,10:58:96:96,0,1738:9,39,10,0 chr1 6170300 . CACT C 277.58 PASS AC=1;AF=0.531;AN=2;DP=572;MQ=60;set=variant2-variant3-variant6-variant7-variant21-variant27-variant28-variant31-variant32-variant33-variant35-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,12:31:99:447,0,981:13,6,7,5 chr1 6170424 . CG C 2986.32 PASS AC=1;AF=0.606;AN=2;DP=3028;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant17-variant18-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:70,43:113:99:1387,0,2443:41,29,26,17 chr1 6170659 . A G 130.62 PASS AC=1;AF=0.5;AN=2;DP=116;MQ=60;set=variant19-variant20-variant30-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:13,11:24:99:208,0,198:7,6,0,11 chr1 6172875 . G A 287.45 PASS AC=1;AF=0.71;AN=2;DP=388;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant13-variant14-variant17-variant18-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,8:10:54:173,0,54:2,0,5,3 chr1 6173649 . A G 924.98 PASS AC=1;AF=0.691;AN=2;DP=925;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,17:24:99:482,0,202:2,5,6,11 chr1 6184092 . A G 3619.87 PASS AC=1;AF=0.714;AN=2;DP=4212;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,88:148:99:2054,0,1348:37,23,49,39 chr1 6184286 . A G 810.22 PASS AC=1;AF=0.719;AN=2;DP=703;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant20-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:10,11:21:99:285,0,325:1,9,4,7 chr1 6186961 . A G 449.81 PASS AC=2;AF=1;AN=2;DP=659;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:585,45,0:0,0,2,13 chr1 6196739 . G A 2868.94 PASS AC=1;AF=0.5;AN=2;DP=223;FS=2.992;FractionInformativeReads=1;MQ=60;MQRankSum=-1.845;QD=12.87;ReadPosRankSum=2.99;SOR=0.508;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:106,117:223:99:2897,0,2570:47,59,58,59 chr1 6202423 . C A 1813.86 PASS AC=1;AF=0.5;AN=2;DP=2151;MQ=60;set=variant5-variant9-variant12-variant17-variant22-variant25-variant29-variant35-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:137,101:238:99:2257,0,3782:63,74,52,49 chr1 6239937 . C CG 3062.91 PASS AC=2;AF=1;AN=2;DP=2786;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,80:80:99:2966,241,0:0,0,50,30 chr1 6257856 . G A 945.97 PASS AC=2;AF=0.656;AN=2;DP=2111;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2029,209,0:0,0,32,38 chr1 6260663 . A C 600.01 PASS AC=2;AF=0.625;AN=2;DP=1510;MQ=60;set=variant-variant2-variant3-variant5-variant9-variant10-variant11-variant13-variant16-variant17-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,73:73:99:2167,219,0:0,0,38,35 chr1 6272137 . A G 2044.73 PASS AC=2;AF=0.6;AN=2;DP=5306;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant19-variant21-variant24-variant25-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,183:184:99:5404,511,0:1,0,91,92 chr1 6278414 . A G 3677.96 PASS AC=2;AF=0.696;AN=2;DP=2605;MQ=60;set=variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant24-variant25-variant27-variant28-variant29-variant32-variant33-variant35-variant36-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,100:101:99:2948,276,0:1,0,42,58 chr1 6279370 . G C 4054.38 PASS AC=2;AF=0.614;AN=2;DP=2036;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant7-variant8-variant9-variant10-variant14-variant15-variant16-variant21-variant24-variant25-variant27-variant28-variant32-variant33-variant35-variant36-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,84:84:99:2533,253,0:0,0,36,48 chr1 6283164 . T G 237.24 PASS AC=1;AF=0.5;AN=2;DP=15;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.766;QD=15.82;ReadPosRankSum=0.177;SOR=0.743;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:6,9:15:99:265,0,135:2,4,3,6 chr1 6283547 . GA G 3497.68 PASS AC=1;AF=0.6;AN=2;DP=2677;MQ=60;set=variant3-variant9-variant15-variant21-variant24-variant25-variant27-variant28-variant32-variant35-variant36-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:91,91:182:99:2696,0,2686:63,28,55,36 chr1 6284680 . C T 2065.29 PASS AC=1;AF=0.545;AN=2;DP=1774;MQ=60;set=variant5-variant10-variant13-variant17-variant19-variant25-variant27-variant29-variant35-variant36-variant42 GT:AD:DP:GQ:PL:SB 0/1:74,75:149:99:1841,0,1934:29,45,26,49 chr1 6291918 . T TA,TAA 232.75 PASS AC=1,0;AF=0.5,0.05;AN=2;DP=389;MQ=60;set=variant5-variant10-variant13-variant17-variant19-variant27-variant29-variant35-variant36-variant42 GT:DP:GQ:SB 0/1:32:99:15,6,10,1 chr1 6296209 . A C 66.22 PASS AC=1;AF=0.75;AN=2;DP=10;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.198;ReadPosRankSum=0.198;set=variant17-variant35 GT:AD:DP:GQ:PL:SB 0/1:5,2:7:69:69,0,124:3,2,2,0 chr1 6307389 . C T 381.21 PASS AC=1;AF=0.789;AN=2;DP=718;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,17:25:99:447,0,161:5,3,8,9 chr1 6419320 . C A 294.65 PASS AC=1;AF=0.5;AN=2;DP=125;FractionInformativeReads=1;MQ=60;set=variant29-variant35-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:20,19:39:99:401,0,524:12,8,8,11 chr1 6453520 . C CG 487.77 PASS AC=2;AF=1;AN=2;DP=1186;FS=0;MQ=60;MQRankSum=-0.65;ReadPosRankSum=1.444;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:1074,81,0:0,0,8,19 chr1 6530965 . C CG 3491.46 PASS AC=2;AF=1;AN=2;DP=5226;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,98:98:99:3319,297,0:0,0,42,56 chr1 6545390 . A T 617.03 PASS AC=1;AF=0.528;AN=2;DP=1027;MQ=60;set=variant-variant7-variant8-variant9-variant17-variant21-variant22-variant24-variant29-variant30-variant32-variant34-variant35-variant36-variant37-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:35,24:59:99:497,0,879:17,18,11,13 chr1 6545839 . C T 672.89 PASS AC=1;AF=0.528;AN=2;DP=981;MQ=60;set=variant-variant7-variant8-variant9-variant17-variant21-variant22-variant24-variant29-variant30-variant32-variant34-variant35-variant36-variant37-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:28,28:56:99:766,0,837:18,10,21,7 chr1 6546037 . A AC,ACC 534.91 PASS AC=1,0;AF=0.455,0.091;AN=2;DP=948;MQ=60;set=variant-variant7-variant24-variant29-variant30-variant32-variant35-variant36-variant37-variant42-variant43 GT:DP:GQ:SB 0/1:97:99:25,45,4,23 chr1 6550376 . T C 210.55 PASS AC=1;AF=0.528;AN=2;DP=249;FractionInformativeReads=1;MQ=60;set=variant-variant7-variant8-variant10-variant17-variant18-variant21-variant22-variant24-variant30-variant32-variant34-variant35-variant36-variant37-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,7:19:99:174,0,384:9,3,4,3 chr1 6550505 . C T 862.83 PASS AC=1;AF=0.529;AN=2;DP=1003;MQ=60;set=variant-variant7-variant8-variant9-variant21-variant22-variant24-variant29-variant30-variant32-variant34-variant35-variant36-variant37-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:40,24:64:99:568,0,994:20,20,14,10 chr1 6550536 . GTCTAAGGC G 1348.59 PASS AC=1;AF=0.525;AN=2;DP=1364;MQ=60;set=variant-variant7-variant8-variant9-variant10-variant17-variant18-variant21-variant22-variant24-variant29-variant30-variant32-variant34-variant35-variant36-variant37-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:37,29:66:99:1036,0,1916:18,19,16,13 chr1 6551692 . C T 603.62 PASS AC=1;AF=0.533;AN=2;DP=1267;set=variant-variant7-variant10-variant17-variant18-variant24-variant29-variant30-variant32-variant35-variant36-variant37-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:51,40:91:99:972,0,1395:26,25,20,20 chr1 6557009 . A C 1269.05 PASS AC=1;AF=0.526;AN=2;DP=1613;FractionInformativeReads=1;MQ=60;set=variant-variant7-variant8-variant9-variant10-variant18-variant21-variant22-variant24-variant29-variant30-variant32-variant34-variant35-variant36-variant37-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:45,57:102:99:1613,0,1192:23,22,29,28 chr1 6579460 . C T 1096.04 PASS AC=1;AF=0.5;AN=2;DP=288;FractionInformativeReads=1;MQ=60;set=variant18-variant35 GT:AD:DP:GQ:PL:SB 0/1:83,78:161:99:1867,0,2051:49,34,42,36 chr1 6579607 . C T 1060.79 PASS AC=1;AF=0.849;AN=2;DP=4428;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,76:132:99:1901,0,1369:26,30,35,41 chr1 6579843 . C T 543.34 PASS AC=1;AF=0.849;AN=2;DP=3133;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,41:83:99:1131,0,892:21,21,23,18 chr1 6580236 . G C 225.3 PASS AC=2;AF=1;AN=2;DP=342;FS=0;MQ=60;MQRankSum=0.747;ReadPosRankSum=0.747;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:450,30,0:0,0,2,8 chr1 6580250 . C T 73.47 PASS AC=1;AF=0.888;AN=2;DP=259;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,6:8:66:246,0,66:0,2,2,4 chr1 6581877 . G A 496.96 PASS AC=1;AF=0.849;AN=2;DP=2012;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,13:29:99:341,0,451:9,7,7,6 chr1 6583231 . G A 1802.25 PASS AC=1;AF=0.538;AN=2;DP=1526;set=variant-variant2-variant8-variant14-variant15-variant22-variant23-variant30-variant31-variant32-variant35-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:71,56:127:99:1941,0,2298:44,27,36,20 chr1 6583232 . A G 1784.46 PASS AC=1;AF=0.538;AN=2;DP=1536;set=variant-variant2-variant8-variant14-variant15-variant22-variant23-variant30-variant31-variant32-variant35-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:73,56:129:99:1941,0,2351:45,28,36,20 chr1 6583627 . G A 148.54 PASS AC=1;AF=0.935;AN=2;DP=78;FS=0;set=variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant16-variant18-variant21-variant22-variant27-variant29-variant31-variant33-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,2:3:36:81,0,36:1,0,2,0 chr1 6583701 . T C 124.46 PASS AC=2;AF=0.872;AN=2;DP=712;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:781,60,0:0,0,16,4 chr1 6584024 . A G 3101.9 PASS AC=2;AF=1;AN=2;DP=3147;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,67:67:99:2421,201,0:0,0,45,22 chr1 6584101 . A G 2408.22 PASS AC=1;AF=0.849;AN=2;DP=8120;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:89,81:170:99:2145,0,2112:48,41,53,28 chr1 6584311 . G GTA 6675.77 PASS AC=2;AF=1;AN=2;DP=7025;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,156:156:99:6710,472,0:0,0,62,94 chr1 6584804 . A T 90.69 PASS AC=1;AF=0.556;AN=2;DP=87;MQ=60;set=variant-variant2-variant15-variant23-variant30-variant31-variant32-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:4,3:7:65:65,0,145:0,4,1,2 chr1 6585021 . A G 727.76 PASS AC=2;AF=1;AN=2;DP=828;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:570,42,0:0,0,13,1 chr1 6585539 . C T 877.11 PASS AC=1;AF=0.86;AN=2;DP=3064;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,35:82:99:829,0,1202:23,24,19,16 chr1 6585804 . C T 2897.12 PASS AC=1;AF=0.86;AN=2;DP=8502;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:114,122:236:99:3008,0,2826:60,54,60,62 chr1 6586070 . C T 3301.43 PASS AC=2;AF=1;AN=2;DP=5460;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,113:113:99:3379,338,0:0,0,46,67 chr1 6591937 . T C 231.21 PASS AC=1;AF=0.86;AN=2;DP=1078;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,16:28:99:575,0,316:10,2,16,0 chr1 6593532 . G A 1034.81 PASS AC=1;AF=0.542;AN=2;DP=951;MQ=60;set=variant-variant2-variant8-variant14-variant15-variant22-variant23-variant30-variant31-variant32-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:38,50:88:99:1235,0,912:18,20,21,29 chr1 6601773 . T C 182.07 PASS AC=1;AF=0.939;AN=2;DP=158;FS=0;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,2:6:72:72,0,165:4,0,2,0 chr1 6602223 . ATT AT,A 196.32 PASS AC=2,0;AF=0.893,0.036;AN=2;DP=571;FS=0;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:7:19:0,0,0,7 chr1 6609559 . C A 381.53 PASS AC=1;AF=0.826;AN=2;DP=998;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,6:16:99:208,0,485:10,0,6,0 chr1 6609563 . CAT C 538.95 PASS AC=1;AF=0.531;AN=2;DP=418;MQ=60;set=variant-variant2-variant8-variant11-variant13-variant14-variant15-variant18-variant22-variant23-variant30-variant31-variant32-variant35-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:9,13:22:99:483,0,339:8,1,12,1 chr1 6609851 . A G 2564.77 PASS AC=2;AF=1;AN=2;DP=3557;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,97:97:99:3208,291,0:0,0,30,67 chr1 6609896 . G A 688.06 PASS AC=1;AF=0.826;AN=2;DP=1731;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,28:52:99:770,0,728:5,19,7,21 chr1 6610366 . T C 408.01 PASS AC=1;AF=0.826;AN=2;DP=1166;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,19:31:99:621,0,349:9,3,16,3 chr1 6610382 . C T 629.57 PASS AC=1;AF=0.826;AN=2;DP=1604;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,25:43:99:752,0,522:15,3,20,5 chr1 6614391 . A C 3608.65 PASS AC=1;AF=0.977;AN=2;DP=2981;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:28,44:72:99:1213,0,601:11,17,21,23 chr1 6614415 . A G 3283.05 PASS AC=2;AF=1;AN=2;DP=3048;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,84:84:99:3092,252,0:0,0,42,42 chr1 6614535 . G A 954.05 PASS AC=1;AF=0.826;AN=2;DP=4212;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,54:100:99:1330,0,1031:22,24,24,30 chr1 6614635 . G GC 385.93 PASS AC=1;AF=0.5;AN=2;DP=53;MQ=60;set=variant18-variant35 GT:AD:DP:GQ:PL:SB 0/1:13,10:23:99:287,0,395:4,9,1,9 chr1 6614653 . C G 237.44 PASS AC=1;AF=0.826;AN=2;DP=970;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,10:19:99:257,0,318:1,8,2,8 chr1 6615444 . G A 714.79 PASS AC=1;AF=0.5;AN=2;DP=97;FractionInformativeReads=1;MQ=60;set=variant18-variant35 GT:AD:DP:GQ:PL:SB 0/1:26,17:43:99:495,0,716:17,9,10,7 chr1 6615690 . A G 123.13 PASS AC=1;AF=0.849;AN=2;DP=1388;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,18:27:99:708,0,589:1,8,5,13 chr1 6615695 . C T 123.13 PASS AC=1;AF=0.833;AN=2;DP=1257;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,18:25:99:713,0,544:1,6,5,13 chr1 6631319 . G A 145.31 PASS AC=2;AF=1;AN=2;DP=684;FS=0;MQ=60;MQRankSum=0.714;ReadPosRankSum=0.51;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:537,42,0:0,0,2,12 chr1 6635231 . A G 4317.86 PASS AC=2;AF=1;AN=2;DP=8324;FS=0;MQ=60;MQRankSum=1.323;ReadPosRankSum=1.689;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,228:228:99:7456,682,0:0,0,133,95 chr1 6636461 . C T 1707.18 PASS AC=2;AF=0.717;AN=2;DP=3197;MQ=60;set=variant4-variant5-variant7-variant9-variant11-variant14-variant16-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant33-variant35-variant36-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,140:140:99:4295,420,0:0,0,86,54 chr1 6639847 . G T 320.52 PASS AC=2;AF=0.563;AN=2;DP=388;FractionInformativeReads=1;MQ=60;set=variant13-variant21-variant23-variant24-variant33-variant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:1856,183,0:0,0,26,36 chr1 6639943 . G A 703.71 PASS AC=1;AF=0.5;AN=2;DP=156;FractionInformativeReads=1;MQ=60;set=variant21-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:38,25:63:99:767,0,1111:27,11,14,11 chr1 6653941 . C T 585.84 PASS AC=1;AF=0.5;AN=2;DP=159;FractionInformativeReads=1;MQ=60;set=variant8-variant35 GT:AD:DP:GQ:PL:SB 0/1:44,51:95:99:1290,0,1119:18,26,19,32 chr1 6685416 . G C 269.89 PASS AC=1;AF=0.5;AN=2;DP=86;FractionInformativeReads=1;MQ=60;set=variant5-variant21-variant35 GT:AD:DP:GQ:PL:SB 0/1:19,19:38:99:414,0,474:6,13,8,11 chr1 6694513 . G T 1984.31 PASS AC=1;AF=0.533;AN=2;DP=1342;FractionInformativeReads=1;MQ=60;set=variant5-variant7-variant8-variant11-variant13-variant14-variant15-variant20-variant21-variant23-variant24-variant27-variant33-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,64:125:99:2498,0,3438:38,23,33,31 chr1 6694514 . A T 1984.31 PASS AC=1;AF=0.533;AN=2;DP=1341;FractionInformativeReads=1;MQ=60;set=variant5-variant7-variant8-variant11-variant13-variant14-variant15-variant20-variant21-variant23-variant24-variant27-variant33-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:62,65:127:99:2498,0,3438:38,24,34,31 chr1 6704635 . A G 3168.36 PASS AC=2;AF=0.943;AN=2;DP=6023;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,144:144:99:4310,432,0:0,0,73,71 chr1 6705874 . G C 2062.55 PASS AC=2;AF=0.594;AN=2;DP=2204;MQ=60;set=variant5-variant7-variant8-variant11-variant13-variant14-variant15-variant20-variant21-variant23-variant24-variant27-variant33-variant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,173:174:99:5050,511,0:1,0,104,69 chr1 6866978 . G A 366.29 PASS AC=2;AF=0.688;AN=2;DP=897;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1422,129,0:0,0,33,10 chr1 6931643 . T TA 334.45 PASS AC=2;AF=0.6;AN=2;DP=370;MQ=60;set=variant5-variant7-variant11-variant13-variant20-variant24-variant27-variant33-variant35-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:998,105,0:0,0,25,9 chr1 7202190 . T C 1763.64 PASS AC=1;AF=0.742;AN=2;DP=3482;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,61:125:99:1587,0,1545:36,28,37,24 chr1 7289606 . T G,A 239.08 PASS AC=2,0;AF=0.986,0.014;AN=2;DP=232;FS=0;MQ=60;set=variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:6:18:0,0,6,0 chr1 7289612 . T G 239.08 PASS AC=2;AF=1;AN=2;DP=266;FS=0;MQ=60;set=variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:270,18,0:0,0,6,0 chr1 7289619 . G A 230.83 PASS AC=2;AF=1;AN=2;DP=314;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:302,21,0:0,0,7,0 chr1 7289777 . G A 887.36 PASS AC=2;AF=0.77;AN=2;DP=2999;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:2093,227,0:0,0,38,38 chr1 7289959 . A G 61.77 PASS AC=2;AF=0.87;AN=2;DP=150;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant19-variant21-variant22-variant24-variant25-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:231,21,0:0,0,2,5 chr1 7527996 . T C 1384.13 PASS AC=1;AF=0.7;AN=2;DP=3665;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,69:123:99:1747,0,1457:13,41,22,47 chr1 7595125 . G A 283.67 PASS AC=1;AF=0.55;AN=2;DP=326;MQ=60;set=variant2-variant5-variant6-variant17-variant21-variant26-variant27-variant31-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:10,12:22:99:342,0,314:2,8,2,10 chr1 7723534 . G A 4134.85 PASS AC=1;AF=0.5;AN=2;DP=3601;MQ=60;set=variant6-variant8-variant18-variant20-variant27-variant28-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:219,195:414:99:4845,0,5844:96,123,88,107 chr1 7723957 . G A 2098.24 PASS AC=1;AF=0.652;AN=2;DP=8791;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant12-variant13-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:169,166:335:99:4124,0,4218:85,84,84,82 chr1 7730879 . C T 623.13 PASS AC=1;AF=0.5;AN=2;DP=311;FractionInformativeReads=1;MQ=60;set=variant6-variant8-variant18-variant20-variant27-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,20:39:99:524,0,498:14,5,13,7 chr1 7737651 . G A 2149.41 PASS AC=1;AF=0.5;AN=2;DP=1430;MQ=60;set=variant6-variant8-variant20-variant27-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:90,123:213:99:3101,0,1989:50,40,69,54 chr1 7737799 . A G 802.62 PASS AC=1;AF=0.657;AN=2;DP=4133;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:64,61:125:99:1527,0,1701:19,45,22,39 chr1 7797096 . C G 704.27 PASS AC=1;AF=0.5;AN=2;DP=354;MQ=60;set=variant6-variant8-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,37:80:99:1005,0,1177:14,29,18,19 chr1 7797734 . T A 1012.26 PASS AC=1;AF=0.816;AN=2;DP=1535;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,21:34:99:619,0,431:3,10,10,11 chr1 7807897 . A G 2841.14 PASS AC=1;AF=0.802;AN=2;DP=4410;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,49:108:99:1190,0,1400:28,31,24,25 chr1 7807966 . GT G 679.59 PASS AC=1;AF=0.756;AN=2;DP=1971;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,18:43:99:349,0,467:6,19,5,13 chr1 7809728 . C CT 378.43 PASS AC=1;AF=0.709;AN=2;DP=1021;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,12:20:99:264,0,159:7,1,12,0 chr1 7810923 . G A 208.44 PASS AC=1;AF=0.5;AN=2;DP=62;FS=0;FractionInformativeReads=1;MQ=60;set=variant6-variant8-variant19-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:8,4:12:99:131,0,284:7,1,4,0 chr1 7811014 . G A 1685.3 PASS AC=1;AF=0.791;AN=2;DP=2474;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,36:54:99:1413,0,1079:12,6,22,14 chr1 7811033 . GAA G 1413.74 PASS AC=1;AF=0.5;AN=2;DP=575;MQ=60;set=variant6-variant8-variant18-variant19-variant35-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,38:61:99:1518,0,1222:15,8,21,17 chr1 7811215 . A G 2823.19 PASS AC=1;AF=0.791;AN=2;DP=3616;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,47:92:99:1211,0,1202:21,24,27,20 chr1 7812398 . A G 262.01 PASS AC=1;AF=0.864;AN=2;DP=198;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant12-variant13-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,4:9:99:141,0,160:4,1,4,0 chr1 7826347 . C T 1229.57 PASS AC=1;AF=0.909;AN=2;DP=1692;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:22,16:38:99:475,0,594:15,7,13,3 chr1 7827903 . C CA,CAA,CAAA 692.23 PASS AC=0,0,1;AF=0.085,0.756,0.073;AN=2;DP=1252;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 0/3:35:99:8,4,15,8 chr1 7828173 . TAAAAA TAAA,TAAAA,T,TAA,TA 988.58 PASS AC=0,1,0,1,0;AF=0.227,0.295,0.193,0.216,0.011;AN=2;DP=3661;set=Intersection GT:DP:GQ:SB 4/2:44:99:3,4,14,23 chr1 7828278 . CA C 1013.14 PASS AC=1;AF=0.849;AN=2;DP=2781;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,26:67:99:510,0,937:25,16,18,8 chr1 7829226 . A G 3168.85 PASS AC=2;AF=1;AN=2;DP=3208;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.544;ReadPosRankSum=0.396;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:2663,216,0:0,0,28,44 chr1 7833485 . G A 1188.45 PASS AC=1;AF=0.587;AN=2;DP=2049;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant13-variant14-variant15-variant17-variant19-variant21-variant22-variant25-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,35:80:99:847,0,1138:23,22,18,17 chr1 7840926 . G C 764.8 PASS AC=1;AF=0.795;AN=2;DP=2170;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:27,26:53:99:798,0,830:9,18,9,17 chr1 7841330 . G A 771.97 PASS AC=1;AF=0.577;AN=2;DP=963;MQ=60;set=variant6-variant8-variant17-variant19-variant21-variant22-variant25-variant35-variant36-variant37-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,45:87:99:1164,0,962:19,23,28,17 chr1 7841549 . A C 563.09 PASS AC=1;AF=0.93;AN=2;DP=588;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,15:20:99:484,0,127:1,4,2,13 chr1 7844680 . T C 422.99 PASS AC=1;AF=0.767;AN=2;DP=1022;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,14:35:99:432,0,644:15,6,9,5 chr1 7845695 . T C 348.01 PASS AC=1;AF=0.725;AN=2;DP=1214;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,11:18:99:363,0,203:2,5,1,10 chr1 7847362 . C CT 1013.52 PASS AC=1;AF=0.989;AN=2;DP=1276;FS=0;MQ=60;MQRankSum=0.68;ReadPosRankSum=-0.211;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:22,8:30:99:158,0,596:15,7,6,2 chr1 7854209 . C T 859.8 PASS AC=1;AF=0.536;AN=2;DP=588;MQ=60;set=variant4-variant6-variant8-variant17-variant19-variant21-variant22-variant25-variant34-variant35-variant36-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,24:48:99:678,0,740:4,20,8,16 chr1 7861153 . C CT 839.38 PASS AC=1;AF=0.658;AN=2;DP=2178;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,21:44:99:572,0,660:14,9,14,7 chr1 7861345 . G A 242.82 PASS AC=1;AF=0.662;AN=2;DP=464;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,13:19:99:427,0,162:1,5,2,11 chr1 7863293 . C T 656.37 PASS AC=1;AF=0.649;AN=2;DP=1298;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,15:28:99:434,0,329:4,9,3,12 chr1 7869915 . G C 2617.21 PASS AC=1;AF=0.989;AN=2;DP=3567;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:61,51:112:99:1382,0,1524:37,24,34,17 chr1 7870048 . T C 4008.62 PASS AC=1;AF=0.966;AN=2;DP=4639;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:66,65:131:99:1621,0,1598:28,38,28,37 chr1 7870144 . A C 2322.83 PASS AC=1;AF=0.989;AN=2;DP=3008;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:30,37:67:99:970,0,806:12,18,15,22 chr1 7880469 . A G 507.77 PASS AC=1;AF=0.663;AN=2;DP=1574;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,23:45:99:651,0,587:12,10,15,8 chr1 7880683 . T G 1829.68 PASS AC=1;AF=0.567;AN=2;DP=1674;MQ=60;set=variant4-variant6-variant8-variant17-variant19-variant21-variant22-variant25-variant34-variant35-variant36-variant37-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,66:121:99:1600,0,1361:25,30,32,34 chr1 7887493 . T C 6582.06 PASS AC=1;AF=0.989;AN=2;DP=12069;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:181,144:325:99:3608,0,4517:96,85,78,66 chr1 7889804 . C G 1071.49 PASS AC=1;AF=0.713;AN=2;DP=3123;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,38:68:99:1058,0,871:21,9,27,11 chr1 7890117 . T C 3473.87 PASS AC=1;AF=0.579;AN=2;DP=4743;set=variant4-variant6-variant8-variant10-variant17-variant19-variant21-variant22-variant23-variant25-variant27-variant30-variant34-variant35-variant36-variant37-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:159,108:267:99:2625,0,4200:75,84,52,56 chr1 7890264 . A G 766.51 PASS AC=1;AF=0.713;AN=2;DP=4483;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:76,71:147:99:1803,0,1974:24,52,24,47 chr1 7897133 . A G 744.37 PASS AC=1;AF=0.567;AN=2;DP=1216;MQ=60;set=variant4-variant6-variant8-variant17-variant19-variant21-variant22-variant25-variant34-variant35-variant36-variant37-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,34:87:99:779,0,1248:30,23,17,17 chr1 7904196 . A G 3446.27 PASS AC=1;AF=0.5;AN=2;DP=2094;MQ=60;set=variant6-variant8-variant19-variant35-variant36-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:138,147:285:99:3854,0,3877:74,64,87,60 chr1 7904247 . C T 11453.9 PASS AC=1;AF=0.989;AN=2;DP=14073;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:172,186:358:99:4772,0,4489:93,79,99,87 chr1 7904475 . G A 20838 PASS AC=1;AF=0.989;AN=2;DP=23485;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:336,262:598:99:6340,0,7952:163,173,124,138 chr1 7906476 . G T 4185.69 PASS AC=1;AF=0.989;AN=2;DP=6794;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:111,72:183:99:1585,0,2787:63,48,38,34 chr1 7906859 . T TAAGA 2352.74 PASS AC=1;AF=0.567;AN=2;DP=1540;MQ=60;set=variant4-variant6-variant8-variant17-variant19-variant21-variant22-variant25-variant34-variant35-variant36-variant37-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,58:104:99:2296,0,2297:22,24,27,31 chr1 7907620 . A ATAAT 3076.95 PASS AC=1;AF=0.667;AN=2;DP=5830;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:91,79:170:99:3371,0,4927:57,34,57,22 chr1 7913184 . CA C,CAA 410.14 PASS AC=1,0;AF=0.511,0.011;AN=2;DP=7987;set=filterInvariant-variant2-variant3-variant4-variant5-variant6-filterInvariant7-variant8-filterInvariant9-variant10-variant11-filterInvariant12-variant13-variant14-variant15-variant16-variant17-variant18-filterInvariant19-filterInvariant20-variant21-variant22-variant23-filterInvariant24-variant25-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant29-variant30-filterInvariant31-filterInvariant32-filterInvariant33-filterInvariant34-variant35-variant36-variant37-variant38-filterInvariant39-variant40-filterInvariant41-filterInvariant42-variant43-variant44 GT:DP:GQ:SB 0/1:166:99:45,47,36,38 chr1 7980364 . CTT CT,CTTT,C,CTTTT,CTTTTT 898.58 PASS AC=1,0,0,0,0;AF=0.415,0.098,0.012,0.012,0.012;AN=2;DP=9879;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-filterInvariant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:201:99:57,68,33,43 chr1 7998963 . T G 2608.56 PASS AC=2;AF=0.989;AN=2;DP=3898;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,121:121:99:3684,362,0:0,0,46,75 chr1 8021778 . T C 2307.24 PASS AC=1;AF=0.765;AN=2;DP=5785;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:135,78:213:99:1775,0,3407:72,63,41,37 chr1 8022171 . C T 451.53 PASS AC=1;AF=0.672;AN=2;DP=1205;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant35-variant36-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,20:53:99:526,0,840:11,22,6,14 chr1 8022800 . CT C,CTT 153.38 PASS AC=1,0;AF=0.472,0.028;AN=2;DP=1297;set=variant2-variant3-filterInvariant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant15-variant16-filterInvariant17-filterInvariant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-filterInvariant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43 GT:DP:GQ:SB 0/1:40:99:20,8,10,2 chr1 8037496 . G A 1506.34 PASS AC=1;AF=0.65;AN=2;DP=4016;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant35-variant36-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:77,71:148:99:1620,0,1828:40,37,38,33 chr1 8064578 . A G 1351.65 PASS AC=1;AF=0.65;AN=2;DP=3474;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant35-variant36-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,74:118:99:1851,0,985:21,23,40,34 chr1 8072466 . C T 1422.24 PASS AC=1;AF=0.65;AN=2;DP=3777;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant35-variant36-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,51:99:99:1475,0,1255:20,28,21,30 chr1 8377828 . G A 314.62 PASS AC=2;AF=0.671;AN=2;DP=1014;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1339,123,0:0,0,30,11 chr1 8384228 . G A 274.98 PASS AC=1;AF=0.5;AN=2;DP=22;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.615;QD=12.5;ReadPosRankSum=0.099;SOR=0.892;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:12,10:22:99:303,0,343:9,3,8,2 chr1 8384268 . T C 1485.9 PASS AC=2;AF=0.989;AN=2;DP=2384;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:1536,144,0:0,0,29,19 chr1 8384575 . G C 97.27 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=2676;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:91,34:125:99:377,0,4069:12,79,34,0 chr1 8390051 . G A 133.71 PASS AC=2;AF=0.643;AN=2;DP=462;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:470,36,0:0,0,9,3 chr1 8390495 . A G 1028.25 PASS AC=2;AF=0.85;AN=2;DP=3622;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,112:112:99:3865,334,0:0,0,57,55 chr1 8395441 . T C 7127.44 PASS AC=1;AF=0.647;AN=2;DP=8006;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:167,132:299:99:3094,0,4002:99,68,80,52 chr1 8395560 . G T 3677.56 PASS AC=1;AF=0.556;AN=2;DP=6296;MQ=60;set=variant2-variant14-variant16-variant17-variant18-variant19-variant21-variant23-variant25-variant26-variant30-variant32-variant33-variant35-variant36-variant37-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:204,184:388:99:4448,0,5004:95,109,71,113 chr1 8404093 . C T 477.99 PASS AC=1;AF=0.625;AN=2;DP=1345;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant13-variant15-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant33-variant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,39:83:99:905,0,1162:19,25,17,22 chr1 8404169 . T A 962.34 PASS AC=2;AF=1;AN=2;DP=2266;FS=0;MQ=60;MQRankSum=0.037;ReadPosRankSum=1.585;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:1981,195,0:0,0,27,38 chr1 8412989 . A G 103.58 PASS AC=1;AF=0.798;AN=2;DP=1287;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,17:33:99:416,0,426:7,9,9,8 chr1 8413317 . A C 849.27 PASS AC=1;AF=0.579;AN=2;DP=1516;MQ=60;set=variant2-variant5-variant11-variant13-variant14-variant17-variant18-variant19-variant21-variant23-variant25-variant30-variant32-variant33-variant35-variant36-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:54,41:95:99:1113,0,1434:26,28,23,18 chr1 8413839 . A G 494.89 PASS AC=1;AF=0.611;AN=2;DP=1037;MQ=60;set=variant2-variant5-variant13-variant14-variant17-variant18-variant19-variant21-variant23-variant25-variant30-variant32-variant33-variant35-variant36-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:31,26:57:99:668,0,818:14,17,14,12 chr1 8414685 . AT A 217.84 PASS AC=1;AF=0.594;AN=2;DP=381;MQ=60;set=variant5-variant13-variant14-variant17-variant19-variant21-variant23-variant25-variant30-variant32-variant33-variant35-variant36-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:10,13:23:99:292,0,193:1,9,7,6 chr1 8415418 . G A 178.92 PASS AC=1;AF=0.579;AN=2;DP=676;MQ=60;set=variant2-variant5-variant9-variant13-variant14-variant17-variant18-variant19-variant21-variant23-variant25-variant30-variant32-variant33-variant35-variant36-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:34,15:49:99:283,0,1008:23,11,9,6 chr1 8418644 . C A 3061.64 PASS AC=1;AF=0.756;AN=2;DP=6604;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:113,84:197:99:3139,0,5501:59,54,47,37 chr1 8418650 . T C 3286.56 PASS AC=1;AF=0.756;AN=2;DP=6765;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:113,85:198:99:3167,0,5507:59,54,50,35 chr1 8419854 . TCGCTCC T 961.26 PASS AC=1;AF=0.5;AN=2;DP=57;FS=1.105;FractionInformativeReads=0.965;MQ=60;MQRankSum=1.17;QD=16.86;ReadPosRankSum=0.699;SOR=0.977;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:28,27:55:99:999,0,1079:18,10,19,8 chr1 8421203 . T C 1300.81 PASS AC=1;AF=0.732;AN=2;DP=5518;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:76,86:162:99:1998,0,1727:39,37,41,45 chr1 8422676 . T C 1765.52 PASS AC=1;AF=0.732;AN=2;DP=6384;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:91,73:164:99:1785,0,2150:50,41,44,29 chr1 8424039 . C G 314.59 PASS AC=1;AF=0.611;AN=2;DP=280;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant23-variant30-variant32-variant33-variant35-variant36-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:13,4:17:86:86,0,381:10,3,4,0 chr1 8425798 . C T 154.9 PASS AC=1;AF=0.583;AN=2;DP=475;MQ=60;set=variant2-variant5-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant23-variant30-variant32-variant33-variant35-variant36-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:17,14:31:99:399,0,406:11,6,12,2 chr1 8425900 . T C 875.76 PASS AC=1;AF=0.611;AN=2;DP=1286;MQ=60;set=variant2-variant5-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant23-variant30-variant32-variant33-variant35-variant36-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:30,43:73:99:1021,0,707:18,12,23,20 chr1 8526142 . G A 3024.9 PASS AC=1;AF=0.689;AN=2;DP=4442;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,59:120:99:1499,0,1431:28,33,33,26 chr1 8557320 . C G 509.76 PASS AC=1;AF=0.686;AN=2;DP=452;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,10:16:99:309,0,227:6,0,7,3 chr1 8557691 . A C 1100.85 PASS AC=1;AF=0.689;AN=2;DP=1200;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,25:40:99:819,0,296:5,10,5,20 chr1 8616404 . C A 328.7 PASS AC=1;AF=0.559;AN=2;DP=409;FractionInformativeReads=1;MQ=60;set=variant7-variant8-variant11-variant12-variant13-variant17-variant19-variant24-variant25-variant27-variant29-variant31-variant35-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,8:20:99:257,0,329:9,3,7,1 chr1 8877520 . AT ATTT,ATT,A 833 PASS AC=1,1,0;AF=0.291,0.395,0.023;AN=2;DP=3598;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-filterInvariant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-filterInvariant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 2/1:55:99:4,7,27,17 chr1 8926285 . A AG 908.96 PASS AC=2;AF=0.683;AN=2;DP=1922;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant11-variant12-variant13-variant15-variant16-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant33-variant34-variant35-variant37-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:2006,183,0:0,0,46,14 chr1 8926329 . C T 1676.04 PASS AC=1;AF=0.5;AN=2;DP=1380;MQ=60;set=variant3-variant4-variant6-variant12-variant16-variant22-variant26-variant31-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:79,56:135:99:1363,0,1860:44,35,33,23 chr1 8930369 . T C 1482.85 PASS AC=2;AF=0.854;AN=2;DP=2070;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:2172,204,0:0,0,44,24 chr1 8930385 . G A 1853.1 PASS AC=2;AF=0.854;AN=2;DP=2569;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,83:83:99:2582,249,0:0,0,53,30 chr1 8935149 . A G 582.26 PASS AC=2;AF=0.857;AN=2;DP=745;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:44:509,44,0:0,0,2,13 chr1 9006104 . T TC 382.38 PASS AC=1;AF=0.63;AN=2;DP=487;MQ=60;set=variant2-variant3-variant4-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant24-variant25-variant26-variant30-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:15,9:24:99:265,0,497:2,13,1,8 chr1 9011586 . T G 1417.19 PASS AC=1;AF=0.797;AN=2;DP=4896;MQ=60;set=variant2-variant3-variant4-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,68:135:99:1765,0,1664:28,39,27,41 chr1 9011722 . G T 441.05 PASS AC=1;AF=0.775;AN=2;DP=1559;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,28:52:99:692,0,588:8,16,10,18 chr1 9018931 . A G 1013.06 PASS AC=1;AF=0.5;AN=2;DP=89;FS=0;FractionInformativeReads=0.989;MQ=60;MQRankSum=0.129;QD=11.38;ReadPosRankSum=-0.805;SOR=0.693;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:44,44:88:99:1041,0,995:27,17,27,17 chr1 9022591 . G A 993.42 PASS AC=1;AF=0.5;AN=2;DP=90;FS=0.799;FractionInformativeReads=1;MQ=60;MQRankSum=0.724;QD=11.04;ReadPosRankSum=-0.813;SOR=0.563;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:48,42:90:99:1022,0,1133:28,20,23,19 chr1 9064609 . AG A 134.82 PASS AC=1;AF=0.529;AN=2;DP=401;MQ=60;set=variant3-variant4-variant5-variant8-variant15-variant17-variant18-variant22-variant25-variant28-variant29-variant30-variant31-variant34-variant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,17:33:99:486,0,429:9,7,14,3 chr1 9070485 . T A 71.28 PASS AC=1;AF=0.778;AN=2;DP=92;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant6-variant7-variant9-variant11-variant16-variant18-variant22-variant23-variant24-variant27-variant33-variant35-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:2,2:4:70:70,0,80:0,2,0,2 chr1 9073801 . C T 1376.71 PASS AC=1;AF=0.611;AN=2;DP=2033;MQ=60;set=variant2-variant3-variant6-variant7-variant9-variant11-variant12-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant31-variant33-variant34-variant35-variant36-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,48:85:99:1191,0,991:12,25,18,30 chr1 9074932 . G A 566.04 PASS AC=1;AF=0.615;AN=2;DP=998;MQ=60;set=variant2-variant3-variant6-variant7-variant9-variant11-variant12-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant31-variant33-variant34-variant35-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,27:58:99:826,0,811:11,20,6,21 chr1 9079154 . C T 140.95 PASS AC=1;AF=0.675;AN=2;DP=329;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant11-variant12-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant33-variant35-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,8:17:99:294,0,330:9,0,8,0 chr1 9084924 . T C 552.78 PASS AC=2;AF=0.841;AN=2;DP=3309;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,85:85:99:2980,254,0:0,0,61,24 chr1 9095202 . C T 1848.88 PASS AC=1;AF=0.805;AN=2;DP=4529;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,54:105:99:1437,0,1248:31,20,33,21 chr1 9101155 . T G 1672.53 PASS AC=1;AF=0.563;AN=2;DP=1019;MQ=60;set=variant7-variant12-variant16-variant19-variant21-variant24-variant25-variant27-variant28-variant32-variant33-variant35-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,33:64:99:812,0,845:16,15,17,16 chr1 9117371 . A G 120.76 PASS AC=1;AF=0.714;AN=2;DP=79;set=variant11-variant20-variant21-variant22-variant27-variant28-variant35 GT:AD:DP:GQ:PL:SB 0/1:4,9:13:87:253,0,87:3,1,6,3 chr1 9129867 . G A 294.47 PASS AC=1;AF=0.607;AN=2;DP=375;MQ=60;set=variant2-variant7-variant12-variant16-variant19-variant21-variant24-variant27-variant28-variant32-variant35-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,13:38:99:310,0,664:8,17,4,9 chr1 9160577 . A G 458.81 PASS AC=1;AF=0.5;AN=2;DP=165;MQ=60;set=variant12-variant21-variant24-variant27-variant35 GT:AD:DP:GQ:PL:SB 0/1:9,23:32:99:561,0,224:4,5,12,11 chr1 9160870 . T TGAGCCCAGGAGTTC 600.24 PASS AC=1;AF=0.686;AN=2;DP=1123;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,20:42:99:772,0,3079:8,14,8,12 chr1 9161550 . G A 1045.3 PASS AC=1;AF=0.703;AN=2;DP=3461;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant34-variant35-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:78,69:147:99:1555,0,1972:34,44,29,40 chr1 9161619 . C T 956.91 PASS AC=1;AF=0.727;AN=2;DP=1955;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,43:88:99:1222,0,1225:15,30,13,30 chr1 9161668 . T C 703.7 PASS AC=1;AF=0.703;AN=2;DP=1500;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant34-variant35-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,30:56:99:891,0,621:10,16,10,20 chr1 9162051 . C T 353.62 PASS AC=1;AF=0.703;AN=2;DP=1193;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant34-variant35-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,15:29:99:385,0,400:6,8,6,9 chr1 9162185 . T G 162.18 PASS AC=1;AF=0.717;AN=2;DP=380;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant32-variant34-variant35-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,2:5:67:67,0,113:0,3,0,2 chr1 9162490 . A G,AAG,AG 4514.84 PASS AC=1,0,0;AF=0.563,0.016,0.125;AN=2;DP=3664;set=variant7-variant11-variant12-variant13-variant3-variant14-variant15-variant5-variant16-variant6-variant17-variant18-variant19-variant21-variant2-variant22-variant23-variant24-variant25-variant26-variant10-variant27-variant28-variant30-variant32-variant34-variant35-variant38-variant39-variant40-variant43-variant44 GT:DP:GQ:SB 0/1:95:99:35,9,34,17 chr1 9163424 . T C 84.76 PASS AC=1;AF=0.87;AN=2;DP=117;FS=0;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant6-variant7-variant10-variant11-variant12-variant14-variant15-variant16-variant19-variant21-variant22-variant24-variant25-variant27-variant28-variant32-variant35-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,2:3:37:81,0,37:1,0,1,1 chr1 9163839 . A G 678.32 PASS AC=1;AF=0.703;AN=2;DP=1680;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant34-variant35-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,31:70:99:752,0,1022:22,17,18,13 chr1 9164133 . G A 791.07 PASS AC=1;AF=0.703;AN=2;DP=2344;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant34-variant35-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,52:91:99:1447,0,982:19,20,23,29 chr1 9164200 . G A,GGGGGGCACTGTGGCCACAA 3358.96 PASS AC=1,0;AF=0.65,0.025;AN=2;DP=2091;MQ=60;set=variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant34-variant35-variant38-variant39-variant40-variant43-variant44 GT:DP:GQ:SB 0/1:116:99:33,25,32,26 chr1 9165685 . G A 2984.1 PASS AC=1;AF=0.536;AN=2;DP=3503;MQ=60;set=variant2-variant3-variant7-variant12-variant16-variant19-variant21-variant24-variant27-variant28-variant32-variant35-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:123,152:275:99:3597,0,2925:62,61,73,79 chr1 9165868 . A G 948.56 PASS AC=2;AF=0.989;AN=2;DP=926;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:803,66,0:0,0,4,18 chr1 9171238 . G T 584.89 PASS AC=1;AF=0.536;AN=2;DP=1479;MQ=60;set=variant2-variant3-variant7-variant12-variant16-variant19-variant21-variant24-variant27-variant28-variant32-variant35-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:58,65:123:99:1568,0,1562:34,24,40,25 chr1 9188226 . G C 958.01 PASS AC=1;AF=0.5;AN=2;DP=98;FractionInformativeReads=1;MQ=60;set=variant24-variant35 GT:AD:DP:GQ:PL:SB 0/1:22,20:42:99:574,0,787:21,1,15,5 chr1 9189313 . G A 42.79 PASS AC=1;AF=0.5;AN=2;DP=22;MQ=60;set=variant16-variant31-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:3,4:7:99:159,0,256:1,2,1,3 chr1 9189318 . A G 42.79 PASS AC=1;AF=0.5;AN=2;DP=22;FS=0;FractionInformativeReads=1;MQ=60;set=variant16-variant31-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:3,4:7:99:159,0,256:1,2,1,3 chr1 9189323 . G T 45.8 PASS AC=1;AF=0.5;AN=2;DP=24;FS=0;FractionInformativeReads=1;set=variant16-variant31-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:3,4:7:99:159,0,256:1,2,1,3 chr1 9189324 . G C 45.8 PASS AC=1;AF=0.5;AN=2;DP=25;FS=0;FractionInformativeReads=1;set=variant16-variant31-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:3,4:7:99:159,0,256:1,2,1,3 chr1 9294783 . CCGCCCCCGCCGCGCG C 52.73 PASS AC=1;AF=0.923;AN=2;DP=39;FS=0;set=variant-variant4-variant6-variant8-variant9-variant11-variant15-variant19-variant21-variant30-variant31-variant32-variant35 GT:AD:DP:GQ:PL:SB 0/1:1,2:3:81:81,0,89:1,0,2,0 chr1 9305445 . A C 2567.55 PASS AC=1;AF=0.563;AN=2;DP=2368;MQ=60;set=variant3-variant10-variant12-variant14-variant16-variant17-variant19-variant23-variant24-variant25-variant26-variant27-variant33-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:106,86:192:99:2044,0,2401:52,54,43,43 chr1 9324213 . C T 3970.78 PASS AC=1;AF=0.583;AN=2;DP=2800;MQ=60;set=variant3-variant10-variant12-variant14-variant16-variant17-variant26-variant27-variant33-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:130,123:253:99:2776,0,3078:69,61,65,58 chr1 9324571 . T C 3002.29 PASS AC=1;AF=0.679;AN=2;DP=10149;MQ=60;set=variant-variant3-variant4-variant6-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:223,165:388:99:4202,0,5791:99,124,64,101 chr1 9324670 . A G 2057.15 PASS AC=1;AF=0.679;AN=2;DP=7099;MQ=60;set=variant-variant3-variant4-variant6-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:176,106:282:99:2537,0,4604:81,95,49,57 chr1 9325703 . C CT 452.02 PASS AC=1;AF=0.824;AN=2;DP=824;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,14:28:99:351,0,352:4,10,3,11 chr1 9326179 . A T 610.76 PASS AC=1;AF=0.577;AN=2;DP=1052;MQ=60;set=variant3-variant10-variant12-variant14-variant15-variant16-variant17-variant26-variant27-variant33-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,41:93:99:952,0,1327:30,22,19,22 chr1 9326887 . CTT C,CT 218.26 PASS AC=1,1;AF=0.721,0.256;AN=2;DP=625;FS=0;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/2:22:99:0,0,7,15 chr1 9327177 . C T 1237.15 PASS AC=1;AF=0.577;AN=2;DP=994;FractionInformativeReads=1;set=variant3-variant10-variant12-variant14-variant15-variant16-variant17-variant26-variant27-variant33-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,46:93:99:1062,0,1024:28,19,26,20 chr1 9327344 . G T 701.83 PASS AC=1;AF=0.577;AN=2;DP=766;MQ=60;set=variant3-variant10-variant12-variant14-variant15-variant16-variant17-variant26-variant27-variant33-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,41:62:99:1135,0,514:8,13,21,20 chr1 9327387 . T G 1580.96 PASS AC=1;AF=0.816;AN=2;DP=1999;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,39:54:99:1117,0,342:8,7,19,20 chr1 9327949 . A C 1975.96 PASS AC=1;AF=0.661;AN=2;DP=4164;MQ=60;set=variant-variant3-variant4-variant6-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:88,88:176:99:2266,0,2242:36,52,32,56 chr1 9331244 . T C 556.2 PASS AC=1;AF=0.679;AN=2;DP=1597;FractionInformativeReads=1;set=variant-variant3-variant4-variant6-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,32:59:99:927,0,634:16,11,20,12 chr1 9331277 . G T 1234.46 PASS AC=1;AF=0.556;AN=2;DP=1399;MQ=60;set=variant3-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant26-variant27-variant33-variant35-variant36-variant37-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,39:76:99:1040,0,834:20,17,21,18 chr1 9331331 . A T 1349.35 PASS AC=1;AF=0.559;AN=2;DP=1182;MQ=60;set=variant3-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant26-variant27-variant33-variant35-variant36-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,37:70:99:965,0,786:15,18,15,22 chr1 9352855 . GGGGGC G 163.65 PASS AC=1;AF=0.6;AN=2;DP=326;MQ=60;set=variant-variant2-variant3-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant24-variant26-variant27-variant28-variant29-variant33-variant35-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,8:12:99:324,0,137:2,2,4,4 chr1 9353015 . CGCCGGG C 1609.09 PASS AC=2;AF=0.989;AN=2;DP=1614;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1620,108,0:0,0,16,20 chr1 9411667 . A G 599.75 PASS AC=2;AF=0.869;AN=2;DP=831;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:520,54,0:0,0,8,10 chr1 9416346 . C T 2592.38 PASS AC=1;AF=0.604;AN=2;DP=4605;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant12-variant14-variant15-variant16-variant18-variant20-variant21-variant23-variant24-variant25-variant28-variant29-variant32-variant34-variant35-variant36-variant40 GT:AD:DP:GQ:PL:SB 0/1:109,126:235:99:3166,0,3016:64,45,64,62 chr1 9427842 . A G 2311.36 PASS AC=1;AF=0.589;AN=2;DP=4592;MQ=60;set=variant-variant2-variant4-variant7-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant19-variant20-variant22-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:104,62:166:99:1435,0,2592:50,54,31,31 chr1 9427869 . G A 2144.33 PASS AC=2;AF=0.888;AN=2;DP=5770;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,145:145:99:4594,434,0:0,0,66,79 chr1 9428520 . G A 1918.95 PASS AC=1;AF=0.556;AN=2;DP=1264;MQ=60;set=variant3-variant15-variant16-variant21-variant23-variant24-variant25-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:80,81:161:99:1808,0,1994:40,40,41,40 chr1 9428685 . T G 1392.61 PASS AC=2;AF=0.881;AN=2;DP=2029;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:2006,177,0:0,0,20,39 chr1 9428769 . G A 732.91 PASS AC=2;AF=1;AN=2;DP=1458;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1348,126,0:0,0,25,18 chr1 9429264 . GT GTT,G 7259.04 PASS AC=1,0;AF=0.568,0.023;AN=2;DP=5308;MQ=60;set=variant-variant4-variant8-variant9-variant11-variant12-variant14-variant16-variant17-variant18-variant26-variant27-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant41-variant43-variant44 GT:DP:GQ:SB 0/1:194:99:49,54,45,46 chr1 9658465 . T G 497.31 PASS AC=2;AF=0.849;AN=2;DP=3709;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,69:69:99:2273,207,0:0,0,48,21 chr1 9658707 . G A 839.09 PASS AC=2;AF=0.837;AN=2;DP=2728;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:2458,231,0:0,0,22,55 chr1 9661061 . A G 882.05 PASS AC=2;AF=0.849;AN=2;DP=2096;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:2048,180,0:0,0,42,18 chr1 9662449 . A C 192.87 PASS AC=1;AF=0.5;AN=2;DP=1208;MQ=60;set=filterInvariant-variant5-filterInvariant11-filterInvariant13-filterInvariant14-filterInvariant19-filterInvariant20-filterInvariant25-filterInvariant27-filterInvariant29-filterInvariant31-filterInvariant32-filterInvariant33-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant38-filterInvariant39-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:49,18:67:99:301,0,5702:3,46,18,0 chr1 9662455 . A C 183.51 PASS AC=1;AF=0.5;AN=2;DP=1274;MQ=60;set=filterInvariant-variant5-filterInvariant11-filterInvariant13-filterInvariant14-filterInvariant19-filterInvariant20-filterInvariant25-filterInvariant26-filterInvariant27-filterInvariant31-filterInvariant32-filterInvariant33-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant38-filterInvariant39-filterInvariant40-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:51,17:68:99:289,0,6077:5,46,17,0 chr1 9662458 . CTACAG C 169.07 PASS AC=1;AF=0.5;AN=2;DP=708;MQ=60;set=variant-variant5-filterInvariant14-variant19-variant25-variant31-variant32-variant34-variant35-filterInvariant36-variant40 GT:AD:DP:GQ:PL:SB 0/1:62,16:78:99:261,0,6528:11,51,16,0 chr1 9664650 . T A 2260.99 PASS AC=1;AF=0.75;AN=2;DP=207;FractionInformativeReads=1;MQ=60;MQRankSum=-1.906;ReadPosRankSum=-0.891;set=variant25-variant35 GT:AD:DP:GQ:PL:SB 0/1:77,59:136:99:1540,0,2030:44,33,31,28 chr1 9668027 . G A 238.16 PASS AC=1;AF=0.5;AN=2;DP=249;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant8-variant14-variant15-variant16-variant17-variant21-variant22-variant26-variant30-variant31-variant32-variant35-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:3,10:13:94:362,0,94:0,3,1,9 chr1 9670483 . T A 950.65 PASS AC=2;AF=0.872;AN=2;DP=4712;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,106:106:99:3307,316,0:0,0,72,34 chr1 9670834 . C T 695.36 PASS AC=2;AF=0.837;AN=2;DP=3046;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,101:101:99:3020,302,0:0,0,38,63 chr1 9671257 . CTT CT,C 149.22 PASS AC=2,0;AF=0.841,0.024;AN=2;DP=1347;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:30:87:0,0,9,21 chr1 9673779 . C A 766.57 PASS AC=2;AF=0.86;AN=2;DP=4643;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:9,132:141:99:3881,321,0:9,0,54,78 chr1 9711621 . C A 295.59 PASS AC=1;AF=0.5;AN=2;DP=29;FS=1.585;FractionInformativeReads=1;MQ=60;MQRankSum=1.129;QD=10.19;ReadPosRankSum=-0.952;SOR=1.14;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:17,12:29:99:324,0,432:11,6,9,3 chr1 9711642 . A G 311.07 PASS AC=1;AF=0.569;AN=2;DP=787;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant12-variant13-variant14-variant17-variant19-variant21-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,19:41:99:401,0,420:13,9,11,8 chr1 9711674 . A G 569.9 PASS AC=1;AF=0.569;AN=2;DP=1037;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant12-variant13-variant14-variant17-variant19-variant21-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,19:41:99:409,0,577:12,10,10,9 chr1 9711737 . T C 805.7 PASS AC=1;AF=0.569;AN=2;DP=1173;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant12-variant13-variant14-variant17-variant19-variant21-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,24:49:99:592,0,691:12,13,10,14 chr1 9711760 . G C 806.81 PASS AC=1;AF=0.569;AN=2;DP=1057;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant12-variant13-variant14-variant17-variant19-variant21-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,23:42:99:530,0,527:9,10,12,11 chr1 9712997 . G A 1570.89 PASS AC=1;AF=0.5;AN=2;DP=146;FS=2.946;FractionInformativeReads=0.993;MQ=60;MQRankSum=-1.074;QD=10.76;ReadPosRankSum=2.992;SOR=0.863;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:74,71:145:99:1599,0,1835:36,38,39,32 chr1 9713386 . C T 511.73 PASS AC=1;AF=0.567;AN=2;DP=1285;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant12-variant13-variant14-variant17-variant19-variant21-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,17:44:99:310,0,752:14,13,8,9 chr1 9713500 . G A 379.5 PASS AC=1;AF=0.565;AN=2;DP=907;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant12-variant13-variant14-variant17-variant19-variant20-variant21-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,13:35:99:347,0,534:11,11,6,7 chr1 9714177 . G A 1134.97 PASS AC=1;AF=0.533;AN=2;DP=2381;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant7-variant9-variant13-variant14-variant19-variant28-variant29-variant32-variant35-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:116,78:194:99:1957,0,2888:65,51,46,32 chr1 9714538 . G GGA 952.28 PASS AC=1;AF=0.581;AN=2;DP=2250;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant12-variant13-variant14-variant17-variant19-variant20-variant21-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:74,38:112:99:1277,0,4405:30,44,16,22 chr1 9714539 . T G 961.31 PASS AC=1;AF=0.581;AN=2;DP=2118;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant12-variant13-variant14-variant17-variant19-variant20-variant21-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:74,33:107:99:1319,0,4402:30,44,12,21 chr1 9714541 . C CCA 909.86 PASS AC=1;AF=0.581;AN=2;DP=2050;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant12-variant13-variant14-variant17-variant19-variant20-variant21-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:69,31:100:99:1205,0,4416:28,41,13,18 chr1 9714543 . A ACCCC 904.54 PASS AC=1;AF=0.581;AN=2;DP=2003;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant12-variant13-variant14-variant17-variant19-variant20-variant21-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,30:98:99:1114,0,4300:28,40,13,17 chr1 9714544 . A AG 907.44 PASS AC=1;AF=0.581;AN=2;DP=1963;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant12-variant13-variant14-variant17-variant19-variant20-variant21-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,27:94:99:1072,0,4303:26,41,9,18 chr1 9770690 . CAG CAGAG,C 158.13 PASS AC=1,0;AF=0.4,0.1;AN=2;DP=656;MQ=60;set=variant2-filterInvariant8-variant9-filterInvariant11-variant13-filterInvariant18-variant19-filterInvariant22-variant26-variant27-variant28-filterInvariant29-filterInvariant30-variant33-variant34-variant35-variant36-variant37-variant41-variant44 GT:DP:GQ:SB 0/1:12:99:3,3,1,5 chr1 9770714 . C G 228.38 PASS AC=1;AF=0.5;AN=2;DP=164;set=variant9-variant19-variant27-variant28-variant33-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:6,9:15:99:259,0,111:3,3,1,8 chr1 9779871 . T C 478.37 PASS AC=1;AF=0.5;AN=2;DP=611;MQ=60;set=variant7-variant9-variant13-variant18-variant19-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,14:31:99:468,0,585:16,1,13,1 chr1 9781412 . C G 1013.07 PASS AC=1;AF=0.671;AN=2;DP=3222;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,57:108:99:1805,0,1588:21,30,25,32 chr1 9782556 . C T 977.85 PASS AC=1;AF=0.657;AN=2;DP=3085;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,47:90:99:1106,0,1198:29,14,26,21 chr1 9782766 . C T 682.37 PASS AC=1;AF=0.5;AN=2;DP=487;FractionInformativeReads=1;MQ=60;set=variant9-variant19-variant27-variant28-variant33-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:39,34:73:99:979,0,982:18,21,10,24 chr1 9784423 . C T 2555.37 PASS AC=1;AF=0.5;AN=2;DP=1462;FractionInformativeReads=1;set=variant9-variant19-variant27-variant28-variant33-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:102,110:212:99:2660,0,2511:47,55,55,55 chr1 9786845 . G C 348.41 PASS AC=1;AF=0.5;AN=2;DP=139;FractionInformativeReads=1;MQ=60;set=variant9-variant27-variant28-variant35 GT:AD:DP:GQ:PL:SB 0/1:18,27:45:99:703,0,503:12,6,17,10 chr1 9787508 . T C 2807.99 PASS AC=2;AF=0.943;AN=2;DP=5790;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,159:159:99:4782,475,0:0,0,73,86 chr1 9787866 . CT C,CTTT 52.31 PASS AC=0,1;AF=0.333,0.167;AN=2;DP=63;MQ=60;set=variant4-variant25-filterInvariant35 GT:DP:GQ:SB 0/2:18:70:5,9,3,1 chr1 9789577 . G A 880.25 PASS AC=1;AF=0.5;AN=2;DP=332;FractionInformativeReads=1;MQ=60;set=variant9-variant27-variant28-variant35 GT:AD:DP:GQ:PL:SB 0/1:59,34:93:99:687,0,1385:27,32,15,19 chr1 9789891 . T C 690.26 PASS AC=1;AF=0.5;AN=2;DP=309;FractionInformativeReads=1;MQ=60;set=variant9-variant27-variant28-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:31,41:72:99:1045,0,779:16,15,22,19 chr1 9792105 . G GA 162.61 PASS AC=2;AF=0.989;AN=2;DP=870;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:371,39,0:0,0,3,10 chr1 9793452 . T A 2374.7 PASS AC=1;AF=0.5;AN=2;DP=816;MQ=60;set=variant9-variant27-variant28-variant35 GT:AD:DP:GQ:PL:SB 0/1:94,136:230:99:3071,0,1940:46,48,69,67 chr1 9794305 . C T 712.58 PASS AC=1;AF=0.5;AN=2;DP=261;FractionInformativeReads=1;MQ=60;set=variant9-variant27-variant28-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:20,23:43:99:638,0,659:4,16,6,17 chr1 9794982 . C T 894.68 PASS AC=1;AF=0.5;AN=2;DP=303;FractionInformativeReads=1;MQ=60;set=variant9-variant27-variant28-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:38,38:76:99:894,0,953:20,18,23,15 chr1 9795250 . G A 758.3 PASS AC=1;AF=0.5;AN=2;DP=283;FractionInformativeReads=1;MQ=60;set=variant9-variant27-variant28-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:34,26:60:99:637,0,902:14,20,10,16 chr1 9795719 . C T 58.61 PASS AC=1;AF=0.5;AN=2;DP=114;FractionInformativeReads=1;MQ=60;set=variant9-variant27-variant28-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:15,8:23:99:276,0,487:4,11,0,8 chr1 9801341 . G A 1379.81 PASS AC=1;AF=0.5;AN=2;DP=641;FractionInformativeReads=1;MQ=60;set=variant9-variant27-variant28-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:75,76:151:99:1775,0,1872:29,46,36,40 chr1 9804693 . C T 958.17 PASS AC=1;AF=0.5;AN=2;DP=294;FractionInformativeReads=1;MQ=60;set=variant9-variant27-variant28-variant35 GT:AD:DP:GQ:PL:SB 0/1:39,49:88:99:1196,0,1135:8,31,18,31 chr1 9811541 . A G 703 PASS AC=1;AF=0.5;AN=2;DP=379;MQ=60;set=variant9-variant27-variant28-variant35-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:32,37:69:99:1016,0,696:19,13,25,12 chr1 9816620 . T C 3377.27 PASS AC=2;AF=0.955;AN=2;DP=4415;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,102:102:99:3171,306,0:0,0,56,46 chr1 9883878 . T C 548.53 PASS AC=2;AF=1;AN=2;DP=1034;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:947,90,0:0,0,14,16 chr1 9883960 . A G 138.55 PASS AC=1;AF=0.5;AN=2;DP=241;MQ=60;set=variant9-variant27-variant28-variant35-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:23,16:39:99:451,0,580:8,15,7,9 chr1 9884399 . T G 1363.62 PASS AC=1;AF=0.5;AN=2;DP=713;MQ=60;set=variant9-variant27-variant28-variant33-variant35-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:27,59:86:99:1494,0,533:17,10,32,27 chr1 9908269 . C T 2203.24 PASS AC=1;AF=0.563;AN=2;DP=2283;MQ=60;set=variant4-variant9-variant10-variant12-variant13-variant18-variant23-variant24-variant25-variant28-variant35-variant37-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:85,84:169:99:1875,0,1923:48,37,48,36 chr1 9908515 . A G 1748.93 PASS AC=2;AF=1;AN=2;DP=2493;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:2151,194,0:0,0,34,31 chr1 9908680 . C T 903.43 PASS AC=1;AF=0.563;AN=2;DP=647;MQ=60;set=variant4-variant9-variant10-variant12-variant13-variant18-variant23-variant24-variant25-variant28-variant35-variant37-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,26:58:99:663,0,989:16,16,13,13 chr1 9910357 . A T 2297.48 PASS AC=1;AF=0.611;AN=2;DP=771;FractionInformativeReads=1;MQ=60;set=variant4-variant9-variant10-variant12-variant13-variant18-variant19-variant20-variant23-variant24-variant25-variant28-variant35-variant37-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,19:39:99:735,0,1104:14,6,8,11 chr1 9910358 . T C 2297.48 PASS AC=1;AF=0.611;AN=2;DP=775;FractionInformativeReads=1;MQ=60;set=variant4-variant9-variant10-variant12-variant13-variant18-variant19-variant20-variant23-variant24-variant25-variant28-variant35-variant37-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,19:40:99:735,0,1104:15,6,8,11 chr1 9970471 . G A 274.33 PASS AC=1;AF=0.533;AN=2;DP=221;FractionInformativeReads=1;MQ=60;set=variant4-variant9-variant10-variant12-variant14-variant18-variant23-variant24-variant25-variant35-variant37-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,9:18:99:294,0,228:4,5,3,6 chr1 9989081 . G A 511.64 PASS AC=1;AF=0.5;AN=2;DP=168;FractionInformativeReads=1;MQ=60;set=variant17-variant32-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:25,18:43:99:506,0,737:19,6,14,4 chr1 10001235 . TTTCG T 3170.84 PASS AC=1;AF=0.857;AN=2;DP=3331;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,43:64:99:1700,0,973:7,14,14,29 chr1 10003320 . G A 1446.75 PASS AC=1;AF=0.884;AN=2;DP=2154;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,18:41:99:540,0,699:16,7,10,8 chr1 10027540 . G A 611.73 PASS AC=1;AF=0.884;AN=2;DP=803;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,8:21:99:241,0,397:3,10,1,7 chr1 10057203 . G T 663.54 PASS AC=1;AF=0.5;AN=2;DP=168;FractionInformativeReads=1;MQ=60;set=variant17-variant32-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:24,17:41:99:456,0,857:19,5,12,5 chr1 10057233 . A C 324.49 PASS AC=1;AF=0.5;AN=2;DP=1107;set=variant2-filterInvariant3-variant4-variant5-variant8-filterInvariant9-variant10-variant12-variant17-variant19-variant21-variant23-filterInvariant26-variant28-filterInvariant29-filterInvariant32-variant34-variant35-filterInvariant36-variant38-variant40-filterInvariant41 GT:AD:DP:GQ:PL:SB 0/1:33,25:58:99:677,0,1391:16,17,25,0 chr1 10057240 . T C 299.96 PASS AC=1;AF=0.5;AN=2;DP=1305;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant12-variant15-variant19-variant21-variant26-variant28-variant30-filterInvariant31-variant32-variant35-variant38-variant40-filterInvariant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:41,28:69:99:801,0,950:20,21,28,0 chr1 10057246 . G C 263.83 PASS AC=1;AF=0.5;AN=2;DP=1177;set=variant-filterInvariant4-variant8-filterInvariant10-filterInvariant12-filterInvariant15-variant17-variant19-filterInvariant21-filterInvariant29-filterInvariant32-variant34-variant35-filterInvariant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:59,21:80:99:546,0,2795:38,21,21,0 chr1 10057251 . G C 235.3 PASS AC=1;AF=0.5;AN=2;DP=940;set=variant-filterInvariant4-variant5-variant8-variant12-filterInvariant19-variant29-filterInvariant32-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:78,20:98:99:526,0,2971:54,24,20,0 chr1 10241135 . TAA TA,T 2290.82 PASS AC=1,0;AF=0.535,0.012;AN=2;DP=10375;MQ=60;set=variant-variant2-variant3-variant4-filterInvariant5-filterInvariant6-variant7-variant8-variant9-filterInvariant10-variant11-filterInvariant12-variant13-filterInvariant14-variant15-filterInvariant16-filterInvariant18-variant19-variant20-filterInvariant21-variant22-filterInvariant23-filterInvariant24-variant25-variant26-variant27-variant28-variant29-filterInvariant30-variant31-variant32-filterInvariant33-variant34-filterInvariant35-variant36-filterInvariant37-variant38-variant39-filterInvariant40-filterInvariant41-variant42-filterInvariant43-filterInvariant44 GT:DP:GQ:SB 0/1:235:99:96,102,16,21 chr1 10335315 . G A 1209.71 PASS AC=1;AF=0.977;AN=2;DP=1349;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:13,8:21:99:257,0,428:9,4,6,2 chr1 10351329 . A G 134.43 PASS AC=1;AF=0.5;AN=2;DP=8;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.684;QD=16.8;ReadPosRankSum=1.221;SOR=1.179;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:3,5:8:99:163,0,114:0,3,0,5 chr1 10357206 . AT A,ATTT,ATT 245.14 PASS AC=1,0,0;AF=0.452,0.024,0.024;AN=2;DP=2586;set=variant-variant2-variant3-filterInvariant4-filterInvariant5-variant6-variant7-filterInvariant8-variant9-variant10-filterInvariant11-variant12-filterInvariant14-variant15-variant16-variant17-filterInvariant18-variant19-variant20-variant21-filterInvariant22-variant23-variant24-filterInvariant25-variant26-variant27-variant28-filterInvariant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-filterInvariant40-variant41-variant43-variant44 GT:DP:GQ:SB 0/1:47:99:10,22,5,10 chr1 10478830 . CA C,CAA 82.92 PASS AC=1,0;AF=0.3,0.2;AN=2;DP=1035;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-filterInvariant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:DP:GQ:SB 0/1:37:99:17,6,12,2 chr1 10502307 . AT A 308.59 PASS AC=2;AF=0.966;AN=2;DP=1116;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:550,57,0:0,0,14,5 chr1 10502710 . A G 5629.8 PASS AC=2;AF=0.966;AN=2;DP=6909;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,175:175:99:4736,522,0:0,0,83,92 chr1 10509703 . C T 1876.54 PASS AC=2;AF=0.966;AN=2;DP=1331;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:1236,90,0:0,0,27,3 chr1 10511330 . AT A,ATT 388.17 PASS AC=2,0;AF=0.672,0.017;AN=2;DP=467;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant12-variant13-variant14-variant15-variant16-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant41-variant42-variant44 GT:DP:GQ:SB 1/1:13:39:0,0,10,3 chr1 10511544 . C T 3636.33 PASS AC=2;AF=0.643;AN=2;DP=3262;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant10-variant13-variant14-variant15-variant16-variant21-variant23-variant24-variant25-variant26-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,115:116:99:3519,337,0:0,1,60,55 chr1 10511589 . T C 3717.06 PASS AC=2;AF=0.966;AN=2;DP=4733;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,104:104:99:3446,312,0:0,0,53,51 chr1 10512056 . T C 7758.98 PASS AC=2;AF=0.966;AN=2;DP=8821;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,201:201:99:6585,603,0:0,0,124,77 chr1 10517944 . CTG C 799.39 PASS AC=2;AF=0.966;AN=2;DP=1599;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1436,102,0:0,0,15,19 chr1 10519090 . C T 518.05 PASS AC=2;AF=0.965;AN=2;DP=373;FS=0;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:316,24,0:0,0,6,2 chr1 10519787 . A T 1123.87 PASS AC=1;AF=0.5;AN=2;DP=3320;set=variant-variant3-variant5-variant6-variant7-variant8-variant10-filterInvariant12-variant13-variant14-variant15-variant16-variant19-filterInvariant21-variant23-variant24-variant25-variant26-variant27-variant29-filterInvariant30-variant31-variant32-variant34-variant35-variant37-variant39-filterInvariant41-variant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,41:61:99:684,0,249:4,16,9,32 chr1 10529194 . T C 2681.74 PASS AC=2;AF=0.677;AN=2;DP=2592;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant10-variant12-variant14-variant15-variant16-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,86:86:99:2656,256,0:0,0,58,28 chr1 10555257 . C T 1584.21 PASS AC=2;AF=0.744;AN=2;DP=2343;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,66:66:99:2298,198,0:0,0,41,25 chr1 10596341 . C T 1324.94 PASS AC=1;AF=0.56;AN=2;DP=3114;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant9-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant27-variant28-variant29-variant30-variant31-variant35-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:86,66:152:99:1439,0,2114:40,46,26,40 chr1 10596388 . A G 1671.53 PASS AC=2;AF=0.989;AN=2;DP=3179;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,100:100:99:3060,300,0:0,0,37,63 chr1 10684512 . A ACAGGGCCCTC 1760.03 PASS AC=1;AF=0.5;AN=2;DP=131;FS=2.514;FractionInformativeReads=0.855;MQ=60;MQRankSum=-0.24;QD=13.44;ReadPosRankSum=-1.296;SOR=0.467;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:63,49:112:99:1797,0,4123:23,40,21,28 chr1 10689942 . G T 1556 PASS AC=1;AF=0.583;AN=2;DP=2724;MQ=60;set=variant-variant2-variant3-variant5-variant8-variant9-variant12-variant13-variant16-variant18-variant21-variant22-variant27-variant31-variant32-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:85,79:164:99:1929,0,2138:39,46,36,43 chr1 10696712 . CAA C,CA 140.66 PASS AC=1,0;AF=0.533,0.133;AN=2;DP=116;MQ=60;set=variant-variant3-variant8-variant9-variant15-variant16-variant19-variant21-variant27-variant28-variant31-variant32-variant35-variant37-variant42 GT:DP:GQ:SB 0/1:5:39:2,0,2,1 chr1 10714294 . G C 1655.57 PASS AC=1;AF=0.5;AN=2;DP=719;MQ=60;set=variant2-variant7-variant13-variant17-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:74,67:141:99:1624,0,1979:28,46,28,39 chr1 10714330 . A AC 1173.46 PASS AC=1;AF=0.559;AN=2;DP=1217;MQ=60;set=variant2-variant7-variant10-variant11-variant13-variant17-variant19-variant20-variant26-variant27-variant28-variant33-variant35-variant37-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,37:81:99:1119,0,1392:14,30,12,25 chr1 10714402 . C T 475.91 PASS AC=1;AF=0.5;AN=2;DP=238;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant13-variant17-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,25:47:99:859,0,735:11,11,12,13 chr1 10856513 . TG T 545.81 PASS AC=1;AF=0.845;AN=2;DP=2583;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,40:71:99:1538,0,1466:17,14,21,19 chr1 10856517 . G A 619.42 PASS AC=1;AF=0.845;AN=2;DP=2578;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,41:73:99:1536,0,1523:18,14,22,19 chr1 10856692 . C T 1337.6 PASS AC=1;AF=0.7;AN=2;DP=3931;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant18-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:62,71:133:99:1669,0,1457:27,35,28,43 chr1 11008497 . G C 4303.27 PASS AC=1;AF=0.548;AN=2;DP=4142;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant9-variant13-variant14-variant20-variant21-variant26-variant27-variant29-variant30-variant33-variant34-variant35-variant36-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:107,121:228:99:3019,0,3012:53,54,59,62 chr1 11008695 . T C 3299.86 PASS AC=1;AF=0.55;AN=2;DP=2249;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant9-variant13-variant14-variant20-variant21-variant27-variant29-variant30-variant33-variant34-variant35-variant36-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,65:133:99:1701,0,1771:32,36,33,32 chr1 11014118 . C T 975.61 PASS AC=1;AF=0.548;AN=2;DP=2730;MQ=60;set=variant-variant3-variant6-variant7-variant9-variant10-variant13-variant14-variant20-variant21-variant27-variant29-variant30-variant33-variant34-variant35-variant36-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:63,48:111:99:1033,0,1681:32,31,22,26 chr1 11015165 . A G 1518.59 PASS AC=1;AF=0.548;AN=2;DP=1573;MQ=60;set=variant-variant3-variant6-variant7-variant9-variant10-variant13-variant14-variant20-variant21-variant27-variant29-variant30-variant33-variant34-variant35-variant36-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,40:83:99:833,0,1102:28,15,23,17 chr1 11015325 . C T 843.87 PASS AC=1;AF=0.548;AN=2;DP=900;MQ=60;set=variant-variant3-variant6-variant7-variant9-variant10-variant13-variant14-variant20-variant21-variant27-variant29-variant30-variant33-variant34-variant35-variant36-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,27:66:99:579,0,1098:11,28,11,16 chr1 11017022 . C CAG 2641.26 PASS AC=1;AF=0.548;AN=2;DP=1924;MQ=60;set=variant-variant3-variant6-variant7-variant9-variant10-variant13-variant14-variant20-variant21-variant27-variant29-variant30-variant33-variant34-variant35-variant36-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,32:86:99:1152,0,2122:33,21,17,15 chr1 11017609 . T C 376.77 PASS AC=1;AF=0.545;AN=2;DP=482;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant9-variant10-variant13-variant14-variant20-variant21-variant27-variant29-variant30-variant33-variant34-variant35-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,9:23:99:336,0,1387:11,3,6,3 chr1 11017617 . G C 376.77 PASS AC=1;AF=0.545;AN=2;DP=531;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant9-variant10-variant13-variant14-variant20-variant21-variant27-variant29-variant30-variant33-variant34-variant35-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,10:28:99:428,0,1618:12,6,7,3 chr1 11017634 . C T 460.43 PASS AC=1;AF=0.545;AN=2;DP=654;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant9-variant10-variant13-variant14-variant20-variant21-variant27-variant29-variant30-variant33-variant34-variant35-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,14:37:99:438,0,1677:14,9,8,6 chr1 11018723 . A G 3338.38 PASS AC=1;AF=0.548;AN=2;DP=3381;MQ=60;set=variant-variant3-variant6-variant7-variant9-variant10-variant13-variant14-variant21-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:70,93:163:99:2400,0,1788:32,38,40,53 chr1 11024353 . A G 1549.3 PASS AC=1;AF=0.609;AN=2;DP=2628;MQ=60;set=variant-variant3-variant6-variant7-variant9-variant10-variant11-variant13-variant14-variant19-variant21-variant27-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,60:125:99:1509,0,1505:25,40,23,37 chr1 11024381 . A G 1184.38 PASS AC=1;AF=0.609;AN=2;DP=1962;MQ=60;set=variant-variant3-variant6-variant7-variant9-variant10-variant11-variant13-variant14-variant19-variant21-variant27-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,42:87:99:1140,0,1125:15,30,15,27 chr1 11024395 . T C 1003.64 PASS AC=1;AF=0.64;AN=2;DP=1666;MQ=60;set=variant-variant3-variant6-variant7-variant9-variant10-variant11-variant13-variant14-variant19-variant21-variant23-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,35:70:99:934,0,985:10,25,12,23 chr1 11072579 . T C 917.48 PASS AC=2;AF=0.942;AN=2;DP=696;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:337,36,0:0,0,7,5 chr1 11072885 . C T 381.29 PASS AC=1;AF=0.826;AN=2;DP=888;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,17:21:93:391,0,93:3,1,6,11 chr1 11079077 . A G 267.07 PASS AC=1;AF=0.826;AN=2;DP=808;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,11:22:99:249,0,379:1,10,3,8 chr1 11080723 . T TG 98.75 PASS AC=2;AF=0.872;AN=2;DP=801;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:630,54,0:0,0,5,13 chr1 11086097 . A AT 1336.83 PASS AC=1;AF=0.826;AN=2;DP=2861;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,44:80:99:1390,0,1103:17,19,19,25 chr1 11086717 . A G 221.67 PASS AC=2;AF=0.86;AN=2;DP=1546;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1390,129,0:0,0,26,17 chr1 11087524 . G A 2327.96 PASS AC=2;AF=0.86;AN=2;DP=5991;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,167:167:99:4830,498,0:0,0,84,83 chr1 11087835 . T C 276.2 PASS AC=2;AF=0.872;AN=2;DP=556;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:497,42,0:0,0,3,11 chr1 11090897 . A G 993.1 PASS AC=1;AF=0.5;AN=2;DP=273;FractionInformativeReads=1;MQ=60;set=variant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,42:98:99:1021,0,1375:16,40,18,24 chr1 11090916 . C A 846.21 PASS AC=1;AF=0.826;AN=2;DP=3007;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,41:76:99:1179,0,858:13,22,10,31 chr1 11094665 . G A 231.25 PASS AC=2;AF=0.907;AN=2;DP=140;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant12-variant15-variant16-variant17-variant18-variant21-variant23-variant24-variant27-variant29-variant30-variant31-variant32-variant35-variant36-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:222,15,0:0,0,5,0 chr1 11094757 . G GA,GAA 377.46 PASS AC=2,0;AF=0.737,0.013;AN=2;DP=721;set=variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:21:42:1,0,11,9 chr1 11095039 . C T 80.93 PASS AC=2;AF=0.872;AN=2;DP=943;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:884,84,0:0,0,12,16 chr1 11097867 . C T 1335.86 PASS AC=1;AF=0.5;AN=2;DP=453;FractionInformativeReads=1;MQ=60;set=variant29-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,46:99:99:1339,0,1340:20,33,25,21 chr1 11104676 . G A 331.62 PASS AC=1;AF=0.802;AN=2;DP=639;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,11:21:99:358,0,373:9,1,8,3 chr1 11104712 . G A 576.02 PASS AC=1;AF=0.802;AN=2;DP=1027;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,14:31:99:348,0,577:14,3,11,3 chr1 11104845 . T C 1450.09 PASS AC=2;AF=0.86;AN=2;DP=4900;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,136:136:99:4136,407,0:0,0,75,61 chr1 11105106 . C T 597.83 PASS AC=1;AF=0.802;AN=2;DP=2689;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,38:74:99:845,0,912:14,22,17,21 chr1 11105122 . C T 504.5 PASS AC=2;AF=0.86;AN=2;DP=2563;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,67:67:99:2617,206,0:0,0,27,40 chr1 11107439 . G T 72.1 PASS AC=1;AF=0.81;AN=2;DP=740;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,13:25:99:392,0,310:5,7,2,11 chr1 11114940 . G T 609.38 PASS AC=1;AF=0.5;AN=2;DP=192;FractionInformativeReads=1;MQ=60;set=variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,45:74:99:1119,0,684:14,15,20,25 chr1 11115177 . CTT CTTT,CT,C 50.09 PASS AC=0,0,1;AF=0.115,0.346,0.038;AN=2;DP=1461;set=filterInvariant-filterInvariant2-filterInvariant3-variant4-filterInvariant5-variant6-variant7-filterInvariant9-filterInvariant10-filterInvariant12-variant16-variant19-filterInvariant20-variant23-variant25-variant26-variant29-filterInvariant34-variant35-filterInvariant36-variant38-variant39-filterInvariant40-variant42-filterInvariant43-variant44 GT:DP:GQ:SB 0/3:50:99:13,19,4,14 chr1 11119177 . C T 380.54 PASS AC=1;AF=0.5;AN=2;DP=37;FractionInformativeReads=1;MQ=60;set=variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,13:20:99:409,0,215:6,1,9,4 chr1 11119899 . T C 4997.74 PASS AC=2;AF=1;AN=2;DP=7102;FS=0;MQ=60;MQRankSum=-0.485;ReadPosRankSum=0.928;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,185:185:99:5562,554,0:0,0,79,106 chr1 11120256 . C T 78.26 PASS AC=1;AF=0.5;AN=2;DP=4;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.727;QD=19.57;ReadPosRankSum=0.727;SOR=0.916;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:1,3:4:25:106,0,25:0,1,2,1 chr1 11126697 . G C 563.33 PASS AC=1;AF=0.5;AN=2;DP=154;FractionInformativeReads=1;MQ=60;set=variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,28:96:99:592,0,1823:33,35,14,14 chr1 11126848 . T C 742.08 PASS AC=1;AF=0.5;AN=2;DP=193;FractionInformativeReads=1;MQ=60;set=variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,26:56:99:628,0,833:13,17,12,14 chr1 11128329 . A G 43.72 PASS AC=1;AF=0.813;AN=2;DP=282;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,4:14:98:98,0,288:2,8,1,3 chr1 11129848 . A G 562.31 PASS AC=1;AF=0.791;AN=2;DP=1662;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,24:51:99:638,0,615:9,18,8,16 chr1 11133934 . CAAAA C,CAAAAAA 58.54 PASS AC=0,1;AF=0.167,0.333;AN=2;DP=59;set=variant23-variant29-variant35 GT:DP:GQ:SB 0/2:12:99:6,0,4,2 chr1 11134157 . T G 866.41 PASS AC=1;AF=0.802;AN=2;DP=2169;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,28:61:99:775,0,973:17,16,14,14 chr1 11134470 . A AT,ATT 30.14 PASS AC=0,1;AF=0.2,0.3;AN=2;DP=239;set=filterInvariant14-filterInvariant23-variant29-variant35-variant44 GT:DP:GQ:SB 0/2:30:99:3,9,3,15 chr1 11134494 . G C 503.23 PASS AC=1;AF=0.5;AN=2;DP=68;FractionInformativeReads=1;MQ=60;set=variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,13:25:99:539,0,595:3,9,2,11 chr1 11136815 . T C 934.76 PASS AC=1;AF=0.5;AN=2;DP=223;FractionInformativeReads=1;MQ=60;set=variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,42:86:99:1075,0,1098:29,15,29,13 chr1 11136838 . A G 1163.39 PASS AC=1;AF=0.5;AN=2;DP=313;FractionInformativeReads=1;MQ=60;set=variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,53:117:99:1248,0,1497:39,25,35,18 chr1 11137661 . A G 1151.93 PASS AC=1;AF=0.5;AN=2;DP=273;FractionInformativeReads=1;MQ=60;set=variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,53:108:99:1297,0,1323:30,25,24,29 chr1 11139731 . G A 497.16 PASS AC=1;AF=0.5;AN=2;DP=186;FractionInformativeReads=1;MQ=60;set=variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,32:68:99:869,0,988:26,10,23,9 chr1 11140610 . GAAAA GAA,G 259.35 PASS AC=0,1;AF=0.25,0.25;AN=2;DP=27;set=variant29-variant35 GT:DP:GQ:SB 0/2:15:99:3,4,2,6 chr1 11141030 . G C 625.58 PASS AC=1;AF=0.5;AN=2;DP=187;FractionInformativeReads=1;MQ=60;set=variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,35:77:99:884,0,1118:21,21,21,14 chr1 11141102 . A G 787.55 PASS AC=1;AF=0.5;AN=2;DP=180;FractionInformativeReads=1;MQ=60;set=variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,27:68:99:790,0,1117:24,17,14,13 chr1 11141187 . C G 913.85 PASS AC=1;AF=0.802;AN=2;DP=5023;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,77:136:99:2039,0,1440:30,29,43,34 chr1 11141406 . T C 357.53 PASS AC=1;AF=0.5;AN=2;DP=81;FractionInformativeReads=1;MQ=60;set=variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,15:27:99:407,0,422:1,11,4,11 chr1 11150682 . C T 1441.78 PASS AC=1;AF=0.5;AN=2;DP=425;MQ=60;set=variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:89,82:171:99:1866,0,2097:43,46,38,44 chr1 11151480 . T C 430.08 PASS AC=1;AF=0.5;AN=2;DP=152;FractionInformativeReads=1;MQ=60;set=variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,21:46:99:515,0,663:17,8,12,9 chr1 11151779 . A G 158.43 PASS AC=1;AF=0.829;AN=2;DP=494;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,5:13:99:142,0,281:1,7,1,4 chr1 11159823 . T C 2167.3 PASS AC=1;AF=0.5;AN=2;DP=788;MQ=60;set=variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:182,127:309:99:2785,0,4115:94,88,69,58 chr1 11159968 . G A 2134.7 PASS AC=1;AF=0.5;AN=2;DP=348;MQ=60;set=variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:72,47:119:99:1584,0,3421:28,44,14,33 chr1 11159989 . T C 1980.08 PASS AC=1;AF=0.5;AN=2;DP=271;MQ=60;set=variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,28:85:99:1093,0,2987:21,36,10,18 chr1 11166713 . T C 2229.47 PASS AC=1;AF=0.5;AN=2;DP=612;MQ=60;set=variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:102,112:214:99:2945,0,2530:43,59,46,66 chr1 11167146 . G A 2103.83 PASS AC=1;AF=0.5;AN=2;DP=669;FractionInformativeReads=1;MQ=60;set=variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:137,103:240:99:2501,0,3645:69,68,53,50 chr1 11167760 . C T 319.9 PASS AC=1;AF=0.5;AN=2;DP=72;FractionInformativeReads=1;MQ=60;set=variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,16:22:99:472,0,198:1,5,5,11 chr1 11169676 . C T 1429.66 PASS AC=1;AF=0.5;AN=2;DP=282;FractionInformativeReads=1;MQ=60;set=variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,52:97:99:1307,0,1043:24,21,28,24 chr1 11171226 . C T 903.92 PASS AC=1;AF=0.5;AN=2;DP=321;FractionInformativeReads=1;MQ=60;set=variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,63:98:99:1523,0,815:16,19,28,35 chr1 11174331 . T C 358.51 PASS AC=1;AF=0.5;AN=2;DP=152;FractionInformativeReads=1;MQ=60;set=variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,24:58:99:703,0,841:22,12,19,5 chr1 11175270 . G T 46.72 PASS AC=1;AF=0.5;AN=2;DP=22;FractionInformativeReads=1;MQ=60;set=variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,6:10:99:233,0,149:3,1,3,3 chr1 11181327 . C T 806.41 PASS AC=1;AF=0.528;AN=2;DP=2398;MQ=60;set=variant-variant3-variant5-variant7-variant11-variant12-variant16-variant19-variant20-variant23-variant24-variant25-variant26-variant32-variant33-variant35-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:75,78:153:99:1924,0,1853:43,32,45,33 chr1 11181457 . G T 1489.28 PASS AC=1;AF=0.5;AN=2;DP=486;FractionInformativeReads=1;MQ=60;set=variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:87,102:189:99:2370,0,2386:35,52,42,60 chr1 11182261 . G A 576.24 PASS AC=1;AF=0.5;AN=2;DP=235;FS=0;FractionInformativeReads=1;MQ=60;set=variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,49:104:99:1167,0,1498:18,37,16,33 chr1 11184489 . C T 1150.38 PASS AC=1;AF=0.5;AN=2;DP=227;FractionInformativeReads=1;MQ=60;set=variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,34:67:99:934,0,884:22,11,26,8 chr1 11186897 . A G 884.51 PASS AC=1;AF=0.5;AN=2;DP=200;FractionInformativeReads=1;MQ=60;set=variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,28:65:99:649,0,1018:16,21,14,14 chr1 11187893 . T C 1609.98 PASS AC=2;AF=0.989;AN=2;DP=1868;MQ=60;MQRankSum=0.892;ReadPosRankSum=0.499;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:1528,141,0:0,0,17,30 chr1 11189191 . G A 483.01 PASS AC=1;AF=0.5;AN=2;DP=87;FractionInformativeReads=1;MQ=60;set=variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,10:35:99:233,0,815:8,17,4,6 chr1 11190646 . G A 2522.8 PASS AC=1;AF=0.528;AN=2;DP=3526;MQ=60;set=variant-variant3-variant5-variant7-variant11-variant12-variant16-variant19-variant20-variant23-variant24-variant25-variant26-variant32-variant33-variant35-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:109,101:210:99:2292,0,2953:52,57,51,50 chr1 11193401 . A C 1160.82 PASS AC=1;AF=0.5;AN=2;DP=127;FractionInformativeReads=1;MQ=60;set=variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,25:42:99:921,0,1539:3,14,6,19 chr1 11193406 . C T 1014.86 PASS AC=1;AF=0.5;AN=2;DP=110;FractionInformativeReads=1;MQ=60;set=variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,18:32:99:824,0,1518:3,11,4,14 chr1 11193408 . C T 1014.86 PASS AC=1;AF=0.5;AN=2;DP=106;FractionInformativeReads=1;MQ=60;set=variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,17:30:99:714,0,1450:3,10,4,13 chr1 11194591 . G A 1553.2 PASS AC=1;AF=0.5;AN=2;DP=427;MQ=60;set=variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:80,69:149:99:1760,0,2069:40,40,28,41 chr1 11194836 . A G 61.77 PASS AC=1;AF=0.75;AN=2;DP=14;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.825;ReadPosRankSum=0.825;set=variant29-variant35 GT:AD:DP:GQ:PL:SB 0/1:8,4:12:99:141,0,313:0,8,0,4 chr1 11206690 . A T 1078.83 PASS AC=1;AF=0.5;AN=2;DP=351;MQ=60;set=variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:83,62:145:99:1326,0,1935:48,35,36,26 chr1 11227360 . G T 555.75 PASS AC=1;AF=0.5;AN=2;DP=66;FractionInformativeReads=1;MQ=60;set=variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,6:20:99:181,0,939:11,3,5,1 chr1 11227365 . C T 589.52 PASS AC=1;AF=0.5;AN=2;DP=72;FractionInformativeReads=1;MQ=60;set=variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,6:22:99:178,0,972:12,4,5,1 chr1 11254843 . T C 527.83 PASS AC=1;AF=0.5;AN=2;DP=203;FractionInformativeReads=1;set=variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,32:73:99:953,0,1085:14,27,14,18 chr1 11255008 . T C 1077.78 PASS AC=1;AF=0.5;AN=2;DP=288;FractionInformativeReads=1;MQ=60;set=variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:63,41:104:99:975,0,1573:34,29,22,19 chr1 11255431 . C T 510.61 PASS AC=1;AF=0.5;AN=2;DP=107;FractionInformativeReads=1;MQ=60;set=variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,19:37:99:623,0,490:9,9,7,12 chr1 11255702 . G A 1607.13 PASS AC=1;AF=0.5;AN=2;DP=327;MQ=60;set=variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,46:99:99:1184,0,1355:28,25,26,20 chr1 11256034 . T C 1092.05 PASS AC=1;AF=0.5;AN=2;DP=194;FractionInformativeReads=1;MQ=60;set=variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,32:63:99:713,0,834:10,21,13,19 chr1 11264828 . A C 545.33 PASS AC=1;AF=0.5;AN=2;DP=76;MQ=60;set=variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,16:29:99:499,0,388:2,11,3,13 chr1 11273418 . T G 209.12 PASS AC=1;AF=0.5;AN=2;DP=45;FractionInformativeReads=1;MQ=60;set=variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,9:15:99:279,0,230:6,0,7,2 chr1 11276126 . A AT 314.96 PASS AC=1;AF=0.5;AN=2;DP=170;FractionInformativeReads=1;MQ=60;set=variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,29:66:99:965,0,1215:23,14,16,13 chr1 11288618 . G A 352.53 PASS AC=1;AF=0.779;AN=2;DP=1653;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,22:46:99:595,0,670:14,10,12,10 chr1 11288633 . G C 463.19 PASS AC=1;AF=0.779;AN=2;DP=1856;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,24:48:99:649,0,648:13,11,13,11 chr1 11288758 . G A 875.54 PASS AC=1;AF=0.779;AN=2;DP=4391;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,48:98:99:1371,0,1416:32,18,30,18 chr1 11294474 . T A 252.98 PASS AC=1;AF=0.779;AN=2;DP=865;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,20:31:99:551,0,358:2,9,6,14 chr1 11297762 . T C 445.51 PASS AC=1;AF=0.779;AN=2;DP=2425;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,48:80:99:1135,0,806:20,12,25,23 chr1 11298739 . T C 348.1 PASS AC=1;AF=0.5;AN=2;DP=82;FractionInformativeReads=1;MQ=60;set=variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,13:28:99:208,0,505:2,13,6,7 chr1 11298790 . T C 114.2 PASS AC=1;AF=0.786;AN=2;DP=625;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,6:12:99:167,0,193:1,5,1,5 chr1 11301714 . A G 881.01 PASS AC=1;AF=0.779;AN=2;DP=5802;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:102,68:170:99:1615,0,2553:54,48,39,29 chr1 11301841 . C A 887.4 PASS AC=1;AF=0.5;AN=2;DP=225;FractionInformativeReads=1;MQ=60;set=variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,37:81:99:902,0,1258:13,31,10,27 chr1 11303153 . C A 618.47 PASS AC=1;AF=0.5;AN=2;DP=110;FS=0;FractionInformativeReads=1;MQ=60;set=variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,22:42:99:716,0,621:17,3,19,3 chr1 11317310 . C T 345.49 PASS AC=1;AF=0.5;AN=2;DP=104;FS=0;FractionInformativeReads=1;MQ=60;set=variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,11:26:99:287,0,389:6,9,4,7 chr1 11318236 . C T 36.49 PASS AC=1;AF=0.88;AN=2;DP=112;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant14-variant15-variant17-variant18-variant21-variant26-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,4:6:73:150,0,73:2,0,2,2 chr1 11347092 . T C 794.38 PASS AC=1;AF=0.5;AN=2;DP=232;MQ=60;set=variant24-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,47:74:99:1194,0,643:13,14,21,26 chr1 11347155 . C CTGTT 589.02 PASS AC=2;AF=0.619;AN=2;DP=1225;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant11-variant17-variant19-variant20-variant23-variant24-variant25-variant26-variant29-variant32-variant33-variant35-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:3195,214,0:0,0,31,39 chr1 11347492 . C T 1300.21 PASS AC=1;AF=0.5;AN=2;DP=337;FractionInformativeReads=1;MQ=60;set=variant24-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,41:81:99:1003,0,964:20,20,21,20 chr1 11561164 . G A 1442.04 PASS AC=1;AF=0.545;AN=2;DP=997;MQ=60;set=variant3-variant7-variant8-variant24-variant25-variant28-variant31-variant35-variant37-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:46,70:116:99:1872,0,1139:28,18,45,25 chr1 11561937 . C T 2373.89 PASS AC=1;AF=0.545;AN=2;DP=2030;MQ=60;set=variant3-variant7-variant8-variant24-variant25-variant28-variant31-variant35-variant37-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:120,100:220:99:2545,0,2893:63,57,47,53 chr1 11562913 . C T 2071.44 PASS AC=1;AF=0.545;AN=2;DP=1381;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant8-variant24-variant25-variant28-variant31-variant35-variant37-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:69,67:136:99:1646,0,1606:32,37,27,40 chr1 11575398 . G A 1214.72 PASS AC=1;AF=0.545;AN=2;DP=1050;MQ=60;set=variant3-variant7-variant8-variant24-variant25-variant28-variant31-variant35-variant37-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:42,54:96:99:1324,0,1282:33,9,34,20 chr1 11579363 . G C 400.99 PASS AC=1;AF=0.5;AN=2;DP=47;FS=0;FractionInformativeReads=1;MQ=59.86;MQRankSum=-1.362;QD=8.53;ReadPosRankSum=-1.007;SOR=0.828;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:30,17:47:99:429,0,783:20,10,12,5 chr1 11584164 . A G 1443.2 PASS AC=1;AF=0.522;AN=2;DP=1874;MQ=60;set=variant3-variant7-variant8-variant10-variant12-variant15-variant16-variant17-variant22-variant24-variant25-variant26-variant28-variant30-variant31-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:46,40:86:99:1082,0,1161:20,26,14,26 chr1 11593640 . A G 887.34 PASS AC=2;AF=0.942;AN=2;DP=1984;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,47:48:98:1407,98,0:1,0,28,19 chr1 11593793 . T TGCACACACGCAC 2861.02 PASS AC=2;AF=1;AN=2;DP=3932;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,96:96:99:4766,335,0:0,0,56,40 chr1 11594400 . T C 738.37 PASS AC=2;AF=0.632;AN=2;DP=2259;MQ=60;set=variant3-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2152,209,0:0,0,41,29 chr1 11595038 . A G 1329.85 PASS AC=1;AF=0.525;AN=2;DP=2379;MQ=60;set=variant5-variant6-variant7-variant11-variant12-variant15-variant16-variant18-variant19-variant20-variant21-variant26-variant29-variant30-variant33-variant35-variant37-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:72,69:141:99:1722,0,1645:34,38,29,40 chr1 11595203 . A G 804.04 PASS AC=1;AF=0.529;AN=2;DP=889;MQ=60;set=variant5-variant6-variant7-variant11-variant15-variant16-variant18-variant19-variant20-variant21-variant26-variant29-variant30-variant33-variant35-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,25:52:99:683,0,637:10,17,11,14 chr1 11596455 . C T 1681.84 PASS AC=1;AF=0.55;AN=2;DP=1189;MQ=60;set=variant3-variant7-variant8-variant24-variant25-variant28-variant31-variant35-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:57,72:129:99:1755,0,1350:34,23,41,31 chr1 11596762 . C T 1169.54 PASS AC=1;AF=0.548;AN=2;DP=1942;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant8-variant12-variant16-variant17-variant22-variant24-variant25-variant26-variant28-variant30-variant31-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:49,42:91:99:1138,0,1352:26,23,15,27 chr1 11596864 . A G 992.22 PASS AC=1;AF=0.55;AN=2;DP=745;MQ=60;set=variant3-variant7-variant8-variant24-variant25-variant28-variant31-variant35-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:59,33:92:99:671,0,1490:31,28,15,18 chr1 11596912 . T C 758.82 PASS AC=1;AF=0.55;AN=2;DP=666;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant8-variant24-variant25-variant28-variant31-variant35-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:53,24:77:99:505,0,1446:23,30,12,12 chr1 11597444 . T TG 739.75 PASS AC=1;AF=0.529;AN=2;DP=1268;set=variant5-variant6-variant7-variant11-variant15-variant16-variant18-variant19-variant20-variant21-variant26-variant29-variant30-variant33-variant35-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,46:91:99:1167,0,1160:23,22,23,23 chr1 11708736 . T C 5505.73 PASS AC=2;AF=0.833;AN=2;DP=7281;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,225:225:99:6670,673,0:0,0,115,110 chr1 11709051 . A AG 651.78 PASS AC=1;AF=0.778;AN=2;DP=1011;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,20:25:11:492,0,11:5,0,14,6 chr1 11709052 . C G,CCCAG,CCCAGCCCAGCCCAG 862.77 PASS AC=0,2,0;AF=0.273,0.625,0.023;AN=2;DP=1260;set=Intersection GT:DP:GQ:SB 2/2:30:99:0,0,23,7 chr1 11714368 . T G 1148.72 PASS AC=2;AF=0.805;AN=2;DP=1743;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1102,110,0:0,0,13,24 chr1 11714793 . A G 422.99 PASS AC=2;AF=0.817;AN=2;DP=1067;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1285,105,0:0,0,6,29 chr1 11714883 . G GGCGGGGC 107.74 PASS AC=2;AF=0.882;AN=2;DP=116;FS=0;MQ=60;set=variant3-variant6-variant7-variant8-variant9-variant11-variant12-variant15-variant18-variant19-variant22-variant24-variant25-variant27-variant35-variant39-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:381,27,0:0,0,5,4 chr1 11714938 . T C 111.22 PASS AC=2;AF=1;AN=2;DP=280;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:384,39,0:0,0,8,5 chr1 11714981 . A G 66.22 PASS AC=2;AF=1;AN=2;DP=298;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:279,24,0:0,0,4,4 chr1 11721854 . C T 1591.04 PASS AC=1;AF=0.714;AN=2;DP=4638;MQ=60;set=variant2-variant3-variant5-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,71:124:99:2075,0,1357:26,27,33,38 chr1 11724092 . G C 386.78 PASS AC=1;AF=0.736;AN=2;DP=1938;MQ=60;set=variant2-variant3-variant5-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,26:56:99:597,0,669:18,12,15,11 chr1 11735652 . G A 2491.08 PASS AC=1;AF=0.528;AN=2;DP=4328;MQ=60;set=variant2-variant6-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant25-variant28-variant35-variant36-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:128,135:263:99:3182,0,2959:77,51,79,56 chr1 11735877 . A G 1891.09 PASS AC=1;AF=0.528;AN=2;DP=2817;MQ=60;set=variant2-variant6-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant25-variant28-variant35-variant36-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:95,95:190:99:2588,0,2263:47,48,45,50 chr1 11737051 . G C 1069.23 PASS AC=1;AF=0.722;AN=2;DP=3683;MQ=60;set=variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,32:100:99:742,0,1653:31,37,14,18 chr1 11740329 . AGGCGTGAGCCAC A 553.9 PASS AC=1;AF=0.563;AN=2;DP=1553;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant19-variant21-variant22-variant24-variant25-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:52,20:72:99:684,0,2122:33,19,13,7 chr1 11740358 . A G 1506.26 PASS AC=1;AF=0.688;AN=2;DP=2911;set=variant2-variant3-variant5-variant6-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,65:94:99:1763,0,937:19,10,39,26 chr1 11741293 . G A 407.06 PASS AC=1;AF=0.5;AN=2;DP=115;FractionInformativeReads=1;MQ=60;set=variant29-variant35 GT:AD:DP:GQ:PL:SB 0/1:36,29:65:99:831,0,1074:22,14,19,10 chr1 11741796 . T A 242.83 PASS AC=1;AF=0.565;AN=2;DP=479;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant9-variant10-variant12-variant19-variant21-variant22-variant24-variant25-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:12,17:29:99:394,0,295:8,4,10,7 chr1 11742074 . C T 43.71 PASS AC=2;AF=0.865;AN=2;DP=326;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:441,45,0:0,0,5,10 chr1 11766889 . A G 172.72 PASS AC=2;AF=0.676;AN=2;DP=719;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1166,105,0:0,0,16,19 chr1 11771988 . A G 1488.58 PASS AC=1;AF=0.5;AN=2;DP=1440;MQ=60;set=variant6-variant8-variant9-variant21-variant23-variant31-variant35-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:104,98:202:99:2324,0,2575:58,46,54,44 chr1 11772303 . A G 1411.14 PASS AC=2;AF=0.825;AN=2;DP=4872;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,130:130:99:4301,390,0:0,0,76,54 chr1 11772340 . G A 1976.94 PASS AC=1;AF=0.5;AN=2;DP=1325;MQ=60;set=variant6-variant8-variant9-variant21-variant23-variant31-variant35-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:79,75:154:99:1835,0,2106:42,37,41,34 chr1 11772526 . A G 945.23 PASS AC=1;AF=0.75;AN=2;DP=2263;MQ=60;set=variant2-variant3-variant5-variant8-variant9-variant11-variant13-variant14-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:44,51:95:99:1370,0,1147:16,28,17,34 chr1 11779499 . T C 663.31 PASS AC=1;AF=0.77;AN=2;DP=1036;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,8:26:99:238,0,555:14,4,5,3 chr1 11779762 . C T 1056.61 PASS AC=1;AF=0.58;AN=2;DP=3246;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant13-variant14-variant21-variant22-variant23-variant26-variant30-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:76,57:133:99:1240,0,2013:37,39,26,31 chr1 11781134 . C G 1522.62 PASS AC=2;AF=0.671;AN=2;DP=3259;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,98:98:99:3324,294,0:0,0,35,63 chr1 11781768 . A G 649.97 PASS AC=2;AF=1;AN=2;DP=1012;FS=0;MQ=60;MQRankSum=0.714;ReadPosRankSum=1.531;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:673,60,0:0,0,7,13 chr1 11782092 . T C 42.2 PASS AC=1;AF=0.6;AN=2;DP=53;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant6-variant11-variant24-variant26-variant27-variant34-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:99:144,0,144:3,1,4,0 chr1 11782506 . T C 1456.85 PASS AC=2;AF=0.708;AN=2;DP=4042;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant18-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,124:124:99:3867,372,0:0,0,66,58 chr1 11782814 . G A 582.55 PASS AC=2;AF=0.671;AN=2;DP=1996;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,69:70:99:2197,165,0:0,1,26,43 chr1 11782886 . C T 282.21 PASS AC=1;AF=0.726;AN=2;DP=1013;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,21:24:14:615,0,14:2,1,5,16 chr1 11783295 . G A 526.8 PASS AC=2;AF=0.671;AN=2;DP=1566;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:1672,171,0:0,0,33,24 chr1 11783646 . CT C 51.41 PASS AC=1;AF=0.583;AN=2;DP=56;FS=0;set=variant3-variant26-variant32-variant33-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:4,6:10:66:113,0,66:2,2,2,4 chr1 11784986 . A G 1862.2 PASS AC=2;AF=0.989;AN=2;DP=3001;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,73:73:99:2342,219,0:0,0,37,36 chr1 11796168 . CGGGCG C 8016.84 PASS AC=2;AF=1;AN=2;DP=7069;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,142:142:99:6269,428,0:0,0,88,54 chr1 11807426 . C T 2030.6 PASS AC=2;AF=0.671;AN=2;DP=6175;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,178:179:99:5427,490,0:1,0,103,75 chr1 11810674 . G A 210.78 PASS AC=2;AF=0.6;AN=2;DP=914;MQ=60;set=variant2-variant5-variant8-variant10-variant14-variant15-variant17-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant32-variant33-variant34-variant35-variant38-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:1701,162,0:0,0,24,30 chr1 11810691 . C T 146.82 PASS AC=2;AF=0.6;AN=2;DP=923;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant8-variant10-variant14-variant15-variant17-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant32-variant33-variant34-variant35-variant38-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:1542,143,0:0,0,21,27 chr1 11810765 . T A 824.99 PASS AC=2;AF=1;AN=2;DP=1953;FS=0;MQ=60;MQRankSum=1.347;ReadPosRankSum=0.577;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1590,152,0:0,0,24,27 chr1 11810844 . A G 698.58 PASS AC=2;AF=0.625;AN=2;DP=589;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant8-variant10-variant14-variant15-variant17-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant32-variant33-filterInvariant34-variant35-variant38-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1361,138,0:0,0,18,28 chr1 11824242 . A C 411.86 PASS AC=2;AF=0.795;AN=2;DP=884;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:940,87,0:0,0,20,9 chr1 11824303 . T C 993.62 PASS AC=2;AF=0.756;AN=2;DP=1608;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:1834,174,0:0,0,37,21 chr1 11824346 . G A 1231.62 PASS AC=2;AF=0.75;AN=2;DP=2087;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,78:78:99:2224,232,0:0,0,46,32 chr1 11824556 . A G 1282.88 PASS AC=2;AF=0.744;AN=2;DP=1620;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1299,117,0:0,0,14,25 chr1 11824575 . T C 1536.01 PASS AC=2;AF=0.795;AN=2;DP=1269;FractionInformativeReads=1;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1555,105,0:0,0,11,23 chr1 11824578 . C T 1536.01 PASS AC=2;AF=0.744;AN=2;DP=1225;FractionInformativeReads=1;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1555,105,0:0,0,11,24 chr1 11825851 . G C 2300.83 PASS AC=2;AF=0.808;AN=2;DP=2084;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1810,168,0:0,0,38,18 chr1 11826630 . C T 3950.11 PASS AC=2;AF=0.808;AN=2;DP=6267;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,196:196:99:5646,583,0:0,0,101,95 chr1 11827180 . A G 2514.27 PASS AC=2;AF=1;AN=2;DP=3712;FS=0;MQRankSum=0.197;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,87:88:99:2604,233,0:1,0,62,25 chr1 11827304 . A G 2165.64 PASS AC=2;AF=1;AN=2;DP=3456;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,92:92:99:2699,275,0:0,0,46,46 chr1 11827355 . A G 1169.09 PASS AC=2;AF=0.808;AN=2;DP=1716;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1546,153,0:0,0,20,31 chr1 11828238 . G A 4150.89 PASS AC=2;AF=0.808;AN=2;DP=6339;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,173:173:99:5389,519,0:0,0,94,79 chr1 11828319 . G A 3768.55 PASS AC=2;AF=0.808;AN=2;DP=6090;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,174:174:99:5374,522,0:0,0,77,97 chr1 11831615 . C T 5209.33 PASS AC=2;AF=0.795;AN=2;DP=4509;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,132:132:99:3930,395,0:0,0,74,58 chr1 11831756 . A G 1206.15 PASS AC=2;AF=0.788;AN=2;DP=1583;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,44:45:93:1370,93,0:1,0,12,32 chr1 11832100 . T A 2778.98 PASS AC=2;AF=0.73;AN=2;DP=2964;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,85:85:99:2679,254,0:0,0,55,30 chr1 11832311 . G C 1113.31 PASS AC=2;AF=0.743;AN=2;DP=1869;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:1933,171,0:0,0,14,43 chr1 11836441 . T C 7923.65 PASS AC=2;AF=0.989;AN=2;DP=7958;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,199:199:99:8961,608,0:0,0,121,78 chr1 11836442 . G A 7432.29 PASS AC=2;AF=0.716;AN=2;DP=6863;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,202:202:99:8961,608,0:0,0,122,80 chr1 11836628 . T C 5274.21 PASS AC=2;AF=0.775;AN=2;DP=6865;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,224:224:99:7076,671,0:0,0,105,119 chr1 11836682 . C T 3739.16 PASS AC=2;AF=0.716;AN=2;DP=4415;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,159:159:99:4961,473,0:0,0,69,90 chr1 11836868 . A G 370.91 PASS AC=2;AF=0.782;AN=2;DP=705;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:767,63,0:0,0,4,17 chr1 11838848 . G T 4221.75 PASS AC=2;AF=0.716;AN=2;DP=5472;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,178:179:99:5948,525,0:0,1,103,75 chr1 11839966 . G A 2011.5 PASS AC=2;AF=0.716;AN=2;DP=3049;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,95:95:99:2759,283,0:0,0,48,47 chr1 11839998 . T C 1831.83 PASS AC=2;AF=0.943;AN=2;DP=3041;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,89:89:99:2708,267,0:0,0,44,45 chr1 11842144 . C G 941.67 PASS AC=2;AF=0.716;AN=2;DP=2131;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2029,209,0:0,0,40,30 chr1 11842431 . C T 211.43 PASS AC=1;AF=0.5;AN=2;DP=20;FractionInformativeReads=1;MQ=60;set=variant26-variant35 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:99:147,0,155:1,3,0,4 chr1 11844330 . C T 5522.19 PASS AC=2;AF=0.708;AN=2;DP=6878;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,232:233:99:6930,684,0:0,1,122,110 chr1 11844520 . C T 1556.17 PASS AC=1;AF=0.5;AN=2;DP=570;FractionInformativeReads=1;MQ=60;set=variant6-variant10-variant18-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:54,65:119:99:1705,0,1342:27,27,30,35 chr1 11844827 . A G 102.92 PASS AC=2;AF=0.988;AN=2;DP=288;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.742;ReadPosRankSum=0.742;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:187,18,0:0,0,1,5 chr1 11845113 . G A 938.93 PASS AC=2;AF=0.989;AN=2;DP=1430;MQ=60;MQRankSum=1.526;ReadPosRankSum=1.443;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1306,117,0:0,0,27,12 chr1 11845169 . T G 2244.83 PASS AC=2;AF=0.716;AN=2;DP=2580;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,92:92:99:2822,276,0:0,0,57,35 chr1 11846092 . G GT 700.62 PASS AC=2;AF=0.977;AN=2;DP=1286;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:616,69,0:0,0,20,3 chr1 11846252 . G A 2679.15 PASS AC=2;AF=0.782;AN=2;DP=4482;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,114:114:99:3427,340,0:0,0,59,55 chr1 11846447 . G A 626.48 PASS AC=2;AF=0.989;AN=2;DP=1061;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1099,108,0:0,0,13,23 chr1 11846659 . ATTTTTTTT ATTTT,A,ATTTTTTTTT,ATTT 363.12 PASS AC=2,0,0,0;AF=0.607,0.143,0.036,0.054;AN=2;DP=182;set=variant2-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant31-variant32-variant33-variant35-variant37-variant39-variant42-variant44 GT:DP:GQ:SB 1/1:4:12:0,0,3,1 chr1 11847334 . G GGAA 2354.32 PASS AC=2;AF=0.716;AN=2;DP=2248;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:2386,165,0:0,0,33,17 chr1 11847759 . C T 3767.72 PASS AC=2;AF=0.694;AN=2;DP=5239;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,147:147:99:4653,441,0:0,0,81,66 chr1 11848879 . A G 1796.01 PASS AC=2;AF=0.977;AN=2;DP=3740;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,81:81:99:2676,242,0:0,0,35,46 chr1 11849447 . A G 2731.45 PASS AC=2;AF=0.989;AN=2;DP=4053;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,110:110:99:3388,330,0:0,0,51,59 chr1 11850365 . T G 3064.38 PASS AC=2;AF=0.769;AN=2;DP=4434;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,140:140:99:4390,419,0:0,0,65,75 chr1 11854457 . G A 9712.27 PASS AC=2;AF=0.977;AN=2;DP=9482;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,237:237:99:7212,710,0:0,0,128,109 chr1 11854755 . G A 3171.03 PASS AC=2;AF=0.681;AN=2;DP=3609;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,108:110:99:3062,279,0:1,1,54,54 chr1 11856378 . G A 1281.75 PASS AC=1;AF=0.593;AN=2;DP=5046;MQ=60;set=variant2-variant3-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant23-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:107,93:200:99:2028,0,2529:48,59,38,55 chr1 11856489 . G A 452.91 PASS AC=1;AF=0.5;AN=2;DP=44;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.433;QD=10.29;ReadPosRankSum=-0.54;SOR=0.83;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:23,21:44:99:481,0,698:5,18,4,17 chr1 11860683 . T C 136.72 PASS AC=2;AF=0.786;AN=2;DP=482;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:594,42,0:0,0,3,11 chr1 11864505 . C CA,CAA 150.88 PASS AC=2,0;AF=0.808,0.077;AN=2;DP=153;MQ=60;set=variant4-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant17-variant18-variant19-variant21-variant24-variant25-variant26-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:4:12:0,0,3,1 chr1 11867044 . T C 237.06 PASS AC=2;AF=0.805;AN=2;DP=1197;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1211,123,0:0,0,27,14 chr1 11876417 . C T 489.01 PASS AC=2;AF=0.694;AN=2;DP=547;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:715,57,0:0,0,15,4 chr1 11884555 . A G 3169.67 PASS AC=2;AF=1;AN=2;DP=4917;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,121:121:99:3726,362,0:0,0,62,59 chr1 11887323 . T C 834.38 PASS AC=1;AF=0.5;AN=2;DP=102;FractionInformativeReads=1;MQ=60;set=variant26-variant35 GT:AD:DP:GQ:PL:SB 0/1:21,30:51:99:752,0,536:8,13,13,17 chr1 11887373 . T TG 391.39 PASS AC=1;AF=0.756;AN=2;DP=1579;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:23,14:37:99:323,0,605:8,15,3,11 chr1 11900035 . G A 246.22 PASS AC=2;AF=1;AN=2;DP=1346;FS=0;MQ=60;MQRankSum=0.037;ReadPosRankSum=-1.216;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:866,66,0:0,0,19,3 chr1 11917620 . T TA 1389.35 PASS AC=1;AF=0.58;AN=2;DP=3092;MQ=60;set=variant-variant3-variant9-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:60,47:107:99:1107,0,1510:32,28,20,27 chr1 11918927 . TCTGCTG TCTG,TCTGCTGCTG,T 2320.3 PASS AC=1,0,0;AF=0.2,0.2,0.1;AN=2;DP=830;MQ=60;set=variant3-variant21-variant34-variant35-variant41 GT:DP:GQ:SB 0/1:112:99:23,32,21,36 chr1 11982544 . T C 3550.75 PASS AC=1;AF=0.767;AN=2;DP=5045;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:69,64:133:99:1618,0,1788:38,31,33,31 chr1 11982676 . A C 2529.17 PASS AC=1;AF=0.5;AN=2;DP=406;FractionInformativeReads=1;MQ=60;set=variant3-variant35 GT:AD:DP:GQ:PL:SB 0/1:86,91:177:99:2235,0,2175:43,43,50,41 chr1 11986553 . A AG 635.67 PASS AC=2;AF=1;AN=2;DP=1448;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1492,120,0:0,0,18,22 chr1 12004479 . TACACAC TACACACACACACACAC,TACACACACACACAC,TACAC,TACACACACACACACACAC,T,TACACACACACACACACACACAC,TAC 367.23 PASS AC=0,0,1,0,0,0,0;AF=0.177,0.113,0.145,0.081,0.065,0.032,0.065;AN=2;DP=624;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-filterInvariant39-variant40-variant43-variant44 GT:DP:GQ:SB 0/3:15:99:5,0,8,2 chr1 12082334 . A T 2367.83 PASS AC=1;AF=0.55;AN=2;DP=3833;MQ=60;set=variant-variant5-variant7-variant9-variant12-variant14-variant16-variant18-variant22-variant24-variant25-variant28-variant29-variant33-variant34-variant35-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:137,97:234:99:2347,0,3644:61,76,43,54 chr1 12082881 . C T 571.85 PASS AC=1;AF=0.55;AN=2;DP=2041;MQ=60;set=variant-variant5-variant7-variant9-variant12-variant14-variant16-variant18-variant22-variant24-variant25-variant28-variant29-variant33-variant34-variant35-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:66,48:114:99:976,0,1731:32,34,23,25 chr1 12082926 . A G 902.26 PASS AC=1;AF=0.726;AN=2;DP=2821;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,37:80:99:883,0,1340:12,31,16,21 chr1 12090001 . T C 1797.6 PASS AC=1;AF=0.55;AN=2;DP=3987;MQ=60;set=variant-variant5-variant7-variant9-variant12-variant14-variant16-variant18-variant22-variant24-variant25-variant28-variant29-variant33-variant34-variant35-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:128,123:251:99:2916,0,2974:65,63,58,65 chr1 12091210 . T C 532.5 PASS AC=1;AF=0.714;AN=2;DP=886;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,13:23:99:472,0,300:8,2,11,2 chr1 12144219 . A G 109.69 PASS AC=2;AF=0.706;AN=2;DP=710;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:826,78,0:0,0,13,13 chr1 12144434 . G A 1030.12 PASS AC=1;AF=0.5;AN=2;DP=724;FractionInformativeReads=1;MQ=60;set=variant6-variant7-variant8-variant9-variant34-variant35-variant36-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:46,34:80:99:835,0,1238:26,20,21,13 chr1 12144662 . T A 800.81 PASS AC=1;AF=0.607;AN=2;DP=1580;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant35-variant37-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:30,40:70:99:1562,0,1587:12,18,18,22 chr1 12144667 . C T 764.28 PASS AC=1;AF=0.607;AN=2;DP=1550;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant35-variant37-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:29,41:70:99:1574,0,1544:12,17,18,23 chr1 12144801 . CTG C 359.89 PASS AC=1;AF=0.62;AN=2;DP=450;MQ=60;set=variant2-variant5-variant7-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant35-variant37-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,10:19:99:375,0,341:3,6,4,6 chr1 12157076 . A C 768.16 PASS AC=1;AF=0.571;AN=2;DP=434;MQ=60;set=variant6-variant9-variant32-variant33-variant34-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:31,29:60:99:754,0,879:21,10,18,11 chr1 12164437 . C T 283.85 PASS AC=1;AF=0.523;AN=2;DP=1259;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant7-variant8-variant9-variant12-variant13-variant16-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant29-variant30-variant32-variant35-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:32,28:60:99:741,0,870:22,10,19,9 chr1 12175729 . C T 2188.64 PASS AC=2;AF=1;AN=2;DP=5523;FS=0;MQ=60;MQRankSum=0.408;ReadPosRankSum=0.324;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,161:161:99:4943,482,0:0,0,86,75 chr1 12175818 . A G 1020.36 PASS AC=1;AF=0.647;AN=2;DP=1615;set=variant2-variant6-variant12-variant13-variant18-variant21-variant22-variant23-variant25-variant26-variant32-variant34-variant35-variant36-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,58:116:99:1408,0,1412:20,38,24,34 chr1 12183174 . A C 357.78 PASS AC=1;AF=0.721;AN=2;DP=1577;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,33:55:99:981,0,618:15,7,21,12 chr1 12185955 . TG T 2320.05 PASS AC=1;AF=0.5;AN=2;DP=318;MQ=60;set=variant26-variant35 GT:AD:DP:GQ:PL:SB 0/1:84,72:156:99:2436,0,2922:45,39,43,29 chr1 12198179 . G A 885.03 PASS AC=1;AF=0.7;AN=2;DP=1230;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant9-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,11:27:99:337,0,546:13,3,10,1 chr1 12198297 . T C 2960.23 PASS AC=2;AF=0.577;AN=2;DP=2887;MQ=60;set=variant6-variant11-variant14-variant18-variant22-variant26-variant27-variant29-variant34-variant35-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,239:239:99:6779,714,0:0,0,134,105 chr1 12198635 . T C 1044.18 PASS AC=1;AF=0.81;AN=2;DP=3240;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,48:103:99:1040,0,1202:24,31,23,25 chr1 12204354 . A G 2601.81 PASS AC=2;AF=0.942;AN=2;DP=2447;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:2143,168,0:0,0,9,47 chr1 12248942 . A G 3468.32 PASS AC=1;AF=0.614;AN=2;DP=1976;MQ=60;set=variant2-variant3-variant9-variant11-variant13-variant15-variant16-variant19-variant20-variant21-variant23-variant28-variant29-variant32-variant34-variant35-variant36-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,35:75:99:929,0,994:14,26,10,25 chr1 12248965 . A G 2292.58 PASS AC=1;AF=0.614;AN=2;DP=1381;MQ=60;set=variant2-variant3-variant9-variant11-variant13-variant15-variant16-variant19-variant20-variant21-variant23-variant28-variant29-variant32-variant34-variant35-variant36-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,19:48:99:553,0,765:10,19,4,15 chr1 12249020 . C T 715.15 PASS AC=1;AF=0.614;AN=2;DP=594;MQ=60;set=variant2-variant3-variant9-variant11-variant13-variant15-variant16-variant19-variant20-variant21-variant23-variant28-variant29-variant32-variant34-variant35-variant36-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,9:26:99:186,0,498:5,12,2,7 chr1 12249031 . A G 786.18 PASS AC=2;AF=0.775;AN=2;DP=927;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:726,54,0:0,0,3,15 chr1 12251191 . T A 649.44 PASS AC=1;AF=0.605;AN=2;DP=349;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant9-variant11-variant15-variant16-variant19-variant21-variant23-variant28-variant29-variant32-variant34-variant35-variant36-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,10:18:99:292,0,280:0,8,1,9 chr1 12251765 . T G 2813.6 PASS AC=1;AF=0.591;AN=2;DP=2773;MQ=60;set=variant2-variant3-variant9-variant11-variant13-variant15-variant16-variant19-variant20-variant21-variant23-variant28-variant29-variant32-variant34-variant35-variant36-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,75:132:99:1847,0,1311:34,23,45,30 chr1 12251808 . T G 4140.96 PASS AC=2;AF=0.677;AN=2;DP=5055;MQ=60;set=variant2-variant3-variant5-variant6-variant8-variant9-variant11-variant13-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,166:166:99:4994,497,0:0,0,88,78 chr1 12252333 . CTGTG CTGTGTG,C,CTG 269.89 PASS AC=0,1,0;AF=0.196,0.375,0.054;AN=2;DP=535;MQ=60;set=variant-variant2-variant3-variant6-variant9-variant11-variant13-variant15-variant16-variant19-variant21-variant23-variant24-variant25-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:26:99:12,1,12,1 chr1 12252892 . C T 557.11 PASS AC=1;AF=0.595;AN=2;DP=548;MQ=60;set=variant2-variant3-variant9-variant11-variant13-variant15-variant16-variant19-variant20-variant21-variant23-variant29-variant32-variant34-variant35-variant36-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,14:40:99:302,0,661:16,10,9,5 chr1 12252955 . T G 1345.87 PASS AC=1;AF=0.595;AN=2;DP=1293;MQ=60;set=variant2-variant3-variant9-variant11-variant13-variant15-variant16-variant19-variant20-variant21-variant23-variant29-variant32-variant34-variant35-variant36-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,31:78:99:753,0,1217:27,20,19,12 chr1 12253351 . T C 978.52 PASS AC=1;AF=0.583;AN=2;DP=512;MQ=60;set=variant2-variant3-variant9-variant11-variant13-variant15-variant16-variant19-variant21-variant23-variant29-variant32-variant35-variant36-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:19,15:34:99:411,0,530:6,13,4,11 chr1 12254201 . G A 1155.02 PASS AC=1;AF=0.605;AN=2;DP=913;MQ=60;set=variant2-variant3-variant9-variant11-variant13-variant15-variant16-variant19-variant21-variant23-variant29-variant32-variant34-variant35-variant36-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:26,19:45:99:520,0,746:7,19,4,15 chr1 12261972 . A G 1838.79 PASS AC=1;AF=0.579;AN=2;DP=1399;MQ=60;set=variant2-variant3-variant11-variant15-variant16-variant20-variant21-variant23-variant28-variant29-variant32-variant34-variant35-variant36-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,35:71:99:837,0,861:22,14,19,16 chr1 12266591 . A G 336.68 PASS AC=1;AF=0.647;AN=2;DP=236;MQ=60;set=variant2-variant3-variant11-variant15-variant16-variant21-variant23-variant24-variant25-variant28-variant29-variant32-variant35-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,6:10:99:199,0,111:3,1,5,1 chr1 12266612 . A G 98.3 PASS AC=1;AF=0.63;AN=2;DP=403;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant9-variant11-variant13-variant15-variant16-variant19-variant20-variant21-variant23-variant24-variant25-variant28-variant29-variant32-variant35-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,7:14:99:226,0,148:4,3,6,1 chr1 12267265 . A G 633.28 PASS AC=1;AF=0.609;AN=2;DP=2211;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,61:105:99:1423,0,1633:20,24,27,34 chr1 12267270 . T G 662.2 PASS AC=1;AF=0.5;AN=2;DP=465;MQ=60;set=variant-variant4-variant5-variant22-variant26-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:55,44:99:99:1144,0,2186:24,31,20,24 chr1 12267292 . C T 1149.03 PASS AC=2;AF=0.784;AN=2;DP=2126;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,90:90:99:2712,267,0:0,0,37,53 chr1 12267971 . G GA 57.32 PASS AC=2;AF=0.821;AN=2;DP=81;FS=0;MQ=60;set=variant4-variant11-variant13-variant14-variant27-variant28-variant29-variant33-variant34-variant35-variant36-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:84,9,0:0,0,2,1 chr1 12267999 . C T 114.39 PASS AC=2;AF=0.758;AN=2;DP=276;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant6-variant8-variant11-variant13-variant14-variant15-variant17-variant18-variant21-variant22-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:86,9,0:0,0,2,1 chr1 12368705 . GT G,GTT 51.71 PASS AC=1,0;AF=0.227,0.273;AN=2;DP=696;MQ=60;set=filterInvariant-filterInvariant6-filterInvariant7-filterInvariant16-filterInvariant18-filterInvariant25-variant26-filterInvariant31-filterInvariant35-filterInvariant39-filterInvariant43 GT:DP:GQ:SB 0/1:39:99:8,22,1,8 chr1 12401868 . A C 1869.57 PASS AC=1;AF=0.791;AN=2;DP=4072;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,62:111:99:1696,0,1236:32,17,40,22 chr1 12418700 . T C 247.45 PASS AC=2;AF=0.989;AN=2;DP=1501;FS=0;MQ=60;MQRankSum=1.79;ReadPosRankSum=-0.271;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,52:52:99:1714,156,0:0,0,19,33 chr1 12434029 . A C 318.05 PASS AC=1;AF=0.5;AN=2;DP=88;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant26-variant35 GT:AD:DP:GQ:PL:SB 0/1:12,13:25:99:345,0,373:3,9,3,10 chr1 12567232 . A G 5205.33 PASS AC=2;AF=1;AN=2;DP=9175;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,260:260:99:7951,779,0:0,0,130,130 chr1 12569355 . G A 2697.17 PASS AC=1;AF=0.5;AN=2;DP=235;FS=2.204;FractionInformativeReads=1;MQ=60;MQRankSum=0.797;QD=11.48;ReadPosRankSum=-1.106;SOR=0.556;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:119,116:235:99:2725,0,2921:66,53,60,56 chr1 12570579 . C CTG,CTGTG,CTGTGTG,CTGTGTGTGTG 473.63 PASS AC=1,0,0,0;AF=0.547,0.07,0.012,0.012;AN=2;DP=1776;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:41:99:6,5,13,17 chr1 12638964 . T C 3833.75 PASS AC=1;AF=0.845;AN=2;DP=8071;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:114,124:238:99:3214,0,2880:54,60,58,66 chr1 12639018 . C T 3619.05 PASS AC=1;AF=0.683;AN=2;DP=5132;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant35-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:95,104:199:99:2713,0,2627:42,53,51,53 chr1 12639168 . A G 4262.3 PASS AC=1;AF=0.805;AN=2;DP=7455;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:93,122:215:99:3038,0,2219:43,50,59,63 chr1 12776134 . C A 796.65 PASS AC=2;AF=0.802;AN=2;DP=3538;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,91:91:99:3092,272,0:0,0,67,24 chr1 12776218 . A C 5005.41 PASS AC=2;AF=0.872;AN=2;DP=8352;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,260:260:99:7967,778,0:0,0,157,103 chr1 12776344 . A T 2228.74 PASS AC=2;AF=0.779;AN=2;DP=9087;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,247:247:99:7877,738,0:0,0,99,148 chr1 12779560 . T C 6294.04 PASS AC=2;AF=0.872;AN=2;DP=6831;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,163:163:99:5084,488,0:0,0,75,88 chr1 12779618 . T C 3901.77 PASS AC=2;AF=0.872;AN=2;DP=4623;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,111:111:99:3608,333,0:0,0,40,71 chr1 12785093 . T G 3006.34 PASS AC=2;AF=0.837;AN=2;DP=3617;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,104:104:99:3253,312,0:0,0,61,43 chr1 12785494 . G T 5028.71 PASS AC=2;AF=0.779;AN=2;DP=6667;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,187:187:99:5856,559,0:0,0,92,95 chr1 12786070 . A G 1374.93 PASS AC=2;AF=0.779;AN=2;DP=2478;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,61:61:99:1962,183,0:0,0,25,36 chr1 12786273 . T C 1799.13 PASS AC=2;AF=0.779;AN=2;DP=2670;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,64:64:99:1944,192,0:0,0,32,32 chr1 12786363 . C T 1871.6 PASS AC=2;AF=0.779;AN=2;DP=3133;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:2395,227,0:0,0,36,40 chr1 12786417 . A G 1421.88 PASS AC=2;AF=0.779;AN=2;DP=3087;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:2004,185,0:0,0,33,29 chr1 12786444 . G A 1236.83 PASS AC=2;AF=0.767;AN=2;DP=2961;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:1890,174,0:0,0,29,29 chr1 12787632 . C T 1817.7 PASS AC=2;AF=0.779;AN=2;DP=2757;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2113,209,0:0,0,38,32 chr1 12787980 . A G 1605.21 PASS AC=2;AF=0.779;AN=2;DP=2359;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:1887,175,0:0,0,31,28 chr1 12788406 . G A 572.58 PASS AC=2;AF=0.841;AN=2;DP=618;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:297,21,0:0,0,6,1 chr1 12820870 . T C 1612.88 PASS AC=2;AF=0.826;AN=2;DP=4221;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,102:102:99:3292,306,0:0,0,38,64 chr1 12821476 . GTT G,GT 114.33 PASS AC=2,0;AF=0.828,0.086;AN=2;DP=251;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant13-variant15-variant17-variant18-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant35-variant36-variant38-variant40-variant41-variant43 GT:DP:GQ:SB 1/1:6:18:0,0,2,4 chr1 12822126 . C T 377.99 PASS AC=2;AF=0.775;AN=2;DP=382;FractionInformativeReads=1;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:82,6,0:0,0,2,0 chr1 12822162 . A G 277.08 PASS AC=2;AF=0.77;AN=2;DP=279;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:131,15,0:0,0,3,2 chr1 12822586 . T C 255.13 PASS AC=2;AF=0.819;AN=2;DP=308;FractionInformativeReads=1;set=variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:222,15,0:0,0,5,0 chr1 12823036 . TA T 134.62 PASS AC=2;AF=0.66;AN=2;DP=743;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant13-variant16-variant17-variant19-variant20-variant21-variant26-variant27-variant30-variant31-variant35-variant36-variant38-filterInvariant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:611,60,0:0,0,8,12 chr1 12823667 . G A 2641.79 PASS AC=2;AF=0.756;AN=2;DP=3973;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,109:109:99:3585,325,0:0,0,70,39 chr1 12835605 . G A 459.72 PASS AC=1;AF=0.5;AN=2;DP=169;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant9-variant13-variant26-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:9,18:27:99:475,0,238:6,3,12,6 chr1 12835868 . T C 2269.28 PASS AC=2;AF=0.813;AN=2;DP=4423;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,139:139:99:4333,417,0:0,0,73,66 chr1 12837169 . C T 618.48 PASS AC=1;AF=0.5;AN=2;DP=78;FS=3.337;FractionInformativeReads=1;MQ=60;MQRankSum=-0.185;QD=7.93;ReadPosRankSum=-0.79;SOR=1.134;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:52,26:78:99:647,0,1278:31,21,18,8 chr1 12837634 . T A,C 3692.81 PASS AC=2,0;AF=0.793,0.012;AN=2;DP=7430;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-filterInvariant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:186:99:0,0,98,88 chr1 12837840 . G C 2198.78 PASS AC=2;AF=0.813;AN=2;DP=2765;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,64:64:99:2254,192,0:0,0,18,46 chr1 12853975 . G T 73.35 PASS AC=1;AF=0.5;AN=2;DP=1739;set=filterInvariant-variant3-variant5-variant6-variant7-variant8-filterInvariant9-filterInvariant11-variant14-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-filterInvariant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-filterInvariant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,11:53:99:181,0,1141:27,15,8,3 chr1 12854021 . G T 1422.74 PASS AC=1;AF=0.5;AN=2;DP=4511;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:71,26:97:99:875,0,3411:47,24,16,10 chr1 12854022 . A T 1506.72 PASS AC=1;AF=0.5;AN=2;DP=4542;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:72,26:98:99:875,0,3411:48,24,16,10 chr1 12854041 . T C 1681.45 PASS AC=1;AF=0.5;AN=2;DP=5169;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:83,27:110:99:866,0,4058:53,30,16,11 chr1 12854052 . C T 461.21 PASS AC=1;AF=0.5;AN=2;DP=5129;FractionInformativeReads=1;set=variant-variant2-variant3-filterInvariant4-variant5-variant6-variant7-variant8-variant9-variant10-filterInvariant11-variant12-variant14-variant15-variant16-variant17-variant19-filterInvariant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-filterInvariant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:98,28:126:99:858,0,4327:62,36,16,12 chr1 12854090 . T A 1050.41 PASS AC=1;AF=0.5;AN=2;DP=6252;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-filterInvariant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:121,27:148:99:737,0,5359:69,52,14,13 chr1 12854097 . T C 1074.33 PASS AC=1;AF=0.5;AN=2;DP=6381;FractionInformativeReads=1;set=variant-variant2-variant3-filterInvariant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-filterInvariant13-variant14-variant15-variant16-variant17-variant19-filterInvariant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:123,27:150:99:741,0,5463:69,54,13,14 chr1 12854105 . A G 1083.36 PASS AC=1;AF=0.5;AN=2;DP=6261;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-filterInvariant13-variant14-variant15-variant16-variant17-variant19-filterInvariant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-filterInvariant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:121,22:143:99:624,0,5369:67,54,11,11 chr1 12854530 . C G 6594.25 PASS AC=2;AF=0.878;AN=2;DP=7267;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,172:172:99:5214,515,0:0,0,74,98 chr1 12854842 . G C 60.54 PASS AC=2;AF=0.692;AN=2;DP=260;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant11-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant26-variant27-variant28-variant30-variant31-variant32-variant35-variant36-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:197,15,0:0,0,5,0 chr1 12855835 . C G 4813.73 PASS AC=2;AF=1;AN=2;DP=7367;FS=0;MQRankSum=-0.498;ReadPosRankSum=1.429;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,211:211:99:9248,638,0:0,0,104,107 chr1 12855845 . G C 4750.21 PASS AC=2;AF=1;AN=2;DP=7147;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,205:205:99:9140,628,0:0,0,97,108 chr1 12856010 . C G 495.81 PASS AC=1;AF=0.5;AN=2;DP=6137;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-filterInvariant7-variant8-filterInvariant9-filterInvariant10-variant12-filterInvariant13-filterInvariant14-variant15-variant16-variant17-filterInvariant18-filterInvariant19-filterInvariant20-variant21-filterInvariant23-variant24-variant25-variant26-variant27-variant28-filterInvariant29-filterInvariant30-variant33-filterInvariant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:104,57:161:99:979,0,2439:41,63,30,27 chr1 12887054 . T C,G 121.14 PASS AC=1,1;AF=0.387,0.226;AN=2;DP=1337;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant44 GT:DP:GQ:SB 1/2:52:99:0,0,32,20 chr1 12887549 . T C 8709.88 PASS AC=2;AF=0.89;AN=2;DP=14300;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,374:374:99:11230,1118,0:0,0,195,179 chr1 12888389 . A C 221.82 PASS AC=1;AF=0.794;AN=2;DP=405;set=variant-variant3-variant4-variant5-filterInvariant6-variant7-variant9-variant10-variant11-variant13-variant14-filterInvariant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant28-filterInvariant30-variant31-variant32-variant33-filterInvariant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,9:10:15:270,0,15:1,0,7,2 chr1 12888601 . G GC 982.02 PASS AC=2;AF=0.943;AN=2;DP=2638;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:1946,174,0:0,0,25,33 chr1 12898472 . C T 2121.05 PASS AC=2;AF=0.932;AN=2;DP=4750;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,148:148:99:4410,444,0:0,0,78,70 chr1 12898654 . A G 1164.51 PASS AC=2;AF=0.667;AN=2;DP=5381;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,176:176:99:5274,527,0:0,0,83,93 chr1 12898673 . G T 3211.34 PASS AC=1;AF=0.85;AN=2;DP=4654;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:87,78:165:99:1939,0,2182:37,50,33,45 chr1 12907282 . G C 2238.04 PASS AC=1;AF=0.5;AN=2;DP=5163;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:62,48:110:99:1859,0,4393:43,19,34,14 chr1 12907284 . T C 2259.66 PASS AC=1;AF=0.5;AN=2;DP=5276;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:64,49:113:99:1859,0,4393:44,20,35,14 chr1 12907285 . G C 2259.66 PASS AC=1;AF=0.5;AN=2;DP=5307;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:64,49:113:99:1859,0,4393:44,20,35,14 chr1 12907316 . T C 1544 PASS AC=1;AF=0.5;AN=2;DP=6705;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:94,60:154:99:1279,0,2617:58,36,35,25 chr1 12907350 . C T 2202.88 PASS AC=1;AF=0.5;AN=2;DP=7839;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:130,51:181:99:1681,0,7649:80,50,24,27 chr1 12907351 . A G 2244.87 PASS AC=1;AF=0.5;AN=2;DP=7873;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:128,50:178:99:1666,0,8013:79,49,23,27 chr1 12907370 . A T 1651.73 PASS AC=1;AF=0.5;AN=2;DP=8362;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-filterInvariant28-variant29-variant30-variant31-variant32-filterInvariant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:165,44:209:99:1369,0,10813:93,72,18,26 chr1 12907379 . T C 1605.19 PASS AC=1;AF=0.5;AN=2;DP=8464;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-filterInvariant9-variant10-variant11-filterInvariant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-filterInvariant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:194,38:232:99:1084,0,12607:104,90,13,25 chr1 12907380 . C A 1599.17 PASS AC=1;AF=0.5;AN=2;DP=8458;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-filterInvariant9-variant10-variant11-filterInvariant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-filterInvariant31-variant32-filterInvariant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:194,39:233:99:1045,0,12568:104,90,14,25 chr1 12907385 . G A 1160.96 PASS AC=1;AF=0.5;AN=2;DP=8540;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-filterInvariant9-variant10-variant11-filterInvariant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-filterInvariant31-variant32-filterInvariant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:194,30:224:99:904,0,12902:105,89,9,21 chr1 12907400 . G A 920.56 PASS AC=1;AF=0.5;AN=2;DP=8841;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-filterInvariant9-variant10-variant11-variant13-variant14-variant15-filterInvariant16-filterInvariant17-variant18-variant19-variant20-variant21-variant22-filterInvariant23-variant24-variant25-variant26-variant27-variant29-filterInvariant30-filterInvariant31-variant32-filterInvariant33-variant34-variant35-filterInvariant36-variant37-variant38-filterInvariant39-variant40-variant41-variant42-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:213,34:247:99:805,0,13874:113,100,11,23 chr1 12907408 . T A 876.23 PASS AC=1;AF=0.5;AN=2;DP=9037;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-filterInvariant9-variant10-variant11-variant13-variant14-variant15-filterInvariant16-variant17-variant18-variant19-variant20-variant21-variant22-filterInvariant23-filterInvariant24-filterInvariant25-variant26-variant27-variant29-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-variant34-variant35-filterInvariant36-variant37-variant38-filterInvariant39-variant40-variant41-variant42-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:218,29:247:99:550,0,13756:110,108,8,21 chr1 12907438 . A G 965.87 PASS AC=1;AF=0.5;AN=2;DP=9198;set=variant-variant2-filterInvariant3-variant4-variant5-variant6-variant7-variant8-filterInvariant9-variant10-variant11-filterInvariant12-filterInvariant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-filterInvariant22-variant23-filterInvariant24-filterInvariant25-variant26-variant27-variant29-variant30-filterInvariant31-filterInvariant32-filterInvariant33-variant35-variant37-variant38-filterInvariant40-variant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:235,39:274:99:874,0,14483:107,128,8,31 chr1 12907446 . C T 924.14 PASS AC=1;AF=0.5;AN=2;DP=8631;FractionInformativeReads=1;set=variant-variant2-filterInvariant3-variant4-variant5-variant6-variant7-variant8-filterInvariant9-variant10-variant11-filterInvariant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-filterInvariant21-filterInvariant22-variant23-variant24-filterInvariant25-variant26-variant27-variant29-variant30-filterInvariant31-filterInvariant32-filterInvariant33-variant35-variant37-variant38-filterInvariant40-variant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:226,35:261:99:777,0,14446:102,124,7,28 chr1 12907450 . T C 854.73 PASS AC=1;AF=0.5;AN=2;DP=8225;FractionInformativeReads=1;set=variant-variant2-filterInvariant3-variant4-variant5-variant6-variant7-variant8-filterInvariant9-variant10-variant11-filterInvariant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-filterInvariant21-filterInvariant22-filterInvariant23-variant24-filterInvariant25-variant26-variant27-variant29-filterInvariant30-filterInvariant32-filterInvariant33-variant35-variant37-variant38-filterInvariant40-variant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:224,34:258:99:747,0,14354:101,123,7,27 chr1 12907457 . A G 869.79 PASS AC=1;AF=0.5;AN=2;DP=8199;set=variant-variant2-filterInvariant3-variant4-variant5-variant6-variant7-variant8-filterInvariant9-variant10-variant11-filterInvariant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-filterInvariant21-filterInvariant22-variant23-filterInvariant24-filterInvariant25-variant26-variant27-variant29-variant30-filterInvariant31-filterInvariant32-filterInvariant33-variant35-variant37-variant38-filterInvariant40-variant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:217,33:250:99:711,0,14133:97,120,7,26 chr1 12907458 . T A 869.79 PASS AC=1;AF=0.5;AN=2;DP=8147;FractionInformativeReads=1;set=variant-variant2-filterInvariant3-variant4-variant5-variant6-variant7-variant8-filterInvariant9-variant10-variant11-filterInvariant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-filterInvariant21-filterInvariant22-variant23-filterInvariant24-filterInvariant25-variant26-variant27-variant29-variant30-filterInvariant31-variant32-filterInvariant33-variant35-variant37-variant38-filterInvariant40-variant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:216,33:249:99:717,0,14000:96,120,7,26 chr1 12907465 . A G 701.84 PASS AC=1;AF=0.5;AN=2;DP=7841;FractionInformativeReads=1;set=variant-variant2-filterInvariant3-filterInvariant4-variant5-variant6-variant7-variant8-filterInvariant9-variant10-variant11-filterInvariant13-variant14-variant15-filterInvariant16-filterInvariant17-variant18-variant19-variant20-filterInvariant21-filterInvariant22-variant23-filterInvariant24-filterInvariant25-variant26-variant27-variant29-filterInvariant30-filterInvariant31-variant32-filterInvariant33-variant35-variant37-variant38-filterInvariant40-variant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:209,29:238:99:583,0,13112:93,116,7,22 chr1 12907469 . C G 620.87 PASS AC=1;AF=0.5;AN=2;DP=7529;FractionInformativeReads=1;set=variant-variant2-filterInvariant3-filterInvariant4-variant5-variant6-variant7-variant8-filterInvariant9-variant10-variant11-filterInvariant13-variant14-variant15-filterInvariant16-variant17-variant18-variant19-variant20-filterInvariant21-filterInvariant22-variant23-filterInvariant24-filterInvariant25-variant26-variant27-variant29-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-variant35-variant37-variant38-variant41-variant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:205,29:234:99:595,0,12824:91,114,7,22 chr1 12907483 . T A 363.88 PASS AC=1;AF=0.5;AN=2;DP=6256;FractionInformativeReads=1;set=filterInvariant-variant2-filterInvariant3-filterInvariant4-variant5-filterInvariant6-variant7-variant8-filterInvariant9-filterInvariant10-variant11-variant14-variant15-filterInvariant16-filterInvariant17-filterInvariant18-variant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant25-variant26-filterInvariant27-variant29-filterInvariant30-filterInvariant32-filterInvariant33-variant35-variant37-variant38-filterInvariant41-variant42-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:191,26:217:99:502,0,11914:81,110,7,19 chr1 12907495 . T C 501.08 PASS AC=1;AF=0.5;AN=2;DP=5918;set=variant-variant2-filterInvariant3-filterInvariant4-variant5-variant6-variant7-variant8-filterInvariant9-filterInvariant10-variant11-variant14-variant15-filterInvariant16-variant17-variant18-variant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-variant26-filterInvariant27-variant29-filterInvariant30-filterInvariant32-filterInvariant33-variant35-variant37-variant38-filterInvariant40-filterInvariant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:180,25:205:99:493,0,11048:73,107,7,18 chr1 12907498 . C T 459.09 PASS AC=1;AF=0.5;AN=2;DP=5811;set=variant-variant2-filterInvariant3-filterInvariant4-variant5-variant6-variant7-variant8-filterInvariant9-filterInvariant10-variant11-variant14-variant15-filterInvariant16-variant17-variant18-variant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-variant26-filterInvariant27-variant29-filterInvariant30-filterInvariant32-filterInvariant33-variant35-variant37-variant38-filterInvariant40-filterInvariant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:172,25:197:99:508,0,10631:69,103,7,18 chr1 12907507 . C T 399.17 PASS AC=1;AF=0.5;AN=2;DP=5737;FractionInformativeReads=1;set=variant-variant2-filterInvariant3-filterInvariant4-variant5-variant6-variant7-variant8-filterInvariant9-filterInvariant10-variant11-variant14-variant15-filterInvariant16-variant17-variant18-variant19-variant20-variant21-filterInvariant22-filterInvariant23-variant24-variant26-filterInvariant27-variant29-variant30-filterInvariant32-variant33-variant34-variant35-variant37-variant38-filterInvariant40-filterInvariant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:157,25:182:99:565,0,9129:62,95,7,18 chr1 12907508 . T C 399.17 PASS AC=1;AF=0.5;AN=2;DP=5666;FractionInformativeReads=1;set=variant-variant2-filterInvariant3-filterInvariant4-variant5-variant6-variant7-variant8-filterInvariant9-filterInvariant10-variant11-variant14-variant15-filterInvariant16-variant17-variant18-variant19-variant20-variant21-filterInvariant22-filterInvariant23-variant24-variant26-variant27-variant29-variant30-filterInvariant32-variant33-variant34-variant35-variant37-variant38-filterInvariant40-filterInvariant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:155,25:180:99:571,0,8971:60,95,7,18 chr1 12907513 . T C 411.21 PASS AC=1;AF=0.5;AN=2;DP=5027;FractionInformativeReads=1;set=variant-variant2-variant3-filterInvariant4-variant5-variant6-variant7-variant8-filterInvariant9-filterInvariant10-variant11-variant14-variant15-filterInvariant16-variant17-variant18-variant19-variant20-filterInvariant21-filterInvariant22-filterInvariant23-variant26-variant27-variant29-variant30-filterInvariant32-filterInvariant33-variant35-variant37-variant38-filterInvariant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:148,23:171:99:511,0,8327:60,88,6,17 chr1 12907518 . T A 489.32 PASS AC=1;AF=0.5;AN=2;DP=4806;FractionInformativeReads=1;set=variant-variant2-variant3-filterInvariant4-variant5-variant6-variant7-variant8-filterInvariant9-filterInvariant10-variant11-variant14-variant15-filterInvariant16-variant17-variant18-variant19-variant20-filterInvariant21-filterInvariant22-variant23-variant26-variant27-variant29-variant30-filterInvariant32-filterInvariant33-variant35-variant37-variant38-filterInvariant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:139,23:162:99:526,0,7787:57,82,6,17 chr1 12907519 . C A 495.34 PASS AC=1;AF=0.5;AN=2;DP=4895;FractionInformativeReads=1;set=variant-variant2-variant3-filterInvariant4-variant5-variant6-variant7-variant8-filterInvariant9-filterInvariant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant20-filterInvariant21-filterInvariant22-variant23-variant26-variant27-variant29-variant30-filterInvariant32-filterInvariant33-variant35-variant37-variant38-filterInvariant40-variant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:139,22:161:99:526,0,7787:57,82,6,16 chr1 12907777 . T C 1518.56 PASS AC=1;AF=0.5;AN=2;DP=11165;set=filterInvariant-variant2-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant7-variant8-filterInvariant9-variant10-filterInvariant11-filterInvariant12-variant13-variant14-variant15-filterInvariant16-filterInvariant17-filterInvariant18-variant19-variant20-variant21-filterInvariant22-variant23-variant24-variant25-variant26-filterInvariant27-variant28-variant29-variant30-filterInvariant31-filterInvariant32-variant33-variant34-variant35-variant36-variant37-variant38-filterInvariant39-filterInvariant40-filterInvariant41-filterInvariant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:205,32:237:99:764,0,8335:102,103,28,4 chr1 12907781 . T C 1677.44 PASS AC=1;AF=0.5;AN=2;DP=11263;set=filterInvariant-variant2-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant7-variant8-filterInvariant9-variant10-filterInvariant11-filterInvariant12-variant13-variant14-variant15-filterInvariant16-filterInvariant17-filterInvariant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-filterInvariant26-filterInvariant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-filterInvariant39-variant40-filterInvariant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:196,37:233:99:934,0,8357:97,99,31,6 chr1 12907798 . A C 2285.86 PASS AC=1;AF=0.5;AN=2;DP=11893;set=filterInvariant-variant2-variant3-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant7-variant8-variant9-variant10-filterInvariant11-filterInvariant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-filterInvariant27-variant28-variant29-variant30-variant31-variant32-filterInvariant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-filterInvariant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:185,51:236:99:1693,0,7858:96,89,43,8 chr1 12907802 . C T 2446.31 PASS AC=1;AF=0.5;AN=2;DP=12057;set=filterInvariant-variant2-variant3-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant7-variant8-variant9-variant10-filterInvariant11-filterInvariant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-filterInvariant26-filterInvariant27-variant28-filterInvariant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-filterInvariant41-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:186,56:242:99:1874,0,7717:97,89,46,10 chr1 12907803 . C T 2446.31 PASS AC=1;AF=0.5;AN=2;DP=12131;set=filterInvariant-variant2-variant3-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant7-variant8-variant9-variant10-filterInvariant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-filterInvariant26-filterInvariant27-variant28-filterInvariant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-filterInvariant41-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:186,59:245:99:1880,0,7633:97,89,48,11 chr1 12907837 . C T 4253.12 PASS AC=1;AF=0.5;AN=2;DP=15041;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:176,131:307:99:3348,0,4721:90,86,93,38 chr1 12907885 . T C 4558.15 PASS AC=1;AF=0.5;AN=2;DP=21324;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-filterInvariant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:266,204:470:99:5114,0,7000:172,94,113,91 chr1 12908236 . G T 2708.3 PASS AC=1;AF=0.5;AN=2;DP=8491;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:120,65:185:99:2145,0,4945:35,85,16,49 chr1 12908243 . A G 2396.39 PASS AC=1;AF=0.5;AN=2;DP=7338;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-filterInvariant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:101,51:152:99:1923,0,4618:28,73,9,42 chr1 12919422 . T C 184.57 PASS AC=1;AF=0.5;AN=2;DP=1640;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,12:36:99:432,0,1277:17,7,8,4 chr1 12919423 . G A 184.57 PASS AC=1;AF=0.5;AN=2;DP=1636;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,12:36:99:432,0,1277:17,7,8,4 chr1 12919459 . G T 50.71 PASS AC=1;AF=0.5;AN=2;DP=1867;set=filterInvariant-variant3-variant4-variant5-variant7-variant8-variant9-filterInvariant14-variant16-filterInvariant18-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant29-variant31-filterInvariant33-variant34-variant35-variant37-variant38-variant39-filterInvariant41-variant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,12:54:99:307,0,1189:29,13,8,4 chr1 12919482 . G C 54.06 PASS AC=1;AF=0.5;AN=2;DP=2985;set=filterInvariant-variant2-variant3-variant4-variant5-variant7-filterInvariant8-filterInvariant9-variant11-filterInvariant13-filterInvariant14-variant15-variant18-filterInvariant19-variant20-variant21-filterInvariant22-variant24-variant25-variant26-variant27-variant29-filterInvariant30-filterInvariant31-variant32-variant33-variant34-filterInvariant35-filterInvariant37-variant38-filterInvariant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:66,10:76:99:148,0,1790:41,25,6,4 chr1 12919505 . G T 46.12 PASS AC=1;AF=0.5;AN=2;DP=3373;FractionInformativeReads=1;set=filterInvariant-variant2-variant3-variant4-variant5-variant7-filterInvariant8-variant9-variant11-variant13-filterInvariant14-variant15-variant18-filterInvariant19-variant20-variant21-variant24-variant25-variant26-variant27-variant29-filterInvariant31-variant32-variant33-variant34-filterInvariant35-variant37-variant38-filterInvariant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:84,8:92:83:83,0,3853:49,35,4,4 chr1 12919506 . A T 43.12 PASS AC=1;AF=0.5;AN=2;DP=3388;set=filterInvariant-variant2-variant3-variant4-variant5-variant7-filterInvariant8-variant9-variant11-variant13-filterInvariant14-variant15-variant18-filterInvariant19-variant20-variant21-variant24-variant25-variant26-variant27-variant29-filterInvariant31-variant32-variant33-variant34-filterInvariant35-filterInvariant37-variant38-filterInvariant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:83,8:91:83:83,0,3853:48,35,4,4 chr1 12919511 . C T,A 37.11 PASS AC=1,0;AF=0.457,0.057;AN=2;DP=3589;set=filterInvariant-filterInvariant2-variant3-variant4-variant5-variant7-filterInvariant8-filterInvariant9-variant10-variant11-variant13-filterInvariant14-variant15-variant18-filterInvariant19-variant20-variant21-variant24-variant25-filterInvariant26-variant27-variant29-variant30-variant32-variant33-variant34-filterInvariant35-filterInvariant37-variant38-filterInvariant39-variant40-variant41-variant42-variant43-filterInvariant44 GT:DP:GQ:SB 0/1:93:80:49,36,4,4 chr1 12921386 . G A 2775.6 PASS AC=1;AF=0.5;AN=2;DP=407;set=variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:93,112:205:99:2804,0,2280:38,55,48,64 chr1 12942119 . C T 3404.46 PASS AC=1;AF=0.708;AN=2;DP=7849;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant13-variant17-variant18-variant19-variant24-variant25-variant26-variant28-variant30-variant31-variant34-variant35-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:187,195:382:99:4252,0,4085:101,86,105,90 chr1 12942289 . C A 1662.99 PASS AC=1;AF=0.5;AN=2;DP=7068;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-filterInvariant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-filterInvariant39-variant40-variant41-variant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:153,42:195:99:1267,0,5679:39,114,24,18 chr1 12942306 . C T 1711.38 PASS AC=1;AF=0.5;AN=2;DP=6123;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-filterInvariant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:109,43:152:99:1401,0,4499:26,83,21,22 chr1 12942384 . T C 164.99 PASS AC=1;AF=0.5;AN=2;DP=2412;set=variant-filterInvariant2-variant3-variant4-variant5-variant6-variant7-variant8-variant12-variant13-variant14-filterInvariant15-variant16-variant17-variant20-filterInvariant21-filterInvariant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,19:67:99:421,0,1698:7,41,2,17 chr1 12942399 . A G 431.52 PASS AC=1;AF=0.5;AN=2;DP=1238;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant13-variant17-variant18-variant19-variant24-variant25-variant26-variant28-filterInvariant30-variant31-filterInvariant34-variant35-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:34,20:54:99:592,0,1256:5,29,2,18 chr1 12942414 . G T 101.4 PASS AC=1;AF=0.5;AN=2;DP=1677;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:27,15:42:99:443,0,1059:3,24,3,12 chr1 12942419 . G GT,GTT 49.23 PASS AC=1,0;AF=0.484,0.016;AN=2;DP=1121;set=filterInvariant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant17-variant21-filterInvariant22-variant24-variant25-variant26-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant39-variant40-filterInvariant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:32:99:3,24,1,4 chr1 12942430 . G C 271.56 PASS AC=1;AF=0.5;AN=2;DP=706;set=variant2-variant5-filterInvariant7-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant30-filterInvariant32-variant34-variant35-variant37-variant38-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,4:26:88:88,0,943:3,19,1,3 chr1 12942862 . G C 37.72 PASS AC=1;AF=0.688;AN=2;DP=564;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,7:16:99:248,0,275:7,2,6,1 chr1 12979729 . G A 246.06 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=2256;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:43,36:79:99:682,0,858:24,19,20,16 chr1 12979845 . T C 204.98 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=1628;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:44,28:72:99:507,0,937:16,28,11,17 chr1 12987833 . A G 143.71 PASS AC=1;AF=0.5;AN=2;DP=734;FractionInformativeReads=1;set=filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant8-filterInvariant9-filterInvariant11-filterInvariant14-filterInvariant15-filterInvariant16-filterInvariant18-filterInvariant19-filterInvariant20-variant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant30-filterInvariant31-filterInvariant32-variant33-filterInvariant34-filterInvariant35-filterInvariant38-filterInvariant39-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:19,5:24:72:72,0,504:15,4,4,1 chr1 12987951 . C T 97.77 DRAGENHardSNP AC=1;AF=0.516;AN=2;DP=3156;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:86,36:122:99:526,0,1760:43,43,19,17 chr1 12988077 . G T 123.24 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=58;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:11,5:16:99:101,0,292:1,10,0,5 chr1 13001186 . C T 3619.63 PASS AC=1;AF=0.58;AN=2;DP=8347;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-filterInvariant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:110,98:208:99:2445,0,2862:85,25,82,16 chr1 13001312 . C G 6578.48 PASS AC=1;AF=0.557;AN=2;DP=21542;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-filterInvariant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:324,346:670:99:6866,0,6734:126,198,148,198 chr1 13001418 . C A 222.95 PASS AC=1;AF=0.5;AN=2;DP=2397;set=filterInvariant2-variant4-variant5-variant6-variant7-variant8-variant13-variant15-variant17-variant18-variant19-filterInvariant20-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant37-variant38-filterInvariant39-variant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:69,39:108:99:911,0,2673:6,63,5,34 chr1 13001428 . C A 1430.99 PASS AC=1;AF=0.545;AN=2;DP=2511;set=variant-filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant7-variant8-variant9-filterInvariant10-filterInvariant11-variant12-variant13-variant14-variant15-variant16-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-variant23-filterInvariant24-variant25-variant26-variant27-variant28-filterInvariant29-variant30-variant31-variant32-variant33-filterInvariant34-variant35-variant36-variant37-variant38-variant39-variant40-filterInvariant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:21,40:61:99:1445,0,793:0,21,1,39 chr1 13001445 . C T 792.11 PASS AC=1;AF=0.536;AN=2;DP=1222;FractionInformativeReads=1;set=variant-filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant8-variant9-filterInvariant10-filterInvariant11-filterInvariant13-filterInvariant14-filterInvariant15-variant16-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-variant23-filterInvariant24-filterInvariant25-variant26-filterInvariant27-filterInvariant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant38-filterInvariant39-filterInvariant40-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:9,17:26:99:713,0,366:1,8,0,17 chr1 13001465 . G T 170.82 PASS AC=1;AF=0.657;AN=2;DP=491;set=variant-filterInvariant2-filterInvariant3-variant4-filterInvariant5-variant6-filterInvariant7-filterInvariant8-variant9-filterInvariant11-filterInvariant14-variant15-filterInvariant17-variant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-variant24-filterInvariant25-variant27-filterInvariant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant33-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant38-filterInvariant39-filterInvariant40-variant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:1,7:8:15:375,0,15:1,0,0,7 chr1 13036587 . C T 2233.04 DRAGENHardSNP AC=2;AF=0.716;AN=2;DP=6391;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,83:83:99:2039,248,0:0,0,42,41 chr1 13052789 . G A 2658.26 PASS AC=1;AF=0.524;AN=2;DP=9927;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:97,129:226:99:3064,0,2253:56,41,75,54 chr1 13052871 . C T 3063.1 PASS AC=1;AF=0.524;AN=2;DP=12047;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-filterInvariant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:124,162:286:99:5768,0,4472:52,72,69,93 chr1 13052907 . T C 5232.75 PASS AC=1;AF=0.636;AN=2;DP=10166;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:96,122:218:99:4796,0,3767:36,60,48,74 chr1 13111821 . C G 223.85 DRAGENHardSNP AC=1;AF=0.717;AN=2;DP=515;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:13,14:27:99:265,0,296:5,8,6,8 chr1 13123665 . T G 492.98 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=247;FS=0;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:36,50:86:99:979,0,618:18,18,25,25 chr1 13141835 . C T 567.97 DRAGENHardSNP AC=1;AF=0.733;AN=2;DP=1254;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:10,21:31:99:478,0,198:2,8,5,16 chr1 13183199 . C G 62.15 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=2739;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:173,16:189:99:142,0,70752:75,98,12,4 chr1 13183213 . T A 84 PASS AC=1;AF=0.5;AN=2;DP=3582;set=filterInvariant2-filterInvariant4-variant5-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant14-filterInvariant15-filterInvariant19-filterInvariant21-variant23-variant25-variant27-filterInvariant29-filterInvariant33-filterInvariant35-variant37-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:157,18:175:99:316,0,67530:70,87,14,4 chr1 13183225 . T C 395.99 PASS AC=1;AF=0.5;AN=2;DP=6346;set=variant2-filterInvariant3-variant4-variant5-filterInvariant6-variant7-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant13-variant14-variant15-filterInvariant16-filterInvariant17-filterInvariant18-variant19-filterInvariant20-variant21-variant23-variant25-filterInvariant26-variant27-variant29-filterInvariant30-filterInvariant33-filterInvariant35-variant37-variant38-filterInvariant39-variant40-variant41-variant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:151,18:169:99:328,0,66304:64,87,14,4 chr1 13183228 . C T 428.95 PASS AC=1;AF=0.5;AN=2;DP=6429;set=variant2-variant3-variant4-filterInvariant5-filterInvariant6-variant7-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant13-variant14-variant15-filterInvariant16-filterInvariant17-filterInvariant18-variant19-filterInvariant20-variant21-variant23-filterInvariant24-variant25-filterInvariant26-variant27-variant29-filterInvariant30-filterInvariant33-variant35-variant37-variant38-filterInvariant39-variant40-variant41-variant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:147,18:165:99:421,0,65355:60,87,14,4 chr1 13183237 . C T 659.97 PASS AC=1;AF=0.5;AN=2;DP=6293;FractionInformativeReads=1;set=variant2-variant3-variant4-filterInvariant5-variant6-filterInvariant7-variant8-variant9-variant10-filterInvariant11-filterInvariant12-variant13-variant14-variant15-variant16-filterInvariant17-variant18-variant19-variant20-variant21-variant23-filterInvariant24-variant25-filterInvariant26-variant27-variant29-variant30-variant33-filterInvariant34-variant35-filterInvariant37-variant38-filterInvariant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:145,25:170:99:646,0,62804:58,87,20,5 chr1 13183238 . T C 662.98 PASS AC=1;AF=0.5;AN=2;DP=6250;FractionInformativeReads=1;set=variant2-variant3-variant4-filterInvariant5-variant6-variant7-variant8-variant9-variant10-variant11-filterInvariant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-filterInvariant24-variant25-filterInvariant26-variant27-variant29-variant30-variant33-filterInvariant34-variant35-filterInvariant37-variant38-filterInvariant39-filterInvariant40-variant41-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:144,26:170:99:691,0,62325:58,86,20,6 chr1 13183243 . T C 765.02 PASS AC=1;AF=0.5;AN=2;DP=6019;FractionInformativeReads=1;set=variant2-variant3-variant4-filterInvariant5-variant6-filterInvariant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant33-filterInvariant34-variant35-filterInvariant37-variant38-filterInvariant39-filterInvariant40-variant41-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:137,31:168:99:1067,0,58759:57,80,24,7 chr1 13183248 . T A 825.08 PASS AC=1;AF=0.5;AN=2;DP=5844;FractionInformativeReads=1;set=variant2-variant3-variant4-filterInvariant5-variant6-filterInvariant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-filterInvariant27-variant29-variant30-variant33-filterInvariant34-variant35-filterInvariant37-variant38-filterInvariant39-filterInvariant40-variant41-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:133,36:169:99:1076,0,56116:56,77,29,7 chr1 13183249 . C A 828.09 PASS AC=1;AF=0.5;AN=2;DP=5802;set=variant2-variant3-variant4-filterInvariant5-variant6-filterInvariant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-filterInvariant21-variant23-variant24-variant25-variant26-filterInvariant27-variant29-variant30-variant33-filterInvariant34-variant35-filterInvariant37-variant38-filterInvariant39-filterInvariant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:133,36:169:99:1085,0,55065:56,77,29,7 chr1 13183439 . T C 9192.24 PASS AC=1;AF=0.784;AN=2;DP=18306;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:75,334:409:99:8905,0,1051:38,37,165,169 chr1 13183511 . T C 5032.46 PASS AC=1;AF=0.5;AN=2;DP=15315;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:213,160:373:99:5623,0,8503:110,103,57,103 chr1 13183528 . A C 4481.77 PASS AC=1;AF=0.5;AN=2;DP=13615;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:208,123:331:99:4659,0,8839:107,101,40,83 chr1 13183532 . C T 4088.45 PASS AC=1;AF=0.5;AN=2;DP=13070;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:207,106:313:99:4068,0,8711:104,103,33,73 chr1 13183533 . C T 3845.54 PASS AC=1;AF=0.5;AN=2;DP=12987;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:206,104:310:99:3867,0,8600:103,103,31,73 chr1 13183567 . C T 1419.8 PASS AC=1;AF=0.5;AN=2;DP=9944;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant7-variant8-variant9-variant10-filterInvariant11-variant12-variant13-variant14-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant18-variant19-variant20-variant21-variant22-variant23-filterInvariant24-variant25-filterInvariant26-filterInvariant27-variant28-filterInvariant29-variant30-filterInvariant31-variant32-variant33-variant34-filterInvariant35-filterInvariant36-filterInvariant37-variant38-variant39-variant40-filterInvariant41-filterInvariant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:208,47:255:99:1251,0,8660:108,100,6,41 chr1 13183573 . G T 1352.33 PASS AC=1;AF=0.5;AN=2;DP=9611;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant8-variant9-filterInvariant10-filterInvariant11-variant12-filterInvariant13-variant14-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant18-variant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant27-variant28-filterInvariant29-filterInvariant30-filterInvariant31-variant32-filterInvariant33-variant34-filterInvariant35-filterInvariant36-filterInvariant37-variant38-variant39-filterInvariant40-filterInvariant41-filterInvariant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:214,36:250:99:1117,0,8889:113,101,3,33 chr1 13183966 . G T 242.88 PASS AC=1;AF=0.5;AN=2;DP=2725;set=variant-variant2-filterInvariant3-variant4-variant5-variant6-variant7-variant10-filterInvariant11-filterInvariant13-variant14-variant17-variant18-variant20-variant21-variant23-variant24-filterInvariant25-variant26-variant27-variant29-variant30-variant32-variant33-variant34-filterInvariant35-filterInvariant36-variant37-variant38-filterInvariant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:111,27:138:99:298,0,3334:35,76,11,16 chr1 13183973 . G A 823.72 PASS AC=1;AF=0.5;AN=2;DP=2851;set=variant-variant2-filterInvariant3-variant4-variant5-variant6-variant7-filterInvariant10-variant11-variant13-variant14-filterInvariant15-filterInvariant16-variant17-variant18-filterInvariant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-filterInvariant34-variant35-filterInvariant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:99,22:121:99:332,0,3223:32,67,8,14 chr1 13219149 . G A 1550.94 PASS AC=1;AF=0.5;AN=2;DP=13062;set=variant-filterInvariant2-variant3-variant4-filterInvariant5-variant6-variant7-variant8-variant9-filterInvariant12-filterInvariant13-filterInvariant14-filterInvariant15-variant16-variant17-filterInvariant18-variant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-variant25-variant26-filterInvariant27-variant28-variant29-filterInvariant30-variant32-filterInvariant33-filterInvariant34-variant35-variant36-filterInvariant37-filterInvariant38-variant39-filterInvariant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:124,129:253:99:3096,0,2713:42,82,38,91 chr1 13365747 . C G 45.74 PASS AC=1;AF=0.654;AN=2;DP=297;FractionInformativeReads=1;set=filterInvariant2-filterInvariant7-filterInvariant12-variant14-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant29-filterInvariant32-variant35-filterInvariant39-variant40-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:23,17:40:99:330,0,513:14,9,11,6 chr1 13365776 . C G 354.41 PASS AC=1;AF=0.625;AN=2;DP=290;set=filterInvariant7-filterInvariant21-filterInvariant29-filterInvariant32-variant35-filterInvariant39-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:26,24:50:99:444,0,535:14,12,12,12 chr1 13414069 . G C 515.82 DRAGENHardSNP AC=2;AF=0.6;AN=2;DP=996;FS=0;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:2,26:28:34:593,34,0:1,1,13,13 chr1 13414082 . T C 1048.45 DRAGENHardSNP AC=1;AF=0.567;AN=2;DP=1854;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:2,26:28:15:1086,0,15:1,1,13,13 chr1 13414089 . G A 1048.45 DRAGENHardSNP AC=1;AF=0.591;AN=2;DP=1012;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:2,26:28:15:1086,0,15:1,1,13,13 chr1 13448180 . A G 496.53 DRAGENHardSNP AC=2;AF=0.86;AN=2;DP=514;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,10:10:33:495,33,0:0,0,10,0 chr1 13448184 . C T 652.76 DRAGENHardSNP AC=2;AF=0.86;AN=2;DP=632;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,12:12:9:540,9,0:0,0,11,1 chr1 13448185 . G C 229.49 DRAGENHardSNP AC=2;AF=0.703;AN=2;DP=607;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:1,13:14:9:540,9,0:1,0,12,1 chr1 13448199 . C T 856.08 DRAGENHardSNP AC=2;AF=0.966;AN=2;DP=1358;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:659,66,0:0,0,19,3 chr1 13448283 . A G 2587.19 DRAGENHardSNP AC=2;AF=1;AN=2;DP=5361;FS=0;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,94:94:99:2324,282,0:0,0,47,47 chr1 13448351 . T C 1765.7 DRAGENHardSNP AC=2;AF=0.943;AN=2;DP=3647;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:1654,186,0:0,0,23,39 chr1 13695787 . C G 1574.97 DRAGENHardSNP AC=1;AF=0.989;AN=2;DP=2527;FS=0;MQRankSum=-2.1;ReadPosRankSum=-0.853;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:35,47:82:99:1111,0,745:25,10,34,13 chr1 13695816 . G A 2318.89 DRAGENHardSNP AC=1;AF=0.989;AN=2;DP=4360;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:58,83:141:99:1812,0,1080:33,25,53,30 chr1 13695974 . T C 960.66 DRAGENHardSNP AC=1;AF=0.989;AN=2;DP=2019;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:24,29:53:99:683,0,485:9,15,5,24 chr1 13839423 . T C 592.95 PASS AC=1;AF=0.5;AN=2;DP=2370;set=filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant7-variant8-variant9-filterInvariant11-filterInvariant12-filterInvariant13-variant14-filterInvariant16-filterInvariant17-variant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant25-filterInvariant27-filterInvariant28-variant30-filterInvariant32-filterInvariant35-filterInvariant38-filterInvariant39-filterInvariant40-variant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,16:76:76:76,0,820:22,38,16,0 chr1 13839427 . T C 196.94 PASS AC=1;AF=0.5;AN=2;DP=1915;set=filterInvariant2-variant3-filterInvariant4-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant12-filterInvariant13-filterInvariant16-filterInvariant19-variant20-filterInvariant21-filterInvariant23-variant25-filterInvariant28-filterInvariant31-filterInvariant35-variant36-filterInvariant38-filterInvariant39-filterInvariant40-filterInvariant42 GT:AD:DP:GQ:PL:SB 0/1:68,16:84:99:158,0,2616:28,40,16,0 chr1 13839437 . A C 39.07 PASS AC=1;AF=0.5;AN=2;DP=1465;set=filterInvariant2-variant4-variant7-variant8-filterInvariant9-filterInvariant11-filterInvariant13-variant25-filterInvariant35-filterInvariant36-variant40-filterInvariant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:107,13:120:72:72,0,3434:50,57,12,1 chr1 13933855 . A G 787.57 PASS AC=1;AF=0.594;AN=2;DP=1064;FractionInformativeReads=1;MQ=60;set=variant6-variant12-variant14-variant20-variant21-variant22-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:31,35:66:99:987,0,909:7,24,9,26 chr1 13936822 . G T 849.31 PASS AC=1;AF=0.686;AN=2;DP=3171;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:50,50:100:99:1106,0,1215:33,17,31,19 chr1 13936839 . G A 1579.89 PASS AC=1;AF=0.5;AN=2;DP=127;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.667;QD=12.44;ReadPosRankSum=-2.407;SOR=0.697;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:57,70:127:99:1608,0,1380:35,22,43,27 chr1 13937089 . G T 1047.97 PASS AC=1;AF=0.686;AN=2;DP=3138;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:45,29:74:99:813,0,1052:20,25,10,19 chr1 13937281 . T C 229.81 PASS AC=2;AF=0.763;AN=2;DP=619;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:245,18,0:0,0,2,4 chr1 13940365 . CTTT CT,CTT,CTTTT,C 63.86 PASS AC=2,0,0,0;AF=0.22,0.42,0.02,0.02;AN=2;DP=552;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant10-variant12-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant26-variant28-filterInvariant31-variant33-variant34-variant35-variant38-variant39-variant40 GT:DP:GQ:SB 1/1:11:3:0,1,1,9 chr1 13940864 . C G 5238.77 PASS AC=2;AF=0.943;AN=2;DP=8146;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,212:212:99:6183,635,0:0,0,113,99 chr1 13941452 . T C 486.78 PASS AC=1;AF=0.5;AN=2;DP=61;FS=0;FractionInformativeReads=0.984;MQ=60;MQRankSum=1.902;QD=7.98;ReadPosRankSum=-0.455;SOR=0.646;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:34,26:60:99:515,0,781:14,20,11,15 chr1 13942731 . T C 4104.16 PASS AC=1;AF=0.6;AN=2;DP=5135;MQ=60;set=variant6-variant12-variant14-variant20-variant21-variant22-variant25-variant27-variant28-variant29-variant32-variant33-variant35-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:167,156:323:99:3720,0,4156:79,88,79,77 chr1 13942866 . T A 2494.51 PASS AC=1;AF=0.5;AN=2;DP=173;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.134;QD=14.42;ReadPosRankSum=-0.427;SOR=0.671;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:87,86:173:99:2523,0,2496:44,43,43,43 chr1 13942890 . TG T 2087.47 PASS AC=1;AF=0.6;AN=2;DP=3044;MQ=60;set=variant6-variant12-variant14-variant20-variant21-variant22-variant25-variant27-variant28-variant29-variant32-variant33-variant35-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:112,94:206:99:2897,0,3539:57,55,48,46 chr1 13942902 . G A 2939.34 PASS AC=1;AF=0.5;AN=2;DP=227;FS=0.485;FractionInformativeReads=1;MQ=60;MQRankSum=2.131;QD=12.95;ReadPosRankSum=-0.661;SOR=0.64;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:107,120:227:99:2968,0,2803:55,52,60,60 chr1 13943470 . G A 3952.23 PASS AC=1;AF=0.5;AN=2;DP=207;FS=5.732;FractionInformativeReads=1;MQ=60;MQRankSum=-1.937;QD=19.09;ReadPosRankSum=0.614;SOR=0.689;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:104,103:207:99:3980,0,5250:57,47,48,55 chr1 13943478 . A T 3864.95 PASS AC=1;AF=0.5;AN=2;DP=213;FS=3.061;FractionInformativeReads=1;MQ=60;MQRankSum=2.101;QD=18.15;ReadPosRankSum=1.014;SOR=0.63;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:112,101:213:99:3893,0,5372:60,52,49,52 chr1 13943653 . AT A,ATT 245.53 PASS AC=2,0;AF=0.733,0.012;AN=2;DP=2028;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-filterInvariant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:34:2:2,2,9,21 chr1 13943724 . T C 449.86 PASS AC=1;AF=0.6;AN=2;DP=432;MQ=60;set=variant6-variant12-variant14-variant20-variant21-variant22-variant25-variant27-variant28-variant29-variant32-variant33-variant35-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:17,12:29:99:318,0,616:9,8,6,6 chr1 13943896 . T TG 863.32 PASS AC=1;AF=0.5;AN=2;DP=45;FS=6.176;FractionInformativeReads=1;MQ=60;MQRankSum=-0.811;QD=19.18;ReadPosRankSum=-0.423;SOR=1.609;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:20,25:45:99:901,0,1148:10,10,8,17 chr1 13943897 . T TG 863.32 PASS AC=1;AF=0.5;AN=2;DP=45;FS=6.176;FractionInformativeReads=1;MQ=60;MQRankSum=0.765;QD=19.18;ReadPosRankSum=-0.423;SOR=1.609;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:20,25:45:99:901,0,1148:10,10,8,17 chr1 13944175 . A C 340.34 PASS AC=1;AF=0.5;AN=2;DP=21;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.616;QD=16.21;ReadPosRankSum=-1.412;SOR=0.458;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:8,13:21:99:369,0,216:5,3,7,6 chr1 13944236 . C CTT 1897.62 PASS AC=2;AF=0.977;AN=2;DP=2092;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:2330,156,0:0,0,31,20 chr1 13944294 . CT C 1851.87 PASS AC=1;AF=0.6;AN=2;DP=971;MQ=60;set=variant6-variant12-variant14-variant20-variant21-variant22-variant25-variant27-variant28-variant29-variant32-variant33-variant35-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:30,43:73:99:1715,0,1130:17,13,22,21 chr1 13944298 . CTT C 1851.91 PASS AC=1;AF=0.6;AN=2;DP=979;FractionInformativeReads=1;MQ=60;set=variant6-variant12-variant14-variant20-variant21-variant22-variant25-variant27-variant28-variant29-variant32-variant33-variant35-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:31,43:74:99:1712,0,1158:17,14,22,21 chr1 13944326 . T C 713 PASS AC=1;AF=0.5;AN=2;DP=72;FS=0.901;FractionInformativeReads=1;MQ=60;MQRankSum=0.153;QD=9.9;ReadPosRankSum=-0.47;SOR=0.52;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:40,32:72:99:741,0,890:18,22,16,16 chr1 14026900 . G A 275.04 PASS AC=1;AF=0.5;AN=2;DP=22;FS=1.86;FractionInformativeReads=1;MQ=60;MQRankSum=-1.615;QD=12.5;ReadPosRankSum=1.286;SOR=0.273;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:12,10:22:99:303,0,338:3,9,4,6 chr1 14031470 . C T 1771.6 PASS AC=1;AF=0.5;AN=2;DP=143;FS=2.095;FractionInformativeReads=1;MQ=60;MQRankSum=0.265;QD=12.39;ReadPosRankSum=1.087;SOR=0.538;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:66,77:143:99:1800,0,1634:28,38,36,41 chr1 14031732 . G C 3749.47 PASS AC=1;AF=0.821;AN=2;DP=4024;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,44:77:99:1182,0,934:17,16,23,21 chr1 14031756 . A C 4514.47 PASS AC=1;AF=0.805;AN=2;DP=4949;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,54:100:99:1442,0,1214:21,25,30,24 chr1 14042298 . C T 768.81 PASS AC=1;AF=0.5;AN=2;DP=42;FS=1.668;FractionInformativeReads=1;MQ=60;MQRankSum=0.256;QD=18.3;ReadPosRankSum=-0.948;SOR=0.358;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:17,25:42:99:797,0,556:2,15,5,20 chr1 14042309 . G A 422.75 PASS AC=1;AF=0.559;AN=2;DP=515;MQ=60;set=variant2-variant4-variant6-variant7-variant12-variant15-variant16-variant20-variant24-variant25-variant27-variant28-variant35-variant36-variant37-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:12,16:28:99:614,0,410:1,11,2,14 chr1 14057258 . G A 263.87 PASS AC=1;AF=0.559;AN=2;DP=354;set=variant2-variant4-variant6-variant7-variant12-variant15-variant16-variant20-variant24-variant25-variant27-variant28-variant35-variant36-variant37-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:15,15:30:99:413,0,340:9,6,11,4 chr1 14059395 . T C 789.49 PASS AC=1;AF=0.559;AN=2;DP=1070;MQ=60;set=variant2-variant4-variant6-variant7-variant12-variant15-variant16-variant20-variant24-variant25-variant27-variant28-variant35-variant36-variant37-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:21,33:54:99:828,0,619:7,14,12,21 chr1 14075773 . C T 557.95 PASS AC=1;AF=0.5;AN=2;DP=24;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.207;QD=23.25;ReadPosRankSum=0.445;SOR=1.201;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:7,17:24:99:586,0,196:6,1,15,2 chr1 14096821 . T C 735.81 PASS AC=1;AF=0.556;AN=2;DP=1260;MQ=60;set=variant2-variant4-variant6-variant7-variant12-variant15-variant16-variant20-variant24-variant25-variant27-variant28-variant29-variant35-variant36-variant37-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:26,34:60:99:889,0,627:12,14,13,21 chr1 14099763 . C T 807.01 PASS AC=1;AF=0.643;AN=2;DP=1519;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant6-variant7-variant10-variant12-variant15-variant16-variant20-variant21-variant24-variant25-variant27-variant28-variant29-variant34-variant35-variant36-variant37-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:24,27:51:99:640,0,708:8,16,9,18 chr1 14105139 . T A 1270.61 PASS AC=1;AF=0.65;AN=2;DP=3165;MQ=60;set=variant2-variant6-variant7-variant10-variant12-variant15-variant16-variant20-variant21-variant24-variant25-variant27-variant28-variant29-variant34-variant35-variant36-variant37-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:79,54:133:99:1346,0,2080:33,46,22,32 chr1 14105298 . G A 1471.28 PASS AC=1;AF=0.643;AN=2;DP=2355;MQ=60;set=variant2-variant4-variant6-variant7-variant10-variant12-variant15-variant16-variant20-variant21-variant24-variant25-variant27-variant28-variant29-variant34-variant35-variant36-variant37-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:52,50:102:99:1287,0,1423:29,23,27,23 chr1 14106394 . A ACTC 1862.76 PASS AC=1;AF=0.62;AN=2;DP=2588;set=variant2-variant4-variant6-variant7-variant10-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant24-variant25-variant27-variant28-variant29-variant34-variant35-variant36-variant37-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,61:113:99:2408,0,2363:27,25,28,33 chr1 14107360 . T A 437.17 PASS AC=1;AF=0.5;AN=2;DP=227;MQ=60;set=variant24-variant35-variant36-variant38 GT:AD:DP:GQ:PL:SB 0/1:41,25:66:99:513,0,972:18,23,11,14 chr1 14109114 . A G 1240.69 PASS AC=1;AF=0.643;AN=2;DP=1540;MQ=60;set=variant2-variant4-variant6-variant7-variant10-variant12-variant15-variant16-variant20-variant21-variant24-variant25-variant27-variant28-variant29-variant34-variant35-variant36-variant37-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:35,26:61:99:680,0,802:17,18,12,14 chr1 14109408 . CTT CT,CTTT,C 206.22 PASS AC=1,0,0;AF=0.459,0.027,0.014;AN=2;DP=2204;set=variant-filterInvariant2-variant3-variant4-filterInvariant5-filterInvariant6-filterInvariant8-variant10-variant11-filterInvariant12-variant13-variant14-variant15-variant16-variant17-filterInvariant18-variant20-filterInvariant21-variant22-variant24-variant25-filterInvariant26-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-filterInvariant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:56:99:15,18,10,13 chr1 14143003 . A G 1398.41 PASS AC=2;AF=0.857;AN=2;DP=4996;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,120:121:99:3517,324,0:1,0,56,64 chr1 14149505 . C A 338.05 PASS AC=2;AF=0.829;AN=2;DP=907;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:739,54,0:0,0,17,1 chr1 14149601 . C T 2646.16 PASS AC=2;AF=0.829;AN=2;DP=4292;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,119:119:99:3675,357,0:0,0,76,43 chr1 14149622 . T C 3249.12 PASS AC=2;AF=0.829;AN=2;DP=5297;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,141:141:99:4127,422,0:0,0,81,60 chr1 14149844 . T A 3251.91 PASS AC=2;AF=0.829;AN=2;DP=4396;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,105:105:99:3110,311,0:0,0,51,54 chr1 14150032 . C T 2486.2 PASS AC=2;AF=0.821;AN=2;DP=3238;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,94:94:99:2914,280,0:0,0,41,53 chr1 14150116 . C T 2186.87 PASS AC=2;AF=0.829;AN=2;DP=2927;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,87:87:99:2653,261,0:0,0,46,41 chr1 14150505 . T C 1064.85 PASS AC=2;AF=0.829;AN=2;DP=1732;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:1619,141,0:0,0,22,25 chr1 14150709 . C T 4528.28 PASS AC=2;AF=0.866;AN=2;DP=3772;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,85:85:99:3933,274,0:0,0,53,32 chr1 14150714 . G A 4589.4 PASS AC=2;AF=0.866;AN=2;DP=3864;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,91:91:99:3983,280,0:0,0,56,35 chr1 14150740 . G T 4073.98 PASS AC=2;AF=0.866;AN=2;DP=4782;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,124:124:99:4088,370,0:0,0,84,40 chr1 14150992 . T C 4915.78 PASS AC=2;AF=0.866;AN=2;DP=6177;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,165:165:99:5360,494,0:0,0,58,107 chr1 14219038 . T C 747.07 PASS AC=1;AF=0.929;AN=2;DP=848;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,7:13:99:209,0,180:5,1,6,1 chr1 14219864 . C A 804.2 PASS AC=1;AF=0.917;AN=2;DP=1808;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,25:63:99:612,0,1009:23,15,13,12 chr1 14220186 . A G 1316.98 PASS AC=1;AF=0.69;AN=2;DP=2781;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant10-variant14-variant17-variant20-variant22-variant24-variant26-variant27-variant31-variant35-variant36-variant37-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,57:125:99:1457,0,1797:44,24,35,22 chr1 14925105 . T G 443.87 PASS AC=1;AF=0.813;AN=2;DP=749;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,5:19:99:127,0,397:6,8,3,2 chr1 15427801 . C T 131.1 PASS AC=1;AF=0.583;AN=2;DP=200;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant6-variant7-variant9-variant16-variant22-variant29-variant31-variant35-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,8:18:99:225,0,290:7,3,6,2 chr1 15427934 . C T 467.66 PASS AC=2;AF=0.667;AN=2;DP=2543;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,85:85:99:2702,254,0:0,0,52,33 chr1 15427982 . G A 602.89 PASS AC=2;AF=0.725;AN=2;DP=3661;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,122:122:99:3899,364,0:0,0,70,52 chr1 15428358 . T C 608.04 PASS AC=2;AF=0.943;AN=2;DP=2827;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:2026,165,0:0,0,18,37 chr1 15428363 . G A 729.76 PASS AC=1;AF=0.5;AN=2;DP=213;MQ=60;set=variant28-variant32-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:33,16:49:99:498,0,923:13,20,2,14 chr1 15428508 . C T 184.18 PASS AC=1;AF=0.556;AN=2;DP=343;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant14-variant15-variant16-variant18-variant21-variant22-variant24-variant25-variant27-variant29-variant30-variant31-variant35-variant37-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,9:13:66:272,0,66:1,3,3,6 chr1 15438990 . G A 827.32 PASS AC=2;AF=0.56;AN=2;DP=3389;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant12-variant15-variant16-variant18-variant21-variant22-variant23-variant25-variant28-variant29-variant31-variant32-variant35-variant36-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,136:138:99:3932,363,0:1,1,72,64 chr1 15441275 . C T 269.01 PASS AC=1;AF=0.686;AN=2;DP=1235;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,16:37:99:442,0,575:11,10,9,7 chr1 15441494 . G A 652.82 PASS AC=1;AF=0.686;AN=2;DP=2286;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,40:62:99:1157,0,586:14,8,20,20 chr1 15441926 . C T 636.82 PASS AC=1;AF=0.686;AN=2;DP=2981;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,33:82:99:745,0,1151:22,27,15,18 chr1 15442028 . T C 446.07 PASS AC=1;AF=0.689;AN=2;DP=1967;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,25:50:99:597,0,623:10,15,13,12 chr1 15442058 . T C 494.31 PASS AC=1;AF=0.548;AN=2;DP=1577;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,28:46:99:718,0,497:9,9,15,13 chr1 15442795 . T C 768.24 PASS AC=1;AF=0.563;AN=2;DP=2208;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,37:81:99:975,0,1157:18,26,19,18 chr1 15443368 . A G 1092.57 PASS AC=2;AF=0.955;AN=2;DP=3302;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,65:66:99:2090,187,0:0,1,31,34 chr1 15443476 . C G 1069.73 PASS AC=1;AF=0.548;AN=2;DP=2283;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,40:90:99:1044,0,1310:28,22,23,17 chr1 15443770 . A G 613.59 PASS AC=2;AF=0.955;AN=2;DP=3504;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,82:82:99:2591,245,0:0,0,36,46 chr1 15443859 . T C 608.99 PASS AC=1;AF=0.662;AN=2;DP=2542;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,40:70:99:1053,0,775:14,16,23,17 chr1 15443898 . G A 851.01 PASS AC=1;AF=0.55;AN=2;DP=2378;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,48:85:99:1180,0,905:20,17,27,21 chr1 15444288 . C T 735.99 PASS AC=1;AF=0.662;AN=2;DP=2332;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,37:72:99:969,0,704:18,17,19,18 chr1 15444487 . G A 338.02 PASS AC=1;AF=0.662;AN=2;DP=1381;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,19:39:99:495,0,493:9,11,8,11 chr1 15444563 . T C 201.9 PASS AC=1;AF=0.676;AN=2;DP=724;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,17:29:99:380,0,282:4,8,7,10 chr1 15444643 . A G 87.74 PASS AC=1;AF=0.683;AN=2;DP=269;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant32-variant35-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,5:11:99:111,0,153:2,4,2,3 chr1 15479261 . GGGC G 647.55 PASS AC=1;AF=0.621;AN=2;DP=968;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant12-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant30-variant31-variant32-variant35-variant37-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,11:22:99:409,0,429:5,6,4,7 chr1 15479265 . G GAA 647.55 PASS AC=1;AF=0.621;AN=2;DP=945;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant12-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant30-variant31-variant32-variant35-variant37-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,11:22:99:409,0,429:5,6,4,7 chr1 15479283 . G A 422.34 PASS AC=2;AF=0.869;AN=2;DP=1109;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-filterInvariant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:388,39,0:0,0,5,8 chr1 15480286 . G C 1140.39 PASS AC=2;AF=0.869;AN=2;DP=6490;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,185:185:99:5654,554,0:0,0,95,90 chr1 15480405 . T C 319.5 PASS AC=2;AF=0.989;AN=2;DP=2903;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,88:88:99:2966,263,0:0,0,22,66 chr1 15480493 . G T 79.67 PASS AC=2;AF=0.869;AN=2;DP=676;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:844,57,0:0,0,5,14 chr1 15480494 . C A 79.67 PASS AC=2;AF=0.869;AN=2;DP=665;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:844,57,0:0,0,5,14 chr1 15490962 . A G 1117.76 PASS AC=1;AF=0.618;AN=2;DP=1709;MQ=60;set=variant2-variant4-variant7-variant8-variant9-variant18-variant21-variant24-variant25-variant28-variant29-variant31-variant34-variant35-variant36-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:53,54:107:99:1366,0,1254:23,30,25,29 chr1 15495110 . A G 2491.7 PASS AC=1;AF=0.625;AN=2;DP=3685;MQ=60;set=variant2-variant4-variant8-variant9-variant18-variant21-variant24-variant25-variant28-variant29-variant31-variant34-variant35-variant36-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:117,100:217:99:2448,0,3012:52,65,49,51 chr1 15497727 . T C 1650.65 PASS AC=2;AF=0.989;AN=2;DP=7102;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,189:189:99:5818,565,0:0,0,113,76 chr1 15497844 . T A 1392.81 PASS AC=2;AF=0.888;AN=2;DP=5227;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,151:151:99:4547,450,0:0,0,56,95 chr1 15497954 . A G 346.81 PASS AC=2;AF=0.897;AN=2;DP=987;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:1010,78,0:0,0,3,23 chr1 15541407 . C T 560.27 PASS AC=1;AF=0.646;AN=2;DP=1376;MQ=60;set=variant-variant4-variant6-variant9-variant11-variant12-variant13-variant15-variant18-variant19-variant21-variant22-variant23-variant24-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:35,30:65:99:718,0,936:23,12,18,12 chr1 15541537 . C T 2883.29 PASS AC=2;AF=0.955;AN=2;DP=4942;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,140:140:99:4576,420,0:0,0,85,55 chr1 15545581 . G A 244.15 PASS AC=1;AF=0.5;AN=2;DP=136;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant12-variant17-variant21-variant25-variant31-variant32-variant35 GT:AD:DP:GQ:PL:SB 0/1:7,10:17:99:219,0,256:7,0,6,4 chr1 15546077 . G A 3812.81 PASS AC=1;AF=0.643;AN=2;DP=6677;MQ=60;set=variant-variant3-variant6-variant7-variant10-variant12-variant13-variant14-variant16-variant17-variant21-variant23-variant25-variant26-variant31-variant32-variant35-variant37-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:155,193:348:99:4847,0,4015:66,89,73,120 chr1 15546761 . G A 474.44 PASS AC=1;AF=0.643;AN=2;DP=1494;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant11-variant13-variant15-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:30,26:56:99:711,0,761:16,14,13,13 chr1 15546825 . A G 650.37 PASS AC=1;AF=0.75;AN=2;DP=2191;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:28,26:54:99:819,0,829:15,13,17,9 chr1 15546872 . CAAA CA,CAA,C 1341.68 PASS AC=0,1,0;AF=0.341,0.466,0.011;AN=2;DP=3897;set=Intersection GT:DP:GQ:SB 0/2:77:99:15,10,37,15 chr1 15573689 . A G 198.47 PASS AC=1;AF=0.652;AN=2;DP=258;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant7-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant26-variant27-variant30-variant34-variant35-variant36-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:7,9:16:99:316,0,264:5,2,6,3 chr1 15573699 . A AC 60.81 PASS AC=1;AF=0.667;AN=2;DP=207;MQ=60;set=variant-variant2-variant6-variant9-variant10-variant11-variant17-variant19-variant20-variant25-variant28-variant29-variant31-variant32-variant35-variant37-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,6:15:99:151,0,360:6,3,4,2 chr1 15573711 . C A 256.63 PASS AC=1;AF=0.63;AN=2;DP=363;MQ=60;set=variant-variant4-variant5-variant7-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant26-variant27-variant30-variant33-variant34-variant35-variant36-variant37-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,8:16:99:312,0,292:5,3,6,2 chr1 15573758 . G A 323.62 PASS AC=1;AF=0.621;AN=2;DP=593;MQ=60;set=variant-variant4-variant5-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant30-variant33-variant34-variant35-variant36-variant37-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,18:29:99:723,0,408:6,5,11,7 chr1 15573769 . G A 501.51 PASS AC=1;AF=0.621;AN=2;DP=670;MQ=60;set=variant-variant4-variant5-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant30-variant33-variant34-variant35-variant36-variant37-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,20:32:99:783,0,444:7,5,11,9 chr1 15573775 . A G 498.51 PASS AC=1;AF=0.683;AN=2;DP=740;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant30-variant33-variant34-variant35-variant36-variant37-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,20:31:99:783,0,444:6,5,11,9 chr1 15573950 . A C 651.37 PASS AC=1;AF=0.621;AN=2;DP=1527;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant30-variant33-variant34-variant35-variant36-variant37-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:41,30:71:99:614,0,849:18,23,15,15 chr1 15574076 . C T 137.09 PASS AC=1;AF=0.625;AN=2;DP=510;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant30-variant33-variant35-variant36-variant37-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:10,9:19:99:226,0,250:3,7,2,7 chr1 15578195 . T C 299.56 PASS AC=1;AF=0.672;AN=2;DP=1032;MQ=60;set=variant-variant4-variant5-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant30-variant33-variant34-variant35-variant36-variant37-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:14,16:30:99:490,0,466:11,3,12,4 chr1 15650784 . T G 151.12 PASS AC=1;AF=0.553;AN=2;DP=327;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant6-variant8-variant9-variant12-variant18-variant20-variant21-variant24-variant25-variant26-variant31-variant32-variant33-variant35-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,9:18:99:328,0,722:9,0,6,3 chr1 15650791 . G C 151.12 PASS AC=1;AF=0.55;AN=2;DP=389;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant6-variant8-variant9-variant12-variant18-variant20-variant21-variant22-variant24-variant25-variant26-variant31-variant32-variant33-variant35-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,10:21:99:402,0,754:11,0,7,3 chr1 15651062 . A G 564.77 PASS AC=1;AF=0.55;AN=2;DP=885;MQ=60;set=variant2-variant3-variant6-variant8-variant9-variant12-variant18-variant20-variant21-variant22-variant24-variant25-variant26-variant31-variant32-variant33-variant35-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:24,33:57:99:896,0,624:7,17,9,24 chr1 15653503 . A G 480.96 PASS AC=1;AF=0.55;AN=2;DP=784;MQ=60;set=variant2-variant3-variant6-variant8-variant9-variant12-variant18-variant20-variant21-variant22-variant24-variant25-variant26-variant31-variant32-variant33-variant35-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:30,26:56:99:636,0,744:18,12,16,10 chr1 15653563 . C T 1045.55 PASS AC=1;AF=0.525;AN=2;DP=1348;MQ=60;set=variant2-variant3-variant6-variant8-variant9-variant12-variant18-variant20-variant21-variant22-variant24-variant25-variant26-variant31-variant32-variant33-variant35-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:45,32:77:99:858,0,1224:26,19,16,16 chr1 15653872 . G A 370.25 PASS AC=1;AF=0.525;AN=2;DP=400;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant6-variant8-variant9-variant12-variant18-variant20-variant21-variant22-variant24-variant25-variant26-variant31-variant32-variant33-variant35-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,6:14:99:187,0,324:0,8,1,5 chr1 15654737 . C CT 306.91 PASS AC=1;AF=0.5;AN=2;DP=873;set=variant2-variant3-variant6-variant8-variant9-variant12-variant18-variant20-variant21-variant22-variant24-variant25-variant26-variant31-variant32-variant33-variant35-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:26,17:43:99:291,0,490:12,14,9,8 chr1 15668276 . G A 700.08 PASS AC=1;AF=0.554;AN=2;DP=1736;MQ=60;set=variant-variant2-variant3-variant6-variant8-variant9-variant10-variant12-variant13-variant15-variant18-variant20-variant21-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,30:71:99:627,0,982:25,16,15,15 chr1 15701350 . T G 264.12 PASS AC=1;AF=0.605;AN=2;DP=241;FractionInformativeReads=1;set=variant4-variant10-variant11-variant16-variant17-variant20-variant23-variant24-variant25-variant26-variant29-variant30-variant35-variant36-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,9:16:99:357,0,616:2,5,3,6 chr1 15701356 . G T,C 407.33 PASS AC=0,1;AF=0.5,0.308;AN=2;DP=393;set=variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:15:99:2,4,3,6 chr1 15701359 . TG T 187.58 PASS AC=1;AF=0.607;AN=2;DP=160;set=variant10-variant11-variant16-variant17-variant20-variant24-variant25-variant26-variant30-variant35-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,9:15:99:360,0,574:2,4,3,6 chr1 15702297 . T G 248 PASS AC=1;AF=0.563;AN=2;DP=910;MQ=60;set=variant-variant4-variant10-variant11-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,24:41:99:620,0,396:5,12,8,16 chr1 15707984 . G A 673.39 PASS AC=1;AF=0.571;AN=2;DP=803;FractionInformativeReads=1;MQ=60;set=variant4-variant10-variant11-variant16-variant17-variant20-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,15:28:99:405,0,381:3,10,4,11 chr1 15708540 . A G 1108.46 PASS AC=1;AF=0.563;AN=2;DP=3591;MQ=60;set=variant-variant4-variant10-variant11-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:75,87:162:99:2261,0,2007:42,33,46,41 chr1 15709555 . A G 1497.12 PASS AC=1;AF=0.571;AN=2;DP=3105;MQ=60;set=variant4-variant10-variant11-variant16-variant17-variant20-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:83,82:165:99:2093,0,2119:42,41,48,34 chr1 15710113 . C G 150.19 PASS AC=1;AF=0.583;AN=2;DP=163;FractionInformativeReads=1;MQ=60;set=variant4-variant16-variant17-variant20-variant22-variant23-variant25-variant26-variant29-variant30-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,5:10:99:195,0,115:3,2,5,0 chr1 15710411 . G C 320.37 PASS AC=1;AF=0.563;AN=2;DP=680;MQ=60;set=variant-variant4-variant10-variant11-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,15:28:99:348,0,334:6,7,6,9 chr1 15714842 . G C 161.19 PASS AC=1;AF=0.571;AN=2;DP=445;MQ=60;set=variant4-variant10-variant11-variant16-variant17-variant20-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,3:17:64:64,0,455:9,5,1,2 chr1 15717838 . A G 141.11 PASS AC=1;AF=0.563;AN=2;DP=699;MQ=60;set=variant-variant4-variant10-variant11-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,17:30:99:461,0,305:4,9,5,12 chr1 15724003 . A G 2468.72 PASS AC=1;AF=0.565;AN=2;DP=6098;MQ=60;set=variant4-variant10-variant11-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:173,137:310:99:3179,0,4097:85,88,65,72 chr1 15724033 . A G 4396.34 PASS AC=1;AF=0.786;AN=2;DP=11420;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:167,126:293:99:2936,0,4034:78,89,59,67 chr1 15754484 . T C 2665.99 PASS AC=2;AF=0.881;AN=2;DP=3790;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,100:100:99:2960,299,0:0,0,56,44 chr1 15755676 . G A 1399.45 PASS AC=1;AF=0.553;AN=2;DP=1838;MQ=60;set=variant4-variant6-variant8-variant11-variant17-variant19-variant21-variant22-variant24-variant25-variant28-variant32-variant33-variant35-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,62:112:99:1598,0,1193:33,17,33,29 chr1 15769139 . G A 734.08 PASS AC=1;AF=0.5;AN=2;DP=553;FractionInformativeReads=1;MQ=60;set=variant6-variant15-variant16-variant28-variant32-variant34-variant35-variant37-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:24,33:57:99:921,0,526:9,15,10,23 chr1 15769876 . G GC 1003.81 PASS AC=2;AF=1;AN=2;DP=2512;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:2418,205,0:0,0,41,27 chr1 15770101 . C A 1601.57 PASS AC=1;AF=0.5;AN=2;DP=2037;FractionInformativeReads=1;MQ=60;set=variant4-variant8-variant12-variant16-variant17-variant19-variant21-variant24-variant32-variant33-variant34-variant35-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,59:127:99:1507,0,1796:31,37,23,36 chr1 15772057 . G T 823.41 PASS AC=1;AF=0.587;AN=2;DP=1629;MQ=60;set=variant2-variant4-variant8-variant12-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant29-variant32-variant33-variant34-variant35-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,29:73:99:772,0,1310:32,12,24,5 chr1 15772933 . A G 185.87 PASS AC=1;AF=0.591;AN=2;DP=584;MQ=60;set=variant2-variant4-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,14:30:99:396,0,536:14,2,10,4 chr1 15783096 . GA G 7299.48 PASS AC=2;AF=1;AN=2;DP=6442;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,151:151:99:4301,453,0:0,0,84,67 chr1 15783117 . C CA 8800.99 PASS AC=2;AF=1;AN=2;DP=7708;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,189:189:99:7087,572,0:0,0,106,83 chr1 15783553 . T TG 4080.93 PASS AC=1;AF=0.5;AN=2;DP=3008;set=variant8-variant12-variant17-variant21-variant32-variant33-variant34-variant35-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:140,153:293:99:4834,0,4361:73,67,83,70 chr1 15788269 . A C 4645.38 PASS AC=1;AF=0.841;AN=2;DP=8342;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:103,110:213:99:2585,0,2455:51,52,54,56 chr1 15788491 . C T 284.61 PASS AC=1;AF=0.594;AN=2;DP=927;FractionInformativeReads=1;MQ=60;set=variant8-variant12-variant17-variant18-variant21-variant22-variant25-variant29-variant32-variant33-variant34-variant35-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,25:66:99:519,0,1137:21,20,14,11 chr1 15788630 . G A 75.15 PASS AC=1;AF=0.6;AN=2;DP=443;FractionInformativeReads=1;set=variant8-variant12-variant17-variant18-variant21-variant22-variant25-variant29-variant32-variant33-variant35-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,19:43:99:475,0,629:7,17,7,12 chr1 15788693 . C T 81.16 PASS AC=1;AF=0.607;AN=2;DP=126;FractionInformativeReads=1;set=variant8-variant12-variant17-variant18-variant21-variant22-variant25-variant29-variant32-variant33-variant35-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:5,3:8:99:111,0,194:0,5,0,3 chr1 15789176 . C T 1354.16 PASS AC=1;AF=0.594;AN=2;DP=1763;FractionInformativeReads=1;set=variant8-variant12-variant17-variant18-variant21-variant22-variant25-variant29-variant32-variant33-variant34-variant35-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,83:148:99:2334,0,1562:42,23,62,21 chr1 15789297 . A C 9700.68 PASS AC=1;AF=0.596;AN=2;DP=9760;set=variant2-variant3-variant4-variant8-variant10-variant12-variant13-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant32-variant33-variant34-variant35-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:189,219:408:99:5336,0,4286:95,94,115,104 chr1 15798603 . T G 893.02 PASS AC=1;AF=0.5;AN=2;DP=87;FS=1.772;FractionInformativeReads=1;MQ=60;MQRankSum=1.489;QD=10.26;ReadPosRankSum=0.183;SOR=0.993;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:48,39:87:99:921,0,1201:23,25,16,23 chr1 15808198 . C T 277.61 PASS AC=2;AF=0.529;AN=2;DP=399;FractionInformativeReads=1;set=variant8-variant14-variant15-variant16-variant20-variant21-variant22-variant23-variant28-variant31-variant32-variant34-variant35-variant36-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:1082,90,0:0,0,7,23 chr1 15808702 . C T 1180.25 PASS AC=2;AF=0.529;AN=2;DP=1380;MQ=60;set=variant8-variant14-variant15-variant16-variant20-variant21-variant22-variant23-variant28-variant31-variant32-variant34-variant35-variant36-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,98:98:99:3273,294,0:0,0,71,27 chr1 15808767 . G A 2976.57 PASS AC=2;AF=0.529;AN=2;DP=3998;MQ=60;set=variant8-variant14-variant15-variant16-variant20-variant21-variant22-variant23-variant28-variant31-variant32-variant34-variant35-variant36-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,265:265:99:7746,791,0:0,0,161,104 chr1 15808872 . G A 3193.08 PASS AC=2;AF=0.529;AN=2;DP=4849;set=variant8-variant14-variant15-variant16-variant20-variant21-variant22-variant23-variant28-variant31-variant32-variant34-variant35-variant36-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,266:267:99:7681,786,0:1,0,112,154 chr1 15809876 . G A 3003.6 PASS AC=2;AF=0.529;AN=2;DP=4478;set=variant8-variant14-variant15-variant16-variant20-variant21-variant22-variant23-variant28-variant31-variant32-variant34-variant35-variant36-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,348:348:99:10504,1038,0:0,0,191,157 chr1 15812432 . A G 1228.22 PASS AC=2;AF=1;AN=2;DP=3887;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,90:90:99:2906,269,0:0,0,61,29 chr1 15813751 . C T 5974.7 PASS AC=2;AF=1;AN=2;DP=8587;FS=0;MQRankSum=1.31;ReadPosRankSum=0.76;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,241:241:99:7515,721,0:0,0,159,82 chr1 15813969 . A C 3785.15 PASS AC=2;AF=0.758;AN=2;DP=3238;set=variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,129:129:99:4470,387,0:0,0,31,98 chr1 15817334 . G A 53.54 PASS AC=2;AF=0.917;AN=2;DP=17;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.026;ReadPosRankSum=-1.026;set=variant19-variant28-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:135,9,0:0,0,3,0 chr1 15819768 . C A 1160.36 PASS AC=2;AF=0.758;AN=2;DP=1047;MQ=60;set=variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:1648,162,0:0,0,32,22 chr1 15820041 . C T 986.3 PASS AC=2;AF=0.526;AN=2;DP=1290;MQ=60;set=variant8-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant25-variant28-variant31-variant32-variant34-variant35-variant36-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:2281,229,0:0,0,36,41 chr1 15820576 . T A 632.26 PASS AC=2;AF=0.758;AN=2;DP=629;MQ=60;set=variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:567,54,0:0,0,5,13 chr1 15820607 . A G 457.08 PASS AC=2;AF=0.742;AN=2;DP=355;FractionInformativeReads=1;MQ=60;set=variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:226,18,0:0,0,1,5 chr1 15820618 . A G 418.54 PASS AC=2;AF=0.758;AN=2;DP=308;MQ=60;set=variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:229,18,0:0,0,1,5 chr1 15822073 . A G 176.64 PASS AC=2;AF=0.526;AN=2;DP=544;MQ=60;set=variant8-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant25-variant28-variant31-variant32-variant34-variant35-variant36-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,31:31:93:1139,93,0:0,0,6,25 chr1 15832383 . G T 632.26 PASS AC=2;AF=0.742;AN=2;DP=607;MQ=60;set=variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:89:1006,89,0:0,0,23,7 chr1 15832543 . T C 2538 PASS AC=2;AF=0.742;AN=2;DP=3224;MQ=60;set=variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,109:109:99:3218,327,0:0,0,51,58 chr1 15834297 . G A 631.63 PASS AC=2;AF=0.742;AN=2;DP=858;MQ=60;set=variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:77:743,77,0:0,0,19,7 chr1 15834491 . G A 1589.46 PASS AC=2;AF=0.742;AN=2;DP=1529;FractionInformativeReads=1;MQ=60;set=variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,61:61:99:1790,182,0:0,0,24,37 chr1 15844615 . A G 2454.62 PASS AC=2;AF=0.742;AN=2;DP=2329;FractionInformativeReads=1;MQ=60;set=variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,87:87:99:2745,261,0:0,0,58,29 chr1 15844718 . G A 1930.55 PASS AC=1;AF=0.5;AN=2;DP=196;FS=0.531;FractionInformativeReads=0.99;MQ=60;MQRankSum=-0.662;QD=9.85;ReadPosRankSum=3.138;SOR=0.63;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:111,83:194:99:1959,0,2911:58,53,42,41 chr1 15844926 . C T 3375.96 PASS AC=2;AF=0.742;AN=2;DP=3196;MQ=60;set=variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,117:117:99:3666,350,0:0,0,50,67 chr1 15845022 . C CTGAG 2249.87 PASS AC=2;AF=0.742;AN=2;DP=1658;MQ=60;set=variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:2364,162,0:0,0,18,36 chr1 15850483 . G A 106.77 PASS AC=2;AF=0.841;AN=2;DP=174;FS=0;FractionInformativeReads=1;MQ=60;set=variant8-variant10-variant12-variant15-variant16-variant19-variant21-variant22-variant23-variant25-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:291,24,0:0,0,3,5 chr1 15850553 . C CGGGGGCG,CGAGGGCG 187.73 PASS AC=2,0;AF=0.769,0.019;AN=2;DP=295;MQ=60;set=variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant25-variant27-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:DP:GQ:SB 1/1:6:24:0,0,3,3 chr1 15850613 . G A 725.38 PASS AC=2;AF=0.742;AN=2;DP=821;FractionInformativeReads=1;MQ=60;set=variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:572,54,0:0,0,10,8 chr1 15850956 . G C 331.77 PASS AC=2;AF=0.78;AN=2;DP=210;FS=0;FractionInformativeReads=1;set=variant8-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant25-variant27-variant28-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:87,6,0:0,0,0,2 chr1 15851064 . A ATCCCCGCACTGACCTCACG 456.23 PASS AC=2;AF=0.776;AN=2;DP=232;MQ=60;set=variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:35:538,35,0:0,0,2,4 chr1 15853276 . T C 960.31 PASS AC=2;AF=0.526;AN=2;DP=1981;FractionInformativeReads=1;set=variant8-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant25-variant28-variant31-variant32-variant34-variant35-variant36-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,101:101:99:3095,303,0:0,0,59,42 chr1 15853289 . T G 2671.28 PASS AC=2;AF=0.742;AN=2;DP=3467;set=variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,105:106:99:3162,307,0:0,1,56,49 chr1 15853551 . C T 279.56 PASS AC=2;AF=0.529;AN=2;DP=341;FractionInformativeReads=1;MQ=60;set=variant8-variant14-variant15-variant16-variant19-variant21-variant22-variant25-variant28-variant31-variant32-variant34-variant35-variant36-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:1046,90,0:0,0,12,18 chr1 15860563 . T A 273.53 PASS AC=2;AF=0.788;AN=2;DP=241;MQ=60;set=variant8-variant10-variant11-variant12-variant13-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:389,33,0:0,0,9,2 chr1 15873386 . A G 1107.07 PASS AC=2;AF=0.526;AN=2;DP=1784;set=variant8-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant25-variant28-variant31-variant32-variant34-variant35-variant36-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,111:111:99:3102,332,0:0,0,51,60 chr1 15873410 . CTTT CTT,CTTTT,CT,C 70.71 PASS AC=0,0,1,1;AF=0.243,0.014,0.243,0.027;AN=2;DP=2177;set=filterInvariant-variant2-filterInvariant3-variant4-variant5-variant7-variant8-filterInvariant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-filterInvariant26-variant27-variant28-variant29-filterInvariant30-variant31-variant32-filterInvariant33-variant34-variant35-variant39-filterInvariant40-variant41-filterInvariant42 GT:DP:GQ:SB 4/3:52:99:4,0,14,34 chr1 15874961 . T A 1176.39 PASS AC=2;AF=0.526;AN=2;DP=1898;MQ=60;set=variant8-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant25-variant28-variant31-variant32-variant34-variant35-variant36-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,107:107:99:3241,320,0:0,0,37,70 chr1 15890342 . CA C 54.94 PASS AC=2;AF=0.615;AN=2;DP=172;set=filterInvariant7-variant15-variant16-variant19-variant20-variant21-variant22-variant28-variant29-variant31-variant35-variant37-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:46:343,46,0:0,0,14,2 chr1 15894959 . T C 2398.33 PASS AC=2;AF=0.526;AN=2;DP=2943;MQ=60;set=variant8-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant25-variant28-variant31-variant32-variant34-variant35-variant36-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,194:194:99:5838,581,0:0,0,98,96 chr1 15896126 . CTT CT,C,CTTTTT,CTTTT,CTTT 33.93 PASS AC=0,0,0,2,0;AF=0.176,0.059,0.029,0.206,0.088;AN=2;DP=252;MQ=60;set=variant2-variant3-variant9-variant10-filterInvariant12-variant14-variant16-variant19-variant22-variant26-variant31-variant33-variant34-variant35-variant36-variant41-variant44 GT:DP:GQ:SB 4/4:5:16:0,0,2,3 chr1 15897020 . C T 263.9 PASS AC=2;AF=0.526;AN=2;DP=415;FractionInformativeReads=1;MQ=60;set=variant8-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant25-variant28-variant31-variant32-variant34-variant35-variant36-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:604,54,0:0,0,10,8 chr1 15897508 . CA C,CAA 319.56 PASS AC=0,1;AF=0.274,0.226;AN=2;DP=11925;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant7-variant8-filterInvariant9-filterInvariant10-filterInvariant12-filterInvariant13-variant14-variant15-variant16-filterInvariant17-variant18-variant19-variant20-variant21-variant22-variant23-filterInvariant24-variant25-filterInvariant26-filterInvariant27-variant28-filterInvariant29-filterInvariant30-variant31-variant32-filterInvariant33-variant34-variant35-variant36-variant37-filterInvariant38-variant39-filterInvariant40-variant41-filterInvariant42-variant44 GT:DP:GQ:SB 0/2:230:99:24,32,78,96 chr1 15899752 . C CA 170.68 PASS AC=2;AF=0.531;AN=2;DP=350;MQ=60;set=variant8-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant25-variant28-variant31-variant32-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,18:19:34:473,34,0:1,0,18,0 chr1 15906696 . CTT CT,CTTT,CTTTT,C,CTTTTT 100.33 PASS AC=0,0,0,1,0;AF=0.167,0.104,0.125,0.104,0.021;AN=2;DP=1188;set=filterInvariant3-variant5-filterInvariant7-filterInvariant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-filterInvariant21-variant24-filterInvariant27-variant28-variant32-variant34-variant35-variant37-filterInvariant38-variant39-variant40-variant41-filterInvariant43 GT:DP:GQ:SB 0/4:25:99:6,3,0,16 chr1 15909441 . C T 197.99 PASS AC=2;AF=0.875;AN=2;DP=100;FractionInformativeReads=1;MQ=60;set=variant8-variant10-variant12-variant15-variant16-variant19-variant21-variant22-variant26-variant27-variant28-variant31-variant33-variant34-variant35-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:135,9,0:0,0,1,2 chr1 15909547 . G A 772.7 PASS AC=2;AF=0.767;AN=2;DP=603;MQ=60;set=variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:370,33,0:0,0,8,3 chr1 15909624 . TGAGTACAG T 2482.96 PASS AC=2;AF=0.758;AN=2;DP=1631;MQ=60;set=variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1612,108,0:0,0,25,11 chr1 15909850 . C G 2429.36 PASS AC=2;AF=0.758;AN=2;DP=2727;MQ=60;set=variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,107:107:99:3246,321,0:0,0,41,66 chr1 15909895 . A G 1315.96 PASS AC=2;AF=0.758;AN=2;DP=1626;MQ=60;set=variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,52:52:99:1638,154,0:0,0,17,35 chr1 15911010 . T G 1997.24 PASS AC=2;AF=0.758;AN=2;DP=1750;FractionInformativeReads=1;MQ=60;set=variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,61:61:99:2085,183,0:0,0,40,21 chr1 15911031 . T G 2264.77 PASS AC=2;AF=0.758;AN=2;DP=2143;MQ=60;set=variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:2451,227,0:0,0,47,29 chr1 15911349 . G A 884.93 PASS AC=2;AF=0.526;AN=2;DP=1431;MQ=60;set=variant8-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant25-variant28-variant31-variant32-variant34-variant35-variant36-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,101:101:99:3412,302,0:0,0,34,67 chr1 15911493 . A G 1948.36 PASS AC=2;AF=0.758;AN=2;DP=1783;MQ=60;set=variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:2181,194,0:0,0,42,23 chr1 15911597 . A G 3182.06 PASS AC=2;AF=0.758;AN=2;DP=2912;MQ=60;set=variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,111:111:99:3320,332,0:0,0,50,61 chr1 15911622 . A AG 3795.08 PASS AC=2;AF=0.758;AN=2;DP=3011;MQ=60;set=variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,107:107:99:3801,322,0:0,0,46,61 chr1 15911730 . T G 611.85 PASS AC=2;AF=0.526;AN=2;DP=610;FractionInformativeReads=1;MQ=60;set=variant8-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant25-variant28-variant31-variant32-variant34-variant35-variant36-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:856,81,0:0,0,9,18 chr1 15944384 . G A 1024.74 PASS AC=1;AF=0.611;AN=2;DP=2211;MQ=60;set=variant8-variant10-variant12-variant15-variant17-variant19-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:63,61:124:99:1311,0,1599:25,38,27,34 chr1 15956610 . A G 380.03 PASS AC=1;AF=0.611;AN=2;DP=399;FractionInformativeReads=1;MQ=60;set=variant8-variant10-variant12-variant15-variant17-variant19-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,11:21:99:355,0,296:7,3,9,2 chr1 15956769 . G T 1383.1 PASS AC=1;AF=0.636;AN=2;DP=2611;FractionInformativeReads=1;MQ=60;set=variant8-variant10-variant12-variant15-variant17-variant19-variant22-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,53:117:99:1365,0,1472:34,30,31,22 chr1 15959886 . C G 852.99 PASS AC=2;AF=0.758;AN=2;DP=1027;MQ=60;set=variant4-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:781,72,0:0,0,17,7 chr1 15959977 . C T 595.74 PASS AC=1;AF=0.636;AN=2;DP=1640;MQ=60;set=variant8-variant10-variant12-variant15-variant17-variant19-variant22-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,43:83:99:965,0,937:21,19,22,21 chr1 15978553 . CTTTTTTT CTTTTTT,CTTTTT,CT,CTT,CTTT,CTTTTTTTTT,C 60.25 PASS AC=0,0,1,0,0,0,0;AF=0.093,0.056,0.222,0.074,0.074,0.037,0.056;AN=2;DP=663;set=variant-variant5-variant6-variant8-variant12-variant13-variant15-variant17-variant19-variant22-filterInvariant23-variant24-filterInvariant25-variant26-variant27-variant29-variant31-variant33-variant34-variant35-filterInvariant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:DP:GQ:SB 0/3:21:99:2,7,0,12 chr1 15986547 . T C 1388.16 PASS AC=1;AF=0.636;AN=2;DP=3020;MQ=60;set=variant8-variant10-variant12-variant15-variant17-variant19-variant22-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:75,66:141:99:1795,0,1839:28,47,24,42 chr1 15988702 . T C 3405.77 PASS AC=1;AF=0.636;AN=2;DP=4843;MQ=60;set=variant8-variant10-variant12-variant15-variant17-variant19-variant22-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:104,124:228:99:2964,0,2599:49,55,63,61 chr1 15988878 . A G 1336.54 PASS AC=1;AF=0.636;AN=2;DP=1844;MQ=60;set=variant8-variant10-variant12-variant15-variant17-variant19-variant22-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,27:68:99:720,0,1213:12,29,8,19 chr1 15988957 . G A 1092.95 PASS AC=2;AF=0.8;AN=2;DP=1610;MQ=60;set=variant2-variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,38:39:81:1330,81,0:1,0,17,21 chr1 15989141 . C G 728.62 PASS AC=1;AF=0.63;AN=2;DP=1169;FractionInformativeReads=1;MQ=60;set=variant8-variant10-variant12-variant13-variant15-variant17-variant19-variant22-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,33:50:99:910,0,384:9,8,18,15 chr1 15989918 . T C 2900.74 PASS AC=1;AF=0.636;AN=2;DP=5799;MQ=60;set=variant8-variant10-variant12-variant15-variant17-variant19-variant22-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:129,116:245:99:2864,0,3228:56,73,46,70 chr1 15990552 . A G 187.51 PASS AC=1;AF=0.636;AN=2;DP=849;FractionInformativeReads=1;MQ=60;set=variant8-variant10-variant12-variant15-variant17-variant19-variant22-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,32:50:99:859,0,459:7,11,15,17 chr1 15990912 . T C 995.53 PASS AC=1;AF=0.636;AN=2;DP=1010;set=variant8-variant10-variant12-variant15-variant17-variant19-variant22-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,18:41:99:649,0,825:22,1,18,0 chr1 15990929 . CA C 280.18 PASS AC=1;AF=0.5;AN=2;DP=3953;set=variant-variant2-variant3-variant4-variant5-filterInvariant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-filterInvariant14-variant15-filterInvariant16-filterInvariant17-variant18-filterInvariant19-filterInvariant20-filterInvariant21-variant22-variant23-variant24-filterInvariant25-variant26-variant27-variant28-variant29-filterInvariant30-variant31-variant32-variant33-filterInvariant34-filterInvariant35-variant36-filterInvariant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,16:65:99:169,0,826:34,15,14,2 chr1 15990983 . T G 2663.97 PASS AC=1;AF=0.63;AN=2;DP=4747;MQ=60;set=variant8-variant10-variant12-variant13-variant15-variant17-variant19-variant22-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:103,90:193:99:2192,0,2636:62,41,56,34 chr1 15992469 . AG A 1435.18 PASS AC=1;AF=0.594;AN=2;DP=1357;MQ=60;set=variant8-variant10-variant15-variant19-variant26-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,33:69:99:1122,0,1246:23,13,21,12 chr1 15993208 . G C 1360.57 PASS AC=1;AF=0.643;AN=2;DP=3049;FractionInformativeReads=1;MQ=60;set=variant8-variant10-variant12-variant15-variant17-variant19-variant22-variant26-variant27-variant29-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:79,66:145:99:1673,0,2063:36,43,27,39 chr1 15993338 . A G 714.13 PASS AC=2;AF=0.729;AN=2;DP=2199;MQ=60;set=variant4-variant5-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,69:69:99:2065,206,0:0,0,24,45 chr1 15993699 . C CA,CAA 119.19 PASS AC=1,0;AF=0.5,0.028;AN=2;DP=429;set=variant4-variant5-variant8-variant14-variant15-variant16-variant20-variant22-variant24-variant25-variant27-variant28-variant31-variant32-variant34-variant35-variant36-variant37 GT:DP:GQ:SB 0/1:27:99:13,5,8,1 chr1 15993713 . A AT,ATT 306.08 PASS AC=1,0;AF=0.625,0.025;AN=2;DP=757;set=variant8-variant10-variant12-variant15-variant17-variant19-variant22-variant26-variant27-variant29-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:DP:GQ:SB 0/1:43:99:15,6,15,7 chr1 16011005 . GGGC GGGCGGC,G 1973.66 PASS AC=2,0;AF=0.714,0.014;AN=2;DP=3203;set=variant4-variant5-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:DP:GQ:SB 1/1:127:99:0,0,84,43 chr1 16011192 . G GGCGACCCTGCTGCCGCAGGGACTC 1251.71 PASS AC=1;AF=0.643;AN=2;DP=1840;MQ=60;set=variant8-variant10-variant12-variant13-variant15-variant17-variant19-variant22-variant26-variant27-variant29-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,64:103:99:2487,0,2271:12,27,19,45 chr1 16042724 . TC T 391.02 PASS AC=1;AF=0.583;AN=2;DP=2090;MQ=60;set=variant8-variant10-variant12-variant15-variant17-variant19-variant26-variant29-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:80,41:121:99:723,0,2595:44,36,21,20 chr1 16042766 . T C 874.28 PASS AC=1;AF=0.643;AN=2;DP=2503;MQ=60;set=variant8-variant10-variant12-variant13-variant15-variant17-variant19-variant22-variant26-variant27-variant29-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,62:116:99:1515,0,1567:23,31,27,35 chr1 16043157 . G A 1082.84 PASS AC=1;AF=0.611;AN=2;DP=1304;MQ=60;set=variant8-variant10-variant12-variant15-variant17-variant19-variant26-variant29-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:63,47:110:99:1052,0,1438:38,25,30,17 chr1 16044401 . G A 898.55 PASS AC=1;AF=0.611;AN=2;DP=1161;FractionInformativeReads=1;MQ=60;set=variant8-variant10-variant12-variant15-variant17-variant19-variant26-variant29-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,36:62:99:993,0,734:19,7,25,11 chr1 16044807 . C G 411.6 PASS AC=1;AF=0.611;AN=2;DP=525;FractionInformativeReads=1;MQ=60;set=variant8-variant10-variant12-variant15-variant17-variant19-variant26-variant29-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,17:33:99:448,0,508:12,4,10,7 chr1 16044929 . A G 1378.97 PASS AC=1;AF=0.611;AN=2;DP=2447;MQ=60;set=variant8-variant10-variant12-variant15-variant17-variant19-variant26-variant29-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,69:133:99:1649,0,1528:36,28,39,30 chr1 16044945 . G A 1451.1 PASS AC=1;AF=0.643;AN=2;DP=3106;MQ=60;set=variant8-variant10-variant12-variant13-variant15-variant17-variant19-variant22-variant26-variant27-variant29-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:66,73:139:99:1668,0,1578:37,29,40,33 chr1 16047726 . T C 403.84 PASS AC=1;AF=0.643;AN=2;DP=783;FractionInformativeReads=1;MQ=60;set=variant8-variant10-variant12-variant13-variant15-variant17-variant19-variant22-variant26-variant27-variant29-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,15:28:99:424,0,299:8,5,13,2 chr1 16048005 . A G 184.4 PASS AC=1;AF=0.643;AN=2;DP=373;FractionInformativeReads=1;MQ=60;set=variant8-variant10-variant12-variant13-variant15-variant17-variant19-variant22-variant26-variant27-variant29-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,12:27:99:294,0,370:5,10,4,8 chr1 16048038 . T C 164.93 PASS AC=1;AF=0.65;AN=2;DP=204;MQ=60;set=variant8-variant10-variant12-variant13-variant15-variant17-variant19-variant22-variant26-variant27-variant29-variant32-variant33-variant35-variant36-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,7:16:99:226,0,267:2,7,1,6 chr1 16051584 . C T 731.65 PASS AC=2;AF=0.989;AN=2;DP=859;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.615;ReadPosRankSum=1.418;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:434,45,0:0,0,9,6 chr1 16053493 . G A 1999.92 PASS AC=1;AF=0.6;AN=2;DP=1454;MQ=60;set=variant2-variant3-variant4-variant10-variant12-variant13-variant16-variant21-variant24-variant26-variant29-variant32-variant33-variant35-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,31:79:99:762,0,1406:27,21,17,14 chr1 16055039 . C T 767.95 PASS AC=1;AF=0.611;AN=2;DP=462;MQ=60;set=variant2-variant3-variant4-variant10-variant13-variant16-variant21-variant24-variant26-variant29-variant32-variant33-variant35-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,16:39:99:428,0,680:18,5,12,4 chr1 16055732 . C T 3077.67 PASS AC=1;AF=0.6;AN=2;DP=2111;MQ=60;set=variant2-variant3-variant4-variant10-variant12-variant13-variant16-variant21-variant24-variant26-variant29-variant32-variant33-variant35-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,68:115:99:1652,0,1073:19,28,25,43 chr1 16056364 . G A 3131.37 PASS AC=1;AF=0.6;AN=2;DP=2485;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant10-variant12-variant13-variant16-variant21-variant24-variant26-variant29-variant32-variant33-variant35-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,70:135:99:1682,0,1470:25,40,27,43 chr1 16058698 . CA C 1939.46 PASS AC=1;AF=0.6;AN=2;DP=1036;MQ=60;set=variant2-variant3-variant4-variant10-variant12-variant13-variant16-variant21-variant24-variant26-variant29-variant32-variant33-variant35-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,43:72:99:1431,0,891:11,18,16,27 chr1 16060678 . T C 3068.81 PASS AC=1;AF=0.6;AN=2;DP=2179;MQ=60;set=variant2-variant3-variant4-variant10-variant12-variant13-variant16-variant21-variant24-variant26-variant29-variant32-variant33-variant35-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,47:103:99:1221,0,1408:27,29,25,22 chr1 16061035 . G C 2830.3 PASS AC=1;AF=0.6;AN=2;DP=1732;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant10-variant12-variant13-variant16-variant21-variant24-variant26-variant29-variant32-variant33-variant35-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,44:92:99:1153,0,1094:22,26,25,19 chr1 16064411 . T C 3808.66 PASS AC=1;AF=0.6;AN=2;DP=2659;MQ=60;set=variant2-variant3-variant4-variant10-variant12-variant13-variant16-variant21-variant24-variant26-variant29-variant32-variant33-variant35-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:91,92:183:99:2136,0,2259:55,36,55,37 chr1 16065276 . AAC A,AACAC 541.8 PASS AC=1,0;AF=0.56,0.02;AN=2;DP=849;set=variant2-variant3-variant4-variant10-filterInvariant11-variant12-variant16-filterInvariant18-filterInvariant20-variant21-variant24-filterInvariant25-variant26-variant29-variant31-variant32-variant33-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:15:99:1,5,3,6 chr1 16065303 . ACACACT A 553.84 PASS AC=1;AF=0.63;AN=2;DP=647;set=variant4-variant5-variant8-variant10-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,6:10:99:240,0,140:1,3,1,5 chr1 16067710 . C T 2550.93 PASS AC=1;AF=0.5;AN=2;DP=595;MQ=60;set=variant15-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:134,105:239:99:2280,0,3458:60,74,49,56 chr1 16069644 . C T 3350.13 PASS AC=1;AF=0.682;AN=2;DP=2409;MQ=60;set=variant2-variant3-variant4-variant7-variant10-variant11-variant12-variant16-variant20-variant21-variant24-variant26-variant29-variant30-variant33-variant35-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,79:143:99:1985,0,1503:23,41,32,47 chr1 16074468 . T A 1287.68 PASS AC=1;AF=0.66;AN=2;DP=1399;MQ=60;set=variant2-variant3-variant4-variant7-variant10-variant11-variant12-variant13-variant16-variant20-variant21-variant23-variant24-variant26-variant29-variant30-variant32-variant33-variant35-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,28:53:99:745,0,637:9,16,9,19 chr1 16074494 . C T 1854.95 PASS AC=1;AF=0.65;AN=2;DP=948;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant12-variant16-variant20-variant21-variant23-variant24-variant26-variant30-variant32-variant33-variant35-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,25:47:99:707,0,581:7,15,6,19 chr1 16094266 . G A 169.45 PASS AC=1;AF=0.5;AN=2;DP=10;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.044;QD=16.94;ReadPosRankSum=0;SOR=0.525;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:1,9:10:16:198,0,16:1,0,4,5 chr1 16095316 . C T 31.67 PASS AC=2;AF=0.737;AN=2;DP=474;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:897,72,0:0,0,4,20 chr1 16096934 . C T 863.91 PASS AC=2;AF=0.731;AN=2;DP=2257;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:1925,175,0:0,0,43,16 chr1 16097237 . G A 144.7 PASS AC=2;AF=0.798;AN=2;DP=1558;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:1021,84,0:0,0,8,20 chr1 16112795 . A G 2442.09 PASS AC=2;AF=0.671;AN=2;DP=3612;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant21-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,120:120:99:3723,360,0:0,0,55,65 chr1 16133838 . A T 1597.2 PASS AC=2;AF=0.571;AN=2;DP=656;FractionInformativeReads=1;MQ=60;set=variant7-variant13-variant17-variant34-variant35-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,92:92:99:3149,274,0:0,0,44,48 chr1 16133987 . T C 2076.03 PASS AC=2;AF=0.571;AN=2;DP=1324;FractionInformativeReads=1;set=variant7-variant13-variant17-variant34-variant35-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,199:199:99:6183,597,0:0,0,108,91 chr1 16134072 . C T 2243.61 PASS AC=2;AF=0.571;AN=2;DP=1495;set=variant7-variant13-variant17-variant34-variant35-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,239:239:99:6977,713,0:0,0,117,122 chr1 16256007 . T C 541.63 PASS AC=2;AF=0.677;AN=2;DP=1607;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant9-variant12-variant13-variant14-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1190,117,0:0,0,25,14 chr1 16259813 . A G 1062.13 PASS AC=2;AF=0.677;AN=2;DP=4117;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant9-variant12-variant13-variant14-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,176:177:99:5406,493,0:1,0,89,87 chr1 16263452 . A G 82.47 PASS AC=2;AF=0.692;AN=2;DP=242;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant9-variant12-variant13-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:485,36,0:0,0,11,1 chr1 16265060 . CTTT CTT,CT,C 252.48 PASS AC=1,0,0;AF=0.268,0.232,0.054;AN=2;DP=501;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant12-variant15-variant18-variant20-variant22-variant23-variant24-variant25-variant27-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant44 GT:DP:GQ:SB 0/1:17:76:8,2,5,2 chr1 16265422 . A G 87.15 PASS AC=2;AF=0.677;AN=2;DP=2408;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant9-variant12-variant13-variant14-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,90:90:99:2654,269,0:0,0,36,54 chr1 16265904 . T A 1913.33 PASS AC=2;AF=0.625;AN=2;DP=738;MQ=60;set=variant7-variant17-variant35-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,186:186:99:5665,556,0:0,0,101,85 chr1 16267040 . A C 493.45 PASS AC=2;AF=0.683;AN=2;DP=1045;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant9-variant12-variant13-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1486,111,0:0,0,4,33 chr1 16269477 . T TG 161.31 PASS AC=2;AF=0.583;AN=2;DP=204;MQ=60;set=variant7-variant17-variant18-variant35-variant40-variant42 GT:AD:DP:GQ:PL:SB 1/1:1,42:43:99:1306,105,0:1,0,31,11 chr1 16269737 . C T 1330.2 PASS AC=2;AF=0.625;AN=2;DP=356;FractionInformativeReads=1;MQ=60;set=variant7-variant17-variant35-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,97:97:99:2819,289,0:0,0,40,57 chr1 16333569 . T G 2299.25 PASS AC=2;AF=0.932;AN=2;DP=3675;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:2617,237,0:0,0,28,51 chr1 16333743 . CA C 170.9 PASS AC=1;AF=0.529;AN=2;DP=737;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant17-variant18-filterInvariant19-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-filterInvariant35-variant36-variant37-variant38-variant39-variant41-variant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:17,6:23:77:77,0,369:11,6,3,3 chr1 16340460 . G T 302.94 PASS AC=2;AF=0.731;AN=2;DP=1084;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:742,60,0:0,0,15,5 chr1 16340761 . T C 768.32 PASS AC=2;AF=0.731;AN=2;DP=3502;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,107:107:99:3354,321,0:0,0,49,58 chr1 16340843 . TC T 1176.42 PASS AC=2;AF=0.775;AN=2;DP=2123;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1643,159,0:0,0,26,27 chr1 16340879 . T G 1175.45 PASS AC=2;AF=0.763;AN=2;DP=1823;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1493,150,0:0,0,20,30 chr1 16340951 . A T 866.65 PASS AC=2;AF=0.775;AN=2;DP=1652;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1150,105,0:0,0,12,23 chr1 16341342 . C A 1347.05 PASS AC=2;AF=0.625;AN=2;DP=418;MQ=60;set=variant7-variant17-variant35-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,111:111:99:3609,331,0:0,0,53,58 chr1 16341354 . T G 1328.31 PASS AC=2;AF=0.731;AN=2;DP=3617;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,116:116:99:3816,348,0:0,0,57,59 chr1 16341560 . G T 957.92 PASS AC=2;AF=0.625;AN=2;DP=275;FractionInformativeReads=1;MQ=60;set=variant7-variant17-variant35-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,85:85:99:2759,255,0:0,0,38,47 chr1 16341649 . C T,G 545.24 PASS AC=2,0;AF=0.628,0.103;AN=2;DP=2378;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:71:99:0,0,38,33 chr1 16341733 . T C 894.05 PASS AC=2;AF=0.731;AN=2;DP=2578;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,73:73:99:2500,219,0:0,0,41,32 chr1 16342237 . A G 765.02 PASS AC=2;AF=0.731;AN=2;DP=2863;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,69:69:99:2019,207,0:0,0,30,39 chr1 16344360 . A G 1163.2 PASS AC=2;AF=0.744;AN=2;DP=5256;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,137:137:99:4315,409,0:0,0,76,61 chr1 16344402 . G A 1576 PASS AC=2;AF=0.731;AN=2;DP=6046;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,157:157:99:4822,469,0:0,0,87,70 chr1 16344494 . G A 1814.37 PASS AC=2;AF=0.731;AN=2;DP=5928;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,185:185:99:5418,553,0:0,0,90,95 chr1 16344625 . C G 870.46 PASS AC=2;AF=0.75;AN=2;DP=3392;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,116:116:99:3668,347,0:0,0,50,66 chr1 16344730 . T C 1292.08 PASS AC=2;AF=0.775;AN=2;DP=2810;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,83:83:99:2679,249,0:0,0,40,43 chr1 16344827 . G A 930.01 PASS AC=2;AF=0.625;AN=2;DP=453;FractionInformativeReads=1;MQ=60;set=variant7-variant17-variant35-variant40 GT:AD:DP:GQ:PL:SB 1/1:1,113:114:99:3395,294,0:0,1,52,61 chr1 16344858 . C T 1104.04 PASS AC=2;AF=0.737;AN=2;DP=4087;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,116:116:99:3374,347,0:0,0,54,62 chr1 16345208 . G A 703.75 PASS AC=2;AF=0.75;AN=2;DP=2444;set=variant-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1598,153,0:0,0,24,27 chr1 16345393 . T C 120.71 PASS AC=2;AF=0.817;AN=2;DP=233;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant26-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:38:399,38,0:0,0,6,7 chr1 16345619 . T C 726.7 PASS AC=2;AF=0.75;AN=2;DP=2928;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,92:92:99:3083,276,0:0,0,64,28 chr1 16348412 . T C 1720.79 PASS AC=2;AF=0.775;AN=2;DP=1961;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,74:74:99:2194,221,0:0,0,39,35 chr1 16350028 . A G 236.43 PASS AC=2;AF=0.792;AN=2;DP=411;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:225,15,0:0,0,4,1 chr1 16350123 . C G 223.62 PASS AC=2;AF=0.75;AN=2;DP=1219;set=variant-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1263,120,0:0,0,26,14 chr1 16350262 . A G 800.28 PASS AC=2;AF=0.6;AN=2;DP=479;FractionInformativeReads=1;MQ=60;set=variant7-variant13-variant17-variant35-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,78:78:99:2692,234,0:0,0,47,31 chr1 16351275 . A G 99.4 PASS AC=2;AF=0.75;AN=2;DP=1297;set=variant-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1175,104,0:0,0,23,12 chr1 16353400 . T C 1909.22 PASS AC=2;AF=0.763;AN=2;DP=1718;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:2148,177,0:0,0,11,48 chr1 16353482 . A G 560.68 PASS AC=2;AF=0.577;AN=2;DP=283;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant7-variant13-variant17-variant22-variant25-variant30-variant32-variant33-variant35-variant40 GT:AD:DP:GQ:PL:SB 1/1:1,16:17:9:591,9,0:1,0,7,9 chr1 16354590 . A T 737.34 PASS AC=2;AF=0.55;AN=2;DP=1134;set=variant-variant2-variant7-variant13-variant17-variant22-variant25-variant32-variant35-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,111:111:99:3180,331,0:0,0,42,69 chr1 16355525 . G A 1075.44 PASS AC=2;AF=0.6;AN=2;DP=572;set=variant7-variant13-variant17-variant35-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,80:80:99:2847,240,0:0,0,24,56 chr1 16355577 . TGGG T,TGGGG 664.44 PASS AC=2,0;AF=0.417,0.167;AN=2;DP=715;set=variant7-variant17-variant18-variant35-variant40-variant42 GT:DP:GQ:SB 1/1:48:99:1,0,19,28 chr1 16355614 . G A 664.7 PASS AC=2;AF=0.6;AN=2;DP=739;set=variant7-filterInvariant13-variant17-variant35-variant40 GT:AD:DP:GQ:PL:SB 1/1:2,76:78:99:2705,152,0:2,0,45,31 chr1 16355877 . G A 2445.65 PASS AC=2;AF=0.6;AN=2;DP=1016;MQ=60;set=variant7-variant13-variant17-variant35-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,201:201:99:6041,599,0:0,0,68,133 chr1 16356187 . C T 1368.1 PASS AC=2;AF=0.6;AN=2;DP=534;MQ=60;set=variant7-variant13-variant17-variant35-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,122:122:99:3598,365,0:0,0,73,49 chr1 16356497 . C G 1487.1 PASS AC=2;AF=0.6;AN=2;DP=460;FractionInformativeReads=1;set=variant7-variant13-variant17-variant35-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,89:89:99:3949,273,0:0,0,46,43 chr1 16356501 . G A 638.79 PASS AC=2;AF=0.757;AN=2;DP=3167;set=variant-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,90:90:99:3925,270,0:0,0,47,43 chr1 16356522 . A G 2357.98 PASS AC=2;AF=0.6;AN=2;DP=481;FractionInformativeReads=1;set=variant7-variant13-variant17-variant35-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,90:90:99:3973,270,0:0,0,40,50 chr1 16356531 . G A 2360.84 PASS AC=2;AF=0.6;AN=2;DP=477;FractionInformativeReads=1;set=variant7-variant13-variant17-variant35-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,89:89:99:4053,274,0:0,0,40,49 chr1 16356533 . T C 2317.38 PASS AC=2;AF=0.6;AN=2;DP=484;FractionInformativeReads=1;set=variant7-variant13-variant17-variant35-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,88:88:99:4004,268,0:0,0,40,48 chr1 16356915 . C G 284.89 PASS AC=2;AF=0.6;AN=2;DP=101;FractionInformativeReads=1;MQ=60;set=variant7-variant13-variant17-variant35-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:717,60,0:0,0,15,5 chr1 16357147 . C T 908.1 PASS AC=2;AF=0.6;AN=2;DP=676;set=variant7-variant13-variant17-variant35-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,138:138:99:4125,413,0:0,0,64,74 chr1 16358085 . C A 1318.95 PASS AC=2;AF=0.6;AN=2;DP=380;FractionInformativeReads=1;set=variant7-variant13-variant17-variant35-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:2951,236,0:0,0,66,13 chr1 16358134 . T C 2789.49 PASS AC=2;AF=0.6;AN=2;DP=1028;MQ=60;set=variant7-variant13-variant17-variant35-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,220:220:99:10015,689,0:0,0,141,79 chr1 16358148 . T C 5555.14 PASS AC=2;AF=0.782;AN=2;DP=8852;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,267:267:99:11214,803,0:0,0,164,103 chr1 16358520 . T C 308.11 PASS AC=2;AF=0.587;AN=2;DP=728;FractionInformativeReads=1;set=variant2-variant5-variant7-variant8-variant9-variant12-variant13-variant14-variant17-variant18-variant21-variant22-variant23-variant24-variant26-variant27-variant30-variant31-variant35-variant37-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1314,108,0:0,0,27,9 chr1 16358932 . T C 3158.63 PASS AC=2;AF=0.782;AN=2;DP=7518;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,235:235:99:6634,702,0:0,0,136,99 chr1 16359051 . C A 800.37 PASS AC=2;AF=0.757;AN=2;DP=5333;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,186:186:99:8172,562,0:0,0,74,112 chr1 16359052 . A G 2029.15 PASS AC=2;AF=0.943;AN=2;DP=6206;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:3,180:183:99:5304,461,0:2,1,70,110 chr1 16359123 . A G 480.75 PASS AC=2;AF=0.782;AN=2;DP=1569;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1479,107,0:0,0,2,34 chr1 16359951 . C T 491.49 PASS AC=2;AF=0.6;AN=2;DP=200;FractionInformativeReads=1;set=variant7-variant13-variant17-variant35-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1328,120,0:0,0,22,18 chr1 16360053 . CT C 529.55 PASS AC=2;AF=0.7;AN=2;DP=194;set=variant7-variant13-variant17-variant35-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:822,66,0:0,0,2,20 chr1 16360137 . C T 613.4 PASS AC=2;AF=0.6;AN=2;DP=224;FractionInformativeReads=1;set=variant7-variant13-variant17-variant35-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1215,102,0:0,0,11,23 chr1 16360190 . A C 445.06 PASS AC=2;AF=0.563;AN=2;DP=309;FractionInformativeReads=1;set=variant7-variant12-variant13-variant17-variant18-variant35-variant40-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:1087,96,0:0,0,12,20 chr1 16360550 . C G 463.39 PASS AC=2;AF=0.75;AN=2;DP=399;set=variant-variant2-variant7-variant13-variant17-variant22-variant25-variant32-variant35-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1547,147,0:0,0,22,27 chr1 16361875 . A G 1669.46 PASS AC=2;AF=0.943;AN=2;DP=2160;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:105,9,0:0,0,3,0 chr1 16361991 . G A 60.72 PASS AC=1;AF=0.5;AN=2;DP=454;FractionInformativeReads=1;set=filterInvariant2-filterInvariant7-filterInvariant32-variant35 GT:AD:DP:GQ:PL:SB 0/1:2,22:24:87:1128,0,87:1,1,19,3 chr1 16362005 . GCCCT G 51.6 PASS AC=1;AF=0.5;AN=2;DP=2221;FractionInformativeReads=1;set=filterInvariant2-filterInvariant3-variant4-filterInvariant6-variant7-filterInvariant10-variant13-variant15-filterInvariant19-filterInvariant25-filterInvariant28-filterInvariant32-variant35-filterInvariant40-filterInvariant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:2,29:31:81:1212,0,81:1,1,19,10 chr1 16362561 . C G 1341.54 PASS AC=2;AF=0.797;AN=2;DP=4961;set=variant-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,181:181:99:6063,543,0:0,0,136,45 chr1 16362621 . G A 3061.94 PASS AC=2;AF=1;AN=2;DP=14271;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,421:421:99:11908,1258,0:0,0,240,181 chr1 16362807 . T A 217.99 PASS AC=2;AF=0.583;AN=2;DP=574;set=variant2-variant7-variant13-variant17-variant35-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,90:90:99:2985,266,0:0,0,17,73 chr1 16366084 . T A 79.68 PASS AC=1;AF=0.5;AN=2;DP=6;FS=0;FractionInformativeReads=1;MQ=35.8;MQRankSum=-0.736;QD=13.28;ReadPosRankSum=-0.736;SOR=1.872;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:1,5:6:24:108,0,24:1,0,1,4 chr1 16366234 . T G 1753.55 PASS AC=2;AF=0.93;AN=2;DP=2241;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:80,6,0:0,0,1,1 chr1 16370215 . A G 378.94 PASS AC=2;AF=0.708;AN=2;DP=1152;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,31:31:92:853,92,0:0,0,16,15 chr1 16370851 . T TACACACACACAC,TACACACACACACACAC,TACACACACACACAC 469.39 PASS AC=0,1,1;AF=0.091,0.273,0.273;AN=2;DP=179;set=variant-variant9-variant13-variant17-variant18-variant22-variant4-variant32-variant33-variant35-variant38 GT:DP:GQ:SB 3/2:15:99:0,0,14,1 chr1 16371932 . A C 1014.81 PASS AC=2;AF=0.943;AN=2;DP=2491;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,99:99:99:3071,296,0:0,0,62,37 chr1 16372282 . GT G 555.45 PASS AC=2;AF=0.567;AN=2;DP=514;MQ=60;set=variant-variant4-variant7-variant9-variant13-variant17-variant18-variant21-variant22-variant25-variant32-variant33-variant35-variant38-variant42 GT:AD:DP:GQ:PL:SB 1/1:1,27:28:74:969,74,0:0,1,15,12 chr1 16372292 . T G 43.43 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=34;FS=22.335;FractionInformativeReads=1;MQ=60;MQRankSum=-0.359;QD=1.28;ReadPosRankSum=-2.362;SOR=4.804;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:24,10:34:72:72,0,890:12,12,0,10 chr1 16374533 . G C 2076.84 PASS AC=2;AF=0.955;AN=2;DP=4444;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,113:113:99:3443,338,0:0,0,56,57 chr1 16374590 . C T 1029.01 PASS AC=2;AF=0.563;AN=2;DP=771;MQ=60;set=variant7-variant9-variant13-variant17-variant18-variant35-variant38-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,102:102:99:2949,302,0:0,0,51,51 chr1 16374972 . T G 2646.71 PASS AC=2;AF=0.625;AN=2;DP=1574;set=variant7-variant9-variant13-variant17-variant18-variant35-variant38-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,254:254:99:8049,761,0:0,0,136,118 chr1 16375063 . C G 7741.67 PASS AC=2;AF=0.932;AN=2;DP=9680;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:3,300:303:99:8513,855,0:1,2,142,158 chr1 16375064 . A C 7741.67 PASS AC=2;AF=0.932;AN=2;DP=9653;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:3,302:305:99:8513,855,0:1,2,142,160 chr1 16375132 . C T 1471.87 PASS AC=2;AF=0.563;AN=2;DP=982;set=variant7-variant9-variant13-variant17-variant18-variant35-variant38-variant42 GT:AD:DP:GQ:PL:SB 1/1:1,167:168:99:5186,492,0:0,1,59,108 chr1 16376191 . C T 704.28 PASS AC=2;AF=0.943;AN=2;DP=1774;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1250,105,0:0,0,28,7 chr1 16376230 . A AT 1795.83 PASS AC=2;AF=0.943;AN=2;DP=3322;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:3420,229,0:0,0,49,26 chr1 16376232 . A T 1804.87 PASS AC=2;AF=0.943;AN=2;DP=3426;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:3420,229,0:0,0,50,26 chr1 16376238 . TC T 1275.67 PASS AC=2;AF=0.943;AN=2;DP=3627;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,82:82:99:2549,246,0:0,0,52,30 chr1 16376278 . G A 1926.88 PASS AC=2;AF=0.943;AN=2;DP=5536;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,136:136:99:3922,407,0:0,0,76,60 chr1 16376319 . T C 2131.62 PASS AC=2;AF=0.943;AN=2;DP=6503;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,150:150:99:4371,448,0:0,0,72,78 chr1 16376458 . T C,A 557.19 PASS AC=2,0;AF=0.932,0.011;AN=2;DP=1786;set=Intersection GT:DP:GQ:SB 1/1:34:99:0,0,8,26 chr1 16376953 . C T 1191.66 PASS AC=2;AF=0.583;AN=2;DP=534;FractionInformativeReads=1;MQ=60;set=variant7-variant9-variant13-variant17-variant35-variant38 GT:AD:DP:GQ:PL:SB 1/1:2,108:110:99:3698,280,0:1,1,82,26 chr1 16377363 . G A 608.25 PASS AC=1;AF=0.5;AN=2;DP=1435;set=variant7-filterInvariant13-filterInvariant17-variant35-filterInvariant40 GT:AD:DP:GQ:PL:SB 0/1:268,95:363:99:1271,0,7167:148,120,48,47 chr1 16377598 . T TG 2490.7 PASS AC=2;AF=0.563;AN=2;DP=2167;MQ=60;set=variant7-variant9-variant13-variant17-variant18-variant35-variant38-variant42 GT:AD:DP:GQ:PL:SB 1/1:3,269:272:99:8258,751,0:1,2,107,162 chr1 16377870 . C T 307.66 PASS AC=2;AF=0.563;AN=2;DP=297;MQ=60;set=variant7-variant9-variant13-variant17-variant18-variant35-variant38-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1482,128,0:0,0,31,12 chr1 16377935 . A G 970.85 PASS AC=2;AF=0.556;AN=2;DP=876;set=variant7-variant9-variant13-variant14-variant17-variant18-variant35-variant38-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,103:103:99:3185,308,0:0,0,67,36 chr1 16377999 . C T 3172.25 PASS AC=2;AF=0.563;AN=2;DP=1260;set=variant7-variant9-variant13-variant17-variant18-variant35-variant38-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,169:169:99:7479,509,0:0,0,92,77 chr1 16378000 . A G 3172.25 PASS AC=2;AF=0.563;AN=2;DP=1266;set=variant7-variant9-variant13-variant17-variant18-variant35-variant38-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,169:169:99:7479,509,0:0,0,92,77 chr1 16378093 . A G 2635.87 PASS AC=2;AF=0.563;AN=2;DP=910;FractionInformativeReads=1;set=variant7-variant9-variant13-variant17-variant18-variant35-variant38-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,140:140:99:6255,421,0:0,0,55,85 chr1 16378099 . G C 2669.42 PASS AC=2;AF=0.563;AN=2;DP=889;FractionInformativeReads=1;set=variant7-variant9-variant13-variant17-variant18-variant35-variant38-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,138:138:99:6266,421,0:0,0,55,83 chr1 16378100 . C A 2591.9 PASS AC=2;AF=0.563;AN=2;DP=878;FractionInformativeReads=1;set=variant7-variant9-variant13-variant17-variant18-variant35-variant38-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,136:136:99:6242,418,0:0,0,54,82 chr1 16378215 . C T 1070.39 PASS AC=2;AF=0.563;AN=2;DP=640;set=variant7-variant9-variant13-variant17-variant18-variant35-variant38-variant42 GT:AD:DP:GQ:PL:SB 1/1:1,84:85:99:2563,209,0:1,0,47,37 chr1 16378331 . G C 741.83 PASS AC=2;AF=0.563;AN=2;DP=473;FractionInformativeReads=1;set=variant7-variant9-variant13-variant17-variant18-variant35-variant38-variant42 GT:AD:DP:GQ:PL:SB 1/1:1,48:49:79:1975,79,0:0,1,15,33 chr1 16378339 . C G 673.19 PASS AC=2;AF=0.563;AN=2;DP=434;FractionInformativeReads=1;set=variant7-variant9-variant13-variant17-variant18-variant35-variant38-variant42 GT:AD:DP:GQ:PL:SB 1/1:1,42:43:64:1820,64,0:0,1,12,30 chr1 16378725 . A T 393.42 PASS AC=2;AF=0.563;AN=2;DP=361;set=variant7-variant9-variant13-variant17-variant18-variant35-variant38-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:1704,162,0:0,0,35,19 chr1 16378931 . A G 1597.71 PASS AC=2;AF=0.571;AN=2;DP=832;set=variant7-variant9-variant13-variant17-variant18-variant35-variant38 GT:AD:DP:GQ:PL:SB 1/1:1,120:121:99:5315,332,0:1,0,44,76 chr1 16378936 . AG A 1563.16 PASS AC=2;AF=0.571;AN=2;DP=789;FractionInformativeReads=1;set=variant7-variant9-variant13-variant17-variant18-variant35-variant38 GT:AD:DP:GQ:PL:SB 1/1:0,118:118:99:5359,361,0:0,0,43,75 chr1 16378938 . G A 1550.45 PASS AC=2;AF=0.571;AN=2;DP=775;FractionInformativeReads=1;set=variant7-variant9-variant13-variant17-variant18-variant35-variant38 GT:AD:DP:GQ:PL:SB 1/1:0,118:118:99:5335,358,0:0,0,42,76 chr1 16378945 . C T 1407.84 PASS AC=2;AF=0.571;AN=2;DP=694;FractionInformativeReads=1;set=variant7-variant9-variant13-variant17-variant18-variant35-variant38 GT:AD:DP:GQ:PL:SB 1/1:0,108:108:99:4995,334,0:0,0,36,72 chr1 16378951 . T C 1302.94 PASS AC=2;AF=0.571;AN=2;DP=635;FractionInformativeReads=1;set=variant7-variant9-variant13-variant17-variant18-variant35-variant38 GT:AD:DP:GQ:PL:SB 1/1:0,99:99:99:4590,307,0:0,0,33,66 chr1 16378954 . G A 1263.98 PASS AC=2;AF=0.571;AN=2;DP=617;FractionInformativeReads=1;set=variant7-variant9-variant13-variant17-variant18-variant35-variant38 GT:AD:DP:GQ:PL:SB 1/1:0,94:94:99:4455,298,0:0,0,31,63 chr1 16378980 . G C 507.78 PASS AC=2;AF=0.563;AN=2;DP=511;set=variant7-variant9-variant13-variant17-variant18-variant26-variant35-variant38 GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:2105,195,0:0,0,22,43 chr1 16378991 . G A 728.56 PASS AC=2;AF=0.571;AN=2;DP=354;set=variant7-variant9-variant13-variant17-variant18-variant35-variant38 GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:2338,163,0:0,0,19,35 chr1 16378998 . T C 641.57 PASS AC=2;AF=0.571;AN=2;DP=309;FractionInformativeReads=1;set=variant7-variant9-variant13-variant17-variant18-variant35-variant38 GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:2226,153,0:0,0,18,31 chr1 16379052 . C G 265.66 PASS AC=2;AF=0.583;AN=2;DP=105;FractionInformativeReads=1;set=variant7-variant9-variant13-variant17-variant35-variant38 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:711,51,0:0,0,2,15 chr1 16380196 . T C 6397.1 PASS AC=2;AF=1;AN=2;DP=13541;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,333:333:99:10031,996,0:0,0,136,197 chr1 16380243 . A G 1336.4 PASS AC=2;AF=0.725;AN=2;DP=6920;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,194:194:99:8287,583,0:0,0,67,127 chr1 16380252 . C T 1300.33 PASS AC=2;AF=0.713;AN=2;DP=6011;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,172:172:99:7828,533,0:0,0,52,120 chr1 16383448 . A C 1435.23 PASS AC=2;AF=1;AN=2;DP=1518;FS=0;FractionInformativeReads=1;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1315,111,0:0,0,11,26 chr1 16383668 . T G 1571.04 PASS AC=2;AF=1;AN=2;DP=3569;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:1535,141,0:0,0,31,16 chr1 16383742 . C G 1372.49 PASS AC=2;AF=0.602;AN=2;DP=6411;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,96:96:99:2810,288,0:0,0,50,46 chr1 16385131 . C A 1322.32 PASS AC=1;AF=0.5;AN=2;DP=1670;set=variant2-variant4-variant9-variant12-variant15-variant17-variant35-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:143,105:248:99:2179,0,3366:82,61,64,41 chr1 16385323 . A G 855.92 PASS AC=1;AF=0.872;AN=2;DP=1584;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:89,56:145:99:1901,0,4957:26,63,15,41 chr1 16385330 . G T 806.49 PASS AC=1;AF=0.875;AN=2;DP=1479;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:84,43:127:99:1640,0,4843:24,60,10,33 chr1 16386247 . T C 211.41 PASS AC=2;AF=1;AN=2;DP=403;FS=0;MQRankSum=0.747;ReadPosRankSum=-0.747;set=variant-variant2-filterInvariant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-filterInvariant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:544,51,0:0,0,11,6 chr1 16386447 . G C 1640.1 PASS AC=2;AF=1;AN=2;DP=3766;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,104:104:99:3176,312,0:0,0,47,57 chr1 16388485 . T C 594.88 PASS AC=1;AF=0.629;AN=2;DP=1359;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-filterInvariant34-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:85,26:111:99:676,0,2269:62,23,25,1 chr1 16388580 . C T,A 1105.58 PASS AC=0,1;AF=0.517,0.083;AN=2;DP=4499;set=variant-variant2-variant5-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant35-variant37-variant39-variant40-variant41-variant42 GT:DP:GQ:SB 0/2:364:99:113,100,97,54 chr1 16388646 . T C 5236.94 PASS AC=1;AF=0.909;AN=2;DP=7934;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:210,212:422:99:5080,0,4670:105,105,101,111 chr1 16388709 . G T 1357.72 PASS AC=1;AF=0.675;AN=2;DP=4999;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:146,144:290:99:3372,0,3546:55,91,52,92 chr1 16388756 . CACCCAT C 1462.84 PASS AC=1;AF=0.5;AN=2;DP=807;set=variant2-variant4-variant6-variant9-variant12-variant15-variant17-variant35-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,68:132:99:2629,0,2451:15,49,16,52 chr1 16388766 . C T 1575.79 PASS AC=1;AF=0.898;AN=2;DP=2429;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:59,66:125:99:2619,0,2302:13,46,15,51 chr1 16451413 . C T 1710.79 PASS AC=2;AF=0.989;AN=2;DP=2883;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,80:80:99:2475,238,0:0,0,40,40 chr1 16460696 . G A 1035.93 PASS AC=1;AF=0.571;AN=2;DP=255;MQ=60;set=variant-variant6-variant15-variant20-variant23-variant25-variant35 GT:AD:DP:GQ:PL:SB 0/1:16,24:40:99:612,0,387:7,9,12,12 chr1 16460743 . TAAC T 1607.63 PASS AC=2;AF=0.989;AN=2;DP=1850;MQ=60;MQRankSum=2.379;ReadPosRankSum=1.256;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:2175,150,0:0,0,26,24 chr1 16525333 . C T 1605.41 PASS AC=1;AF=0.542;AN=2;DP=751;MQ=60;set=variant-variant6-variant8-variant11-variant13-variant20-variant23-variant25-variant32-variant35-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:23,43:66:99:1084,0,575:14,9,21,22 chr1 16528218 . G T 200.3 PASS AC=1;AF=0.65;AN=2;DP=1255;MQ=60;set=variant2-variant3-variant4-variant5-variant8-variant9-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,20:40:99:506,0,561:10,10,12,8 chr1 16528469 . GCC G 277.24 PASS AC=1;AF=0.775;AN=2;DP=1405;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,18:43:99:652,0,4318:8,17,4,14 chr1 16528472 . TACCCTAGGGACC T 277.05 PASS AC=1;AF=0.775;AN=2;DP=1356;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,18:42:99:651,0,4320:7,17,4,14 chr1 16528843 . A G 1646.85 PASS AC=2;AF=0.722;AN=2;DP=1470;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1825,150,0:0,0,38,12 chr1 16532498 . G A 2527.42 PASS AC=1;AF=0.542;AN=2;DP=1264;MQ=60;set=variant-variant6-variant8-variant11-variant13-variant20-variant23-variant25-variant32-variant35-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:55,36:91:99:1016,0,1482:29,26,21,15 chr1 16533022 . C T 1234.59 PASS AC=1;AF=0.78;AN=2;DP=2651;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,23:70:99:554,0,1247:14,33,6,17 chr1 16533830 . AATTC A 283.9 PASS AC=1;AF=0.795;AN=2;DP=706;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,7:16:99:267,0,444:4,5,3,4 chr1 16535804 . G C 46.96 PASS AC=1;AF=0.78;AN=2;DP=627;FractionInformativeReads=1;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,7:21:99:190,0,401:4,10,1,6 chr1 16542366 . G A 1147.36 PASS AC=1;AF=0.542;AN=2;DP=607;MQ=60;set=variant-variant6-variant8-variant11-variant13-variant20-variant23-variant25-variant32-variant35-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:28,21:49:99:528,0,821:21,7,12,9 chr1 16542937 . T G 1208.87 PASS AC=1;AF=0.568;AN=2;DP=865;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant8-variant9-variant11-variant13-variant17-variant18-variant20-variant23-variant25-variant32-variant33-variant34-variant35-variant36-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,29:54:99:816,0,747:20,5,23,6 chr1 16543175 . A C 2259.04 PASS AC=2;AF=1;AN=2;DP=4450;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,115:115:99:3674,343,0:0,0,39,76 chr1 16543390 . G A 342.51 PASS AC=1;AF=0.545;AN=2;DP=112;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant8-variant11-variant13-variant23-variant25-variant32-variant35-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,6:10:99:190,0,107:3,1,4,2 chr1 16555105 . C T 316.48 PASS AC=1;AF=0.58;AN=2;DP=336;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant8-variant9-variant11-variant13-variant15-variant17-variant18-variant20-variant23-variant25-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,10:12:56:252,0,56:1,1,6,4 chr1 16555882 . C T 803.6 PASS AC=1;AF=0.58;AN=2;DP=622;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant8-variant9-variant11-variant13-variant15-variant17-variant18-variant20-variant23-variant25-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,11:19:99:385,0,292:7,1,11,0 chr1 16558838 . C A 1151.95 PASS AC=1;AF=0.613;AN=2;DP=3628;MQ=60;set=variant2-variant3-variant4-variant5-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,93:136:99:2394,0,971:16,27,37,56 chr1 16559541 . C G 2152.72 PASS AC=1;AF=0.6;AN=2;DP=2374;MQ=60;set=variant-variant2-variant6-variant8-variant9-variant11-variant13-variant15-variant17-variant18-variant20-variant23-variant25-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:72,51:123:99:1203,0,1959:24,48,17,34 chr1 16562968 . C A 566.73 PASS AC=2;AF=0.821;AN=2;DP=1013;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:986,87,0:0,0,21,8 chr1 16563635 . A G 1113.87 PASS AC=2;AF=0.821;AN=2;DP=1911;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:1523,141,0:0,0,21,26 chr1 16574040 . TC T 8576.12 PASS AC=1;AF=0.558;AN=2;DP=5874;set=variant-variant2-variant6-variant7-variant8-variant9-variant11-variant13-variant15-variant17-variant18-variant20-variant23-variant25-variant27-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:157,130:287:99:3928,0,4832:85,72,75,55 chr1 16574316 . T C 1715.98 PASS AC=2;AF=0.821;AN=2;DP=2558;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,67:67:99:2461,201,0:0,0,17,50 chr1 16574382 . A C 619.59 PASS AC=1;AF=0.574;AN=2;DP=818;MQ=60;set=variant-variant2-variant6-variant7-variant8-variant9-variant11-variant13-variant15-variant17-variant18-variant20-variant23-variant25-variant27-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,17:34:99:547,0,511:4,13,3,14 chr1 16575030 . T C 485.74 PASS AC=1;AF=0.558;AN=2;DP=951;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant7-variant8-variant9-variant11-variant13-variant15-variant17-variant18-variant20-variant23-variant25-variant27-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,13:27:99:379,0,390:5,9,10,3 chr1 16576437 . ACAAT A 4310.74 PASS AC=1;AF=0.536;AN=2;DP=1584;MQ=60;set=variant-variant6-variant8-variant11-variant13-variant15-variant18-variant20-variant23-variant32-variant34-variant35-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:45,76:121:99:3001,0,2303:18,27,32,44 chr1 16576836 . A G 1458.3 PASS AC=1;AF=0.574;AN=2;DP=1386;MQ=60;set=variant-variant2-variant6-variant7-variant8-variant9-variant11-variant13-variant15-variant17-variant18-variant20-variant23-variant25-variant27-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,23:52:99:506,0,614:13,16,10,13 chr1 16577908 . G C 2454.84 PASS AC=1;AF=0.574;AN=2;DP=3581;set=variant-variant2-variant6-variant7-variant8-variant9-variant11-variant13-variant15-variant17-variant18-variant20-variant23-variant25-variant27-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:72,88:160:99:2165,0,1918:36,36,46,42 chr1 16579070 . C T 805.92 PASS AC=1;AF=0.556;AN=2;DP=620;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant7-variant8-variant9-variant11-variant13-variant15-variant17-variant18-variant20-variant23-variant25-variant27-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,10:20:99:346,0,253:3,7,2,8 chr1 16583030 . C CA 1520.66 PASS AC=1;AF=0.558;AN=2;DP=1143;MQ=60;set=variant-variant2-variant6-variant7-variant8-variant9-variant11-variant13-variant15-variant17-variant18-variant20-variant23-variant25-variant27-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,13:36:99:310,0,592:14,9,11,2 chr1 16621183 . C T 1496.67 PASS AC=2;AF=0.821;AN=2;DP=2105;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,66:66:99:2106,198,0:0,0,42,24 chr1 16632188 . G A 1163.82 PASS AC=1;AF=0.536;AN=2;DP=726;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant8-variant11-variant13-variant15-variant18-variant20-variant23-variant32-variant34-variant35-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:27,29:56:99:599,0,646:17,10,17,12 chr1 16641899 . C T 905.19 PASS AC=1;AF=0.613;AN=2;DP=3029;MQ=60;set=variant2-variant3-variant4-variant5-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,49:89:99:1315,0,1116:18,22,19,30 chr1 16693985 . TTC T 222.61 PASS AC=1;AF=0.545;AN=2;DP=120;MQ=60;set=variant-variant6-variant8-variant11-variant15-variant20-variant23-variant32-variant34-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:2,8:10:56:318,0,56:1,1,3,5 chr1 16713555 . G C 7023.43 PASS AC=1;AF=0.536;AN=2;DP=2913;MQ=60;set=variant-variant6-variant8-variant11-variant13-variant15-variant18-variant20-variant23-variant32-variant34-variant35-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:123,101:224:99:2374,0,2868:69,54,51,50 chr1 16714095 . C T 4253.74 PASS AC=1;AF=0.536;AN=2;DP=1849;MQ=60;set=variant-variant6-variant8-variant11-variant13-variant15-variant18-variant20-variant23-variant32-variant34-variant35-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:80,62:142:99:1481,0,2088:38,42,33,29 chr1 16722100 . C CT 5173.9 PASS AC=1;AF=0.567;AN=2;DP=3726;MQ=60;set=variant-variant6-variant8-variant11-variant13-variant15-variant18-variant20-variant23-variant32-variant34-variant35-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:127,124:251:99:2718,0,2785:66,61,51,73 chr1 16722934 . C G 2386.77 PASS AC=1;AF=0.536;AN=2;DP=1017;MQ=60;set=variant-variant6-variant8-variant11-variant13-variant15-variant18-variant20-variant23-variant32-variant34-variant35-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:52,45:97:99:1111,0,1351:30,22,24,21 chr1 16723084 . G A 1249.38 PASS AC=1;AF=0.613;AN=2;DP=4052;MQ=60;set=variant2-variant3-variant4-variant5-variant8-variant9-variant11-variant12-variant14-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,58:108:99:1638,0,1297:25,25,31,27 chr1 16723139 . C A 3627.86 PASS AC=1;AF=0.536;AN=2;DP=1880;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant8-variant11-variant13-variant15-variant18-variant20-variant23-variant32-variant34-variant35-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:49,58:107:99:1519,0,1357:24,25,32,26 chr1 16723268 . T C 3646.68 PASS AC=1;AF=0.567;AN=2;DP=1868;MQ=60;set=variant-variant6-variant8-variant11-variant13-variant15-variant18-variant20-variant23-variant32-variant34-variant35-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:61,43:104:99:1123,0,1726:25,36,17,26 chr1 16725818 . A G 604.94 PASS AC=1;AF=0.536;AN=2;DP=299;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant8-variant11-variant13-variant15-variant18-variant20-variant23-variant32-variant34-variant35-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:14,21:35:99:503,0,380:11,3,13,8 chr1 16726036 . A G 1425.38 PASS AC=1;AF=0.536;AN=2;DP=960;MQ=60;set=variant-variant6-variant8-variant11-variant13-variant15-variant18-variant20-variant23-variant32-variant34-variant35-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:47,29:76:99:772,0,1147:24,23,14,15 chr1 16727305 . G GCTT 2437.16 PASS AC=1;AF=0.567;AN=2;DP=1501;MQ=60;set=variant-variant6-variant8-variant11-variant13-variant15-variant18-variant20-variant23-variant32-variant34-variant35-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:77,44:121:99:1622,0,3610:34,43,21,23 chr1 16730413 . C T 1350.84 PASS AC=1;AF=0.538;AN=2;DP=1204;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant8-variant11-variant13-variant15-variant18-variant20-variant23-variant32-variant34-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:53,54:107:99:1347,0,1408:24,29,27,27 chr1 16730582 . C G 436.88 PASS AC=1;AF=0.621;AN=2;DP=834;MQ=60;set=variant2-variant3-variant4-variant5-variant8-variant9-variant11-variant12-variant14-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant35-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:30,16:46:99:340,0,673:10,20,7,9 chr1 16731646 . T C 5055.85 PASS AC=2;AF=1;AN=2;DP=4060;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,91:91:99:3973,274,0:0,0,30,61 chr1 16731647 . G C 5055.85 PASS AC=2;AF=0.716;AN=2;DP=3311;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,85:87:99:3116,212,0:1,1,27,58 chr1 16731653 . C T 1348.61 PASS AC=1;AF=0.617;AN=2;DP=2439;MQ=60;set=variant2-variant3-variant4-variant5-variant8-variant9-variant11-variant12-variant14-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant35-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,33:78:99:1043,0,1231:16,29,8,25 chr1 16731661 . T C 2819.83 PASS AC=2;AF=0.716;AN=2;DP=2690;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,69:71:99:2561,167,0:1,1,22,47 chr1 16731756 . G T 728.07 PASS AC=1;AF=0.538;AN=2;DP=168;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant8-variant11-variant13-variant15-variant18-variant20-variant23-variant32-variant34-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,9:13:94:285,0,94:1,3,2,7 chr1 16748311 . G C 2716.83 PASS AC=1;AF=0.5;AN=2;DP=204;FS=0;FractionInformativeReads=0.995;MQ=60;MQRankSum=-1.194;QD=13.32;ReadPosRankSum=1.232;SOR=0.721;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:95,108:203:99:2745,0,2377:61,34,70,38 chr1 16778265 . G T 300.2 PASS AC=2;AF=0.661;AN=2;DP=1793;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant10-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,73:73:99:2113,218,0:0,0,41,32 chr1 16786087 . T C 1315.25 PASS AC=2;AF=1;AN=2;DP=2379;FS=0;MQ=60;MQRankSum=-0.896;ReadPosRankSum=0.478;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:1921,195,0:0,0,35,30 chr1 16802890 . G A 972.96 PASS AC=2;AF=0.667;AN=2;DP=3529;set=variant-variant2-variant3-variant4-variant6-variant7-variant10-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,137:138:99:4293,400,0:1,0,79,58 chr1 16862273 . C A 162.23 PASS AC=1;AF=0.5;AN=2;DP=1200;FractionInformativeReads=1;set=filterInvariant3-filterInvariant6-variant13-filterInvariant17-filterInvariant18-variant22-variant23-filterInvariant25-variant28-variant32-variant33-filterInvariant35-filterInvariant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:74,11:85:96:96,0,2705:62,12,9,2 chr1 16862282 . G A 83.76 PASS AC=1;AF=0.5;AN=2;DP=1294;FractionInformativeReads=1;set=filterInvariant-filterInvariant7-variant15-variant20-variant21-variant26-variant29-filterInvariant30-variant34-variant35-variant37-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:83,26:109:99:486,0,2774:70,13,21,5 chr1 16862296 . G C 413.55 PASS AC=1;AF=0.5;AN=2;DP=5770;set=variant-filterInvariant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-filterInvariant11-variant12-variant13-variant14-filterInvariant16-variant17-filterInvariant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:127,31:158:99:612,0,4040:102,25,29,2 chr1 16862340 . G A 517.76 PASS AC=1;AF=0.5;AN=2;DP=9650;set=variant-filterInvariant3-variant5-variant6-filterInvariant7-variant8-filterInvariant9-filterInvariant11-variant14-variant17-filterInvariant18-variant23-variant24-variant25-variant26-variant27-filterInvariant29-filterInvariant30-variant31-variant32-filterInvariant33-variant34-filterInvariant35-filterInvariant37-variant38-variant39-filterInvariant40 GT:AD:DP:GQ:PL:SB 0/1:328,43:371:99:164,0,8996:250,78,31,12 chr1 16862454 . T G 19431.9 PASS AC=1;AF=0.5;AN=2;DP=59379;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:654,789:1443:99:30160,0,24872:353,301,443,346 chr1 16862461 . T A 19801.3 PASS AC=1;AF=0.5;AN=2;DP=60743;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:520,948:1468:99:37127,0,18173:277,243,521,427 chr1 16862472 . G C 1447.53 PASS AC=1;AF=0.5;AN=2;DP=35296;set=filterInvariant3-filterInvariant4-filterInvariant6-filterInvariant7-filterInvariant10-filterInvariant12-variant13-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-variant28-variant30-filterInvariant31-variant32-filterInvariant33-filterInvariant35-filterInvariant37-filterInvariant38 GT:AD:DP:GQ:PL:SB 0/1:1395,144:1539:99:1505,0,56066:743,652,73,71 chr1 16862502 . A G 24850.1 PASS AC=1;AF=0.5;AN=2;DP=67059;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:558,1076:1634:99:26010,0,11044:266,292,554,522 chr1 16862574 . C T 1538.71 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=3859;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:1284,160:1444:99:166,0,33839:555,729,68,92 chr1 16862708 . T G 2252.72 PASS AC=1;AF=0.5;AN=2;DP=9082;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:82,171:253:99:6473,0,2979:19,63,23,148 chr1 16862712 . G T 2103.78 PASS AC=1;AF=0.5;AN=2;DP=8023;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:73,143:216:99:6138,0,2980:16,57,18,125 chr1 16862714 . T G 2112.33 PASS AC=1;AF=0.5;AN=2;DP=7572;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:72,134:206:99:5742,0,2862:15,57,16,118 chr1 16862719 . G A 68.47 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=173;FS=0;FractionInformativeReads=1;MQ=37.83;MQRankSum=-1.797;QD=0.4;ReadPosRankSum=-0.51;SOR=0.454;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:155,18:173:97:97,0,5643:24,131,3,15 chr1 16862732 . A G 185.05 PASS AC=1;AF=0.5;AN=2;DP=3714;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-filterInvariant27-variant28-filterInvariant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-filterInvariant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:54,30:84:99:736,0,1540:10,44,0,30 chr1 16862774 . CTG C 40.63 PASS AC=1;AF=0.5;AN=2;DP=176;set=filterInvariant13-variant22-filterInvariant25-filterInvariant28-variant32-variant35 GT:AD:DP:GQ:PL:SB 0/1:26,5:31:99:105,0,1100:2,24,0,5 chr1 16863238 . T C 344.84 PASS AC=1;AF=0.5;AN=2;DP=2232;FractionInformativeReads=1;set=filterInvariant3-variant6-filterInvariant7-filterInvariant10-filterInvariant16-variant22-variant23-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant27-filterInvariant31-variant32-filterInvariant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:144,8:152:68:68,0,5952:82,62,8,0 chr1 16863257 . A G 450.56 PASS AC=1;AF=0.5;AN=2;DP=4141;set=filterInvariant3-variant6-variant7-variant8-filterInvariant9-variant10-filterInvariant14-filterInvariant19-filterInvariant20-variant22-variant23-variant24-variant25-variant26-variant27-variant31-variant32-variant35-variant38-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:188,25:213:99:606,0,7838:103,85,21,4 chr1 16863259 . T G 30.52 PASS AC=1;AF=0.5;AN=2;DP=6112;set=filterInvariant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-filterInvariant14-filterInvariant16-filterInvariant17-variant19-filterInvariant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-filterInvariant33-variant35-filterInvariant36-filterInvariant37-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:191,29:220:99:606,0,7838:105,86,25,4 chr1 16863304 . T C 1608 PASS AC=1;AF=0.5;AN=2;DP=12986;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:231,102:333:99:3651,0,9584:120,111,69,33 chr1 16863308 . G T 1720.68 PASS AC=1;AF=0.5;AN=2;DP=13359;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:236,108:344:99:3904,0,9711:119,117,70,38 chr1 16863313 . C T 519.76 PASS AC=1;AF=0.5;AN=2;DP=11712;set=variant-filterInvariant2-variant3-variant4-variant5-variant6-variant7-variant8-filterInvariant9-variant10-filterInvariant12-filterInvariant13-variant14-variant17-variant19-filterInvariant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-filterInvariant29-variant30-variant31-variant32-filterInvariant33-filterInvariant34-filterInvariant35-variant36-variant37-variant38-variant39-filterInvariant40-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:298,64:362:99:620,0,11444:156,142,39,25 chr1 16863314 . A G 1849.58 PASS AC=1;AF=0.5;AN=2;DP=14109;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:241,126:367:99:4317,0,9670:121,120,75,51 chr1 16863328 . T G 1912.66 PASS AC=1;AF=0.5;AN=2;DP=14723;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:237,145:382:99:3627,0,5654:116,121,85,60 chr1 16863352 . C T 2181.66 PASS AC=1;AF=0.5;AN=2;DP=14974;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:228,161:389:99:4765,0,5544:106,122,90,71 chr1 16863382 . A T 485.63 PASS AC=1;AF=0.5;AN=2;DP=7685;set=variant-filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant7-variant11-variant12-filterInvariant13-variant15-variant16-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant20-variant21-filterInvariant26-variant29-filterInvariant30-filterInvariant34-variant35-variant36-filterInvariant37-filterInvariant40-filterInvariant41-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:282,68:350:99:783,0,7152:130,152,38,30 chr1 16863398 . A C 2229.72 PASS AC=1;AF=0.5;AN=2;DP=11865;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-filterInvariant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:173,139:312:99:3771,0,4062:75,98,65,74 chr1 16863484 . C A 130.51 PASS AC=1;AF=0.5;AN=2;DP=1462;set=filterInvariant2-filterInvariant4-filterInvariant6-filterInvariant7-filterInvariant10-filterInvariant12-variant13-filterInvariant16-variant18-filterInvariant19-filterInvariant22-variant23-filterInvariant25-variant28-variant30-variant31-variant32-filterInvariant33-variant35-filterInvariant38 GT:AD:DP:GQ:PL:SB 0/1:67,12:79:99:221,0,2160:14,53,1,11 chr1 16863514 . C T 84.93 PASS AC=1;AF=0.5;AN=2;DP=1116;set=variant2-variant3-variant4-variant7-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-filterInvariant22-variant26-filterInvariant28-variant29-filterInvariant31-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,15:47:99:393,0,1241:0,32,3,12 chr1 16890421 . G A 283.53 PASS AC=1;AF=0.5;AN=2;DP=20908;set=filterInvariant-variant2-variant3-variant4-variant5-variant6-variant7-filterInvariant8-variant9-variant10-variant12-variant13-variant14-filterInvariant15-variant16-variant17-filterInvariant18-variant19-variant20-filterInvariant21-variant22-variant23-variant24-variant25-filterInvariant26-variant27-variant28-variant29-variant30-variant31-variant32-filterInvariant33-variant34-variant35-variant36-variant37-variant38-variant39-filterInvariant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:322,253:575:99:6463,0,9719:227,95,174,79 chr1 16890428 . T A 1340.61 PASS AC=1;AF=0.5;AN=2;DP=15328;set=variant-filterInvariant2-variant3-filterInvariant4-variant5-variant11-filterInvariant12-variant14-variant15-filterInvariant16-filterInvariant18-filterInvariant19-variant20-variant21-variant22-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant27-variant31-filterInvariant32-filterInvariant33-filterInvariant35-variant37-filterInvariant38-filterInvariant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:536,80:616:99:1028,0,18591:360,176,62,18 chr1 16890441 . C T 656.94 PASS AC=1;AF=0.5;AN=2;DP=19798;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant4-variant5-variant6-variant7-variant8-variant9-variant11-filterInvariant13-variant14-filterInvariant15-filterInvariant16-variant17-filterInvariant18-variant23-variant24-filterInvariant25-filterInvariant26-filterInvariant27-variant28-variant30-variant32-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant38-variant39-filterInvariant40-variant41-filterInvariant42-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:605,91:696:99:807,0,17990:410,195,57,34 chr1 16890484 . G C 378.63 PASS AC=1;AF=0.5;AN=2;DP=29575;set=filterInvariant-filterInvariant2-filterInvariant4-variant5-variant6-variant7-variant8-variant9-filterInvariant11-filterInvariant13-filterInvariant14-filterInvariant15-filterInvariant16-variant17-filterInvariant18-variant23-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant27-variant28-variant30-filterInvariant31-variant32-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant38-variant39-filterInvariant40-variant41-filterInvariant42-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:889,145:1034:99:1350,0,24731:525,364,78,67 chr1 16890598 . T A 13968 PASS AC=1;AF=0.534;AN=2;DP=55757;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:369,1102:1471:99:37765,0,9824:150,219,521,581 chr1 16890602 . T G 1476.86 PASS AC=1;AF=0.5;AN=2;DP=34777;set=filterInvariant2-variant3-variant4-variant6-filterInvariant7-variant9-variant10-variant12-variant14-variant19-variant20-variant22-variant23-variant25-variant27-variant28-filterInvariant29-filterInvariant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-filterInvariant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:845,628:1473:99:18502,0,28955:378,467,288,340 chr1 16890607 . G A 1031.57 PASS AC=1;AF=0.5;AN=2;DP=27794;set=filterInvariant3-filterInvariant4-filterInvariant6-variant9-variant10-filterInvariant12-variant14-filterInvariant19-filterInvariant20-filterInvariant22-filterInvariant23-variant25-variant27-filterInvariant28-filterInvariant31-filterInvariant32-variant35-filterInvariant36-filterInvariant37-variant38-variant39-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:1142,282:1424:99:4150,0,45512:518,624,125,157 chr1 16890639 . C T 5891.41 PASS AC=1;AF=0.5;AN=2;DP=42627;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-filterInvariant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-filterInvariant20-variant21-variant22-filterInvariant23-variant24-variant25-variant26-variant27-variant28-filterInvariant29-variant30-variant31-variant32-variant33-filterInvariant34-variant35-variant37-variant38-filterInvariant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:1000,204:1204:99:3149,0,43515:425,575,81,123 chr1 16890644 . C T 4350.45 PASS AC=1;AF=0.5;AN=2;DP=43309;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-filterInvariant11-variant12-variant14-variant15-filterInvariant16-filterInvariant17-filterInvariant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-filterInvariant33-variant34-variant35-variant36-variant37-variant38-variant39-filterInvariant40-variant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:340,816:1156:99:21882,0,9784:128,212,348,468 chr1 16890671 . T C 17120.1 PASS AC=1;AF=0.545;AN=2;DP=34126;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:115,753:868:99:31189,0,4277:36,79,281,472 chr1 16890672 . G A 17120.1 PASS AC=1;AF=0.545;AN=2;DP=33755;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:114,741:855:99:30958,0,4296:36,78,271,470 chr1 16890760 . G A 1328.16 PASS AC=1;AF=0.511;AN=2;DP=8098;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:73,124:197:99:3876,0,2789:13,60,26,98 chr1 16891154 . A G 135.1 PASS AC=1;AF=0.5;AN=2;DP=616;FractionInformativeReads=1;set=filterInvariant9-filterInvariant10-filterInvariant14-filterInvariant28-filterInvariant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:86,18:104:99:248,0,3118:59,27,12,6 chr1 16891158 . A C 339.26 PASS AC=1;AF=0.5;AN=2;DP=3343;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-filterInvariant12-variant14-filterInvariant15-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-filterInvariant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-filterInvariant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:58,48:106:99:1447,0,1498:40,18,33,15 chr1 16891207 . T C 184.11 PASS AC=1;AF=0.5;AN=2;DP=2004;set=filterInvariant6-variant9-filterInvariant10-filterInvariant14-filterInvariant20-filterInvariant23-filterInvariant25-filterInvariant28-variant32-filterInvariant35-filterInvariant36-filterInvariant38-filterInvariant39 GT:AD:DP:GQ:PL:SB 0/1:136,19:155:99:211,0,4278:117,19,16,3 chr1 16891243 . C G 6249.01 PASS AC=2;AF=0.795;AN=2;DP=12817;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,295:295:99:9909,891,0:0,0,206,89 chr1 16891333 . C T 1424.06 PASS AC=1;AF=0.5;AN=2;DP=14211;set=filterInvariant3-variant5-variant6-variant9-variant10-filterInvariant12-filterInvariant14-variant19-variant20-filterInvariant22-variant23-variant24-variant25-filterInvariant27-variant28-filterInvariant30-filterInvariant31-variant32-variant35-variant36-filterInvariant37-variant38-variant39-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:500,157:657:99:2856,0,13686:263,237,88,69 chr1 16891485 . C T 2686.74 PASS AC=1;AF=0.536;AN=2;DP=11178;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-filterInvariant10-variant11-variant12-filterInvariant13-variant14-variant15-variant16-filterInvariant17-variant18-variant19-variant20-filterInvariant21-variant22-variant23-variant24-variant25-filterInvariant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:71,180:251:99:5864,0,1257:30,41,40,140 chr1 16892310 . T G 2858.92 PASS AC=1;AF=0.511;AN=2;DP=11165;set=variant-filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-variant13-variant14-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-variant26-filterInvariant27-filterInvariant28-filterInvariant29-variant30-filterInvariant31-filterInvariant32-filterInvariant33-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant38-filterInvariant39-variant40-filterInvariant41-filterInvariant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:73,296:369:99:8694,0,1226:57,16,53,243 chr1 16892407 . A G 475.99 PASS AC=1;AF=0.5;AN=2;DP=6759;set=variant-variant2-variant3-filterInvariant4-variant5-filterInvariant6-variant7-variant8-filterInvariant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-filterInvariant24-filterInvariant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-filterInvariant40-variant41-filterInvariant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:187,62:249:99:1067,0,6341:112,75,38,24 chr1 16892419 . A G 108.43 PASS AC=1;AF=0.5;AN=2;DP=7050;set=variant-filterInvariant2-variant3-variant4-variant5-variant6-filterInvariant7-variant8-variant9-variant10-variant12-variant14-filterInvariant15-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:151,128:279:99:2876,0,4452:89,62,77,51 chr1 16892545 . C T 1935.61 PASS AC=1;AF=0.5;AN=2;DP=3003;set=variant3-filterInvariant5-filterInvariant10-variant24-filterInvariant28-filterInvariant35-filterInvariant36-filterInvariant38-filterInvariant39 GT:AD:DP:GQ:PL:SB 0/1:322,46:368:99:254,0,9529:177,145,25,21 chr1 16892561 . C T 3684.59 PASS AC=2;AF=1;AN=2;DP=12177;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,391:391:99:14176,1176,0:0,0,215,176 chr1 16892578 . ACT A 1687.29 PASS AC=1;AF=0.5;AN=2;DP=12202;set=variant-variant2-filterInvariant3-variant4-variant5-variant6-variant7-variant8-filterInvariant9-filterInvariant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-filterInvariant23-variant24-variant25-variant26-variant27-variant28-filterInvariant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:307,113:420:99:3793,0,12322:172,135,57,56 chr1 16892811 . A G 15973.6 PASS AC=1;AF=0.5;AN=2;DP=19468;set=variant3-variant4-variant5-variant6-variant9-variant10-filterInvariant12-filterInvariant14-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant28-filterInvariant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:409,448:857:99:10906,0,9169:189,220,214,234 chr1 16893033 . G A 2496.89 PASS AC=2;AF=0.705;AN=2;DP=20912;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-filterInvariant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,448:448:99:13762,1340,0:0,0,261,187 chr1 16893884 . G A 4200.18 PASS AC=1;AF=0.5;AN=2;DP=39214;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-filterInvariant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-filterInvariant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:334,1017:1351:99:30376,0,7046:83,251,241,776 chr1 16894277 . G T 464.12 PASS AC=1;AF=0.5;AN=2;DP=2088;set=variant-variant3-filterInvariant4-variant6-variant8-variant9-variant10-variant15-variant20-variant21-filterInvariant22-variant24-filterInvariant25-variant27-variant28-variant30-variant31-filterInvariant32-variant34-variant35-filterInvariant37-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:79,34:113:99:789,0,2544:63,16,28,6 chr1 16894323 . C A 486.05 PASS AC=1;AF=0.5;AN=2;DP=6141;set=variant-filterInvariant2-variant3-variant4-filterInvariant5-variant6-filterInvariant7-variant8-variant9-variant10-variant12-filterInvariant13-variant14-variant15-variant19-variant20-variant21-variant22-variant23-variant24-variant25-filterInvariant26-variant27-variant28-filterInvariant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-filterInvariant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:112,97:209:99:2154,0,2832:84,28,63,34 chr1 16894376 . A G 249.37 PASS AC=1;AF=0.5;AN=2;DP=6009;set=filterInvariant-filterInvariant2-filterInvariant3-variant4-variant5-variant6-variant7-variant8-variant13-filterInvariant14-filterInvariant16-filterInvariant17-filterInvariant23-filterInvariant25-filterInvariant26-filterInvariant27-variant30-variant32-filterInvariant35-filterInvariant36-filterInvariant38-filterInvariant39-filterInvariant40-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:274,36:310:63:63,0,6814:153,121,20,16 chr1 16894450 . C T 447.42 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=269;FS=6.043;FractionInformativeReads=1;MQ=29.38;MQRankSum=-1.526;QD=1.66;ReadPosRankSum=-2.865;SOR=0.456;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:224,45:269:99:476,0,5762:92,132,23,22 chr1 16895392 . AC A 127.2 PASS AC=1;AF=0.5;AN=2;DP=2912;set=variant-variant2-variant3-variant4-filterInvariant5-filterInvariant7-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-filterInvariant24-variant26-variant28-filterInvariant29-variant30-variant31-filterInvariant32-filterInvariant33-variant34-filterInvariant35-variant36-variant37-filterInvariant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:78,13:91:99:150,0,2347:53,25,10,3 chr1 16895634 . T G 4365.94 PASS AC=1;AF=0.682;AN=2;DP=12386;set=variant-filterInvariant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-filterInvariant11-filterInvariant12-variant13-variant14-filterInvariant15-variant16-variant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-variant23-variant24-filterInvariant25-variant26-variant27-filterInvariant28-filterInvariant29-variant30-variant31-variant32-variant33-filterInvariant34-variant35-variant36-variant37-variant38-variant39-variant40-filterInvariant41-filterInvariant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,214:271:99:5549,0,844:26,31,62,152 chr1 16900883 . T G 62.88 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=4035;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:97,17:114:99:142,0,2229:58,39,11,6 chr1 16901247 . G T 41.81 PASS AC=1;AF=0.5;AN=2;DP=2427;FractionInformativeReads=1;set=filterInvariant2-filterInvariant3-variant4-filterInvariant5-filterInvariant6-filterInvariant7-variant8-filterInvariant9-filterInvariant10-filterInvariant12-filterInvariant13-filterInvariant14-filterInvariant15-filterInvariant19-filterInvariant20-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant27-filterInvariant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-filterInvariant34-filterInvariant35-variant36-filterInvariant37-filterInvariant38-filterInvariant39-filterInvariant41-filterInvariant42-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:44,47:91:99:1017,0,1044:7,37,4,43 chr1 16901259 . T A 283.75 PASS AC=1;AF=0.5;AN=2;DP=1398;set=filterInvariant3-filterInvariant4-variant6-filterInvariant7-filterInvariant10-filterInvariant12-filterInvariant14-filterInvariant19-filterInvariant20-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-variant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-variant35-variant36-filterInvariant37-filterInvariant38-filterInvariant39-filterInvariant41-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:37,33:70:99:691,0,871:8,29,1,32 chr1 16901539 . G T 414.33 PASS AC=1;AF=0.5;AN=2;DP=2455;set=variant3-variant4-variant6-filterInvariant9-variant10-filterInvariant12-variant19-variant20-filterInvariant22-variant23-variant25-variant28-filterInvariant31-variant32-variant35-filterInvariant36-variant37-variant38-variant39-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:76,39:115:99:1318,0,3030:59,17,25,14 chr1 16901549 . A G 1055.29 PASS AC=1;AF=0.5;AN=2;DP=4898;set=variant-variant3-variant4-variant6-variant8-variant10-variant12-variant15-variant19-variant20-variant21-variant22-variant23-filterInvariant24-variant25-variant27-variant28-variant30-filterInvariant31-filterInvariant32-filterInvariant33-variant34-variant35-variant36-variant37-variant38-variant39-filterInvariant40-filterInvariant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:85,34:119:99:1172,0,3365:66,19,21,13 chr1 16901627 . C A 815.96 PASS AC=1;AF=0.5;AN=2;DP=10017;set=variant3-filterInvariant4-variant5-variant6-filterInvariant8-filterInvariant10-variant11-filterInvariant12-variant13-filterInvariant17-filterInvariant18-filterInvariant19-variant20-filterInvariant21-variant22-filterInvariant23-variant26-filterInvariant27-filterInvariant28-filterInvariant29-variant35-variant36-variant37-variant38-variant39-filterInvariant40-variant41-variant42-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:229,54:283:99:596,0,5769:126,103,17,37 chr1 16901668 . T C 1062.77 PASS AC=1;AF=0.5;AN=2;DP=11084;set=variant-variant2-variant3-variant4-variant5-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant25-variant26-filterInvariant27-variant29-variant31-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:156,112:268:99:2341,0,3776:66,90,53,59 chr1 16901710 . C G 1081.82 PASS AC=1;AF=0.5;AN=2;DP=6655;set=variant-filterInvariant3-variant6-filterInvariant7-variant8-filterInvariant10-variant13-variant15-filterInvariant19-variant20-variant21-filterInvariant22-filterInvariant23-variant27-filterInvariant28-filterInvariant29-variant30-filterInvariant34-filterInvariant35-variant36-filterInvariant37-variant38-variant39-filterInvariant41-variant42-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:180,27:207:99:159,0,5936:72,108,4,23 chr1 16901714 . G A 3515.06 PASS AC=1;AF=0.56;AN=2;DP=10585;set=variant-variant2-variant3-variant4-variant5-variant6-filterInvariant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-filterInvariant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:89,100:189:99:2704,0,2110:32,57,34,66 chr1 16902727 . G C 357.93 PASS AC=1;AF=0.5;AN=2;DP=2947;set=variant3-variant4-variant6-filterInvariant7-variant9-variant10-filterInvariant12-filterInvariant13-variant14-filterInvariant19-filterInvariant20-filterInvariant22-variant23-variant25-filterInvariant27-filterInvariant28-filterInvariant29-filterInvariant31-variant32-variant35-filterInvariant36-filterInvariant37-variant38-variant39-filterInvariant41-filterInvariant42-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:83,55:138:99:1175,0,2046:64,19,43,12 chr1 16902750 . T C 190.7 PASS AC=1;AF=0.5;AN=2;DP=3998;set=filterInvariant3-filterInvariant7-filterInvariant8-filterInvariant9-variant10-filterInvariant12-filterInvariant18-filterInvariant20-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant27-filterInvariant31-variant33-filterInvariant35-filterInvariant38-variant39-filterInvariant40-filterInvariant42 GT:AD:DP:GQ:PL:SB 0/1:200,41:241:99:370,0,4923:131,69,27,14 chr1 16902804 . C A 271.37 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=3075;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:281,52:333:99:296,0,6691:155,126,29,23 chr1 16902884 . T C 240.51 PASS AC=1;AF=0.5;AN=2;DP=4946;set=variant-filterInvariant2-filterInvariant3-filterInvariant4-variant11-filterInvariant12-variant15-filterInvariant16-variant19-variant20-variant21-variant22-variant26-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant33-variant34-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:229,44:273:99:479,0,7411:103,126,16,28 chr1 16902894 . A G 1350.96 PASS AC=1;AF=0.648;AN=2;DP=8122;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-filterInvariant11-filterInvariant12-variant13-variant14-filterInvariant15-variant16-variant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-variant23-variant24-variant25-variant26-variant27-variant28-filterInvariant29-variant30-variant31-variant32-variant33-filterInvariant34-variant35-variant36-variant37-variant38-variant39-variant40-filterInvariant41-filterInvariant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:109,122:231:99:3569,0,2450:52,57,47,75 chr1 16903639 . A C 86.33 PASS AC=1;AF=0.5;AN=2;DP=201;FractionInformativeReads=1;set=variant2-filterInvariant5-variant16-variant28-filterInvariant35-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,6:34:64:64,0,948:25,3,5,1 chr1 16903651 . C A 70.81 PASS AC=1;AF=0.5;AN=2;DP=245;FractionInformativeReads=1;set=variant2-filterInvariant5-variant16-variant28-filterInvariant35-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,8:42:84:84,0,1106:31,3,6,2 chr1 16903663 . C T 521.83 PASS AC=1;AF=0.5;AN=2;DP=2211;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,25:53:99:799,0,858:22,6,25,0 chr1 16903674 . C T 434.01 PASS AC=1;AF=0.5;AN=2;DP=2747;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,36:72:99:1459,0,1643:30,6,36,0 chr1 16903683 . T A 539.53 PASS AC=1;AF=0.5;AN=2;DP=3406;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,54:93:99:1851,0,1672:33,6,47,7 chr1 16903912 . T A 1325.53 PASS AC=1;AF=0.698;AN=2;DP=4925;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant8-variant9-filterInvariant10-variant11-variant12-filterInvariant13-variant14-variant15-filterInvariant16-filterInvariant17-variant18-variant19-variant20-variant21-variant22-filterInvariant23-variant24-filterInvariant25-filterInvariant26-filterInvariant27-variant28-variant29-variant31-filterInvariant32-variant33-variant34-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant38-filterInvariant39-filterInvariant40-variant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:60,76:136:99:2411,0,1317:27,33,2,74 chr1 16905718 . A C 62.07 PASS AC=1;AF=0.5;AN=2;DP=627;FractionInformativeReads=1;set=variant3-variant4-variant7-variant9-variant10-variant11-variant12-variant15-variant17-variant18-variant19-variant20-variant21-variant22-filterInvariant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant37-filterInvariant39-variant40-variant41-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,5:21:99:143,0,545:2,14,0,5 chr1 16905788 . A G 79.68 PASS AC=1;AF=0.5;AN=2;DP=402;FractionInformativeReads=1;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-filterInvariant21-variant22-variant24-variant25-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,4:15:99:135,0,519:3,8,0,4 chr1 16905789 . T C 79.68 PASS AC=1;AF=0.5;AN=2;DP=393;FractionInformativeReads=1;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-filterInvariant21-variant22-variant24-variant25-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,4:14:99:135,0,519:2,8,0,4 chr1 16907107 . A C 508.11 PASS AC=1;AF=0.5;AN=2;DP=5289;set=variant-filterInvariant2-variant3-filterInvariant4-variant5-variant9-variant11-variant12-variant14-variant15-filterInvariant16-variant18-variant19-variant20-variant21-variant22-variant24-filterInvariant25-filterInvariant26-variant31-variant32-variant33-filterInvariant34-variant35-variant37-filterInvariant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:183,38:221:99:760,0,8814:164,19,32,6 chr1 16907110 . T C 3285.55 PASS AC=1;AF=0.5;AN=2;DP=8583;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:64,172:236:99:7361,0,3730:56,8,150,22 chr1 16907124 . A C 4836.66 PASS AC=1;AF=0.5;AN=2;DP=11837;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:87,236:323:99:8910,0,4227:71,16,188,48 chr1 16907165 . G A 1321.35 PASS AC=1;AF=0.5;AN=2;DP=16925;set=variant-variant2-variant3-filterInvariant4-filterInvariant5-filterInvariant7-filterInvariant11-filterInvariant12-variant14-variant15-variant16-filterInvariant18-filterInvariant19-variant20-variant21-filterInvariant22-variant26-filterInvariant28-filterInvariant30-filterInvariant31-filterInvariant32-variant34-variant35-variant36-variant37-filterInvariant41-filterInvariant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:592,110:702:99:1542,0,17817:420,172,82,28 chr1 16907328 . G T 17721.3 PASS AC=1;AF=0.511;AN=2;DP=60220;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:401,1447:1848:99:35403,0,6004:174,227,670,777 chr1 16907766 . A G 1790.32 PASS AC=1;AF=0.602;AN=2;DP=4209;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:39,77:116:99:2381,0,1172:35,4,71,6 chr1 16907854 . T A 6896.79 PASS AC=1;AF=0.5;AN=2;DP=25314;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:275,371:646:99:14972,0,10374:178,97,248,123 chr1 16907871 . C T 8073.31 PASS AC=1;AF=0.5;AN=2;DP=31480;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:338,470:808:99:16965,0,11735:209,129,292,178 chr1 16908115 . A G 3270.17 PASS AC=1;AF=0.5;AN=2;DP=13012;set=variant-variant2-variant3-variant4-variant5-variant6-filterInvariant7-variant8-variant9-variant10-variant11-variant12-filterInvariant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-filterInvariant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-filterInvariant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:168,150:318:99:4270,0,4613:50,118,39,111 chr1 16908914 . G A 88.37 PASS AC=1;AF=0.5;AN=2;DP=1554;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-filterInvariant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,17:44:99:357,0,670:22,5,12,5 chr1 16908989 . C T 186.1 PASS AC=1;AF=0.5;AN=2;DP=1331;set=variant2-variant3-filterInvariant4-variant7-variant11-variant12-variant15-filterInvariant16-variant18-variant20-variant21-variant22-variant26-variant30-filterInvariant31-variant32-variant33-variant34-variant35-variant36-variant37-filterInvariant40-filterInvariant41-filterInvariant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:47,14:61:99:204,0,1153:28,19,8,6 chr1 16909002 . TG T 118.66 PASS AC=1;AF=0.5;AN=2;DP=163;set=variant10-variant14-variant23-filterInvariant35 GT:AD:DP:GQ:PL:SB 0/1:57,8:65:78:78,0,1719:29,28,5,3 chr1 16909052 . C T 607.85 PASS AC=2;AF=0.966;AN=2;DP=1649;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-filterInvariant40-variant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1479,129,0:0,0,12,31 chr1 16909057 . A C 124.99 PASS AC=1;AF=0.5;AN=2;DP=85;FractionInformativeReads=1;set=variant10-variant23-filterInvariant35 GT:AD:DP:GQ:PL:SB 0/1:36,4:40:60:60,0,1474:11,25,0,4 chr1 16909061 . T G 100.02 PASS AC=1;AF=0.5;AN=2;DP=116;set=variant10-variant23-filterInvariant31-filterInvariant35 GT:AD:DP:GQ:PL:SB 0/1:35,4:39:63:63,0,1445:10,25,0,4 chr1 16909100 . G C 38.96 PASS AC=1;AF=0.5;AN=2;DP=825;FS=0;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant5-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant29-filterInvariant30-filterInvariant31-variant32-filterInvariant33-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant38-filterInvariant39-filterInvariant40-filterInvariant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:11,11:22:99:284,0,303:0,11,0,11 chr1 16909129 . T C 81.22 PASS AC=1;AF=0.523;AN=2;DP=748;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant13-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-variant25-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant38-filterInvariant39-filterInvariant40-variant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:8,13:21:99:396,0,196:0,8,0,13 chr1 16910064 . A G 2984.01 PASS AC=1;AF=0.534;AN=2;DP=10210;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:117,158:275:99:4109,0,2791:77,40,113,45 chr1 16910350 . C A 64.03 PASS AC=1;AF=0.5;AN=2;DP=35;FractionInformativeReads=1;set=variant-variant35-variant42-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:5,3:8:80:80,0,150:1,4,0,3 chr1 16912014 . A C 474.91 PASS AC=1;AF=0.5;AN=2;DP=614;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,10:19:99:379,0,317:3,6,1,9 chr1 16912015 . G A 43.56 PASS AC=1;AF=0.5;AN=2;DP=403;set=variant-variant3-variant4-variant5-variant9-variant11-variant15-variant16-variant20-variant21-variant22-variant24-variant25-variant26-variant31-variant32-variant33-variant35-variant37-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:16,3:19:73:73,0,866:4,12,0,3 chr1 16913584 . A C 656.15 PASS AC=1;AF=0.526;AN=2;DP=5700;set=variant10-variant12-filterInvariant13-variant14-variant15-filterInvariant18-variant19-variant20-filterInvariant25-filterInvariant26-filterInvariant29-filterInvariant31-variant34-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:174,65:239:99:1124,0,4253:92,82,26,39 chr1 16913612 . G A 292.39 PASS AC=1;AF=0.529;AN=2;DP=3902;set=filterInvariant10-variant12-filterInvariant13-variant14-variant15-filterInvariant18-variant19-variant20-variant22-filterInvariant25-variant34-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:177,46:223:99:751,0,4293:87,90,16,30 chr1 16914139 . C A 1736.14 PASS AC=1;AF=0.5;AN=2;DP=5556;set=variant-variant5-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant25-variant26-variant29-variant31-variant34-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:149,67:216:99:1603,0,5152:110,39,46,21 chr1 16914160 . G A 601.13 PASS AC=1;AF=0.5;AN=2;DP=11282;set=variant-variant2-filterInvariant3-filterInvariant4-variant5-filterInvariant6-filterInvariant7-filterInvariant9-filterInvariant10-filterInvariant11-variant12-variant13-variant14-filterInvariant15-variant16-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant27-variant28-variant29-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-filterInvariant34-variant35-filterInvariant36-variant37-variant38-filterInvariant39-filterInvariant40-variant41-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:190,77:267:99:2675,0,7924:119,71,67,10 chr1 16914168 . C G 1250.03 PASS AC=1;AF=0.5;AN=2;DP=12956;set=variant-filterInvariant2-filterInvariant3-filterInvariant4-variant5-filterInvariant6-filterInvariant7-filterInvariant8-variant9-filterInvariant10-filterInvariant11-filterInvariant12-variant13-variant14-filterInvariant15-variant16-variant17-variant18-filterInvariant19-filterInvariant20-variant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-variant26-filterInvariant27-filterInvariant28-variant29-filterInvariant30-variant31-filterInvariant32-filterInvariant33-filterInvariant34-variant35-filterInvariant36-filterInvariant37-variant38-filterInvariant39-filterInvariant40-variant41-filterInvariant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:216,87:303:99:2841,0,8442:135,81,77,10 chr1 16914252 . C T 789.41 PASS AC=1;AF=0.5;AN=2;DP=20324;set=filterInvariant2-variant3-variant4-filterInvariant5-variant6-filterInvariant7-variant9-variant10-variant12-filterInvariant13-variant14-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant28-filterInvariant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-filterInvariant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:401,396:797:99:8492,0,9877:207,194,217,179 chr1 16914306 . A G 1406.82 PASS AC=1;AF=0.5;AN=2;DP=22571;set=variant2-variant3-variant4-filterInvariant5-variant6-filterInvariant7-variant9-variant10-variant12-filterInvariant13-variant14-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant28-filterInvariant29-filterInvariant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-filterInvariant41-filterInvariant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:423,477:900:99:9869,0,9412:194,229,215,262 chr1 16914393 . G T 582.76 PASS AC=1;AF=0.5;AN=2;DP=5379;set=filterInvariant3-filterInvariant4-variant6-variant10-variant14-variant19-variant20-variant23-filterInvariant24-filterInvariant28-filterInvariant29-variant32-variant35-filterInvariant36-variant37-variant38-filterInvariant39-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:283,85:368:99:1600,0,16187:86,197,23,62 chr1 16914396 . C T 1199.27 PASS AC=1;AF=0.5;AN=2;DP=12760;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:151,196:347:99:7175,0,7301:47,104,51,145 chr1 16914415 . A G 712.43 PASS AC=1;AF=0.5;AN=2;DP=8760;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:107,111:218:99:4566,0,6416:28,79,22,89 chr1 16916358 . G C 2143.08 PASS AC=1;AF=0.548;AN=2;DP=5054;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:88,27:115:99:570,0,2102:49,39,17,10 chr1 16916515 . G A 71.75 PASS AC=1;AF=0.5;AN=2;DP=4799;set=filterInvariant2-filterInvariant3-variant4-variant11-variant15-filterInvariant16-filterInvariant18-filterInvariant19-variant20-filterInvariant21-variant22-filterInvariant26-filterInvariant28-variant34-variant35-filterInvariant36-variant37-filterInvariant40-filterInvariant41-filterInvariant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:173,39:212:99:540,0,4707:86,87,25,14 chr1 16916569 . A G 505.8 PASS AC=1;AF=0.5;AN=2;DP=9782;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-filterInvariant13-variant14-variant15-variant16-filterInvariant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:96,89:185:99:1850,0,2263:42,54,47,42 chr1 16916603 . C A 3327.64 PASS AC=1;AF=0.693;AN=2;DP=7718;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:36,118:154:99:2934,0,703:12,24,46,72 chr1 16918255 . A C 385.75 PASS AC=1;AF=0.5;AN=2;DP=6328;set=variant-variant2-filterInvariant3-variant4-variant5-filterInvariant6-variant7-variant8-filterInvariant9-filterInvariant11-filterInvariant12-variant13-variant14-filterInvariant15-variant16-filterInvariant17-variant18-variant19-variant20-variant21-variant22-variant23-filterInvariant24-variant25-variant26-filterInvariant28-filterInvariant29-variant30-filterInvariant31-filterInvariant32-filterInvariant34-variant35-filterInvariant36-filterInvariant37-filterInvariant38-filterInvariant39-variant40-filterInvariant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:124,28:152:99:487,0,3912:102,22,23,5 chr1 16918465 . A G 729.1 PASS AC=1;AF=0.5;AN=2;DP=26855;set=filterInvariant-variant2-variant3-variant4-variant5-filterInvariant7-filterInvariant10-variant11-variant12-variant14-variant15-variant16-filterInvariant17-filterInvariant18-filterInvariant19-variant20-filterInvariant21-variant22-filterInvariant23-filterInvariant24-filterInvariant25-variant26-variant28-filterInvariant29-filterInvariant30-variant31-filterInvariant33-filterInvariant34-variant35-filterInvariant36-variant37-variant38-filterInvariant39-filterInvariant40-filterInvariant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:541,76:617:99:1599,0,14194:249,292,21,55 chr1 16918502 . A G 5971.79 PASS AC=1;AF=0.5;AN=2;DP=21919;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:147,291:438:99:7468,0,2998:64,83,112,179 chr1 16918717 . C T 440.5 PASS AC=1;AF=0.5;AN=2;DP=2959;set=variant3-filterInvariant4-filterInvariant5-variant6-variant9-variant10-variant12-variant13-variant14-filterInvariant17-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-filterInvariant33-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:50,62:112:99:1455,0,1279:28,22,37,25 chr1 16918734 . G C 446.86 PASS AC=1;AF=0.5;AN=2;DP=3235;set=variant3-filterInvariant4-variant6-variant9-variant10-variant12-variant13-variant14-filterInvariant17-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-filterInvariant33-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:58,66:124:99:1494,0,1378:33,25,36,30 chr1 16918888 . C G 219.01 PASS AC=1;AF=0.5;AN=2;DP=2263;set=variant-variant3-variant4-variant5-variant6-filterInvariant7-filterInvariant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-filterInvariant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:34,15:49:99:361,0,868:13,21,3,12 chr1 16950261 . G C 644.43 PASS AC=1;AF=0.5;AN=2;DP=4899;set=variant-filterInvariant2-variant3-variant4-variant5-filterInvariant9-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-filterInvariant21-variant24-variant25-variant26-variant27-filterInvariant31-filterInvariant34-variant35-variant37-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:203,43:246:99:701,0,6299:140,63,29,14 chr1 16950470 . C T 467.23 PASS AC=1;AF=0.5;AN=2;DP=4180;set=variant-variant5-filterInvariant9-filterInvariant11-filterInvariant12-variant13-variant14-variant15-variant18-filterInvariant20-variant21-filterInvariant22-filterInvariant25-filterInvariant26-filterInvariant31-filterInvariant35-filterInvariant37-filterInvariant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:219,38:257:99:332,0,6362:70,149,16,22 chr1 16953672 . C T 690.72 PASS AC=1;AF=0.5;AN=2;DP=9689;set=variant2-filterInvariant3-variant4-variant6-filterInvariant7-filterInvariant9-variant10-filterInvariant12-filterInvariant13-variant14-variant19-variant20-variant23-filterInvariant24-filterInvariant25-variant28-variant29-filterInvariant30-variant32-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant39-filterInvariant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:403,63:466:99:630,0,11574:274,129,41,22 chr1 16953881 . C G 2461.43 PASS AC=1;AF=0.5;AN=2;DP=12528;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-filterInvariant9-filterInvariant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-filterInvariant23-filterInvariant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:306,159:465:99:3685,0,9415:96,210,53,106 chr1 16953889 . G C 502.34 PASS AC=1;AF=0.5;AN=2;DP=9403;set=variant-variant2-filterInvariant3-filterInvariant4-variant5-variant9-variant11-variant12-filterInvariant13-filterInvariant14-variant15-filterInvariant16-variant18-variant19-filterInvariant20-variant21-variant22-filterInvariant23-variant24-filterInvariant25-filterInvariant26-filterInvariant27-variant29-variant31-variant33-variant34-filterInvariant35-variant36-variant37-filterInvariant38-variant40-filterInvariant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:370,57:427:99:294,0,12722:113,257,19,38 chr1 16955128 . A G 323.58 PASS AC=1;AF=0.5;AN=2;DP=5956;set=variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant11-filterInvariant16-variant19-variant20-filterInvariant21-variant23-filterInvariant24-variant25-variant27-variant28-filterInvariant29-filterInvariant31-filterInvariant32-filterInvariant33-filterInvariant34-variant35-variant36-variant38-variant39-variant40-filterInvariant41-variant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:198,61:259:99:1088,0,5189:85,113,27,34 chr1 16955289 . A G 48.67 PASS AC=1;AF=0.5;AN=2;DP=1929;MQ=60;set=variant-variant5-variant9-filterInvariant11-variant12-variant13-variant14-variant15-variant18-variant20-variant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant26-variant29-variant31-variant33-variant34-variant35-filterInvariant37-filterInvariant38-filterInvariant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:68,18:86:99:332,0,1765:26,42,5,13 chr1 16969381 . C T 2261.75 PASS AC=1;AF=0.523;AN=2;DP=14454;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:111,290:401:99:7555,0,2222:52,59,131,159 chr1 16971948 . C G 56.64 PASS AC=1;AF=0.5;AN=2;DP=6045;set=filterInvariant-variant2-variant3-variant4-variant5-variant6-filterInvariant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:118,43:161:99:936,0,3582:86,32,30,13 chr1 16972067 . C T 690.83 PASS AC=1;AF=0.5;AN=2;DP=14829;set=variant-variant2-variant3-filterInvariant4-variant5-variant6-filterInvariant7-filterInvariant9-variant11-variant12-variant13-variant14-variant15-variant16-filterInvariant18-filterInvariant19-filterInvariant20-variant21-variant22-variant25-filterInvariant26-variant27-filterInvariant28-filterInvariant30-variant31-variant32-filterInvariant34-filterInvariant35-filterInvariant37-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:494,71:565:99:341,0,18195:262,232,38,33 chr1 16972068 . A G 2913.55 PASS AC=1;AF=0.5;AN=2;DP=18980;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-filterInvariant17-variant18-variant19-variant20-variant21-variant22-variant23-filterInvariant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:345,221:566:99:5994,0,8379:179,166,121,100 chr1 16972134 . C T 210.67 PASS AC=1;AF=0.5;AN=2;DP=11824;set=filterInvariant4-variant5-variant9-variant10-variant13-filterInvariant15-variant16-filterInvariant17-variant18-variant19-filterInvariant21-filterInvariant22-filterInvariant23-variant24-variant25-variant27-filterInvariant28-variant29-filterInvariant30-filterInvariant31-variant33-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant39-variant41-variant42-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:441,71:512:99:533,0,11109:218,223,26,45 chr1 16972189 . C A 1198.01 PASS AC=1;AF=0.5;AN=2;DP=5948;set=variant7-variant10-filterInvariant13-variant17-variant18-variant19-variant20-variant21-variant24-variant26-variant28-variant29-variant30-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:224,117:341:99:2501,0,5630:93,131,48,69 chr1 16972920 . C T 3794.73 PASS AC=1;AF=0.5;AN=2;DP=28313;set=variant2-variant3-variant4-variant6-filterInvariant7-variant9-variant10-variant12-variant13-variant14-variant19-variant20-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:1111,281:1392:99:4019,0,28629:620,491,157,124 chr1 16972940 . G A 6661.85 PASS AC=1;AF=0.513;AN=2;DP=41528;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-filterInvariant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:643,897:1540:99:21575,0,14332:338,305,478,419 chr1 16973152 . A G 2710.95 PASS AC=1;AF=0.513;AN=2;DP=16123;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:207,323:530:99:9347,0,4902:104,103,162,161 chr1 16973184 . G A 2493.29 PASS AC=1;AF=0.5;AN=2;DP=16940;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-filterInvariant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-filterInvariant22-filterInvariant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-filterInvariant31-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:258,291:549:99:7240,0,7164:141,117,146,145 chr1 16973388 . C T 110.61 PASS AC=1;AF=0.525;AN=2;DP=5866;set=filterInvariant3-filterInvariant4-variant5-filterInvariant9-filterInvariant10-variant11-variant15-filterInvariant16-filterInvariant19-variant21-filterInvariant26-variant34-variant35-filterInvariant36-filterInvariant39-variant40-variant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:303,72:375:99:1923,0,16392:158,145,39,33 chr1 16973400 . G A 227.7 PASS AC=1;AF=0.522;AN=2;DP=6330;set=filterInvariant4-variant5-filterInvariant9-variant11-filterInvariant12-filterInvariant13-variant15-variant16-filterInvariant18-filterInvariant19-variant21-variant25-filterInvariant26-filterInvariant29-variant33-variant34-variant35-filterInvariant36-variant40-variant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:315,62:377:99:1808,0,17111:159,156,38,24 chr1 16973423 . C T 75.13 PASS AC=1;AF=0.5;AN=2;DP=3306;set=filterInvariant-filterInvariant5-variant11-filterInvariant15-variant21-filterInvariant26-variant34-filterInvariant35-filterInvariant36-variant40-filterInvariant41-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:318,44:362:99:749,0,16914:169,149,33,11 chr1 16973919 . A G 1701.58 PASS AC=1;AF=0.5;AN=2;DP=40043;set=filterInvariant-variant2-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant13-filterInvariant14-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant27-variant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant38-filterInvariant39-filterInvariant40-filterInvariant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:625,492:1117:99:8941,0,12748:337,288,259,233 chr1 16973996 . A G 2704.38 PASS AC=1;AF=0.5;AN=2;DP=25098;set=filterInvariant-variant2-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant10-variant11-filterInvariant12-filterInvariant13-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant27-variant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-filterInvariant34-filterInvariant35-filterInvariant37-filterInvariant38-filterInvariant41-filterInvariant42-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:686,121:807:99:2413,0,26039:274,412,38,83 chr1 16974010 . G C 1226.82 PASS AC=1;AF=0.5;AN=2;DP=18974;set=filterInvariant-variant2-filterInvariant3-variant4-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant13-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant27-variant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-filterInvariant34-filterInvariant35-filterInvariant37-filterInvariant38-filterInvariant41-filterInvariant42 GT:AD:DP:GQ:PL:SB 0/1:570,89:659:99:1967,0,23510:220,350,29,60 chr1 16974021 . G A 2594.63 PASS AC=1;AF=0.5;AN=2;DP=16953;set=filterInvariant-variant2-variant3-variant4-variant5-filterInvariant7-variant8-filterInvariant9-filterInvariant10-variant11-filterInvariant12-filterInvariant13-variant14-variant15-variant16-filterInvariant17-variant18-filterInvariant19-variant20-variant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant27-variant28-filterInvariant29-variant30-filterInvariant31-variant34-filterInvariant35-variant36-variant37-filterInvariant39-variant40-filterInvariant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:301,251:552:99:5079,0,6666:107,194,94,157 chr1 16974243 . G C 209.6 PASS AC=1;AF=0.5;AN=2;DP=3318;set=variant2-filterInvariant3-filterInvariant9-variant11-filterInvariant13-filterInvariant15-variant16-filterInvariant17-variant18-filterInvariant19-variant21-filterInvariant24-variant25-variant29-filterInvariant31-filterInvariant33-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant40-variant41-filterInvariant42-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:176,21:197:63:63,0,6824:151,25,21,0 chr1 16974256 . G C 2620.2 PASS AC=1;AF=0.511;AN=2;DP=9597;set=filterInvariant-variant2-filterInvariant3-filterInvariant4-variant5-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant10-variant11-filterInvariant12-variant13-filterInvariant14-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-filterInvariant34-filterInvariant35-variant36-filterInvariant37-variant38-filterInvariant39-variant40-filterInvariant41-variant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:123,135:258:99:4402,0,3420:89,34,135,0 chr1 16974511 . G A 532.37 PASS AC=1;AF=0.5;AN=2;DP=27099;set=filterInvariant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-filterInvariant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-filterInvariant22-filterInvariant23-variant24-variant25-variant26-variant27-filterInvariant28-variant29-variant30-variant31-filterInvariant32-variant33-variant34-filterInvariant35-variant36-filterInvariant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:713,119:832:99:1007,0,20335:380,333,57,62 chr1 16974637 . T C 4034.58 PASS AC=1;AF=0.5;AN=2;DP=35195;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-filterInvariant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-filterInvariant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:715,315:1030:99:8943,0,17582:358,357,121,194 chr1 16974662 . C A 3091.65 PASS AC=1;AF=0.5;AN=2;DP=23683;set=variant5-variant9-variant10-variant12-variant13-filterInvariant15-variant16-filterInvariant17-variant18-variant19-variant20-filterInvariant21-variant22-variant23-variant24-variant25-variant27-filterInvariant28-variant29-filterInvariant30-variant31-filterInvariant32-variant33-variant34-variant35-variant36-filterInvariant37-filterInvariant38-variant39-filterInvariant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:742,178:920:99:2585,0,29353:341,401,60,118 chr1 16974666 . C T 2542.03 PASS AC=1;AF=0.5;AN=2;DP=22851;set=variant-variant2-variant3-variant4-filterInvariant5-variant7-filterInvariant8-filterInvariant9-filterInvariant10-variant11-filterInvariant12-variant14-variant15-variant16-filterInvariant17-variant18-variant19-variant20-variant21-filterInvariant25-variant26-filterInvariant27-filterInvariant28-variant29-variant30-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:514,389:903:99:7654,0,15763:209,305,182,207 chr1 16974758 . G A 1248.58 PASS AC=1;AF=0.514;AN=2;DP=8461;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant4-variant5-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant15-filterInvariant16-filterInvariant17-variant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant39-filterInvariant40-filterInvariant41-variant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:211,108:319:99:3362,0,5805:113,98,8,100 chr1 16974786 . G C 426.13 PASS AC=1;AF=0.5;AN=2;DP=5939;set=filterInvariant-filterInvariant2-filterInvariant3-variant5-filterInvariant9-filterInvariant10-filterInvariant11-variant12-variant13-filterInvariant15-filterInvariant16-variant18-filterInvariant21-variant22-filterInvariant25-filterInvariant26-variant33-variant34-filterInvariant35-filterInvariant36-filterInvariant39-filterInvariant40-variant41-variant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:256,26:282:99:241,0,7928:131,125,0,26 chr1 16974869 . G C 5080.64 PASS AC=1;AF=0.571;AN=2;DP=15360;set=variant2-variant3-variant4-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant19-variant20-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:237,238:475:99:6020,0,5712:132,105,142,96 chr1 16974915 . C T 354.63 PASS AC=1;AF=0.529;AN=2;DP=7229;set=filterInvariant2-filterInvariant11-filterInvariant15-variant16-filterInvariant18-filterInvariant20-variant21-filterInvariant26-filterInvariant29-variant34-filterInvariant35-filterInvariant36-filterInvariant40-filterInvariant41-filterInvariant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:604,74:678:99:604,0,24093:313,291,56,18 chr1 16974972 . C T 802.72 PASS AC=1;AF=0.519;AN=2;DP=18860;set=filterInvariant-variant2-variant3-variant4-variant5-variant7-filterInvariant9-variant11-variant15-variant16-variant18-variant19-variant20-variant21-variant26-variant29-filterInvariant30-variant34-variant35-variant36-variant37-filterInvariant39-variant40-variant41-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:609,237:846:99:3927,0,16206:282,327,157,80 chr1 16975002 . C T 1585.79 PASS AC=1;AF=0.513;AN=2;DP=28075;set=variant-variant2-variant3-variant4-variant5-variant7-filterInvariant9-filterInvariant10-variant11-variant12-variant13-filterInvariant14-variant15-variant16-filterInvariant17-variant18-variant19-variant20-variant21-variant22-filterInvariant24-filterInvariant25-variant26-filterInvariant27-filterInvariant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:534,333:867:99:6508,0,14187:243,291,205,128 chr1 16975084 . G A 920.06 PASS AC=1;AF=0.5;AN=2;DP=14394;set=filterInvariant7-filterInvariant10-filterInvariant17-filterInvariant19-filterInvariant20-variant21-filterInvariant24-filterInvariant26-filterInvariant28-variant29-variant30-variant34-variant35-variant36-filterInvariant37-filterInvariant39-variant40-filterInvariant41-variant42-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:697,249:946:99:4105,0,18255:369,328,124,125 chr1 16975202 . T C 5578.5 PASS AC=1;AF=0.5;AN=2;DP=31112;set=variant2-filterInvariant3-filterInvariant4-variant5-variant7-variant9-variant10-filterInvariant11-variant12-variant13-variant14-filterInvariant15-variant16-variant17-variant18-filterInvariant19-variant21-variant22-filterInvariant23-variant24-variant25-variant27-variant28-filterInvariant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant41-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:799,262:1061:99:4071,0,20152:389,410,130,132 chr1 16975230 . G C 5755.78 PASS AC=1;AF=0.705;AN=2;DP=33096;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:89,834:923:99:21764,0,110:44,45,387,447 chr1 16975724 . GC G 455.51 PASS AC=1;AF=0.5;AN=2;DP=6070;set=variant-variant2-variant3-variant4-variant5-filterInvariant7-filterInvariant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-filterInvariant23-variant24-variant25-variant26-filterInvariant27-variant30-variant31-variant34-variant35-variant36-variant37-filterInvariant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:130,38:168:99:849,0,4138:67,63,22,16 chr1 16975868 . T A 479.95 PASS AC=1;AF=0.516;AN=2;DP=4642;set=variant-variant2-variant3-variant4-variant5-filterInvariant7-variant9-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-filterInvariant23-filterInvariant24-variant25-variant26-filterInvariant27-filterInvariant30-filterInvariant31-variant34-filterInvariant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:99,22:121:99:272,0,2480:45,54,7,15 chr1 16975912 . CCCTGTT C 62.36 PASS AC=1;AF=0.5;AN=2;DP=1757;set=filterInvariant-variant2-variant3-variant4-variant5-filterInvariant9-variant11-filterInvariant14-variant15-variant16-variant18-variant20-variant21-variant26-filterInvariant27-variant34-filterInvariant35-filterInvariant37-filterInvariant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:80,8:88:96:96,0,3264:40,40,1,7 chr1 16975994 . T C 97.74 PASS AC=1;AF=0.516;AN=2;DP=3085;set=filterInvariant2-filterInvariant3-variant5-variant9-variant10-variant11-variant12-variant13-variant15-variant16-filterInvariant17-variant18-variant19-variant20-variant21-filterInvariant22-variant24-variant25-filterInvariant26-variant27-filterInvariant28-variant29-filterInvariant30-variant31-variant33-variant34-variant35-variant36-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:101,26:127:99:463,0,2441:52,49,22,4 chr1 16976032 . A C 448.16 PASS AC=1;AF=0.5;AN=2;DP=4400;set=variant2-variant3-variant4-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant19-variant20-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-filterInvariant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:112,51:163:99:915,0,2789:63,49,25,26 chr1 16976193 . C T 99.19 PASS AC=1;AF=0.515;AN=2;DP=5967;set=filterInvariant3-variant5-filterInvariant6-variant9-variant10-variant11-variant12-variant13-variant15-variant16-filterInvariant17-variant18-filterInvariant19-variant20-variant21-variant22-variant24-filterInvariant25-variant26-variant27-filterInvariant28-variant29-filterInvariant31-variant33-variant34-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant39-filterInvariant40-variant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:164,29:193:99:338,0,4488:100,64,5,24 chr1 16976539 . A G 232.05 PASS AC=1;AF=0.513;AN=2;DP=4751;set=variant2-variant3-variant4-variant5-variant6-filterInvariant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-filterInvariant26-variant27-variant28-filterInvariant29-variant30-variant31-variant32-filterInvariant33-variant34-variant35-variant36-variant37-variant40-variant41-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,58:116:99:1377,0,1528:35,23,45,13 chr1 16976569 . G A 380.55 PASS AC=1;AF=0.5;AN=2;DP=8060;set=variant2-filterInvariant3-variant4-variant5-filterInvariant6-filterInvariant7-variant9-variant10-variant11-variant14-variant15-variant16-variant17-filterInvariant18-variant19-variant20-variant21-variant23-variant24-variant25-filterInvariant26-variant27-filterInvariant29-variant30-variant31-filterInvariant32-filterInvariant33-variant34-variant35-filterInvariant37-filterInvariant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:196,99:295:99:1934,0,5199:126,70,72,27 chr1 16976641 . C T 48.8 PASS AC=1;AF=0.5;AN=2;DP=22201;set=filterInvariant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant12-variant13-filterInvariant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-filterInvariant23-variant24-variant25-variant27-variant28-filterInvariant29-variant30-variant31-variant32-variant33-filterInvariant34-filterInvariant35-variant37-filterInvariant38-filterInvariant39-variant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:617,145:762:99:1238,0,25418:319,298,76,69 chr1 16976649 . C T 2947.95 PASS AC=1;AF=0.5;AN=2;DP=20832;set=variant2-variant3-variant4-variant5-variant9-variant10-variant11-filterInvariant12-variant13-filterInvariant14-variant15-variant16-variant17-variant18-filterInvariant19-variant20-variant21-filterInvariant22-variant24-variant25-variant27-filterInvariant28-filterInvariant29-filterInvariant31-filterInvariant32-variant33-variant34-variant35-variant37-filterInvariant38-variant39-variant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:635,155:790:99:4210,0,14642:318,317,80,75 chr1 16976679 . G A 1400.21 PASS AC=1;AF=0.5;AN=2;DP=21684;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-filterInvariant16-variant17-variant18-filterInvariant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-filterInvariant29-variant30-variant31-variant32-variant33-filterInvariant34-variant35-variant36-variant37-variant38-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:578,137:715:99:1551,0,15340:264,314,75,62 chr1 16976681 . G T 799.96 PASS AC=1;AF=0.5;AN=2;DP=16039;set=filterInvariant2-filterInvariant3-filterInvariant4-variant5-variant9-variant10-variant11-filterInvariant13-variant16-filterInvariant17-variant18-variant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant24-variant25-filterInvariant28-filterInvariant29-filterInvariant31-variant33-filterInvariant34-filterInvariant35-variant36-filterInvariant37-variant38-filterInvariant39-filterInvariant40-filterInvariant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:578,134:712:99:1351,0,15320:274,304,63,71 chr1 16976772 . G T 226.95 PASS AC=1;AF=0.5;AN=2;DP=3223;set=variant-filterInvariant5-filterInvariant7-filterInvariant9-variant10-filterInvariant13-filterInvariant14-variant15-filterInvariant17-variant18-variant19-variant20-variant21-variant26-filterInvariant27-variant29-variant30-variant34-variant35-filterInvariant36-filterInvariant37-filterInvariant41-filterInvariant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:96,40:136:99:812,0,2548:26,70,5,35 chr1 16976786 . G C 433.21 PASS AC=1;AF=0.5;AN=2;DP=1284;set=variant-filterInvariant5-variant6-variant8-filterInvariant10-filterInvariant15-filterInvariant20-variant21-variant26-variant27-variant29-variant30-variant34-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:63,18:81:99:350,0,1777:15,48,0,18 chr1 17017675 . C A 3900.56 PASS AC=1;AF=0.524;AN=2;DP=17980;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-filterInvariant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:159,200:359:99:4469,0,3789:74,85,90,110 chr1 17017717 . C T 1147.63 PASS AC=1;AF=0.5;AN=2;DP=10038;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant26-variant27-variant29-variant31-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:198,65:263:99:1989,0,8876:79,119,23,42 chr1 17017734 . C T 877.23 PASS AC=1;AF=0.5;AN=2;DP=8029;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant26-variant27-variant29-variant31-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:165,57:222:99:1891,0,8187:59,106,15,42 chr1 17022952 . C A 11693.4 PASS AC=2;AF=0.932;AN=2;DP=20684;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,465:466:99:13563,1380,0:0,1,259,206 chr1 17023110 . G A 405.18 PASS AC=1;AF=0.5;AN=2;DP=19688;set=filterInvariant-variant2-variant3-variant4-variant5-variant9-variant11-variant12-variant13-variant14-variant15-filterInvariant16-filterInvariant18-filterInvariant19-variant20-variant21-variant22-variant24-variant25-filterInvariant26-filterInvariant27-variant31-variant32-filterInvariant33-filterInvariant34-variant35-variant37-variant38-filterInvariant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:498,153:651:99:2627,0,13123:248,250,77,76 chr1 17023143 . C T 415.59 PASS AC=1;AF=0.5;AN=2;DP=22679;set=filterInvariant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-filterInvariant18-variant19-variant20-variant21-variant22-variant24-variant25-filterInvariant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-filterInvariant34-variant35-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:477,127:604:99:2127,0,12933:225,252,58,69 chr1 17023182 . C G 6145.8 PASS AC=1;AF=0.5;AN=2;DP=22464;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:137,410:547:99:11587,0,2868:65,72,205,205 chr1 17023209 . G A 1630.24 PASS AC=1;AF=0.5;AN=2;DP=8015;set=variant2-variant7-variant10-variant13-variant16-variant25-filterInvariant26-variant28-variant30-variant31-variant32-variant34-variant35-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:378,132:510:99:2625,0,11071:197,181,66,66 chr1 17023376 . C T 2593.56 PASS AC=1;AF=0.5;AN=2;DP=42153;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-filterInvariant18-variant19-variant20-variant21-variant22-variant24-variant25-filterInvariant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:780,249:1029:99:4299,0,20357:375,405,128,121 chr1 17023403 . G A 2594.41 PASS AC=1;AF=0.5;AN=2;DP=32572;set=variant-variant2-variant3-variant4-variant5-variant9-variant11-variant12-variant13-variant14-variant15-filterInvariant16-filterInvariant18-variant19-variant20-variant21-variant22-variant24-variant25-filterInvariant26-filterInvariant27-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:740,243:983:99:4086,0,19373:338,402,117,126 chr1 17023483 . C T 1419.68 PASS AC=1;AF=0.5;AN=2;DP=18766;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-filterInvariant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:376,128:504:99:2566,0,10313:130,246,37,91 chr1 17023509 . T C 1217.62 PASS AC=1;AF=0.5;AN=2;DP=11889;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:239,78:317:99:1761,0,8613:66,173,19,59 chr1 17023511 . C A 13983.3 PASS AC=1;AF=0.659;AN=2;DP=12692;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:159,150:309:99:4946,0,4550:44,115,38,112 chr1 17023569 . T C 5032.01 PASS AC=2;AF=0.909;AN=2;DP=3717;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,91:91:99:3725,274,0:0,0,9,82 chr1 17025992 . G A 682.13 PASS AC=1;AF=0.5;AN=2;DP=6791;set=variant-variant2-variant3-variant4-variant5-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-filterInvariant25-variant26-variant27-variant31-variant32-filterInvariant33-filterInvariant34-variant35-variant37-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:148,62:210:99:1121,0,6011:91,57,34,28 chr1 17026004 . C G 4742.66 PASS AC=1;AF=0.524;AN=2;DP=9741;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-filterInvariant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,166:233:99:4323,0,2176:36,31,100,66 chr1 17026043 . G GGCGGCA,GGCA,GGCAGCAGCA 240.48 PASS AC=0,1,0;AF=0.051,0.436,0.013;AN=2;DP=12430;set=filterInvariant-variant2-variant3-variant4-variant5-filterInvariant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant43-variant44 GT:DP:GQ:SB 0/2:299:99:121,102,41,35 chr1 17026087 . G A 2582.11 PASS AC=1;AF=0.5;AN=2;DP=13055;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:259,74:333:99:1142,0,6818:127,132,38,36 chr1 17029462 . A G 390.68 PASS AC=1;AF=0.5;AN=2;DP=5548;set=filterInvariant2-variant3-variant4-variant5-variant9-variant11-variant12-variant13-variant14-variant15-filterInvariant16-variant18-filterInvariant19-variant20-variant21-variant22-variant24-variant25-filterInvariant26-variant31-variant32-variant33-filterInvariant34-variant35-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:150,39:189:99:543,0,3655:88,62,24,15 chr1 17029513 . C G 2233.74 PASS AC=1;AF=0.563;AN=2;DP=7022;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-filterInvariant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:112,56:168:99:1058,0,2671:58,54,26,30 chr1 17030325 . A G 2257.9 PASS AC=1;AF=0.583;AN=2;DP=3569;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,73:97:99:2240,0,383:15,9,51,22 chr1 17030336 . C T 1046.55 PASS AC=1;AF=0.5;AN=2;DP=3347;MQ=60;set=variant-variant2-filterInvariant3-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant13-variant14-variant15-filterInvariant16-variant17-filterInvariant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant31-variant32-variant33-variant34-variant35-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:83,26:109:99:538,0,2370:55,28,19,7 chr1 17030504 . T A 2786.23 PASS AC=1;AF=0.5;AN=2;DP=11266;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:213,80:293:99:2744,0,10223:111,102,39,41 chr1 17030515 . G A 3138.57 PASS AC=1;AF=0.5;AN=2;DP=12237;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:229,84:313:99:2826,0,11214:122,107,40,44 chr1 17030518 . C T 3210.33 PASS AC=1;AF=0.5;AN=2;DP=12496;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:239,83:322:99:2860,0,11473:127,112,40,43 chr1 17030519 . T G 3216.35 PASS AC=1;AF=0.5;AN=2;DP=12620;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:244,84:328:99:2860,0,11473:130,114,41,43 chr1 17030590 . G A 2458.17 PASS AC=1;AF=0.5;AN=2;DP=15584;set=variant-filterInvariant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-filterInvariant22-variant24-filterInvariant25-filterInvariant26-variant27-variant29-variant31-variant33-filterInvariant34-variant35-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:293,68:361:99:934,0,7949:150,143,32,36 chr1 17030716 . G A 1940.21 PASS AC=1;AF=0.5;AN=2;DP=5500;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant37-filterInvariant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:99,40:139:99:1017,0,2866:28,71,9,31 chr1 17030729 . C T 923.14 PASS AC=1;AF=0.5;AN=2;DP=4093;set=variant-filterInvariant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant14-variant15-variant16-filterInvariant17-filterInvariant18-variant19-variant20-variant21-filterInvariant26-filterInvariant27-variant29-filterInvariant31-variant34-variant35-variant36-variant37-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:86,17:103:99:245,0,2888:17,69,5,12 chr1 17033758 . A G 7140.75 PASS AC=1;AF=0.512;AN=2;DP=15223;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:90,249:339:99:7154,0,1809:55,35,154,95 chr1 17033805 . C T 5734.92 PASS AC=1;AF=0.5;AN=2;DP=18201;set=variant-variant2-variant5-variant6-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-filterInvariant30-variant31-variant32-variant33-variant34-variant35-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:392,148:540:99:2665,0,10539:223,169,83,65 chr1 17033854 . C T 12121.9 PASS AC=1;AF=0.5;AN=2;DP=29014;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:149,525:674:99:13532,0,2373:75,74,276,249 chr1 17034041 . T C 14198.5 PASS AC=2;AF=0.693;AN=2;DP=15527;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,372:372:99:12297,1116,0:0,0,170,202 chr1 17034125 . C CAGCT 5556.62 PASS AC=1;AF=0.5;AN=2;DP=9986;set=variant-variant2-variant5-variant6-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:200,73:273:99:2396,0,8089:79,121,29,44 chr1 17034140 . C G 52.34 PASS AC=1;AF=0.5;AN=2;DP=4315;set=filterInvariant2-filterInvariant7-variant9-filterInvariant10-variant16-filterInvariant19-variant24-variant25-filterInvariant28-variant29-variant30-filterInvariant31-filterInvariant32-filterInvariant33-variant35-variant39-variant40-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:217,35:252:99:571,0,6859:93,124,11,24 chr1 17034167 . G A 511.72 PASS AC=1;AF=0.5;AN=2;DP=5587;set=variant-variant2-variant3-variant4-filterInvariant7-variant9-filterInvariant10-filterInvariant11-variant12-variant13-variant16-variant18-filterInvariant21-variant22-variant24-variant25-variant29-filterInvariant30-filterInvariant31-filterInvariant32-variant33-filterInvariant35-variant36-variant38-variant39-variant40-variant41-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:165,22:187:99:204,0,4884:64,101,9,13 chr1 17034250 . C G 755.61 PASS AC=1;AF=0.561;AN=2;DP=2078;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,34:48:99:1010,0,488:9,5,19,15 chr1 17034268 . G A 222.21 PASS AC=1;AF=0.5;AN=2;DP=1318;set=variant-variant5-variant6-variant8-variant10-filterInvariant11-variant14-filterInvariant17-variant19-variant20-filterInvariant21-variant26-filterInvariant27-variant29-variant35-filterInvariant36-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:44,15:59:99:345,0,1690:29,15,9,6 chr1 17034285 . C G 191.25 PASS AC=1;AF=0.5;AN=2;DP=1769;set=variant2-variant7-filterInvariant9-variant10-variant16-filterInvariant17-variant19-variant24-variant25-filterInvariant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,14:78:99:386,0,2637:38,26,10,4 chr1 17034297 . G A 457 PASS AC=1;AF=0.5;AN=2;DP=1987;set=variant2-variant7-filterInvariant9-variant10-variant16-filterInvariant17-variant19-variant24-variant25-filterInvariant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:63,17:80:99:452,0,2602:37,26,12,5 chr1 17034455 . CGCGCGCGT C 1366.12 PASS AC=1;AF=0.5;AN=2;DP=14834;set=variant-variant2-variant5-variant9-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant31-variant32-variant33-variant34-variant35-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:367,108:475:99:3403,0,15395:197,170,59,49 chr1 17034513 . G A 1583.03 PASS AC=1;AF=0.5;AN=2;DP=469;FS=1.339;FractionInformativeReads=0.996;MQ=58.47;MQRankSum=0.234;QD=3.38;ReadPosRankSum=1.127;SOR=0.651;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:360,107:467:99:1611,0,9113:170,190,55,52 chr1 17044433 . C T 81.08 PASS AC=1;AF=0.5;AN=2;DP=1151;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant19-variant20-variant21-variant26-variant27-variant29-filterInvariant31-variant34-variant35-variant36-variant37-variant38-variant41-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,10:35:99:296,0,864:22,3,10,0 chr1 17044457 . G C 793.85 PASS AC=2;AF=0.875;AN=2;DP=2664;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:2108,180,0:0,0,48,12 chr1 17044511 . T C 2005.33 PASS AC=1;AF=0.583;AN=2;DP=6442;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,94:123:99:2579,0,527:21,8,56,38 chr1 17044589 . G A 155.14 PASS AC=1;AF=0.514;AN=2;DP=11031;set=filterInvariant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-filterInvariant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-filterInvariant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:174,69:243:99:1383,0,4480:90,84,35,34 chr1 17044662 . G C 435.09 PASS AC=1;AF=0.5;AN=2;DP=7400;set=variant-variant2-variant3-variant4-variant5-variant9-variant11-variant12-variant13-variant14-variant15-filterInvariant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-filterInvariant26-filterInvariant27-variant31-variant32-variant33-variant35-variant37-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:169,42:211:99:681,0,4432:70,99,19,23 chr1 17044695 . A G 491.95 PASS AC=1;AF=0.5;AN=2;DP=3893;set=variant2-variant3-variant4-variant6-variant7-variant10-variant12-variant13-variant14-variant16-filterInvariant17-variant18-variant19-variant22-variant23-variant24-variant25-variant28-variant30-variant31-variant32-variant33-variant35-filterInvariant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:125,31:156:99:580,0,3312:48,77,11,20 chr1 17046361 . A T 1766.84 PASS AC=1;AF=0.5;AN=2;DP=5813;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:78,66:144:99:1687,0,2085:50,28,48,18 chr1 17046439 . C A 1602.77 PASS AC=1;AF=0.5;AN=2;DP=5605;set=variant2-variant7-variant10-filterInvariant16-variant25-filterInvariant26-variant28-variant30-variant32-variant34-variant35-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:300,67:367:99:1022,0,10674:194,106,44,23 chr1 17046456 . T C 5225.26 PASS AC=1;AF=0.5;AN=2;DP=17844;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-filterInvariant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:211,210:421:99:5455,0,6126:126,85,132,78 chr1 17046549 . G A 4332.86 PASS AC=1;AF=0.513;AN=2;DP=29686;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:395,309:704:99:7091,0,9408:200,195,155,154 chr1 17046595 . T C 7070.5 PASS AC=1;AF=0.5;AN=2;DP=28024;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-filterInvariant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:303,367:670:99:8898,0,8814:136,167,162,205 chr1 17046613 . C T 14940.8 PASS AC=1;AF=0.524;AN=2;DP=25768;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:126,479:605:99:17203,0,1856:55,71,202,277 chr1 17046698 . C G 1268.91 PASS AC=1;AF=0.5;AN=2;DP=7980;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-filterInvariant17-filterInvariant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-filterInvariant27-variant28-variant30-variant31-variant32-variant33-filterInvariant34-variant35-variant36-variant37-variant38-variant41-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:91,102:193:99:2793,0,2516:25,66,30,72 chr1 17083671 . C G 836.95 PASS AC=1;AF=0.5;AN=2;DP=4245;set=variant-filterInvariant5-variant6-filterInvariant7-variant8-variant9-variant10-variant13-variant14-variant15-filterInvariant16-variant17-variant18-filterInvariant19-variant20-variant21-variant22-filterInvariant23-filterInvariant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-filterInvariant33-variant34-variant35-variant36-variant37-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:91,52:143:99:992,0,1959:47,44,28,24 chr1 17083685 . C A 826.47 PASS AC=1;AF=0.5;AN=2;DP=4431;set=variant-filterInvariant5-variant6-filterInvariant7-variant8-variant9-variant10-variant13-variant14-variant15-filterInvariant16-variant17-variant18-variant19-variant20-variant21-variant22-filterInvariant23-filterInvariant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-filterInvariant33-variant34-variant35-variant36-variant37-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:89,52:141:99:965,0,1982:44,45,27,25 chr1 17083807 . T C 306.73 PASS AC=2;AF=0.658;AN=2;DP=3381;set=variant-filterInvariant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-filterInvariant12-variant13-variant14-variant15-variant16-variant17-filterInvariant18-variant19-variant20-variant22-variant24-variant25-variant26-variant28-filterInvariant29-filterInvariant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:856,72,0:0,0,5,19 chr1 17084006 . C T 725.92 PASS AC=1;AF=0.5;AN=2;DP=7200;set=variant-filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant7-variant8-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant13-filterInvariant14-filterInvariant15-filterInvariant16-variant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-variant22-filterInvariant23-variant24-filterInvariant25-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant29-filterInvariant30-variant31-variant32-filterInvariant33-variant34-filterInvariant35-filterInvariant36-variant37-filterInvariant38-variant39-filterInvariant41-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:126,82:208:99:1945,0,3120:96,30,72,10 chr1 17084367 . A G 546.27 PASS AC=1;AF=0.5;AN=2;DP=2637;set=variant2-filterInvariant7-filterInvariant12-variant13-filterInvariant22-variant25-variant28-filterInvariant31-filterInvariant32-filterInvariant35 GT:AD:DP:GQ:PL:SB 0/1:361,46:407:99:140,0,10051:174,187,18,28 chr1 17084536 . TGGAACA T 274.23 PASS AC=1;AF=0.5;AN=2;DP=5563;set=variant-variant2-variant3-variant4-variant5-variant7-filterInvariant8-filterInvariant9-variant11-variant12-variant13-variant14-variant15-variant16-variant18-filterInvariant19-variant21-variant22-variant26-variant27-filterInvariant30-variant34-filterInvariant35-filterInvariant36-variant37-filterInvariant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:201,18:219:99:141,0,10123:92,109,7,11 chr1 17084755 . T C 353.26 PASS AC=1;AF=0.597;AN=2;DP=2062;set=variant-filterInvariant5-variant6-filterInvariant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant17-filterInvariant18-variant19-filterInvariant20-variant26-filterInvariant27-variant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant33-variant34-variant35-variant36-variant37-filterInvariant38-filterInvariant41-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,49:76:99:1183,0,680:11,16,14,35 chr1 17084815 . G A 324.96 PASS AC=1;AF=0.545;AN=2;DP=1609;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-filterInvariant15-variant16-variant17-filterInvariant18-variant19-filterInvariant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-filterInvariant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-filterInvariant41-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,11:31:99:262,0,601:12,8,8,3 chr1 17084948 . A C 761.89 PASS AC=1;AF=0.5;AN=2;DP=13778;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-filterInvariant9-variant11-filterInvariant12-variant13-filterInvariant14-variant15-variant16-filterInvariant17-variant18-variant19-variant20-variant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-variant26-filterInvariant28-filterInvariant29-variant30-variant34-variant35-variant36-variant37-variant39-variant40-variant41-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:379,152:531:99:3024,0,9682:250,129,110,42 chr1 17084968 . G C 2030.43 PASS AC=1;AF=0.5;AN=2;DP=20741;set=variant-variant2-variant3-variant4-variant5-variant6-filterInvariant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:484,212:696:99:4076,0,11886:302,182,136,76 chr1 17085006 . C T 409.03 PASS AC=1;AF=0.5;AN=2;DP=5139;set=filterInvariant21-filterInvariant28-variant30-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant40 GT:AD:DP:GQ:PL:SB 0/1:748,167:915:99:1578,0,16765:375,373,83,84 chr1 17085165 . G C,T 1891.84 PASS AC=2,0;AF=0.864,0.125;AN=2;DP=3457;set=variant-filterInvariant2-variant3-variant4-filterInvariant5-variant6-variant7-variant8-variant9-filterInvariant10-variant11-variant12-variant13-variant14-variant15-filterInvariant16-variant17-variant18-filterInvariant19-filterInvariant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-filterInvariant35-filterInvariant36-variant37-variant38-variant39-variant40-filterInvariant41-filterInvariant42-filterInvariant43-variant44 GT:DP:GQ:SB 1/1:30:90:0,0,0,30 chr1 17085255 . A G 2348.32 PASS AC=1;AF=0.543;AN=2;DP=3263;set=variant-filterInvariant2-variant6-variant8-variant9-filterInvariant10-variant11-variant15-filterInvariant16-variant17-variant21-variant24-variant25-variant26-variant27-variant29-variant30-filterInvariant31-variant32-variant34-filterInvariant35-filterInvariant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:27,7:34:99:123,0,761:27,0,6,1 chr1 17085265 . T C 452.98 PASS AC=2;AF=0.661;AN=2;DP=3163;FractionInformativeReads=1;set=variant-filterInvariant2-variant3-variant4-filterInvariant5-filterInvariant7-variant9-filterInvariant10-variant11-variant14-variant15-filterInvariant16-filterInvariant17-filterInvariant19-filterInvariant20-variant21-variant25-variant26-variant29-filterInvariant30-filterInvariant31-variant32-filterInvariant34-filterInvariant35-variant36-variant37-variant38-filterInvariant41-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1845,123,0:0,0,41,0 chr1 17085267 . A G 452.98 PASS AC=2;AF=0.661;AN=2;DP=3246;FractionInformativeReads=1;set=variant-filterInvariant2-variant3-variant4-filterInvariant5-filterInvariant7-variant9-filterInvariant10-variant11-variant14-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant19-filterInvariant20-variant21-variant25-filterInvariant26-variant29-filterInvariant30-filterInvariant31-variant32-filterInvariant34-filterInvariant35-variant36-variant37-variant38-filterInvariant41-filterInvariant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1845,123,0:0,0,41,0 chr1 17085412 . C T 3609.81 PASS AC=1;AF=0.5;AN=2;DP=44576;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-filterInvariant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:817,428:1245:99:15811,0,35470:490,327,283,145 chr1 17085427 . T C 8636.79 PASS AC=1;AF=0.5;AN=2;DP=51112;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:924,508:1432:99:17044,0,38017:537,387,323,185 chr1 17085502 . T C 16196 PASS AC=1;AF=0.5;AN=2;DP=54761;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:797,749:1546:99:18164,0,17644:423,374,377,372 chr1 17085542 . G A 1224.3 PASS AC=1;AF=0.5;AN=2;DP=37775;set=filterInvariant2-variant3-filterInvariant4-filterInvariant5-variant6-filterInvariant7-variant9-variant10-filterInvariant12-variant16-variant17-variant19-filterInvariant20-filterInvariant22-variant23-variant24-variant25-variant27-variant28-variant29-filterInvariant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:1109,337:1446:99:6388,0,41069:509,600,178,159 chr1 17085564 . A G 8043.65 PASS AC=1;AF=0.5;AN=2;DP=42874;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-filterInvariant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:900,407:1307:99:11864,0,24287:392,508,200,207 chr1 17085589 . AGCGCTG A 205.37 PASS AC=1;AF=0.5;AN=2;DP=12500;set=filterInvariant3-filterInvariant4-variant6-variant9-variant10-filterInvariant23-variant25-variant27-variant28-filterInvariant31-filterInvariant35-filterInvariant36-filterInvariant37-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:1035,106:1141:99:1199,0,42698:462,573,29,77 chr1 17085614 . G A 2031.53 PASS AC=1;AF=0.5;AN=2;DP=9838;set=variant6-filterInvariant7-filterInvariant10-variant16-filterInvariant17-variant30-filterInvariant31-variant32-filterInvariant34-filterInvariant35-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:947,143:1090:99:1079,0,28102:410,537,59,84 chr1 17085671 . C G 5784.23 PASS AC=1;AF=0.5;AN=2;DP=31784;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-filterInvariant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:702,331:1033:99:9079,0,18716:289,413,141,190 chr1 17085677 . G A 1534.5 PASS AC=1;AF=0.5;AN=2;DP=28718;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant11-filterInvariant12-variant13-filterInvariant15-variant16-variant17-variant18-variant19-filterInvariant20-variant21-variant22-variant23-variant24-variant25-filterInvariant26-variant27-variant28-variant29-filterInvariant30-variant31-filterInvariant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-filterInvariant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:799,212:1011:99:2801,0,30286:345,454,86,126 chr1 17085712 . C G,T 178.02 PASS AC=0,1;AF=0.013,0.488;AN=2;DP=25661;set=filterInvariant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant12-variant13-filterInvariant14-filterInvariant15-variant16-filterInvariant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-filterInvariant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-filterInvariant39-filterInvariant40-variant41-variant42-variant43 GT:DP:GQ:SB 0/2:940:99:320,399,80,141 chr1 17085795 . G T 341.36 PASS AC=1;AF=0.5;AN=2;DP=12829;set=filterInvariant5-variant9-variant10-variant13-variant18-variant19-filterInvariant22-variant23-variant24-variant25-variant27-variant28-variant29-filterInvariant31-filterInvariant32-variant33-filterInvariant34-filterInvariant35-filterInvariant36-variant38-filterInvariant39-filterInvariant41-variant42-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:640,113:753:99:973,0,17485:301,339,34,79 chr1 17085834 . G T 5877.73 PASS AC=1;AF=0.807;AN=2;DP=18352;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:156,400:556:99:10093,0,2897:68,88,176,224 chr1 17085908 . C G 1602.37 PASS AC=1;AF=0.521;AN=2;DP=7488;set=variant-variant5-filterInvariant6-variant8-filterInvariant9-variant10-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant26-variant27-variant29-filterInvariant31-variant34-variant35-variant36-variant37-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:306,87:393:99:1454,0,7429:126,180,29,58 chr1 17085995 . G C 37.59 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=110;FS=93.144;FractionInformativeReads=0.982;MQ=46.52;MQRankSum=-0.396;QD=0.34;ReadPosRankSum=-0.924;SOR=5.13;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:96,12:108:66:66,0,3616:11,85,12,0 chr1 17085999 . CCCCG C 338.9 PASS AC=1;AF=0.5;AN=2;DP=1498;set=variant6-variant7-variant9-variant10-variant15-variant16-variant17-variant18-variant19-variant20-filterInvariant26-variant30-filterInvariant31-variant32-variant34-variant35-variant37-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,32:86:99:1097,0,1943:21,33,1,31 chr1 17086003 . G C 32.99 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=102;FS=56.151;FractionInformativeReads=0.99;MQ=46.9;MQRankSum=0.308;QD=0.32;ReadPosRankSum=0.459;SOR=4.395;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:93,8:101:61:61,0,3617:15,78,8,0 chr1 17086007 . A C 43.23 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=82;FS=50.025;FractionInformativeReads=0.988;MQ=45.21;MQRankSum=1.322;QD=0.53;ReadPosRankSum=-1.496;SOR=4.395;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:73,8:81:71:71,0,3334:14,59,8,0 chr1 17086010 . T C 84.2 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=73;FS=54.874;FractionInformativeReads=1;MQ=43.89;MQRankSum=1.121;QD=1.15;ReadPosRankSum=-2.64;SOR=4.395;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:65,8:73:99:112,0,2928:10,55,8,0 chr1 17086012 . A C 99.06 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=74;FS=45.528;FractionInformativeReads=1;MQ=43.34;MQRankSum=1.108;QD=1.34;ReadPosRankSum=-2.216;SOR=4.16;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:67,7:74:99:127,0,2759:12,55,7,0 chr1 17086052 . T C 161.06 PASS AC=2;AF=1;AN=2;DP=1498;FS=0;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-filterInvariant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1416,129,0:0,0,25,18 chr1 17086450 . C G 211.68 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=395;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:14,6:20:88:88,0,320:4,10,3,3 chr1 17086464 . T C 172.69 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=385;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:14,6:20:88:88,0,320:4,10,3,3 chr1 17086870 . T C 331.16 PASS AC=2;AF=1;AN=2;DP=226;FS=0;MQRankSum=-2.325;ReadPosRankSum=0.066;set=filterInvariant5-filterInvariant9-filterInvariant10-filterInvariant15-filterInvariant20-variant25-variant27-filterInvariant29-filterInvariant34-filterInvariant35-filterInvariant43 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:820,75,0:0,0,25,0 chr1 17086941 . C T 992.37 PASS AC=1;AF=0.5;AN=2;DP=8169;set=variant-filterInvariant2-filterInvariant7-variant8-variant10-variant13-variant15-filterInvariant18-variant21-filterInvariant22-filterInvariant24-variant25-filterInvariant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-filterInvariant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:221,53:274:99:869,0,6284:170,51,40,13 chr1 17087244 . AC A 3814.71 PASS AC=1;AF=0.5;AN=2;DP=16616;set=variant-variant5-filterInvariant6-variant8-variant9-variant10-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant29-variant31-variant34-variant35-variant36-variant37-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:614,144:758:99:2392,0,19714:316,298,62,82 chr1 17087262 . C T 4213.48 PASS AC=1;AF=0.5;AN=2;DP=24368;set=variant-variant2-variant3-variant4-filterInvariant5-variant6-variant7-variant8-filterInvariant9-variant10-variant11-variant12-variant13-variant15-filterInvariant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-filterInvariant42 GT:AD:DP:GQ:PL:SB 0/1:624,178:802:99:3300,0,18628:294,330,106,72 chr1 17087292 . A G 633.47 PASS AC=1;AF=0.5;AN=2;DP=22999;set=filterInvariant-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-variant9-variant10-variant11-filterInvariant12-filterInvariant13-variant16-filterInvariant17-filterInvariant18-variant19-variant21-filterInvariant22-filterInvariant23-variant24-filterInvariant25-filterInvariant26-variant27-filterInvariant28-variant29-filterInvariant31-filterInvariant32-filterInvariant33-variant34-filterInvariant35-filterInvariant36-variant39-variant41-filterInvariant42-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:753,92:845:99:1673,0,31218:336,417,83,9 chr1 17087299 . T C 5785.07 PASS AC=1;AF=0.5;AN=2;DP=26797;set=variant-filterInvariant3-filterInvariant4-filterInvariant5-variant6-variant8-variant9-variant10-variant11-filterInvariant12-variant13-variant15-variant16-variant17-filterInvariant18-variant19-filterInvariant20-variant21-filterInvariant22-filterInvariant23-variant24-variant25-variant26-variant27-filterInvariant28-variant29-filterInvariant30-variant31-filterInvariant32-variant33-variant34-variant35-filterInvariant36-variant39-variant41-filterInvariant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:749,104:853:99:2099,0,31746:332,417,91,13 chr1 17087305 . G C 1321.83 PASS AC=1;AF=0.5;AN=2;DP=27470;set=variant-filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant5-variant6-variant9-variant10-variant11-filterInvariant12-variant13-filterInvariant15-variant16-variant17-variant18-variant19-filterInvariant20-variant21-filterInvariant22-filterInvariant23-variant24-variant25-filterInvariant26-variant27-filterInvariant28-variant29-variant31-filterInvariant32-variant33-variant34-variant35-filterInvariant36-filterInvariant37-filterInvariant38-variant39-filterInvariant40-variant41-filterInvariant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:745,113:858:99:2357,0,30773:332,413,98,15 chr1 17087365 . C G 7328.19 PASS AC=1;AF=0.511;AN=2;DP=34433;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:103,831:934:99:25662,0,835:57,46,504,327 chr1 17087465 . G A 1275.79 PASS AC=1;AF=0.5;AN=2;DP=67839;set=filterInvariant-variant2-variant3-variant4-variant5-variant6-filterInvariant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-filterInvariant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:1142,796:1938:99:16760,0,28073:613,529,411,385 chr1 17087521 . G A 8999.97 PASS AC=1;AF=0.5;AN=2;DP=44376;set=variant-filterInvariant2-filterInvariant4-filterInvariant6-variant8-filterInvariant11-filterInvariant12-variant13-variant15-variant17-filterInvariant18-variant21-variant22-filterInvariant23-filterInvariant26-variant27-variant28-filterInvariant29-variant30-variant32-variant34-filterInvariant35-filterInvariant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:1950,243:2193:99:365,0,62738:900,1050,116,127 chr1 17087541 . GGTGCT G 10847.3 PASS AC=1;AF=0.5;AN=2;DP=78083;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:1261,748:2009:99:27145,0,50330:567,694,334,414 chr1 17087582 . G A 12021.1 PASS AC=1;AF=0.5;AN=2;DP=62467;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-filterInvariant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:819,776:1595:99:24056,0,20077:347,472,326,450 chr1 17087593 . C T 1806.03 PASS AC=1;AF=0.5;AN=2;DP=24030;set=filterInvariant3-filterInvariant4-variant5-variant6-variant9-variant10-filterInvariant20-variant23-variant25-variant27-variant28-filterInvariant32-variant35-filterInvariant36-filterInvariant37-variant38-variant39-variant42-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:1095,373:1468:99:6803,0,39844:453,642,151,222 chr1 17087682 . A G 560.58 PASS AC=1;AF=0.5;AN=2;DP=9820;set=variant-variant4-variant5-variant6-variant7-variant8-variant11-variant16-variant17-filterInvariant18-variant21-filterInvariant22-variant23-variant26-variant27-filterInvariant28-variant29-variant30-filterInvariant31-variant32-filterInvariant34-filterInvariant35-filterInvariant37-variant38-variant39-variant40-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:373,51:424:99:446,0,10553:100,273,11,40 chr1 17090902 . A AT 34.39 PASS AC=1;AF=0.5;AN=2;DP=3974;set=filterInvariant-variant2-variant3-filterInvariant5-filterInvariant9-variant10-variant11-filterInvariant12-variant13-filterInvariant16-variant18-variant20-filterInvariant24-filterInvariant26-filterInvariant27-variant28-variant29-filterInvariant30-filterInvariant31-filterInvariant33-filterInvariant34-filterInvariant35-variant37-filterInvariant38-variant39-variant40-variant41-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:142,20:162:99:224,0,4575:84,58,10,10 chr1 17197525 . T G 215.56 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=1014;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:137,18:155:99:121,0,3871:85,52,17,1 chr1 17197563 . G T 3422.53 PASS AC=1;AF=0.511;AN=2;DP=12451;set=variant-variant2-variant3-variant4-variant5-filterInvariant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-filterInvariant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:210,74:284:99:2769,0,9828:117,93,54,20 chr1 17197571 . G A 585.5 PASS AC=1;AF=0.5;AN=2;DP=13564;set=variant-variant2-variant3-variant4-filterInvariant5-filterInvariant6-variant7-filterInvariant8-variant9-filterInvariant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-filterInvariant38-variant39-filterInvariant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:223,91:314:99:3228,0,10421:121,102,65,26 chr1 17197595 . A C 795.33 PASS AC=1;AF=0.5;AN=2;DP=16079;set=variant-variant2-variant3-variant4-filterInvariant5-filterInvariant6-variant7-variant8-variant9-filterInvariant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-filterInvariant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:244,150:394:99:5768,0,11127:128,116,99,51 chr1 17197609 . T C 884.83 PASS AC=1;AF=0.5;AN=2;DP=17002;set=variant-variant2-variant3-variant4-variant5-filterInvariant6-variant7-variant8-variant9-filterInvariant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-filterInvariant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:247,180:427:99:6960,0,11274:125,122,118,62 chr1 17197615 . C A 854.81 PASS AC=1;AF=0.5;AN=2;DP=17214;set=variant-variant2-variant3-variant4-variant5-filterInvariant6-variant7-variant8-variant9-filterInvariant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-filterInvariant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:247,190:437:99:7285,0,11225:120,127,123,67 chr1 17197619 . A G 857.66 PASS AC=1;AF=0.5;AN=2;DP=17252;set=variant-variant2-variant3-variant4-variant5-filterInvariant6-variant7-variant8-variant9-filterInvariant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-filterInvariant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:248,195:443:99:7315,0,11076:120,128,124,71 chr1 17197666 . T C 805.62 PASS AC=1;AF=0.5;AN=2;DP=5226;set=variant5-filterInvariant7-variant8-variant14-filterInvariant22-variant23-filterInvariant26-filterInvariant27-filterInvariant30-variant31-variant33-filterInvariant35-variant38-filterInvariant39 GT:AD:DP:GQ:PL:SB 0/1:359,68:427:99:490,0,11309:173,186,38,30 chr1 17197690 . T G 718.7 PASS AC=1;AF=0.5;AN=2;DP=13678;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:123,232:355:99:9247,0,4635:47,76,113,119 chr1 17197694 . G A 667.42 PASS AC=1;AF=0.5;AN=2;DP=13199;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:119,223:342:99:9255,0,4562:45,74,108,115 chr1 17197710 . G C 520.04 PASS AC=1;AF=0.5;AN=2;DP=11298;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:95,202:297:99:8235,0,3726:31,64,94,108 chr1 17197715 . G A 541.82 PASS AC=1;AF=0.5;AN=2;DP=10737;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:91,190:281:99:7960,0,3559:27,64,83,107 chr1 17197721 . C T 327.8 PASS AC=1;AF=0.5;AN=2;DP=1620;set=filterInvariant4-filterInvariant12-filterInvariant19-filterInvariant22-filterInvariant28-variant32-filterInvariant35 GT:AD:DP:GQ:PL:SB 0/1:233,26:259:95:95,0,10005:86,147,12,14 chr1 17197725 . C G 193.59 PASS AC=1;AF=0.5;AN=2;DP=8613;set=variant-variant2-variant3-variant4-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-filterInvariant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-filterInvariant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:120,117:237:99:3048,0,4728:40,80,49,68 chr1 17197758 . C G 355.1 PASS AC=1;AF=0.5;AN=2;DP=5775;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:37,105:142:99:4152,0,1369:9,28,30,75 chr1 17197764 . G A,C 303.47 PASS AC=1,0;AF=0.402,0.098;AN=2;DP=4789;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:122:99:7,26,24,65 chr1 17197771 . G A 331.31 PASS AC=1;AF=0.5;AN=2;DP=4571;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:28,83:111:99:3566,0,1076:5,23,21,62 chr1 17197777 . T G 214.37 PASS AC=1;AF=0.5;AN=2;DP=4083;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:27,76:103:99:3317,0,1027:4,23,16,60 chr1 17197779 . G A 223.4 PASS AC=1;AF=0.5;AN=2;DP=3837;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:33,69:102:99:2826,0,1238:4,29,15,54 chr1 17197798 . A G 122.32 PASS AC=1;AF=0.5;AN=2;DP=2488;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:19,52:71:99:2207,0,677:2,17,11,41 chr1 17197817 . C A 109.62 PASS AC=1;AF=0.5;AN=2;DP=1840;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:16,35:51:99:1421,0,566:1,15,6,29 chr1 17197818 . C G 112.63 PASS AC=1;AF=0.5;AN=2;DP=1821;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:16,35:51:99:1421,0,566:1,15,6,29 chr1 17198145 . GAC G 49.44 PASS AC=1;AF=0.5;AN=2;DP=531;set=filterInvariant3-variant4-variant5-variant6-variant7-variant12-variant13-variant17-filterInvariant19-variant20-variant22-variant24-variant25-variant26-variant28-variant31-variant35-variant37-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:17,9:26:99:327,0,703:12,5,5,4 chr1 17198209 . A C 115.19 PASS AC=1;AF=0.5;AN=2;DP=2151;set=variant2-filterInvariant3-variant4-variant5-variant7-variant9-variant11-variant12-variant13-filterInvariant14-variant15-variant16-variant17-variant18-variant20-variant22-variant24-variant25-variant26-variant28-variant29-variant30-variant31-filterInvariant32-filterInvariant33-variant34-variant35-variant36-variant37-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,20:72:99:653,0,2371:39,13,11,9 chr1 17198211 . C A 125.38 PASS AC=1;AF=0.5;AN=2;DP=2235;set=variant2-filterInvariant3-variant4-variant5-variant7-variant9-variant11-variant12-variant13-filterInvariant14-variant15-variant16-variant17-variant18-variant20-variant22-variant24-variant25-variant26-variant28-variant29-variant30-variant31-filterInvariant32-filterInvariant33-variant34-variant35-variant36-variant37-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,19:72:99:644,0,2463:39,14,10,9 chr1 17198215 . A C 119.39 PASS AC=1;AF=0.5;AN=2;DP=2393;set=filterInvariant2-filterInvariant3-variant4-variant5-variant7-variant9-variant11-variant12-variant13-filterInvariant14-variant15-variant16-variant17-variant18-variant20-filterInvariant22-variant24-variant25-variant26-variant28-variant29-variant30-variant31-filterInvariant32-filterInvariant33-variant34-variant35-variant36-variant37-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,18:78:99:568,0,2582:45,15,9,9 chr1 17198518 . T G 168.67 PASS AC=2;AF=0.95;AN=2;DP=101;FractionInformativeReads=1;set=filterInvariant-filterInvariant3-variant4-filterInvariant5-variant7-filterInvariant9-filterInvariant12-variant16-variant17-filterInvariant19-filterInvariant21-variant22-variant27-filterInvariant32-filterInvariant35-variant36-filterInvariant40-variant41-variant42-filterInvariant44 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:67,6,0:0,0,0,2 chr1 17248500 . A G 5266.57 PASS AC=2;AF=0.581;AN=2;DP=14037;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,238:238:99:7674,713,0:0,0,154,84 chr1 17248532 . A G 16093 PASS AC=2;AF=1;AN=2;DP=19294;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,330:330:99:10079,989,0:0,0,189,141 chr1 17249395 . A G 1910.57 PASS AC=1;AF=0.739;AN=2;DP=4324;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:30,25:55:99:722,0,915:7,23,6,19 chr1 17251055 . C T 2247.32 PASS AC=2;AF=0.581;AN=2;DP=5606;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,87:87:99:2662,259,0:0,0,36,51 chr1 17270751 . G A 948.08 PASS AC=1;AF=0.542;AN=2;DP=4169;set=variant5-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant22-variant25-variant26-variant28-variant30-variant31-variant34-variant35-variant37-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:58,57:115:99:1432,0,1501:27,31,26,31 chr1 17275337 . C T 34.96 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=236;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:117,21:138:99:111,0,3324:68,49,10,11 chr1 17281003 . T C 1167.54 PASS AC=2;AF=0.767;AN=2;DP=1712;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1460,123,0:0,0,14,27 chr1 17287414 . T C 230.24 PASS AC=1;AF=0.534;AN=2;DP=628;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant14-variant16-variant17-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,13:22:99:317,0,142:4,5,6,7 chr1 17295679 . T C 5743.89 PASS AC=2;AF=0.864;AN=2;DP=7385;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,202:202:99:5675,601,0:0,0,91,111 chr1 17297289 . C T 328.65 PASS AC=2;AF=0.768;AN=2;DP=670;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:529,48,0:0,0,4,12 chr1 17299014 . A C 1770.26 PASS AC=2;AF=0.898;AN=2;DP=2468;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:2,58:60:99:1515,123,0:1,1,28,30 chr1 17301672 . T C 705.77 PASS AC=1;AF=0.554;AN=2;DP=2318;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant14-variant16-variant17-variant19-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant35-variant36-variant37-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:39,62:101:99:1592,0,963:22,17,30,32 chr1 17301780 . A G 234.08 PASS AC=1;AF=0.547;AN=2;DP=2146;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant14-variant16-variant17-variant19-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:56,34:90:99:868,0,1476:30,26,15,19 chr1 17303589 . C T 2869.01 PASS AC=1;AF=0.588;AN=2;DP=9277;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:131,161:292:99:3909,0,3024:63,68,84,77 chr1 17303792 . C T 711.02 PASS AC=1;AF=0.813;AN=2;DP=1366;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:15,20:35:99:581,0,458:5,10,4,16 chr1 17307264 . TGG T,TG 2519.71 PASS AC=0,1;AF=0.352,0.409;AN=2;DP=4243;MQ=60;set=Intersection GT:DP:GQ:SB 0/2:120:99:29,19,43,29 chr1 17312743 . C T 1966.77 PASS AC=1;AF=0.536;AN=2;DP=3672;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant14-variant16-variant17-variant19-variant21-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:62,69:131:99:1672,0,1850:26,36,31,38 chr1 17313157 . G A 358.57 PASS AC=1;AF=0.518;AN=2;DP=1077;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant14-variant16-variant17-variant19-variant21-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:16,19:35:99:517,0,531:3,13,6,13 chr1 17313343 . G A 583.01 PASS AC=1;AF=0.518;AN=2;DP=2309;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant14-variant16-variant17-variant19-variant21-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:43,44:87:99:1016,0,928:26,17,27,17 chr1 17313654 . C T 2537.46 PASS AC=1;AF=0.518;AN=2;DP=4411;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant14-variant16-variant17-variant19-variant21-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:81,95:176:99:2327,0,2019:39,42,49,46 chr1 17314942 . G A 2067.71 PASS AC=1;AF=0.518;AN=2;DP=5791;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant14-variant16-variant17-variant19-variant21-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:128,87:215:99:2129,0,3507:50,78,29,58 chr1 17319011 . G A 2895.84 PASS AC=1;AF=0.6;AN=2;DP=6010;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:149,90:239:99:2025,0,3739:70,79,42,48 chr1 17319287 . C T 1123.71 PASS AC=1;AF=0.6;AN=2;DP=1329;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:29,22:51:99:575,0,873:10,19,6,16 chr1 17323449 . T C 316.86 PASS AC=1;AF=0.851;AN=2;DP=355;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,4:16:91:91,0,333:7,5,2,2 chr1 17328301 . T C 161.25 PASS AC=1;AF=0.688;AN=2;DP=460;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,5:12:90:90,0,159:4,3,3,2 chr1 17331676 . A G 506.5 PASS AC=1;AF=0.65;AN=2;DP=2091;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,22:50:99:597,0,844:8,20,10,12 chr1 17345073 . G GC 933.71 PASS AC=2;AF=0.649;AN=2;DP=1078;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1271,102,0:0,0,25,9 chr1 17359386 . T C 297.52 PASS AC=2;AF=0.583;AN=2;DP=1206;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant14-variant16-variant17-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,52:52:99:1633,156,0:0,0,35,17 chr1 17359676 . C A 2925.73 PASS AC=2;AF=0.943;AN=2;DP=4233;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,100:100:99:3125,300,0:0,0,36,64 chr1 17371152 . T C 444.83 PASS AC=2;AF=0.639;AN=2;DP=552;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,23:24:40:959,40,0:1,0,20,3 chr1 17371494 . C T 76.42 PASS AC=2;AF=0.625;AN=2;DP=109;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant16-variant17-variant19-variant21-variant23-variant24-variant26-variant29-variant31-variant32-variant35-variant37-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:178,15,0:0,0,1,4 chr1 17380207 . G C 50.74 PASS AC=1;AF=0.5;AN=2;DP=47;MQ=60;set=variant6-variant18-variant21-variant28-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:4,5:9:60:110,0,60:1,3,5,0 chr1 17380497 . G T 2537.19 PASS AC=2;AF=0.943;AN=2;DP=4391;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,98:98:99:3039,292,0:0,0,45,53 chr1 17393707 . AAG A 126.11 PASS AC=2;AF=0.542;AN=2;DP=215;set=variant5-filterInvariant7-filterInvariant9-variant13-variant19-variant20-variant24-variant26-variant34-variant35-variant36-variant42 GT:AD:DP:GQ:PL:SB 1/1:1,4:5:1:128,1,0:1,0,3,1 chr1 17393748 . AAC A 162.42 PASS AC=2;AF=0.677;AN=2;DP=789;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant35-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:536,42,0:0,0,9,5 chr1 17394048 . T A 469.15 PASS AC=2;AF=0.672;AN=2;DP=1976;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:2355,228,0:0,0,38,38 chr1 17394374 . C A 426.46 PASS AC=2;AF=0.672;AN=2;DP=1892;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,66:66:99:1998,197,0:0,0,29,37 chr1 17394613 . T C 775.28 PASS AC=2;AF=0.89;AN=2;DP=1726;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1928,138,0:0,0,24,20 chr1 17394623 . C T 691.77 PASS AC=2;AF=0.89;AN=2;DP=1827;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:2002,141,0:0,0,25,22 chr1 17395480 . G A 1770.09 PASS AC=2;AF=0.672;AN=2;DP=6095;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,202:202:99:6392,604,0:0,0,103,99 chr1 17395521 . G A 1471.15 PASS AC=2;AF=0.672;AN=2;DP=6387;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,219:220:99:6492,647,0:1,0,116,103 chr1 17396498 . T C 162.37 PASS AC=2;AF=0.672;AN=2;DP=624;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:604,54,0:0,0,12,6 chr1 17396703 . T C 442.49 PASS AC=2;AF=0.672;AN=2;DP=3172;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,93:93:99:2781,278,0:0,0,41,52 chr1 17398066 . G C 983.51 PASS AC=2;AF=0.714;AN=2;DP=3027;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,115:115:99:5073,346,0:0,0,45,70 chr1 17398069 . T C 983.51 PASS AC=2;AF=0.714;AN=2;DP=2917;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,109:109:99:4999,337,0:0,0,40,69 chr1 17401283 . C T 93.91 PASS AC=2;AF=0.714;AN=2;DP=947;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:992,84,0:0,0,22,6 chr1 17402116 . G T 1278.74 PASS AC=2;AF=0.714;AN=2;DP=5241;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,143:143:99:4322,427,0:0,0,73,70 chr1 17402135 . T C 1143.73 PASS AC=2;AF=0.714;AN=2;DP=5404;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,157:158:99:4827,463,0:1,0,80,77 chr1 17402159 . G A 1149.4 PASS AC=2;AF=0.714;AN=2;DP=5756;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,181:181:99:5423,540,0:0,0,95,86 chr1 17402255 . C T 1240.92 PASS AC=2;AF=0.714;AN=2;DP=7245;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,195:195:99:5881,581,0:0,0,97,98 chr1 17402347 . C T 3192.5 PASS AC=2;AF=0.955;AN=2;DP=7460;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,165:165:99:5052,492,0:0,0,66,99 chr1 17402418 . A G 751.28 PASS AC=2;AF=0.714;AN=2;DP=2865;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,84:84:99:2729,252,0:0,0,28,56 chr1 17405809 . G A 481.47 PASS AC=2;AF=0.661;AN=2;DP=2406;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant12-variant14-variant16-variant17-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,84:84:99:2501,252,0:0,0,43,41 chr1 17405916 . C T 307.13 PASS AC=2;AF=0.661;AN=2;DP=1538;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant12-variant14-variant16-variant17-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:1591,162,0:0,0,21,33 chr1 17405949 . C T 210.27 PASS AC=2;AF=0.656;AN=2;DP=1085;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant12-variant14-variant16-variant17-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1132,114,0:0,0,13,25 chr1 17406015 . C T 242.98 PASS AC=2;AF=0.913;AN=2;DP=537;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:310,24,0:0,0,1,7 chr1 17406045 . C T 85.33 PASS AC=2;AF=0.7;AN=2;DP=202;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant10-variant12-variant14-variant16-variant17-variant21-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant35-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:178,15,0:0,0,1,4 chr1 17410364 . G A 1295.36 PASS AC=2;AF=0.661;AN=2;DP=2927;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant12-variant14-variant16-variant17-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,111:112:99:3234,325,0:1,0,47,64 chr1 17418883 . A G 1443.29 PASS AC=1;AF=0.92;AN=2;DP=1757;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:15,18:33:99:696,0,1023:13,2,15,3 chr1 17418894 . A G 702.69 PASS AC=1;AF=0.742;AN=2;DP=1494;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,18:36:99:692,0,1133:16,2,15,3 chr1 17419066 . T C 688.47 PASS AC=1;AF=0.742;AN=2;DP=3231;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,60:106:99:1415,0,990:18,28,25,35 chr1 17422226 . C T 190.14 PASS AC=1;AF=0.742;AN=2;DP=920;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,15:30:99:457,0,368:10,5,12,3 chr1 17422302 . T C 834.87 PASS AC=1;AF=0.735;AN=2;DP=2942;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,58:103:99:1457,0,1140:31,14,37,21 chr1 17431277 . G T 667.04 PASS AC=1;AF=0.763;AN=2;DP=1020;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,14:30:99:359,0,438:9,7,8,6 chr1 17431618 . A G 2723.54 PASS AC=1;AF=0.805;AN=2;DP=3861;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,52:95:99:1435,0,1036:14,29,16,36 chr1 17431681 . C A 1451.29 PASS AC=1;AF=0.756;AN=2;DP=1385;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,19:30:99:583,0,387:2,9,5,14 chr1 17531582 . G A 536.16 PASS AC=2;AF=0.6;AN=2;DP=714;MQ=60;set=variant2-variant6-variant7-variant8-variant11-variant13-variant15-variant18-variant24-variant33-variant35-variant36-variant37-variant39-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:1651,144,0:0,0,34,14 chr1 17550121 . G A 153.7 PASS AC=1;AF=0.5;AN=2;DP=619;MQ=60;set=variant6-variant8-variant10-variant11-variant12-variant18-variant19-variant24-variant27-variant28-variant32-variant35-variant36-variant37-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:22,28:50:99:707,0,550:13,9,18,10 chr1 17550225 . T C 1548.81 PASS AC=2;AF=1;AN=2;DP=3621;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,93:93:99:2883,278,0:0,0,47,46 chr1 17550314 . G A 807.36 PASS AC=1;AF=0.5;AN=2;DP=728;MQ=60;set=variant5-variant6-variant8-variant10-variant11-variant19-variant28-variant35-variant37-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:39,29:68:99:754,0,927:17,22,12,17 chr1 17551034 . A T 505.74 PASS AC=1;AF=0.671;AN=2;DP=517;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,10:16:99:356,0,204:0,6,0,10 chr1 17552875 . A G 1476.45 PASS AC=2;AF=0.893;AN=2;DP=1981;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1477,147,0:0,0,19,30 chr1 17555316 . C G 859.66 PASS AC=1;AF=0.638;AN=2;DP=785;MQ=60;set=variant2-variant4-variant6-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,18:38:99:589,0,604:7,13,5,13 chr1 17557039 . T C 234.96 PASS AC=1;AF=0.621;AN=2;DP=1222;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:27,20:47:99:547,0,742:19,8,12,8 chr1 17557133 . A C 765.95 PASS AC=1;AF=0.636;AN=2;DP=3587;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:80,45:125:99:1152,0,1938:42,38,26,19 chr1 17557178 . C T 1030.53 PASS AC=1;AF=0.643;AN=2;DP=3356;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant17-variant18-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:80,55:135:99:1172,0,1934:38,42,28,27 chr1 17557310 . G A 651.18 PASS AC=1;AF=0.656;AN=2;DP=1044;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:20,10:30:99:264,0,583:5,15,2,8 chr1 17559196 . T C 428.34 PASS AC=1;AF=0.611;AN=2;DP=1356;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant17-variant18-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant37-variant38-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:32,23:55:99:661,0,998:26,6,18,5 chr1 17563967 . T C 1537.17 PASS AC=2;AF=0.694;AN=2;DP=6154;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant18-variant19-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,230:230:99:6830,689,0:0,0,100,130 chr1 17564990 . T C 48.19 PASS AC=2;AF=0.733;AN=2;DP=347;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant18-variant19-variant20-variant22-variant24-variant26-variant27-variant29-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:506,51,0:0,0,11,6 chr1 17565414 . G C 49.73 PASS AC=1;AF=0.536;AN=2;DP=174;MQ=60;set=variant-variant3-variant4-variant7-variant9-variant13-variant18-variant20-variant22-variant27-variant29-variant35-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:13,13:26:99:304,0,345:4,9,5,8 chr1 17566369 . G A 348.95 PASS AC=1;AF=0.538;AN=2;DP=360;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant7-variant9-variant13-variant20-variant22-variant27-variant29-variant35-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:20,7:27:99:214,0,620:4,16,1,6 chr1 17570286 . T C 638.33 PASS AC=2;AF=0.697;AN=2;DP=1729;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant18-variant19-variant20-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1447,132,0:0,0,30,14 chr1 17570466 . T C 518.33 PASS AC=2;AF=0.697;AN=2;DP=3315;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant18-variant19-variant20-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,124:124:99:4082,372,0:0,0,67,57 chr1 17572420 . C A 771.67 PASS AC=1;AF=0.5;AN=2;DP=149;FractionInformativeReads=1;MQ=60;set=variant33-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:22,18:40:99:430,0,475:9,13,9,9 chr1 17575645 . A C 1586.22 PASS AC=1;AF=0.5;AN=2;DP=1201;MQ=60;set=variant11-variant24-variant26-variant28-variant33-variant34-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:72,75:147:99:1841,0,1652:40,32,41,34 chr1 17585837 . A C 379.38 PASS AC=1;AF=0.727;AN=2;DP=66;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant9-variant13-variant18-variant27-variant29-variant34-variant35-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:5,3:8:99:111,0,113:3,2,3,0 chr1 17586010 . G A 1043.74 PASS AC=1;AF=0.5;AN=2;DP=661;FractionInformativeReads=1;MQ=60;set=variant11-variant21-variant24-variant26-variant28-variant33-variant34-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:36,36:72:99:858,0,995:23,13,22,14 chr1 17586134 . A G 1876.33 PASS AC=1;AF=0.5;AN=2;DP=1134;MQ=60;set=variant11-variant21-variant24-variant26-variant28-variant33-variant34-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:75,77:152:99:1901,0,1489:34,41,43,34 chr1 17588689 . T A 824.27 PASS AC=1;AF=0.5;AN=2;DP=267;MQ=60;set=variant33-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:46,55:101:99:1469,0,1110:24,22,25,30 chr1 17593144 . C G,T 469.22 PASS AC=1,0;AF=0.656,0.016;AN=2;DP=2631;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant18-variant19-variant20-variant22-variant24-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:DP:GQ:SB 0/1:102:99:38,18,25,21 chr1 17593316 . G A 1460.7 PASS AC=1;AF=0.5;AN=2;DP=797;MQ=60;set=variant11-variant24-variant26-variant28-variant33-variant34-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:66,53:119:99:1203,0,1708:28,38,19,34 chr1 17596980 . CA CAA,C 68.58 PASS AC=1,0;AF=0.423,0.115;AN=2;DP=234;set=variant3-variant4-variant6-variant9-variant12-variant13-variant18-variant20-variant27-variant30-variant35-variant40-variant42 GT:DP:GQ:SB 0/1:14:99:1,6,0,7 chr1 17597181 . A G 91.46 PASS AC=2;AF=0.677;AN=2;DP=371;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant18-variant19-variant20-variant22-variant24-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:472,45,0:0,0,8,7 chr1 17597721 . A G 393.43 PASS AC=1;AF=0.65;AN=2;DP=508;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant6-variant10-variant11-variant12-variant18-variant19-variant24-variant26-variant28-variant33-variant34-variant35-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:16,17:33:99:527,0,428:3,13,4,13 chr1 17601083 . C T 991.2 PASS AC=1;AF=0.603;AN=2;DP=3289;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant28-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:59,50:109:99:1115,0,1539:29,30,23,27 chr1 17604437 . C T 1161.24 PASS AC=1;AF=0.542;AN=2;DP=1149;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant13-variant14-variant24-variant26-variant28-variant29-variant33-variant35-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,54:121:99:1282,0,1726:24,43,20,34 chr1 17610156 . C T 473.52 PASS AC=1;AF=0.533;AN=2;DP=730;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant11-variant13-variant14-variant16-variant24-variant26-variant28-variant29-variant33-variant34-variant35-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,29:52:99:747,0,645:10,13,13,16 chr1 17610466 . A C 768.58 PASS AC=1;AF=0.603;AN=2;DP=1831;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant28-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:36,44:80:99:1018,0,980:17,19,21,23 chr1 17610602 . A C 1029.44 PASS AC=1;AF=0.784;AN=2;DP=1014;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,11:22:99:338,0,429:7,4,7,4 chr1 17610607 . C G 397.36 PASS AC=1;AF=0.533;AN=2;DP=360;MQ=60;set=variant2-variant5-variant11-variant13-variant14-variant16-variant24-variant26-variant28-variant29-variant33-variant34-variant35-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,11:22:99:391,0,447:7,4,7,4 chr1 17610618 . A G 40.56 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=21;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.018;QD=1.93;ReadPosRankSum=-1.378;SOR=2.225;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:19,2:21:69:69,0,744:13,6,0,2 chr1 17610624 . T G 31.25 PASS AC=1;AF=0.5;AN=2;DP=39;MQ=60;set=filterInvariant27-variant35 GT:AD:DP:GQ:PL:SB 0/1:15,3:18:99:123,0,632:13,2,0,3 chr1 17610630 . T G 50.67 PASS AC=1;AF=0.5;AN=2;DP=56;MQ=60;set=filterInvariant4-variant35 GT:AD:DP:GQ:PL:SB 0/1:15,7:22:99:122,0,644:14,1,0,7 chr1 17635036 . G C 965.62 PASS AC=2;AF=1;AN=2;DP=1266;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,30:30:89:958,89,0:0,0,14,16 chr1 17635072 . A G 678.63 PASS AC=2;AF=0.989;AN=2;DP=1040;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:748,72,0:0,0,11,13 chr1 17635141 . C A 516.88 PASS AC=2;AF=1;AN=2;DP=521;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:432,36,0:0,0,4,8 chr1 17660802 . A ATT,AT 136.82 PASS AC=0,1;AF=0.7,0.033;AN=2;DP=371;set=variant-variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant39-variant41-variant42-variant43 GT:DP:GQ:SB 0/2:9:52:1,2,2,4 chr1 17661805 . A G 1428.81 PASS AC=1;AF=0.718;AN=2;DP=2037;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,36:60:99:854,0,567:13,11,22,14 chr1 17662705 . G C 1738.06 PASS AC=1;AF=0.5;AN=2;DP=563;MQ=60;set=variant30-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:94,122:216:99:2937,0,2167:43,51,60,62 chr1 17666508 . C T 618.19 PASS AC=1;AF=0.645;AN=2;DP=903;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,9:22:99:241,0,448:3,10,3,6 chr1 17666547 . G A 177.49 PASS AC=2;AF=0.682;AN=2;DP=297;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant10-variant12-variant13-variant14-variant17-filterInvariant20-variant21-variant22-variant23-variant26-variant28-variant29-variant32-variant33-variant35-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:370,33,0:0,0,2,9 chr1 17668270 . A G 251.9 PASS AC=1;AF=0.731;AN=2;DP=719;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,13:22:99:374,0,208:6,3,10,3 chr1 17674358 . T A 546.12 PASS AC=1;AF=0.5;AN=2;DP=110;FractionInformativeReads=1;MQ=60;set=variant30-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:20,11:31:99:278,0,559:14,6,8,3 chr1 17674402 . C T 1114.69 PASS AC=1;AF=0.672;AN=2;DP=2041;MQ=60;set=variant-variant3-variant4-variant7-variant8-variant9-variant11-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,25:66:99:544,0,1069:25,16,16,9 chr1 17681277 . T C 327.66 PASS AC=2;AF=0.868;AN=2;DP=556;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:465,42,0:0,0,4,10 chr1 17683041 . T C 2627.58 PASS AC=2;AF=0.841;AN=2;DP=5356;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,109:109:99:3456,326,0:0,0,39,70 chr1 17683157 . A G 456.49 PASS AC=2;AF=0.833;AN=2;DP=956;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:662,54,0:0,0,5,13 chr1 17685174 . T C 1764.3 PASS AC=2;AF=0.859;AN=2;DP=2070;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1557,147,0:0,0,33,16 chr1 17685718 . A C 39.69 PASS AC=1;AF=0.5;AN=2;DP=35;FractionInformativeReads=1;set=variant18-variant29-variant35-variant36-variant39 GT:AD:DP:GQ:PL:SB 0/1:9,4:13:99:140,0,1283:1,8,4,0 chr1 17685724 . A C 36.68 PASS AC=1;AF=0.5;AN=2;DP=33;FractionInformativeReads=1;set=variant18-variant29-variant35-variant36-variant39 GT:AD:DP:GQ:PL:SB 0/1:7,4:11:99:146,0,1241:0,7,4,0 chr1 17685729 . CGACTGCCATCAGT CCTGCCATCAGT,C 73.65 PASS AC=0,1;AF=0.167,0.333;AN=2;DP=30;FractionInformativeReads=1;set=variant29-variant35-variant36 GT:DP:GQ:SB 0/2:13:99:1,8,4,0 chr1 17707739 . T C 2537.85 PASS AC=2;AF=0.837;AN=2;DP=3208;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:2621,231,0:0,0,20,57 chr1 17707798 . C T 1094.39 PASS AC=1;AF=0.767;AN=2;DP=1231;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,18:35:99:417,0,458:5,12,5,13 chr1 17708349 . G A 1009.46 PASS AC=1;AF=0.65;AN=2;DP=1031;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant7-variant10-variant11-variant12-variant13-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,21:49:99:641,0,874:23,5,20,1 chr1 17708528 . G A 2587.7 PASS AC=1;AF=0.5;AN=2;DP=1036;MQ=60;set=variant9-variant16-variant27-variant35 GT:AD:DP:GQ:PL:SB 0/1:141,133:274:99:3169,0,3454:70,71,70,63 chr1 17718418 . C T 287.25 PASS AC=1;AF=0.625;AN=2;DP=354;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant7-variant10-variant11-variant12-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,5:14:99:107,0,309:7,2,4,1 chr1 17718671 . AG A 1033.03 PASS AC=2;AF=1;AN=2;DP=3104;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:2307,196,0:0,0,24,41 chr1 17720391 . G A 2097.97 PASS AC=1;AF=0.655;AN=2;DP=3319;MQ=60;set=variant2-variant6-variant7-variant10-variant11-variant12-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:66,41:107:99:929,0,1917:44,22,27,14 chr1 17720439 . T C 4316.55 PASS AC=1;AF=0.774;AN=2;DP=6413;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:102,67:169:99:1433,0,2596:63,39,41,26 chr1 17720615 . A C 2479.76 PASS AC=1;AF=0.774;AN=2;DP=4636;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:70,69:139:99:1607,0,1959:24,46,31,38 chr1 17720686 . AG A 788.69 PASS AC=1;AF=0.774;AN=2;DP=2769;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,35:64:99:921,0,721:11,18,14,21 chr1 17721388 . C T 252.51 PASS AC=1;AF=0.774;AN=2;DP=462;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,10:12:38:290,0,38:2,0,7,3 chr1 17721407 . C T 253.59 PASS AC=1;AF=0.5;AN=2;DP=49;FractionInformativeReads=1;MQ=60;set=variant16-variant27-variant35 GT:AD:DP:GQ:PL:SB 0/1:11,5:16:99:129,0,291:7,4,5,0 chr1 17721695 . GTTT GTT,G,GT,GTTTT 1277.23 PASS AC=0,1,0,0;AF=0.326,0.43,0.012,0.012;AN=2;DP=2239;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:31:99:6,9,4,12 chr1 17721715 . G T 528.75 PASS AC=1;AF=0.571;AN=2;DP=489;set=variant2-variant7-variant10-variant11-variant17-variant18-variant24-variant25-variant26-variant31-variant34-variant35-variant36-variant42 GT:AD:DP:GQ:PL:SB 0/1:12,17:29:99:675,0,1010:5,7,4,13 chr1 17721721 . TGA T 1654.6 PASS AC=1;AF=0.655;AN=2;DP=873;set=variant2-variant6-variant7-variant10-variant11-variant12-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,16:28:99:678,0,968:5,7,4,12 chr1 17723476 . C CCA 1256.83 PASS AC=1;AF=0.655;AN=2;DP=1081;MQ=60;set=variant2-variant6-variant7-variant10-variant11-variant12-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,16:39:99:614,0,906:17,6,14,2 chr1 17723739 . G A 1026.23 PASS AC=1;AF=0.655;AN=2;DP=1210;MQ=60;set=variant2-variant6-variant7-variant10-variant11-variant12-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,18:42:99:421,0,721:6,18,5,13 chr1 17725011 . T C 52.67 PASS AC=1;AF=0.737;AN=2;DP=512;MQ=60;set=variant-variant2-filterInvariant4-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,6:11:76:116,0,76:3,2,3,3 chr1 17725358 . C G 515.71 PASS AC=1;AF=0.75;AN=2;DP=3069;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,44:93:99:959,0,1157:20,29,21,23 chr1 17739586 . G A 1037.38 PASS AC=1;AF=0.667;AN=2;DP=768;MQ=60;set=variant2-variant6-variant7-variant10-variant11-variant12-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:16,10:26:99:354,0,477:12,4,10,0 chr1 17739820 . T C 1537.04 PASS AC=1;AF=0.756;AN=2;DP=2208;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,27:51:99:692,0,671:9,15,9,18 chr1 17764627 . G A 915.4 PASS AC=1;AF=0.648;AN=2;DP=1251;MQ=60;set=variant2-variant6-variant7-variant10-variant11-variant12-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:31,23:54:99:563,0,786:20,11,16,7 chr1 17907505 . A G 513.75 PASS AC=1;AF=0.75;AN=2;DP=675;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,14:28:99:412,0,444:2,12,3,11 chr1 17907575 . C T 66.22 PASS AC=1;AF=0.828;AN=2;DP=184;FS=0;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant15-variant16-variant18-variant20-variant22-variant23-variant24-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:76:117,0,76:1,2,0,3 chr1 17907607 . C T 61.77 PASS AC=2;AF=0.953;AN=2;DP=135;FS=0;FractionInformativeReads=1;set=variant-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:94,9,0:0,0,1,2 chr1 17913714 . G A 66.22 PASS AC=2;AF=0.952;AN=2;DP=308;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:239,21,0:0,0,5,2 chr1 17914846 . C T 183.13 PASS AC=2;AF=0.895;AN=2;DP=1097;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:73:849,73,0:0,0,23,2 chr1 17929980 . C G 376.05 PASS AC=1;AF=0.6;AN=2;DP=2715;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant31-variant32-variant34-variant35-variant37-variant38-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,66:113:99:1444,0,1020:28,19,36,30 chr1 17981184 . A C 1675.39 PASS AC=1;AF=0.536;AN=2;DP=2018;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant7-variant13-variant15-variant18-variant22-variant29-variant30-variant31-variant35-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:77,65:142:99:1553,0,1851:33,44,29,36 chr1 17982559 . G A 988.33 PASS AC=1;AF=0.536;AN=2;DP=1327;MQ=60;set=variant2-variant6-variant7-variant13-variant15-variant18-variant22-variant29-variant30-variant31-variant35-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:72,40:112:99:867,0,1732:33,39,18,22 chr1 17991052 . T C 3978.13 PASS AC=2;AF=1;AN=2;DP=6329;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,173:173:99:5060,519,0:0,0,85,88 chr1 17991196 . A G 911.94 PASS AC=1;AF=0.531;AN=2;DP=828;MQ=60;set=variant2-variant6-variant7-variant10-variant13-variant15-variant18-variant22-variant29-variant30-variant31-variant35-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,29:50:99:779,0,583:6,15,10,19 chr1 18016162 . G A 250.14 PASS AC=1;AF=0.577;AN=2;DP=190;FractionInformativeReads=1;set=variant2-variant6-variant7-variant15-variant18-variant22-variant30-variant31-variant35-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,6:15:99:176,0,283:6,3,5,1 chr1 18016402 . A G 1166.66 PASS AC=1;AF=0.536;AN=2;DP=1569;MQ=60;set=variant2-variant6-variant7-variant15-variant18-variant22-variant29-variant30-variant31-variant35-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,77:128:99:1937,0,1178:23,28,35,42 chr1 18016441 . T C 735.43 PASS AC=1;AF=0.536;AN=2;DP=1106;MQ=60;set=variant2-variant6-variant7-variant15-variant18-variant22-variant29-variant30-variant31-variant35-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,52:92:99:1374,0,985:17,23,19,33 chr1 18016491 . G A 287.57 PASS AC=1;AF=0.536;AN=2;DP=458;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant7-variant15-variant18-variant22-variant29-variant30-variant31-variant35-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,26:44:99:757,0,509:6,12,5,21 chr1 18017522 . T C 1960.66 PASS AC=1;AF=0.849;AN=2;DP=2121;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,33:64:99:868,0,794:21,10,20,13 chr1 18017558 . A G 3148.13 PASS AC=1;AF=0.849;AN=2;DP=3112;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,54:103:99:1246,0,1129:28,21,29,25 chr1 18017704 . C T 2430.23 PASS AC=1;AF=0.849;AN=2;DP=2266;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,33:64:99:760,0,847:12,19,12,21 chr1 18021406 . T C 3104.12 PASS AC=1;AF=0.849;AN=2;DP=6683;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:92,74:166:99:1832,0,2233:47,45,44,30 chr1 18023154 . A G 291.22 PASS AC=1;AF=0.849;AN=2;DP=725;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,9:16:99:258,0,198:5,2,7,2 chr1 18023290 . C T 2120.58 PASS AC=1;AF=0.849;AN=2;DP=3917;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,46:98:99:1229,0,1251:28,24,26,20 chr1 18023365 . C T 3592.28 PASS AC=1;AF=0.837;AN=2;DP=6230;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:80,61:141:99:1377,0,2082:44,36,31,30 chr1 18023509 . T C 2590.79 PASS AC=1;AF=0.837;AN=2;DP=4793;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:74,61:135:99:1582,0,1868:36,38,33,28 chr1 18023690 . A G 3854.74 PASS AC=1;AF=0.837;AN=2;DP=6429;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:89,89:178:99:2182,0,2040:44,45,48,41 chr1 18023997 . G GC 2815.45 PASS AC=1;AF=0.837;AN=2;DP=3725;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,47:95:99:1438,0,1508:22,26,22,25 chr1 18149510 . G T 3967.72 PASS AC=2;AF=0.696;AN=2;DP=3113;MQ=60;set=variant2-variant3-variant5-variant7-variant10-variant14-variant15-variant17-variant19-variant20-variant22-variant26-variant27-variant28-variant30-variant32-variant34-variant35-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,146:146:99:4432,436,0:0,0,86,60 chr1 18149566 . C A 5831.69 PASS AC=2;AF=0.717;AN=2;DP=5006;MQ=60;set=variant2-variant3-variant5-variant7-variant10-variant14-variant15-variant17-variant19-variant20-variant22-variant24-variant27-variant28-variant30-variant32-variant34-variant35-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,201:202:99:6118,593,0:1,0,112,89 chr1 18152582 . C T 4549.3 PASS AC=1;AF=0.571;AN=2;DP=3582;MQ=60;set=variant3-variant7-variant14-variant15-variant19-variant20-variant22-variant24-variant26-variant30-variant31-variant32-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:135,143:278:99:3489,0,3500:64,71,69,74 chr1 18434199 . CG C 87.15 PASS AC=2;AF=1;AN=2;DP=16;FS=0;MQ=60;set=variant3-variant4-variant22-variant35 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:124,12,0:0,0,3,1 chr1 18434518 . G C 373.54 PASS AC=2;AF=0.652;AN=2;DP=602;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:609,63,0:0,0,10,11 chr1 18434981 . T C 88.71 PASS AC=1;AF=0.5;AN=2;DP=69;FractionInformativeReads=1;MQ=60;set=variant7-variant12-variant13-variant16-variant23-variant32-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:4,3:7:99:111,0,162:0,4,0,3 chr1 18691614 . T C 837.86 PASS AC=1;AF=0.556;AN=2;DP=525;MQ=60;set=variant27-variant30-variant31-variant33-variant35-variant36-variant37-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:29,43:72:99:1072,0,826:24,5,29,14 chr1 18691665 . G T 1129.53 PASS AC=1;AF=0.556;AN=2;DP=1067;MQ=60;set=variant27-variant30-variant31-variant33-variant35-variant36-variant37-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:79,76:155:99:1627,0,1958:50,29,40,36 chr1 18702988 . T C 549.5 PASS AC=2;AF=1;AN=2;DP=632;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:334,24,0:0,0,0,8 chr1 18703544 . G A 2824.52 PASS AC=1;AF=0.556;AN=2;DP=1995;MQ=60;set=variant27-variant30-variant31-variant33-variant35-variant36-variant37-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:137,97:234:99:2585,0,3740:47,90,26,71 chr1 18704829 . G A 1581.89 PASS AC=1;AF=0.5;AN=2;DP=539;MQ=60;set=variant33-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:85,99:184:99:2357,0,2093:37,48,49,50 chr1 18704862 . A G 4971.26 PASS AC=1;AF=0.672;AN=2;DP=4380;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant16-variant17-variant19-variant23-variant24-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:87,95:182:99:2613,0,2155:36,51,42,53 chr1 18807339 . T C 448.35 PASS AC=1;AF=0.656;AN=2;DP=983;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,12:27:99:355,0,420:11,4,9,3 chr1 18807897 . C G 5234.8 PASS AC=1;AF=0.671;AN=2;DP=9458;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:135,107:242:99:2644,0,3492:78,57,59,48 chr1 18807953 . C A 5525.9 PASS AC=1;AF=0.6;AN=2;DP=6867;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant14-variant15-variant17-variant18-variant21-variant25-variant26-variant27-variant28-variant30-variant31-variant35-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:170,125:295:99:2831,0,4222:96,74,70,55 chr1 18808292 . C A 5091.97 PASS AC=1;AF=0.671;AN=2;DP=8628;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:148,111:259:99:2540,0,3774:73,75,53,58 chr1 18808465 . T A 2146.46 PASS AC=1;AF=0.671;AN=2;DP=4305;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,71:139:99:1814,0,1688:27,41,33,38 chr1 18808526 . A C 2354.86 PASS AC=1;AF=0.671;AN=2;DP=4818;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,65:125:99:1522,0,1545:30,30,37,28 chr1 18809896 . A T 3924.27 PASS AC=1;AF=0.634;AN=2;DP=5174;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,56:123:99:2027,0,3572:30,37,24,32 chr1 18809916 . G A 3807.75 PASS AC=1;AF=0.563;AN=2;DP=2758;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant15-variant17-variant18-variant21-variant25-variant26-variant27-variant28-variant30-variant31-variant35-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:66,53:119:99:1999,0,3513:28,38,22,31 chr1 18810344 . G T 2284.54 PASS AC=1;AF=0.622;AN=2;DP=2728;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,31:63:99:808,0,878:20,12,19,12 chr1 18811668 . T C 705.26 PASS AC=1;AF=0.707;AN=2;DP=1722;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,30:56:99:757,0,626:12,14,16,14 chr1 18812176 . G A 632.34 PASS AC=1;AF=0.625;AN=2;DP=601;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant15-variant17-variant18-variant21-variant24-variant25-variant26-variant27-variant30-variant31-variant35-variant38-variant39-filterInvariant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,9:24:99:191,0,488:4,11,3,6 chr1 19027239 . A G 1003.67 PASS AC=1;AF=0.528;AN=2;DP=1862;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant10-variant11-variant14-variant15-variant18-variant22-variant25-variant27-variant28-variant29-variant32-variant34-variant35-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,59:117:99:1496,0,1325:33,25,32,27 chr1 19029546 . A G 396 PASS AC=1;AF=0.528;AN=2;DP=515;MQ=60;set=variant-variant3-variant4-variant10-variant11-variant14-variant15-variant18-variant22-variant25-variant27-variant28-variant29-variant32-variant34-variant35-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,22:37:99:636,0,408:11,4,18,4 chr1 19071182 . A G 330.35 PASS AC=2;AF=0.72;AN=2;DP=776;set=variant2-variant3-variant4-variant6-variant9-variant10-variant11-variant12-variant13-filterInvariant14-variant15-variant16-variant17-variant18-variant21-variant22-variant24-variant28-variant29-variant32-variant35-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:15:734,15,0:0,0,16,2 chr1 19071183 . A AATGG,G,AATGGATGG 699.95 PASS AC=0,2,0;AF=0.172,0.516,0.016;AN=2;DP=998;set=variant6-variant10-variant11-variant12-variant3-variant-variant13-variant14-variant4-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant39-variant41-variant42-variant43 GT:DP:GQ:SB 2/2:24:30:0,1,17,6 chr1 19071187 . G GATAA,GATGGATAA,GATGGATGGATGGATGGATAA 221.98 PASS AC=1,0,0;AF=0.444,0.056,0.028;AN=2;DP=588;set=variant3-variant6-variant9-variant10-variant11-filterInvariant14-variant15-filterInvariant19-variant20-variant21-variant24-filterInvariant25-variant29-variant32-variant35-variant39-variant41-variant43 GT:DP:GQ:SB 0/1:27:99:9,4,12,2 chr1 19071191 . G GATGGATGGATGGATGGATAA,GATGGATGGATGGATAA,GATAA,GATGGATAA,GATGGATGGATAA 288.77 PASS AC=0,0,1,0,0;AF=0.042,0.167,0.208,0.125,0.042;AN=2;DP=398;set=variant2-variant3-variant4-variant10-variant12-variant16-variant13-variant18-variant27-variant35-filterInvariant41-variant43 GT:DP:GQ:SB 0/3:28:99:14,8,6,0 chr1 19071752 . T C 339.76 PASS AC=2;AF=0.797;AN=2;DP=1861;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant32-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:2119,186,0:0,0,31,31 chr1 19072926 . A G 269.05 PASS AC=2;AF=0.75;AN=2;DP=930;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant32-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:965,81,0:0,0,10,17 chr1 19073190 . C T 685.08 PASS AC=1;AF=0.5;AN=2;DP=382;FractionInformativeReads=1;MQ=60;set=variant9-variant11-variant14-variant16-variant35 GT:AD:DP:GQ:PL:SB 0/1:46,30:76:99:728,0,1178:25,21,15,15 chr1 19075225 . A G 2525.49 PASS AC=2;AF=0.792;AN=2;DP=5802;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant32-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,167:167:99:5193,500,0:0,0,94,73 chr1 19166100 . C T 879.65 PASS AC=1;AF=0.5;AN=2;DP=92;FS=3.958;FractionInformativeReads=1;MQ=60;MQRankSum=0.319;QD=9.56;ReadPosRankSum=-0.764;SOR=0.91;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:55,37:92:99:908,0,1380:29,26,16,21 chr1 19166294 . G A 812.53 PASS AC=1;AF=0.522;AN=2;DP=3265;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant17-variant18-variant19-variant20-variant28-variant29-variant34-variant35-variant36-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:81,77:158:99:1972,0,2182:43,38,41,36 chr1 19166894 . G A 1783.86 PASS AC=1;AF=0.5;AN=2;DP=139;FS=2.146;FractionInformativeReads=1;MQ=60;MQRankSum=0.398;QD=12.83;ReadPosRankSum=2.426;SOR=0.923;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:72,67:139:99:1812,0,1705:37,35,38,29 chr1 19168181 . AG A 707.51 PASS AC=1;AF=0.5;AN=2;DP=60;FS=0;FractionInformativeReads=0.983;MQ=60;MQRankSum=-0.191;QD=11.79;ReadPosRankSum=1.412;SOR=0.665;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:33,26:59:99:745,0,986:18,15,14,12 chr1 19168478 . GA GAA,G 31.06 PASS AC=2,0;AF=0.545,0.114;AN=2;DP=270;MQ=60;set=variant-variant3-variant6-variant7-variant10-variant11-variant17-variant19-variant20-variant21-variant22-variant24-variant27-variant28-variant34-variant35-variant38-variant39-variant40-variant41-variant43-variant44 GT:DP:GQ:SB 1/1:3:12:0,0,1,2 chr1 19176254 . C T 136.09 PASS AC=1;AF=0.529;AN=2;DP=220;FractionInformativeReads=1;MQ=60;set=variant5-variant7-variant11-variant13-variant23-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:4,15:19:99:442,0,101:1,3,4,11 chr1 19181015 . G C 2309.48 PASS AC=1;AF=0.597;AN=2;DP=7284;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant29-variant31-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:128,133:261:99:3410,0,3589:69,59,61,72 chr1 19181082 . A C 1900.97 PASS AC=1;AF=0.597;AN=2;DP=8445;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant29-variant31-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:152,147:299:99:3597,0,3688:82,70,74,73 chr1 19181393 . T C 2864.41 PASS AC=1;AF=0.597;AN=2;DP=9541;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant29-variant31-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:158,153:311:99:3594,0,3846:74,84,80,73 chr1 19184077 . A G 1121.51 PASS AC=1;AF=0.597;AN=2;DP=5193;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant29-variant31-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:92,86:178:99:2184,0,2336:39,53,33,53 chr1 19184176 . G A 349.37 PASS AC=1;AF=0.583;AN=2;DP=1137;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant6-variant7-variant9-variant10-variant11-variant14-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant29-variant35-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,20:49:99:583,0,845:7,22,3,17 chr1 19186129 . G C 2378.41 PASS AC=2;AF=0.869;AN=2;DP=5309;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,139:139:99:4061,416,0:0,0,67,72 chr1 19186246 . G A 905.45 PASS AC=1;AF=0.5;AN=2;DP=111;FS=0.709;FractionInformativeReads=1;MQ=60;MQRankSum=-1.378;QD=8.16;ReadPosRankSum=-0.333;SOR=0.621;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:66,45:111:99:934,0,1793:31,35,22,23 chr1 19186260 . C T 659.69 PASS AC=1;AF=0.625;AN=2;DP=2681;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,44:103:99:947,0,1550:26,33,21,23 chr1 19186320 . G C 1359.12 PASS AC=2;AF=0.829;AN=2;DP=2261;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:2092,204,0:0,0,29,39 chr1 19197849 . T C 164.94 PASS AC=1;AF=0.533;AN=2;DP=160;FractionInformativeReads=1;MQ=60;set=variant6-variant7-variant8-variant13-variant15-variant18-variant25-variant26-variant27-variant28-variant35-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,4:9:99:112,0,142:4,1,3,1 chr1 19198064 . T G 436.7 PASS AC=1;AF=0.604;AN=2;DP=894;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant9-variant11-variant14-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant29-variant35-variant36-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,28:56:99:724,0,784:17,11,17,11 chr1 19198100 . C G 665.33 PASS AC=1;AF=0.604;AN=2;DP=1155;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant9-variant11-variant14-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant29-variant35-variant36-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,39:71:99:976,0,790:19,13,22,17 chr1 19198141 . T C 773.78 PASS AC=1;AF=0.604;AN=2;DP=1575;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant9-variant11-variant14-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant29-variant35-variant36-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,47:93:99:1263,0,1077:23,23,28,19 chr1 19198414 . G A 1134.78 PASS AC=1;AF=0.604;AN=2;DP=1841;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant9-variant11-variant14-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant29-variant35-variant36-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,32:73:99:1217,0,2431:17,24,11,21 chr1 19198418 . C T 1131.13 PASS AC=1;AF=0.604;AN=2;DP=1830;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant6-variant9-variant11-variant14-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant29-variant35-variant36-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,31:72:99:1214,0,2452:16,25,11,20 chr1 19198576 . A G 2628.54 PASS AC=1;AF=0.795;AN=2;DP=4213;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,40:88:99:1013,0,1141:26,22,24,16 chr1 19198627 . G A 1955.05 PASS AC=1;AF=0.604;AN=2;DP=3432;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant9-variant11-variant14-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant29-variant35-variant36-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,53:118:99:1310,0,1584:37,28,30,23 chr1 19198895 . A G 679.37 PASS AC=1;AF=0.614;AN=2;DP=951;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant11-variant14-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant29-variant35-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,19:39:99:477,0,537:10,10,10,9 chr1 19199487 . A G 1280.38 PASS AC=1;AF=0.619;AN=2;DP=2783;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant11-variant14-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant29-variant35-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:76,74:150:99:1724,0,1907:34,42,37,37 chr1 19200895 . C T 438.63 PASS AC=1;AF=0.63;AN=2;DP=1668;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant9-variant11-variant14-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant29-variant35-variant36-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,38:78:99:926,0,1096:26,14,27,11 chr1 19201184 . G C 480.36 PASS AC=1;AF=0.784;AN=2;DP=1019;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,24:40:99:854,0,403:5,11,3,21 chr1 19201211 . T TG 149.77 PASS AC=1;AF=0.784;AN=2;DP=617;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,16:26:99:517,0,293:2,8,2,14 chr1 19201956 . A G 2312.56 PASS AC=1;AF=0.803;AN=2;DP=4851;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:94,54:148:99:1160,0,2223:45,49,29,25 chr1 19202770 . T C 1545.44 PASS AC=2;AF=0.977;AN=2;DP=4067;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,95:95:99:3011,285,0:0,0,51,44 chr1 19202896 . G A 1560.2 PASS AC=1;AF=0.721;AN=2;DP=2641;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,51:91:99:1360,0,944:21,19,20,31 chr1 19202917 . T C 1972.77 PASS AC=1;AF=0.776;AN=2;DP=2630;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,47:87:99:1804,0,1734:20,20,18,29 chr1 19202926 . T C 1942.93 PASS AC=1;AF=0.776;AN=2;DP=2432;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,45:80:99:1749,0,1647:16,19,18,27 chr1 19203997 . C G 723.36 PASS AC=1;AF=0.75;AN=2;DP=3932;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:84,60:144:99:1296,0,1987:39,45,29,31 chr1 19204154 . G A 245.42 PASS AC=2;AF=0.872;AN=2;DP=776;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:764,72,0:0,0,8,16 chr1 19204173 . A G 167.92 PASS AC=2;AF=0.905;AN=2;DP=740;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:659,60,0:0,0,6,14 chr1 19208145 . G GGGTTGCCT 1086.83 PASS AC=2;AF=0.989;AN=2;DP=2348;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:2327,156,0:0,0,32,16 chr1 19208944 . A G 1221.18 PASS AC=2;AF=0.989;AN=2;DP=1365;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1698,150,0:0,0,38,12 chr1 19209543 . A G 2520.27 PASS AC=2;AF=0.989;AN=2;DP=3586;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,100:100:99:3352,299,0:0,0,72,28 chr1 19215834 . T C 6975.49 PASS AC=2;AF=0.943;AN=2;DP=14701;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,384:384:99:11386,1148,0:0,0,208,176 chr1 19238001 . TTTTATTTATTTA TTTTATTTATTTATTTA,TTTTA,T 137.32 PASS AC=2,0,0;AF=0.632,0.184,0.026;AN=2;DP=581;set=variant4-variant5-variant10-variant11-variant12-variant14-variant15-variant17-filterInvariant20-variant24-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant40-variant42 GT:DP:GQ:SB 1/1:3:7:0,0,0,3 chr1 19243589 . A G 2939.97 PASS AC=2;AF=0.658;AN=2;DP=5092;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,145:145:99:4433,434,0:0,0,60,85 chr1 19245984 . T G 106.44 PASS AC=1;AF=0.5;AN=2;DP=116;MQ=60;set=variant18-filterInvariant35 GT:AD:DP:GQ:PL:SB 0/1:64,14:78:99:155,0,3492:61,3,0,14 chr1 19245989 . A G 100.89 PASS AC=1;AF=0.5;AN=2;DP=119;MQ=60;set=variant18-filterInvariant35 GT:AD:DP:GQ:PL:SB 0/1:59,18:77:99:161,0,3450:56,3,0,18 chr1 19282981 . A C 2396.44 PASS AC=2;AF=0.989;AN=2;DP=2818;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,66:66:99:2349,198,0:0,0,26,40 chr1 19408294 . G GC 1004.19 PASS AC=1;AF=0.586;AN=2;DP=3324;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant14-variant15-variant17-variant18-variant19-variant21-variant24-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,54:111:99:1402,0,1528:22,35,16,38 chr1 19408380 . T C 748.75 PASS AC=1;AF=0.621;AN=2;DP=1703;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant14-variant15-variant17-variant18-variant19-variant21-variant24-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,25:46:99:773,0,607:6,15,8,17 chr1 19411129 . A G 998.15 PASS AC=1;AF=0.658;AN=2;DP=3675;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,46:100:99:957,0,1260:25,29,23,23 chr1 19412464 . C T 193.45 PASS AC=1;AF=0.622;AN=2;DP=602;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,6:15:99:208,0,346:9,0,6,0 chr1 19413261 . T A 1256.98 PASS AC=1;AF=0.622;AN=2;DP=6157;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:109,74:183:99:1700,0,2535:62,47,46,28 chr1 19413420 . T G 508.17 PASS AC=1;AF=0.658;AN=2;DP=1965;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,33:59:99:951,0,745:6,20,8,25 chr1 19415304 . C T 580.63 PASS AC=1;AF=0.622;AN=2;DP=1606;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,21:43:99:571,0,622:15,7,16,5 chr1 19420392 . G A 647.13 PASS AC=1;AF=0.658;AN=2;DP=2386;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,29:56:99:827,0,686:15,12,21,8 chr1 19426199 . G A 195.86 PASS AC=1;AF=0.658;AN=2;DP=1095;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,15:27:99:379,0,376:2,10,6,9 chr1 19433449 . A G 141.5 PASS AC=1;AF=0.658;AN=2;DP=789;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,22:29:99:531,0,150:3,4,8,14 chr1 19437185 . G T 958.34 PASS AC=1;AF=0.5;AN=2;DP=605;MQ=60;set=variant3-variant4-variant6-variant8-variant14-variant15-variant24-variant28-variant29-variant34-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,27:47:99:822,0,529:15,5,21,6 chr1 19440107 . A G 1615.39 PASS AC=1;AF=0.658;AN=2;DP=4931;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,70:137:99:1869,0,1703:34,33,40,30 chr1 19441212 . A G 274.66 PASS AC=1;AF=0.662;AN=2;DP=665;FractionInformativeReads=1;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,11:17:99:394,0,205:6,0,10,1 chr1 19441723 . ACTCT A 310.62 PASS AC=1;AF=0.559;AN=2;DP=361;MQ=60;set=variant-variant7-variant8-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant25-variant27-variant28-variant30-variant33-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:6,10:16:99:339,0,282:5,1,3,7 chr1 19444912 . CTT CT,CTTTTT,C 81.56 PASS AC=1,0,0;AF=0.433,0.033,0.033;AN=2;DP=354;set=variant2-filterInvariant3-variant4-variant8-variant12-variant19-filterInvariant22-variant26-variant32-variant34-variant35-variant37-filterInvariant39-variant40-variant43 GT:DP:GQ:SB 0/1:14:90:4,4,0,6 chr1 19446587 . C T 250.11 PASS AC=1;AF=0.5;AN=2;DP=293;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant6-variant8-variant14-variant15-variant24-variant28-variant29-variant34-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,12:20:99:343,0,252:7,1,10,2 chr1 19447498 . T C 209.05 PASS AC=1;AF=0.671;AN=2;DP=575;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,6:15:99:210,0,363:9,0,6,0 chr1 19447843 . C G 699.95 PASS AC=1;AF=0.622;AN=2;DP=2550;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,44:75:99:1151,0,918:16,15,20,24 chr1 19448326 . C T 1013.12 PASS AC=1;AF=0.632;AN=2;DP=3332;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,43:88:99:1078,0,1039:27,18,24,19 chr1 19448608 . C G 61.22 PASS AC=1;AF=0.694;AN=2;DP=330;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,5:9:99:198,0,114:1,3,0,5 chr1 19454267 . C T 1787.01 PASS AC=1;AF=0.5;AN=2;DP=494;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant24-variant35 GT:AD:DP:GQ:PL:SB 0/1:75,57:132:99:1269,0,1889:32,43,25,32 chr1 19470749 . G C 93.12 PASS AC=1;AF=0.662;AN=2;DP=1314;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,14:28:99:456,0,389:5,9,3,11 chr1 19484299 . G A 1952.77 PASS AC=1;AF=0.5;AN=2;DP=438;FractionInformativeReads=1;MQ=60;set=variant3-variant24-variant35 GT:AD:DP:GQ:PL:SB 0/1:77,46:123:99:1006,0,1927:40,37,26,20 chr1 19486839 . T C 147.6 PASS AC=1;AF=0.658;AN=2;DP=1217;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,13:14:3:408,0,3:0,1,4,9 chr1 19491857 . T C 1867.19 PASS AC=1;AF=0.658;AN=2;DP=4645;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,59:123:99:1455,0,1640:28,36,31,28 chr1 19499560 . T C 1797.84 PASS AC=1;AF=0.5;AN=2;DP=1820;MQ=60;set=variant3-variant4-variant5-variant6-variant8-variant14-variant15-variant24-variant28-variant29-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:79,77:156:99:2079,0,2161:40,39,30,47 chr1 19499835 . G C 1315.27 PASS AC=1;AF=0.658;AN=2;DP=3288;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,38:76:99:1118,0,981:18,20,12,26 chr1 19500729 . G A 725.88 PASS AC=1;AF=0.658;AN=2;DP=2276;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,26:54:99:599,0,684:19,9,17,9 chr1 19510394 . A G 1358.39 PASS AC=1;AF=0.658;AN=2;DP=5362;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:90,57:147:99:1281,0,2263:49,41,29,28 chr1 19544010 . CA C,CAA 148.77 PASS AC=0,1;AF=0.214,0.286;AN=2;DP=839;set=filterInvariant2-variant3-variant13-variant24-filterInvariant28-variant35-filterInvariant41 GT:DP:GQ:SB 0/2:109:99:33,20,38,18 chr1 19554099 . T G 39.17 PASS AC=1;AF=0.649;AN=2;DP=836;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,13:24:99:388,0,262:3,8,3,10 chr1 19557713 . G C 196.42 PASS AC=1;AF=0.639;AN=2;DP=651;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,15:25:99:511,0,256:6,4,13,2 chr1 19563461 . CAAAAA CAA,CAAA,CAAAA,CA,CAAAAAA,C 122.48 PASS AC=0,0,1,0,0,0;AF=0.119,0.095,0.214,0.071,0.048,0.024;AN=2;DP=277;set=variant3-variant4-variant5-variant8-variant10-variant13-variant15-variant17-variant18-variant20-variant22-variant23-variant25-variant27-variant28-variant35-variant39-variant40-variant41-variant43-variant44 GT:DP:GQ:SB 0/3:11:44:2,2,6,1 chr1 19566881 . C T 1894.77 PASS AC=1;AF=0.5;AN=2;DP=1344;MQ=60;set=variant3-variant4-variant5-variant6-variant8-variant14-variant15-variant24-variant28-variant29-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,44:109:99:1043,0,1676:33,32,24,20 chr1 19578053 . C G 4235.9 PASS AC=1;AF=0.5;AN=2;DP=4058;MQ=60;set=variant3-variant4-variant5-variant6-variant11-variant13-variant14-variant24-variant28-variant29-variant34-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:148,157:305:99:3978,0,3921:63,85,67,90 chr1 19578404 . G A 3596.51 PASS AC=1;AF=0.5;AN=2;DP=3102;MQ=60;set=variant3-variant4-variant5-variant6-variant11-variant13-variant14-variant24-variant28-variant29-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:112,129:241:99:3060,0,3044:53,59,61,68 chr1 19581226 . G A 1153.09 PASS AC=1;AF=0.553;AN=2;DP=1457;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant6-variant11-variant13-variant14-variant17-variant20-variant21-variant23-variant24-variant28-variant29-variant31-variant34-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,34:65:99:888,0,750:16,15,19,15 chr1 19581442 . GA GAAA,GAA,G 855.95 PASS AC=1,0,0;AF=0.5,0.025,0.025;AN=2;DP=1025;MQ=60;set=variant3-variant4-variant5-variant6-variant11-variant13-variant14-variant17-variant20-variant21-variant23-variant24-variant28-variant29-variant31-variant34-variant35-variant39-filterInvariant43-variant44 GT:DP:GQ:SB 0/1:54:99:13,17,9,15 chr1 19581467 . C T 961.33 PASS AC=1;AF=0.553;AN=2;DP=670;MQ=60;set=variant3-variant4-variant5-variant6-variant11-variant13-variant14-variant17-variant20-variant21-variant23-variant24-variant28-variant29-variant31-variant34-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,20:44:99:669,0,1156:9,15,8,12 chr1 19582338 . C A 1211.78 PASS AC=1;AF=0.5;AN=2;DP=748;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant6-variant11-variant13-variant14-variant24-variant28-variant29-variant34-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,18:40:99:499,0,630:15,7,12,6 chr1 19582563 . G A 1599.12 PASS AC=1;AF=0.814;AN=2;DP=6236;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:77,79:156:99:1816,0,1836:34,43,33,46 chr1 19583400 . A G 1713.52 PASS AC=2;AF=0.955;AN=2;DP=2679;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:2497,237,0:0,0,42,37 chr1 19583684 . C T 958.37 PASS AC=1;AF=0.553;AN=2;DP=1254;MQ=60;set=variant3-variant4-variant5-variant6-variant11-variant13-variant14-variant17-variant20-variant21-variant23-variant24-variant28-variant29-variant31-variant34-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,24:74:99:526,0,1308:23,27,15,9 chr1 19583725 . T C 1139.02 PASS AC=1;AF=0.553;AN=2;DP=1108;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant6-variant11-variant13-variant14-variant17-variant20-variant21-variant23-variant24-variant28-variant29-variant31-variant34-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,26:63:99:708,0,1121:16,21,18,8 chr1 19584004 . G A 1674.83 PASS AC=1;AF=0.553;AN=2;DP=1857;FractionInformativeReads=1;set=variant3-variant4-variant5-variant6-variant11-variant13-variant14-variant17-variant20-variant21-variant23-variant24-variant28-variant29-variant31-variant34-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,53:100:99:1378,0,1194:18,29,17,36 chr1 19585545 . G A 185.02 PASS AC=1;AF=0.814;AN=2;DP=1190;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,13:27:99:408,0,349:4,10,2,11 chr1 19585903 . G A 62.44 PASS AC=1;AF=0.588;AN=2;DP=163;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant6-variant11-variant13-variant14-variant20-variant21-variant24-variant28-variant29-variant31-variant34-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,6:10:99:164,0,149:3,1,4,2 chr1 19585933 . G A 64.07 PASS AC=1;AF=0.5;AN=2;DP=168;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant6-variant11-variant13-variant14-variant24-variant28-variant29-variant34-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:6,6:12:99:153,0,197:5,1,4,2 chr1 19586015 . G T 234.85 PASS AC=1;AF=0.553;AN=2;DP=626;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant6-variant11-variant13-variant14-variant17-variant20-variant21-variant23-variant24-variant28-variant29-variant31-variant34-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,18:30:99:477,0,270:7,5,11,7 chr1 19586294 . A G 581.92 PASS AC=1;AF=0.553;AN=2;DP=1228;MQ=60;set=variant3-variant4-variant5-variant6-variant11-variant13-variant14-variant17-variant20-variant21-variant23-variant24-variant28-variant29-variant31-variant34-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,22:73:99:409,0,1321:21,30,11,11 chr1 19586360 . T C 657.93 PASS AC=1;AF=0.5;AN=2;DP=601;MQ=60;set=variant3-variant4-variant5-variant6-variant11-variant13-variant14-variant24-variant28-variant29-variant34-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,9:48:99:140,0,1080:14,25,5,4 chr1 19586571 . T C 452.17 PASS AC=1;AF=0.5;AN=2;DP=408;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant6-variant11-variant13-variant14-variant24-variant28-variant29-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,16:35:99:413,0,413:9,10,8,8 chr1 19586684 . G A 73.61 PASS AC=1;AF=0.5;AN=2;DP=164;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant6-variant11-variant13-variant14-variant24-variant28-variant29-variant34-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,10:15:99:240,0,128:2,3,4,6 chr1 19595137 . C T 1477.02 PASS AC=1;AF=0.738;AN=2;DP=3738;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,61:108:99:1516,0,1105:29,18,39,22 chr1 19595194 . A G 1907.67 PASS AC=1;AF=0.5;AN=2;DP=1530;MQ=60;set=variant3-variant4-variant5-variant6-variant11-variant14-variant24-variant28-variant34-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:85,76:161:99:1599,0,1920:42,43,40,36 chr1 19595892 . G A 1187.92 PASS AC=1;AF=0.738;AN=2;DP=3849;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,56:109:99:1614,0,1443:13,40,14,42 chr1 19596124 . C T 1509.39 PASS AC=1;AF=0.738;AN=2;DP=1825;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,27:50:99:689,0,709:18,5,18,9 chr1 19596156 . G T 2367.83 PASS AC=1;AF=0.738;AN=2;DP=2769;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,43:90:99:1023,0,1163:29,18,24,19 chr1 19600386 . C T 3050.31 PASS AC=1;AF=0.5;AN=2;DP=3085;set=variant3-variant4-variant5-variant6-variant11-variant14-variant24-variant28-variant34-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:137,168:305:99:4371,0,3315:85,52,102,66 chr1 19600538 . C T 1447.53 PASS AC=1;AF=0.5;AN=2;DP=1316;set=variant3-variant4-variant5-variant6-variant11-variant14-variant24-variant28-variant34-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,74:134:99:1934,0,1356:21,39,22,52 chr1 19609254 . T C 1834.13 PASS AC=2;AF=0.83;AN=2;DP=9083;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,225:225:99:6699,674,0:0,0,102,123 chr1 19609522 . G A 634.81 PASS AC=2;AF=0.842;AN=2;DP=1147;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1057,108,0:0,0,13,23 chr1 19611227 . G A 340.65 PASS AC=1;AF=0.559;AN=2;DP=2164;set=variant-variant7-variant8-variant9-variant16-variant19-variant20-variant22-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:95,74:169:99:1714,0,2324:41,54,35,39 chr1 19611241 . T C 692.34 PASS AC=2;AF=0.818;AN=2;DP=5419;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,150:150:99:4517,449,0:0,0,64,86 chr1 19635011 . C T 1481.05 PASS AC=1;AF=0.5;AN=2;DP=1369;MQ=60;set=variant3-variant4-variant5-variant6-variant11-variant14-variant24-variant28-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:80,76:156:99:1889,0,1959:44,36,46,30 chr1 19638309 . A G 2421.34 PASS AC=2;AF=0.872;AN=2;DP=4583;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,130:130:99:4252,389,0:0,0,88,42 chr1 19638642 . AGCCGGGGGCCCC A 485.6 PASS AC=1;AF=0.5;AN=2;DP=91;MQ=60;set=variant8-variant35 GT:AD:DP:GQ:PL:SB 0/1:28,22:50:99:840,0,3721:12,16,10,12 chr1 19638883 . T C 1822.71 PASS AC=2;AF=0.756;AN=2;DP=3055;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:2553,237,0:0,0,45,34 chr1 19650982 . C T 139.66 PASS AC=1;AF=0.571;AN=2;DP=476;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant8-variant11-variant13-variant15-variant16-variant17-variant22-variant23-variant25-variant28-variant29-variant30-variant33-variant34-variant35-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,14:36:99:306,0,681:17,5,9,5 chr1 19651087 . G A 1594.17 PASS AC=1;AF=0.5;AN=2;DP=959;MQ=60;set=variant3-variant4-variant8-variant11-variant32-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:63,69:132:99:1603,0,2442:37,26,40,29 chr1 19651102 . A G 745.29 PASS AC=1;AF=0.571;AN=2;DP=2744;MQ=60;set=variant-variant2-variant8-variant11-variant13-variant15-variant16-variant17-variant22-variant23-variant25-variant28-variant29-variant30-variant33-variant34-variant35-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:73,67:140:99:1703,0,2732:41,32,41,26 chr1 19651277 . G A 245.57 PASS AC=1;AF=0.571;AN=2;DP=1098;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant8-variant11-variant13-variant15-variant16-variant17-variant22-variant23-variant25-variant28-variant29-variant30-variant33-variant34-variant35-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,35:73:99:1028,0,974:13,25,8,27 chr1 19651300 . T C 179.09 PASS AC=1;AF=0.571;AN=2;DP=741;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant8-variant11-variant13-variant15-variant16-variant17-variant22-variant23-variant25-variant28-variant29-variant30-variant33-variant34-variant35-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,25:49:99:769,0,690:6,18,5,20 chr1 19651330 . C T 154.78 PASS AC=1;AF=0.571;AN=2;DP=458;MQ=60;set=variant-variant2-variant8-variant11-variant13-variant15-variant16-variant17-variant22-variant23-variant25-variant28-variant29-variant30-variant33-variant34-variant35-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,15:29:99:447,0,422:2,12,3,12 chr1 19652063 . G A 1359.77 PASS AC=1;AF=0.571;AN=2;DP=2607;MQ=60;set=variant-variant2-variant8-variant11-variant13-variant15-variant16-variant17-variant22-variant23-variant25-variant28-variant29-variant30-variant33-variant34-variant35-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,86:138:99:2029,0,1437:28,24,41,45 chr1 19652127 . AGTT A 908.95 PASS AC=1;AF=0.571;AN=2;DP=1362;MQ=60;set=variant-variant2-variant8-variant11-variant13-variant15-variant16-variant17-variant22-variant23-variant25-variant28-variant29-variant30-variant33-variant34-variant35-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,47:75:99:1450,0,919:15,13,17,30 chr1 19652132 . T G,TGGGGG 895.82 PASS AC=1,0;AF=0.625,0.042;AN=2;DP=653;MQ=60;set=variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-filterInvariant42-variant43-variant44 GT:DP:GQ:SB 0/1:66:99:17,32,10,7 chr1 19652133 . G GGT 139.39 PASS AC=1;AF=0.5;AN=2;DP=986;MQ=60;set=variant3-variant4-variant7-variant8-variant9-variant10-filterInvariant11-variant13-variant14-variant20-variant21-variant26-variant27-variant31-variant32-variant35-variant36-variant39-variant40-variant41-filterInvariant42 GT:AD:DP:GQ:PL:SB 0/1:56,17:73:99:283,0,2111:20,36,10,7 chr1 19652135 . G GGT 909.07 PASS AC=1;AF=0.595;AN=2;DP=1272;MQ=60;set=variant-variant2-variant8-variant11-variant13-variant15-variant16-variant17-variant22-variant23-variant25-variant28-variant29-variant30-variant33-variant34-variant35-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,48:70:99:1679,0,888:11,11,17,31 chr1 19652684 . G C 493.98 PASS AC=1;AF=0.571;AN=2;DP=1026;MQ=60;set=variant-variant2-variant8-variant11-variant13-variant15-variant16-variant17-variant22-variant23-variant25-variant28-variant29-variant30-variant33-variant34-variant35-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,35:67:99:887,0,772:21,11,23,12 chr1 19653256 . A G 588.58 PASS AC=1;AF=0.571;AN=2;DP=877;MQ=60;set=variant-variant2-variant8-variant11-variant13-variant15-variant16-variant17-variant22-variant23-variant25-variant28-variant29-variant30-variant33-variant34-variant35-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,21:46:99:712,0,917:5,20,3,18 chr1 19654666 . GTTT G 319.71 PASS AC=1;AF=0.571;AN=2;DP=432;MQ=60;set=variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant20-variant21-variant26-variant27-variant31-variant32-variant35-variant36-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:3,13:16:99:537,0,121:1,2,2,11 chr1 19665456 . CA C 323.42 PASS AC=1;AF=0.5;AN=2;DP=1014;MQ=60;set=variant3-variant4-variant7-variant8-variant11-variant20-variant21-variant24-variant26-variant32-variant35-variant36-variant37-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:44,33:77:99:908,0,1515:22,22,13,20 chr1 19665497 . A C 451.2 PASS AC=1;AF=0.565;AN=2;DP=956;MQ=60;set=variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant20-variant21-variant24-variant26-variant27-variant31-variant32-variant35-variant36-variant37-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:32,16:48:99:503,0,810:9,23,1,15 chr1 19669235 . A G 1254.54 PASS AC=1;AF=0.571;AN=2;DP=1715;MQ=60;set=variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant20-variant21-variant26-variant27-variant31-variant32-variant35-variant36-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:53,53:106:99:1440,0,1277:33,20,36,17 chr1 19675262 . GGC G 433.04 PASS AC=1;AF=0.5;AN=2;DP=265;MQ=60;set=variant11-variant16-variant22-variant35 GT:AD:DP:GQ:PL:SB 0/1:36,26:62:99:476,0,785:22,14,18,8 chr1 19675263 . GC G 107.49 PASS AC=1;AF=0.533;AN=2;DP=2414;MQ=60;set=filterInvariant-filterInvariant3-filterInvariant4-variant7-variant8-filterInvariant9-variant10-variant11-variant13-filterInvariant15-variant17-variant20-filterInvariant21-filterInvariant22-variant23-variant25-variant26-filterInvariant27-filterInvariant28-variant29-variant31-filterInvariant32-variant34-variant35-variant36-variant38-filterInvariant39-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:31,19:50:99:291,0,663:19,12,15,4 chr1 19683301 . G T 754.96 PASS AC=1;AF=0.682;AN=2;DP=2823;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant18-variant19-variant20-variant21-variant24-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,46:89:99:1169,0,1017:18,25,21,25 chr1 19775113 . T C 1149.1 PASS AC=1;AF=0.643;AN=2;DP=1823;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant7-variant9-variant10-variant11-variant12-variant14-variant20-variant21-variant26-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:40,47:87:99:1118,0,1100:30,10,26,21 chr1 19775246 . C T 2023.13 PASS AC=1;AF=0.643;AN=2;DP=4228;MQ=60;set=variant2-variant3-variant4-variant7-variant9-variant10-variant11-variant12-variant14-variant20-variant21-variant26-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:111,114:225:99:2783,0,3108:66,45,68,46 chr1 19775492 . A G 1218.15 PASS AC=1;AF=0.643;AN=2;DP=1642;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant7-variant9-variant10-variant11-variant12-variant14-variant20-variant21-variant26-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:44,48:92:99:1295,0,1264:18,26,18,30 chr1 19775811 . G A 238.83 PASS AC=2;AF=0.756;AN=2;DP=1627;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1182,114,0:0,0,16,22 chr1 19923313 . T A 145.99 PASS AC=2;AF=0.646;AN=2;DP=911;MQ=60;set=variant-variant4-variant8-variant9-variant11-variant15-variant16-variant19-variant20-variant22-variant24-variant25-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1439,135,0:0,0,29,16 chr1 19935118 . T TA 73.03 PASS AC=2;AF=0.646;AN=2;DP=1076;MQ=60;set=variant-variant4-variant8-variant9-variant11-variant15-variant16-variant19-variant20-variant22-variant24-variant25-variant30-variant31-variant32-filterInvariant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1126,111,0:0,0,10,26 chr1 19953118 . G T 431.57 PASS AC=2;AF=0.966;AN=2;DP=718;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:348,24,0:0,0,7,1 chr1 19956374 . T G 2002.12 PASS AC=2;AF=0.852;AN=2;DP=5792;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,132:132:99:4501,396,0:0,0,38,94 chr1 19969611 . A G 630.88 PASS AC=2;AF=0.975;AN=2;DP=561;FS=0;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:549,51,0:0,0,10,7 chr1 19970888 . G T 72.61 PASS AC=1;AF=0.5;AN=2;DP=18;FractionInformativeReads=1;MQ=60;set=variant11-variant35 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:75:104,0,75:2,2,0,4 chr1 19981451 . A G 888.26 PASS AC=2;AF=0.742;AN=2;DP=1547;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,48:50:99:1531,101,0:1,1,31,17 chr1 19981791 . A G 2202.11 PASS AC=2;AF=0.75;AN=2;DP=5107;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,186:186:99:5637,557,0:0,0,98,88 chr1 19983863 . T TG,TGG 705.39 PASS AC=0,2;AF=0.038,0.85;AN=2;DP=930;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 2/2:17:51:0,0,16,1 chr1 19984100 . G GC 1834.48 PASS AC=2;AF=1;AN=2;DP=3743;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2384,219,0:0,0,42,28 chr1 19984461 . C T 921.31 PASS AC=2;AF=0.878;AN=2;DP=1594;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:1072,90,0:0,0,14,16 chr1 19992066 . T C 1553.15 PASS AC=2;AF=0.703;AN=2;DP=6157;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,173:173:99:5406,519,0:0,0,93,80 chr1 20008600 . C T 102.99 PASS AC=1;AF=0.841;AN=2;DP=352;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,5:13:70:70,0,203:6,2,3,2 chr1 20008880 . G T 440.93 PASS AC=1;AF=0.817;AN=2;DP=2257;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,20:50:99:444,0,833:18,12,11,9 chr1 20020993 . A G 3419.04 PASS AC=1;AF=0.854;AN=2;DP=5675;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:78,48:126:99:1750,0,4418:39,39,20,28 chr1 20020994 . C T 3419.04 PASS AC=1;AF=0.703;AN=2;DP=5031;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:77,47:124:99:1750,0,4418:39,38,19,28 chr1 20027049 . A C 196.61 PASS AC=1;AF=0.576;AN=2;DP=744;set=variant2-variant4-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,9:23:99:299,0,470:12,2,9,0 chr1 20027404 . G A 934.41 PASS AC=1;AF=0.58;AN=2;DP=1770;MQ=60;set=variant2-variant4-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant17-variant20-variant22-variant23-variant24-variant26-variant29-variant31-variant33-variant35-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,30:55:99:790,0,753:9,16,9,21 chr1 20027423 . T G 682.08 PASS AC=1;AF=0.6;AN=2;DP=1763;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant29-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,27:46:99:747,0,421:8,11,7,20 chr1 20066485 . G A 2360.05 PASS AC=1;AF=0.5;AN=2;DP=854;FractionInformativeReads=1;MQ=60;set=variant8-variant9-variant28-variant31-variant35-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:74,69:143:99:2570,0,3905:30,44,22,47 chr1 20066490 . T C 2338.35 PASS AC=1;AF=0.5;AN=2;DP=833;FractionInformativeReads=1;MQ=60;set=variant8-variant9-variant28-variant31-variant35-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:70,65:135:99:2518,0,3889:27,43,20,45 chr1 20067186 . T C 1057.74 PASS AC=1;AF=0.5;AN=2;DP=398;MQ=60;set=variant8-variant9-variant28-variant31-variant35-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,35:58:99:989,0,652:15,8,27,8 chr1 20097285 . T G 518.42 PASS AC=1;AF=0.538;AN=2;DP=686;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant16-variant23-variant27-variant28-variant30-variant33-variant35-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:31,32:63:99:890,0,937:8,23,10,22 chr1 20097370 . T C 662.04 PASS AC=1;AF=0.6;AN=2;DP=578;MQ=60;set=variant2-variant3-variant4-variant7-variant8-variant9-variant11-variant13-variant15-variant16-variant20-variant21-variant23-variant24-variant27-variant28-variant29-variant30-variant33-variant35-variant36-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:15,11:26:99:292,0,436:6,9,5,6 chr1 20097822 . G A 1524.71 PASS AC=1;AF=0.538;AN=2;DP=1607;MQ=60;set=variant2-variant7-variant16-variant23-variant27-variant28-variant30-variant33-variant35-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:72,62:134:99:1471,0,1703:38,34,30,32 chr1 20097941 . G T 1981.68 PASS AC=1;AF=0.643;AN=2;DP=1966;set=variant2-variant3-variant4-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:28,39:67:99:1011,0,669:9,19,12,27 chr1 20140389 . A T 314.84 PASS AC=1;AF=0.5;AN=2;DP=178;FractionInformativeReads=1;MQ=60;set=variant7-variant9-variant12-variant15-variant23-variant26-variant35-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,15:23:99:463,0,256:8,0,12,3 chr1 20141528 . C T 3107.41 PASS AC=1;AF=0.5;AN=2;DP=5272;MQ=60;set=variant5-variant7-variant8-variant16-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant30-variant31-variant34-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:186,167:353:99:3958,0,4792:83,103,73,94 chr1 20141882 . CA C 75.17 PASS AC=2;AF=1;AN=2;DP=366;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:337,27,0:0,0,2,7 chr1 20216860 . G A 2177.96 PASS AC=2;AF=0.716;AN=2;DP=2337;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:1793,170,0:0,0,39,18 chr1 20237881 . AT ATT,ATTT,A 318.35 PASS AC=1,1,0;AF=0.257,0.189,0.149;AN=2;DP=3760;set=variant2-filterInvariant4-variant5-filterInvariant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-filterInvariant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant29-filterInvariant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-filterInvariant39-variant41-variant42-variant43-filterInvariant44 GT:DP:GQ:SB 1/2:63:99:1,8,10,44 chr1 20238343 . A G 1416.26 PASS AC=2;AF=0.73;AN=2;DP=2224;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:2350,231,0:0,0,34,43 chr1 20238860 . C G 518.01 PASS AC=2;AF=0.65;AN=2;DP=906;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant19-variant20-variant21-variant23-variant27-variant31-variant32-variant35-variant36-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:1731,173,0:0,0,25,33 chr1 20246876 . C T 2034.74 PASS AC=1;AF=0.5;AN=2;DP=1467;MQ=60;set=variant11-variant12-variant14-variant19-variant23-variant27-variant31-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:70,103:173:99:2310,0,1585:33,37,50,53 chr1 20248646 . G A 1211.15 PASS AC=1;AF=0.5;AN=2;DP=458;FractionInformativeReads=1;MQ=60;set=variant9-variant11-variant12-variant14-variant19-variant23-variant26-variant27-variant31-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:23,14:37:99:516,0,1464:18,5,14,0 chr1 20248651 . A G 1238.67 PASS AC=1;AF=0.5;AN=2;DP=487;FractionInformativeReads=1;MQ=60;set=variant9-variant11-variant12-variant14-variant19-variant23-variant26-variant27-variant31-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:23,15:38:99:552,0,1439:18,5,15,0 chr1 20248709 . A G 1478.57 PASS AC=1;AF=0.5;AN=2;DP=1260;MQ=60;set=variant9-variant11-variant12-variant14-variant19-variant23-variant26-variant27-variant31-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:53,50:103:99:1207,0,1346:35,18,32,18 chr1 20250336 . A G 198.66 PASS AC=1;AF=0.556;AN=2;DP=188;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant8-variant9-variant11-variant13-variant16-variant18-variant19-variant21-variant23-variant26-variant27-variant35-variant36-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,7:16:99:267,0,482:3,6,2,5 chr1 20250339 . A G 198.66 PASS AC=1;AF=0.553;AN=2;DP=187;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant8-variant9-variant11-variant13-variant16-variant18-variant19-variant21-variant23-variant26-variant27-variant34-variant35-variant36-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,7:16:99:267,0,482:3,6,2,5 chr1 20301963 . C T 651.84 PASS AC=1;AF=0.5;AN=2;DP=50;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.039;QD=13.04;ReadPosRankSum=1.207;SOR=0.682;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:23,27:50:99:680,0,481:12,11,14,13 chr1 20304857 . G A 432.84 PASS AC=2;AF=0.563;AN=2;DP=854;MQ=60;set=variant2-variant6-variant9-variant16-variant17-variant19-variant21-variant23-variant26-variant27-variant30-variant32-variant34-variant35-variant36-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:1669,164,0:0,0,38,17 chr1 20304926 . G A 1171.95 PASS AC=2;AF=0.563;AN=2;DP=1702;MQ=60;set=variant2-variant6-variant9-variant16-variant17-variant19-variant21-variant23-variant26-variant27-variant30-variant32-variant34-variant35-variant36-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,116:116:99:3406,347,0:0,0,63,53 chr1 20305466 . GCACACA G,GCACA,GCACGCACACACACACACA,GCACGCACACACACACACACACA,GCA,GCACACACA 679.96 PASS AC=0,2,0,0,0,0;AF=0.114,0.705,0.034,0.023,0.045,0.011;AN=2;DP=988;set=Intersection GT:DP:GQ:SB 2/2:12:35:0,0,3,9 chr1 20306146 . G C 416.87 PASS AC=2;AF=0.6;AN=2;DP=542;MQ=60;set=variant2-variant6-variant9-variant16-variant19-variant21-variant23-variant26-variant27-variant30-variant32-variant34-variant35-variant36-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:965,102,0:0,0,17,17 chr1 20395401 . C A 1378.59 PASS AC=2;AF=0.691;AN=2;DP=1569;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,31:31:92:963,92,0:0,0,22,9 chr1 20411234 . T A 269.86 PASS AC=1;AF=0.604;AN=2;DP=794;MQ=60;set=variant2-variant3-variant6-variant7-variant9-variant11-variant12-variant15-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38 GT:AD:DP:GQ:PL:SB 0/1:22,14:36:99:402,0,569:15,7,12,2 chr1 20411332 . C T 900.53 PASS AC=1;AF=0.609;AN=2;DP=2518;MQ=60;set=variant2-variant3-variant6-variant7-variant9-variant11-variant12-variant15-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant38 GT:AD:DP:GQ:PL:SB 0/1:50,78:128:99:1986,0,1192:27,23,50,28 chr1 20438701 . C T 111.22 PASS AC=2;AF=0.63;AN=2;DP=186;MQ=60;set=variant2-variant4-variant5-variant6-variant9-variant10-variant12-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant33-variant35-variant37-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:177,12,0:0,0,3,1 chr1 20439313 . C G 1061.3 PASS AC=2;AF=0.7;AN=2;DP=4616;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,125:125:99:3712,375,0:0,0,68,57 chr1 20439522 . T A 826.76 PASS AC=2;AF=0.7;AN=2;DP=2917;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,78:80:99:2394,189,0:1,1,38,40 chr1 20442054 . T C 1663.2 PASS AC=2;AF=0.782;AN=2;DP=4351;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,111:111:99:3681,333,0:0,0,43,68 chr1 20442587 . T C 94.89 PASS AC=1;AF=0.611;AN=2;DP=233;MQ=60;set=variant4-variant5-variant9-variant13-variant14-variant15-variant16-variant18-variant19-variant23-variant26-variant27-variant30-variant35-variant37-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,4:10:99:109,0,241:6,0,3,1 chr1 20442691 . C T 3369.83 PASS AC=1;AF=0.604;AN=2;DP=1776;MQ=60;set=variant3-variant7-variant8-variant11-variant12-variant14-variant16-variant19-variant21-variant22-variant24-variant26-variant27-variant28-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,38:79:99:899,0,1096:27,14,26,12 chr1 20446170 . GT G 328.34 PASS AC=2;AF=1;AN=2;DP=650;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:420,39,0:0,0,1,12 chr1 20466076 . G A 802.49 PASS AC=1;AF=0.5;AN=2;DP=57;FS=6.015;FractionInformativeReads=1;MQ=60;MQRankSum=0.301;QD=14.08;ReadPosRankSum=1.098;SOR=0.22;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:23,34:57:99:831,0,627:5,18,13,21 chr1 20470148 . C T 717.26 PASS AC=1;AF=0.577;AN=2;DP=964;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant21-variant24-variant35-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:43,33:76:99:992,0,1182:15,28,10,23 chr1 20476391 . C T 3580.07 PASS AC=2;AF=0.646;AN=2;DP=4740;MQ=60;set=variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant16-variant18-variant20-variant21-variant23-variant24-variant27-variant29-variant30-variant34-variant35-variant36-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,230:230:99:6971,687,0:0,0,102,128 chr1 20487743 . C T 262.21 PASS AC=2;AF=0.781;AN=2;DP=348;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant20-variant21-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:360,27,0:0,0,7,2 chr1 20488689 . T C 30.19 PASS AC=2;AF=0.779;AN=2;DP=783;FractionInformativeReads=1;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:724,63,0:0,0,16,5 chr1 20488746 . C G 371.59 PASS AC=1;AF=0.55;AN=2;DP=513;FractionInformativeReads=1;MQ=60;set=variant5-variant12-variant16-variant20-variant27-variant29-variant34-variant35-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:28,19:47:99:498,0,774:19,9,12,7 chr1 20489393 . C G 211.34 PASS AC=1;AF=0.625;AN=2;DP=808;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant21-variant23-variant24-variant32-variant34-variant35-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:19,15:34:99:451,0,602:10,9,8,7 chr1 20490518 . T C 923.22 PASS AC=2;AF=0.786;AN=2;DP=5529;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:2,178:180:99:5490,490,0:1,1,93,85 chr1 20499168 . T C 1304.31 PASS AC=1;AF=0.605;AN=2;DP=909;MQ=60;set=variant2-variant5-variant7-variant8-variant12-variant15-variant16-variant20-variant25-variant27-variant28-variant29-variant30-variant34-variant35-variant36-variant37-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:33,21:54:99:583,0,918:23,10,15,6 chr1 20501442 . T C 962.83 PASS AC=2;AF=0.694;AN=2;DP=2826;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant20-variant21-variant23-variant24-variant27-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,107:107:99:3419,321,0:0,0,52,55 chr1 20503710 . G A 300.08 PASS AC=2;AF=0.828;AN=2;DP=215;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant20-variant21-variant23-variant24-variant25-variant28-variant29-variant31-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:221,18,0:0,0,5,1 chr1 20512652 . A C 2312.64 PASS AC=2;AF=1;AN=2;DP=4195;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,96:96:99:2613,287,0:0,0,48,48 chr1 20519808 . G A 474.91 PASS AC=1;AF=0.571;AN=2;DP=662;MQ=60;set=variant2-variant6-variant7-variant8-variant12-variant19-variant22-variant30-variant34-variant35-variant36-variant37-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:43,35:78:99:969,0,1155:29,14,20,15 chr1 20520732 . T C 1609.34 PASS AC=1;AF=0.618;AN=2;DP=1010;MQ=60;set=variant2-variant6-variant7-variant8-variant12-variant19-variant22-variant25-variant27-variant30-variant34-variant35-variant36-variant37-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:50,26:76:99:609,0,1301:24,26,12,14 chr1 20617419 . T C 1198.05 PASS AC=1;AF=0.6;AN=2;DP=1644;MQ=60;set=variant-variant3-variant4-variant6-variant11-variant16-variant17-variant22-variant23-variant24-variant27-variant31-variant35-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:57,52:109:99:1309,0,1376:31,26,27,25 chr1 20617658 . A AGTGTGTGT,AGTGTGTGTGT,AGTGT,AGTGTGTGTGTGT,AGT,ACTGTGTGT,AGTGTGT 31.48 PASS AC=0,2,0,0,0,0,0;AF=0.3,0.125,0.05,0.075,0.05,0.025,0.025;AN=2;DP=330;set=variant4-filterInvariant5-variant6-variant11-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant27-variant31-variant34-variant35-variant36-variant38-variant41-variant42-variant44 GT:DP:GQ:SB 2/2:11:31:0,0,3,8 chr1 20617671 . A G 40.45 PASS AC=2;AF=0.727;AN=2;DP=268;set=variant3-variant4-variant6-variant11-variant14-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant27-variant31-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:440,30,0:0,0,2,8 chr1 20637043 . C T 1402.4 PASS AC=1;AF=0.607;AN=2;DP=2078;MQ=60;set=variant-variant3-variant4-variant6-variant11-variant16-variant17-variant22-variant23-variant24-variant27-variant31-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:100,87:187:99:2160,0,2388:60,40,51,36 chr1 20637374 . T C 452.09 PASS AC=2;AF=0.8;AN=2;DP=1720;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant31-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,57:58:99:1939,132,0:0,1,13,44 chr1 20640572 . G A 475.39 PASS AC=1;AF=0.5;AN=2;DP=32;FS=3.743;FractionInformativeReads=1;MQ=60;MQRankSum=-0.681;QD=14.86;ReadPosRankSum=-0.525;SOR=0.205;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:12,20:32:99:504,0,407:10,2,13,7 chr1 20643944 . G C 172.18 PASS AC=1;AF=0.556;AN=2;DP=367;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant11-variant13-variant16-variant17-variant18-variant23-variant24-variant27-variant29-variant31-variant35-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,9:23:99:321,0,483:10,4,9,0 chr1 20644752 . G A 178.56 PASS AC=1;AF=0.529;AN=2;DP=480;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant11-variant16-variant17-variant21-variant22-variant23-variant24-variant27-variant31-variant35-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,13:28:99:441,0,412:11,4,12,1 chr1 20649814 . T C 1758.66 PASS AC=2;AF=0.685;AN=2;DP=4481;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant11-variant13-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant31-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,203:205:99:6122,565,0:1,1,119,84 chr1 20656824 . A G 273.9 PASS AC=1;AF=0.538;AN=2;DP=943;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant11-variant16-variant17-variant22-variant27-variant31-variant35-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,50:84:99:1337,0,989:7,27,18,32 chr1 20657352 . T C 1475.11 PASS AC=2;AF=0.685;AN=2;DP=4364;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant11-variant13-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant31-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,177:177:99:5105,531,0:0,0,91,86 chr1 20659684 . A G 166.45 PASS AC=1;AF=0.533;AN=2;DP=139;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant11-variant16-variant17-variant22-variant23-variant24-variant27-variant31-variant35-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,6:14:99:228,0,240:2,6,0,6 chr1 20662938 . A G 990.64 PASS AC=1;AF=0.531;AN=2;DP=1925;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant11-variant13-variant16-variant17-variant22-variant23-variant24-variant27-variant31-variant35-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:86,71:157:99:1733,0,2087:48,38,35,36 chr1 20664128 . T C 865.67 PASS AC=1;AF=0.545;AN=2;DP=849;MQ=60;set=variant5-variant8-variant18-variant20-variant25-variant27-variant35-variant36-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,50:94:99:1338,0,1092:27,17,29,21 chr1 20671833 . C A 1170.96 PASS AC=1;AF=0.667;AN=2;DP=2679;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant11-variant13-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant31-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,51:93:99:1178,0,1179:30,12,30,21 chr1 20676932 . T A 138.19 PASS AC=1;AF=0.688;AN=2;DP=334;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant11-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant31-variant34-variant35-variant36-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,6:13:99:190,0,268:1,6,1,5 chr1 20680760 . A G 1069.12 PASS AC=1;AF=0.68;AN=2;DP=2017;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant11-variant13-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant31-variant34-variant35-variant36-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,45:84:99:1353,0,971:25,14,28,17 chr1 20808838 . T TCCCCCCC,TCCCCCC,TCCCCCCCCC 31.51 PASS AC=0,1,0;AF=0.2,0.2,0.1;AN=2;DP=37;set=variant6-variant16-variant19-variant35-variant40 GT:DP:GQ:SB 0/2:6:99:0,2,4,0 chr1 20808846 . A C 40.7 PASS AC=1;AF=0.5;AN=2;DP=35;FractionInformativeReads=1;set=variant6-variant16-variant19-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:3,4:7:99:149,0,215:1,2,4,0 chr1 20808851 . A C 37.69 PASS AC=1;AF=0.5;AN=2;DP=40;FractionInformativeReads=1;set=variant6-variant16-variant19-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:6,4:10:99:144,0,254:2,4,4,0 chr1 20809349 . CGTGT CGTGTGT,CGT,CGTGTGTGTGTGTGT,CGTGTGTGTGTGT,CGTGTGTGTGT,CGTGTGTGT,C 3059.03 PASS AC=0,1,1,0,0,0,0;AF=0.318,0.136,0.091,0.023,0.148,0.045,0.011;AN=2;DP=8181;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-filterInvariant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 2/3:106:99:0,0,51,55 chr1 20826243 . C T 987.05 PASS AC=1;AF=0.5;AN=2;DP=462;FractionInformativeReads=1;MQ=60;set=variant3-variant15-variant17-variant25-variant27-variant35-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:26,39:65:99:1004,0,528:15,11,20,19 chr1 20826782 . CCT C 1367.07 PASS AC=1;AF=0.615;AN=2;DP=1925;MQ=60;set=variant3-variant5-variant6-variant9-variant10-variant11-variant15-variant17-variant19-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:43,28:71:99:997,0,1732:26,17,15,13 chr1 20826910 . G A 1367.8 PASS AC=1;AF=0.615;AN=2;DP=2607;MQ=60;set=variant3-variant5-variant6-variant9-variant10-variant11-variant15-variant17-variant19-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:59,33:92:99:855,0,1656:29,30,17,16 chr1 20827031 . A G 1275.01 PASS AC=1;AF=0.565;AN=2;DP=1798;MQ=60;set=variant3-variant6-variant9-variant10-variant11-variant15-variant17-variant23-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:38,41:79:99:962,0,1005:18,20,19,22 chr1 20829560 . G A 567.43 PASS AC=1;AF=0.6;AN=2;DP=1179;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant12-variant13-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant33-variant35-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,16:43:99:402,0,711:17,10,12,4 chr1 20834610 . C A 1694.55 PASS AC=1;AF=0.5;AN=2;DP=2054;MQ=60;set=variant16-variant17-variant20-variant22-variant23-variant24-variant25-variant26-variant28-variant33-variant35-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:78,90:168:99:2206,0,1942:35,43,43,47 chr1 20879156 . A G 1347.35 PASS AC=1;AF=0.556;AN=2;DP=1875;MQ=60;set=variant2-variant3-variant5-variant13-variant14-variant17-variant19-variant21-variant25-variant27-variant29-variant31-variant32-variant35-variant36-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:73,58:131:99:1411,0,1775:36,37,33,25 chr1 20880905 . A G 399.29 PASS AC=1;AF=0.556;AN=2;DP=1052;MQ=60;set=variant2-variant3-variant5-variant13-variant14-variant17-variant19-variant21-variant25-variant27-variant29-variant31-variant32-variant35-variant36-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:34,39:73:99:940,0,793:19,15,19,20 chr1 20881309 . T A 1128.29 PASS AC=1;AF=0.556;AN=2;DP=1358;MQ=60;set=variant2-variant3-variant5-variant13-variant14-variant17-variant19-variant21-variant25-variant27-variant29-variant31-variant32-variant35-variant36-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:46,34:80:99:862,0,1217:23,23,17,17 chr1 20931774 . A G 367.46 PASS AC=1;AF=0.654;AN=2;DP=310;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant21-variant22-variant26-variant28-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:7,7:14:99:218,0,186:3,4,3,4 chr1 20940258 . T A 4242.68 PASS AC=2;AF=1;AN=2;DP=4635;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,84:84:99:2608,252,0:0,0,50,34 chr1 20945520 . C A 79.68 PASS AC=2;AF=0.779;AN=2;DP=272;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:181,15,0:0,0,1,4 chr1 20960230 . C T 1334.89 PASS AC=1;AF=0.5;AN=2;DP=1546;MQ=60;set=variant2-variant3-variant4-variant7-variant10-variant11-variant12-variant18-variant21-variant23-variant26-variant31-variant32-variant33-variant35-variant37-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:43,57:100:99:1369,0,1074:26,17,33,24 chr1 20960493 . T G 115.13 PASS AC=1;AF=0.5;AN=2;DP=22;FS=21.475;FractionInformativeReads=0.955;MQ=60;MQRankSum=0.634;QD=5.23;ReadPosRankSum=-3.021;SOR=4.164;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:14,7:21:99:143,0,487:9,5,0,7 chr1 20960497 . T G 31.6 PASS AC=1;AF=0.5;AN=2;DP=27;MQ=60;set=variant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:11,7:18:99:149,0,422:8,3,0,7 chr1 20964328 . A G 83.95 PASS AC=2;AF=0.886;AN=2;DP=1103;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:893,75,0:0,0,19,6 chr1 20971911 . G C 190.35 PASS AC=1;AF=0.5;AN=2;DP=202;FS=0;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant7-variant10-variant11-variant18-variant21-variant23-variant26-variant31-variant32-variant33-variant35-variant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:13,6:19:99:213,0,502:12,1,6,0 chr1 20971980 . CA CAA,CAAAA,CAAA,CAAAAA,C 116.03 PASS AC=1,0,0,0,0;AF=0.269,0.103,0.205,0.026,0.013;AN=2;DP=1436;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-filterInvariant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:32:57:5,3,20,4 chr1 20972048 . G A 656.75 PASS AC=2;AF=0.886;AN=2;DP=3429;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,89:89:99:2856,265,0:0,0,43,46 chr1 20974802 . A G 654.36 PASS AC=1;AF=0.5;AN=2;DP=1023;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant7-variant10-variant11-variant12-variant18-variant21-variant23-variant26-variant31-variant32-variant33-variant35-variant37-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:33,24:57:99:637,0,880:21,12,13,11 chr1 20976759 . C T 85.73 PASS AC=2;AF=0.886;AN=2;DP=878;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:721,66,0:0,0,15,7 chr1 20977221 . A T 983.42 PASS AC=2;AF=0.886;AN=2;DP=3264;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:2334,214,0:0,0,29,43 chr1 20977365 . C G 608.8 PASS AC=2;AF=0.886;AN=2;DP=2815;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:1963,186,0:0,0,32,30 chr1 20977449 . G T 854.27 PASS AC=2;AF=0.75;AN=2;DP=3280;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,74:75:99:2286,203,0:1,0,43,31 chr1 20977599 . C G 1361 PASS AC=1;AF=0.5;AN=2;DP=2510;MQ=60;set=variant2-variant3-variant4-variant7-variant10-variant11-variant12-variant18-variant21-variant23-variant26-variant31-variant32-variant33-variant35-variant37-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:71,86:157:99:2158,0,1992:42,29,51,35 chr1 20977854 . A ATTC 15809.4 PASS AC=1;AF=0.613;AN=2;DP=21617;MQ=60;set=variant-variant3-variant5-variant7-variant8-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:358,331:689:99:8136,0,14264:187,171,167,164 chr1 20978058 . G A 1538.04 PASS AC=2;AF=0.75;AN=2;DP=4537;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,134:134:99:4573,402,0:0,0,35,99 chr1 20978570 . G A 88.71 PASS AC=1;AF=0.5;AN=2;DP=6;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.406;QD=14.78;ReadPosRankSum=0.988;SOR=2.093;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:99:117,0,119:2,1,3,0 chr1 20978832 . T C 954.21 PASS AC=2;AF=0.886;AN=2;DP=5274;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,124:124:99:3729,372,0:0,0,69,55 chr1 20979307 . G GT 1700.62 PASS AC=2;AF=0.75;AN=2;DP=6132;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,193:193:99:6510,586,0:0,0,92,101 chr1 20980880 . G A 218.98 PASS AC=1;AF=0.629;AN=2;DP=1797;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant7-variant8-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,28:54:99:680,0,566:13,13,15,13 chr1 20981806 . G A 852.03 PASS AC=2;AF=1;AN=2;DP=933;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:629,57,0:0,0,14,5 chr1 20982631 . G A 391.32 PASS AC=1;AF=0.716;AN=2;DP=3749;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,71:122:99:1760,0,1142:25,26,33,38 chr1 20987873 . G C 5606.94 PASS AC=2;AF=1;AN=2;DP=10130;FS=0;MQ=60;MQRankSum=-0.997;ReadPosRankSum=1.147;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,260:260:99:7635,778,0:0,0,131,129 chr1 20991193 . T G 76.29 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=40;FS=74.887;FractionInformativeReads=0.975;MQ=60;MQRankSum=0.592;QD=1.91;ReadPosRankSum=-3.363;SOR=5.545;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:24,15:39:99:105,0,303:21,3,0,15 chr1 20991273 . G A 107.51 PASS AC=1;AF=0.5;AN=2;DP=256;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant7-variant10-variant11-variant12-variant18-variant21-variant23-variant31-variant32-variant33-variant35-variant37-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,5:10:99:151,0,151:1,4,1,4 chr1 20992606 . G T 640.48 PASS AC=1;AF=0.629;AN=2;DP=2349;MQ=60;set=variant-variant3-variant5-variant7-variant8-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,45:100:99:1014,0,1470:35,20,29,16 chr1 20992819 . G C 920.03 PASS AC=2;AF=0.826;AN=2;DP=4997;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,129:129:99:3786,386,0:0,0,55,74 chr1 20992933 . G C 385.68 PASS AC=2;AF=1;AN=2;DP=864;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:977,84,0:0,0,8,20 chr1 21011273 . T TC 492.05 PASS AC=2;AF=0.563;AN=2;DP=318;MQ=60;set=variant4-variant5-variant13-variant17-variant20-variant27-variant35-variant39 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1275,114,0:0,0,24,13 chr1 21011346 . A G 840.7 PASS AC=2;AF=0.563;AN=2;DP=713;MQ=60;set=variant4-variant5-variant13-variant17-variant20-variant27-variant35-variant39 GT:AD:DP:GQ:PL:SB 1/1:0,91:91:99:2866,273,0:0,0,58,33 chr1 21012575 . G A 1005.86 PASS AC=2;AF=0.611;AN=2;DP=595;MQ=60;set=variant3-variant4-variant5-variant13-variant20-variant24-variant34-variant35-variant39 GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:1951,194,0:0,0,27,38 chr1 21014541 . T G 340.32 PASS AC=2;AF=0.583;AN=2;DP=155;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant13-variant17-variant35-variant39 GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1324,102,0:0,0,5,29 chr1 21016487 . C T 424.04 PASS AC=2;AF=0.667;AN=2;DP=620;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant11-variant12-variant13-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant29-variant30-variant34-variant35-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:2,23:25:25:563,25,0:1,1,13,10 chr1 21016906 . G T 233.57 PASS AC=2;AF=0.667;AN=2;DP=644;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant8-variant11-variant12-variant13-variant17-variant19-variant20-variant21-variant24-variant25-variant27-variant29-variant30-variant34-variant35-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:749,75,0:0,0,9,16 chr1 21024901 . C T 1131.1 PASS AC=1;AF=0.737;AN=2;DP=5132;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:93,103:196:99:2328,0,2247:52,41,56,47 chr1 21040079 . C A 596.88 PASS AC=1;AF=0.75;AN=2;DP=4400;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,60:128:99:1439,0,1579:28,40,25,35 chr1 21042157 . C T 1248.57 PASS AC=1;AF=0.5;AN=2;DP=533;MQ=60;set=variant2-variant21-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:82,84:166:99:2068,0,1822:31,51,33,51 chr1 21042300 . C G 251.5 PASS AC=1;AF=0.757;AN=2;DP=637;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,12:15:88:414,0,88:0,3,2,10 chr1 21043790 . T C 511.53 PASS AC=1;AF=0.764;AN=2;DP=1816;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,30:50:99:911,0,568:14,6,20,10 chr1 21043913 . T C 3066.23 PASS AC=1;AF=0.764;AN=2;DP=8355;set=variant-variant2-variant3-variant4-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:163,136:299:99:3476,0,3609:98,65,91,45 chr1 21043926 . T C 3559.31 PASS AC=1;AF=0.763;AN=2;DP=10695;set=variant-variant2-variant3-variant4-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:182,158:340:99:4067,0,4001:107,75,99,59 chr1 21044161 . A G 2844.55 PASS AC=1;AF=0.75;AN=2;DP=7725;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:126,130:256:99:3176,0,3365:41,85,49,81 chr1 21044219 . A C 1205.19 PASS AC=2;AF=0.863;AN=2;DP=4095;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,124:125:99:3736,364,0:1,0,46,78 chr1 21044362 . CG C 373.97 PASS AC=2;AF=1;AN=2;DP=497;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:597,48,0:0,0,9,7 chr1 21047092 . A T 968.13 PASS AC=1;AF=0.743;AN=2;DP=3366;set=variant-variant2-variant3-variant4-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,43:87:99:1031,0,1234:25,19,26,17 chr1 21047404 . A G 1207.54 PASS AC=1;AF=0.5;AN=2;DP=707;FractionInformativeReads=1;MQ=60;set=variant2-variant14-variant21-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:79,86:165:99:2016,0,2027:34,45,45,41 chr1 21047725 . A G 995.55 PASS AC=1;AF=0.73;AN=2;DP=3101;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,36:89:99:997,0,1435:18,35,9,27 chr1 21050719 . C T 3315.33 PASS AC=1;AF=0.5;AN=2;DP=636;FractionInformativeReads=1;MQ=60;set=variant29-variant35 GT:AD:DP:GQ:PL:SB 0/1:157,182:339:99:4625,0,3879:89,68,102,80 chr1 21050958 . C T 1660.19 PASS AC=1;AF=0.808;AN=2;DP=7150;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:121,117:238:99:2852,0,3278:51,70,44,73 chr1 21052693 . G T 285.17 PASS AC=1;AF=0.5;AN=2;DP=97;FractionInformativeReads=1;MQ=60;set=variant2-variant14-variant21-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,14:20:99:446,0,168:1,5,2,12 chr1 21054726 . A G 389.38 PASS AC=1;AF=0.729;AN=2;DP=729;MQ=60;set=variant2-variant3-variant4-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,4:20:80:80,0,384:6,10,3,1 chr1 21058655 . G A 49.73 PASS AC=1;AF=0.705;AN=2;DP=186;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant11-variant13-variant15-variant16-variant17-variant18-variant21-variant23-variant26-variant28-variant29-variant33-variant35-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,5:9:99:150,0,123:4,0,1,4 chr1 21069129 . A C 465.51 PASS AC=1;AF=0.683;AN=2;DP=715;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant6-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant24-variant25-variant27-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,8:17:99:222,0,306:8,1,7,1 chr1 21074221 . T C 463.17 PASS AC=1;AF=0.5;AN=2;DP=88;MQ=60;set=variant2-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,13:27:99:465,0,505:0,14,1,12 chr1 21083867 . T TA 89.37 PASS AC=2;AF=1;AN=2;DP=9;FS=0;MQ=60;SOR=1.179;set=variant27-variant35 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:108,9,0:0,0,1,2 chr1 21091861 . G T 1633.48 PASS AC=1;AF=0.673;AN=2;DP=2786;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant15-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant33-variant35-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:53,46:99:99:1150,0,1211:31,22,28,18 chr1 21099846 . A G 228.49 PASS AC=1;AF=0.694;AN=2;DP=550;MQ=60;set=variant-variant2-variant3-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant24-variant25-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,9:16:99:354,0,209:6,1,9,0 chr1 21100836 . A AACAC,AAC,AACACAC 1737.3 PASS AC=1,0,0;AF=0.607,0.018,0.018;AN=2;DP=2928;MQ=60;set=variant-variant2-variant3-variant6-variant9-variant10-variant12-variant13-variant15-variant16-variant18-variant19-variant21-variant24-variant25-variant27-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:DP:GQ:SB 0/1:100:99:36,26,23,15 chr1 21100916 . T G 2220.71 PASS AC=1;AF=0.5;AN=2;DP=613;FractionInformativeReads=1;MQ=60;set=variant2-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:121,87:208:99:2092,0,2849:62,59,44,43 chr1 21101163 . A G 1018.79 PASS AC=2;AF=1;AN=2;DP=1235;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.208;ReadPosRankSum=1.595;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,31:31:93:1084,93,0:0,0,11,20 chr1 21101200 . G C 190.98 PASS AC=1;AF=0.5;AN=2;DP=41;FractionInformativeReads=1;MQ=60;set=variant2-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,6:16:99:181,0,309:2,8,1,5 chr1 21102502 . CAAAA CAAAAA,CAA,CAAA,CAAAAAAA,C,CAAAAAA 41.96 PASS AC=0,0,1,0,0,0;AF=0.188,0.031,0.219,0.063,0.031,0.031;AN=2;DP=209;set=variant-variant3-variant6-variant7-variant13-variant14-variant15-variant19-variant25-filterInvariant27-variant31-variant35-variant36-variant38-variant40-variant44 GT:DP:GQ:SB 0/3:12:70:3,2,4,3 chr1 21106204 . GA GAA,G,GAAA,GAAAA 228.49 PASS AC=1,0,0,0;AF=0.271,0.083,0.271,0.021;AN=2;DP=407;MQ=60;set=variant2-variant3-variant4-variant6-variant9-variant10-variant15-variant17-variant20-variant22-variant24-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant44 GT:DP:GQ:SB 0/1:17:99:7,0,8,2 chr1 21133286 . CA C 57.39 DRAGENHardINDEL AC=1;AF=0.5;AN=2;DP=1323;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:271,40:311:70:70,0,6095:144,127,21,19 chr1 21133496 . CT C,CTT 451.55 PASS AC=1,0;AF=0.333,0.167;AN=2;DP=804;MQ=60;set=variant2-filterInvariant5-filterInvariant7-filterInvariant9-filterInvariant10-filterInvariant12-variant15-filterInvariant34-variant35-variant37-variant38-variant44 GT:DP:GQ:SB 0/1:61:99:7,25,9,20 chr1 21167404 . A G 2430.39 PASS AC=2;AF=1;AN=2;DP=3309;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.887;ReadPosRankSum=1.518;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,74:74:99:2184,222,0:0,0,41,33 chr1 21175855 . C A 1305.15 PASS AC=2;AF=0.989;AN=2;DP=1135;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:784,66,0:0,0,18,4 chr1 21176042 . A C 259.36 PASS AC=1;AF=0.5;AN=2;DP=108;MQ=60;set=variant2-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,18:38:99:364,0,463:8,12,6,12 chr1 21179969 . G A 996.08 PASS AC=2;AF=0.989;AN=2;DP=1855;FS=0;MQ=60;MQRankSum=1.25;ReadPosRankSum=1.031;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1283,126,0:0,0,27,15 chr1 21180013 . C T 761.12 PASS AC=1;AF=0.5;AN=2;DP=176;FractionInformativeReads=1;MQ=60;set=variant2-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,33:55:99:923,0,498:13,9,21,12 chr1 21180181 . C T 404.05 PASS AC=1;AF=0.707;AN=2;DP=1191;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant33-variant35-variant36-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:25,17:42:99:403,0,657:7,18,6,11 chr1 21180250 . G A 172.12 PASS AC=1;AF=0.7;AN=2;DP=481;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant33-variant35-variant36-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,5:11:99:148,0,199:1,5,1,4 chr1 21188703 . A T 1079.77 PASS AC=1;AF=0.707;AN=2;DP=2827;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant33-variant35-variant36-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:40,43:83:99:835,0,841:21,19,20,23 chr1 21191416 . T G 381.83 PASS AC=2;AF=0.727;AN=2;DP=1052;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant33-variant35-variant36-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:1054,96,0:0,0,12,20 chr1 21191430 . A G 383.05 PASS AC=1;AF=0.692;AN=2;DP=757;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant15-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant33-variant35-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:16,12:28:99:368,0,389:7,9,4,8 chr1 21219681 . C T 500.23 PASS AC=1;AF=0.5;AN=2;DP=65;FractionInformativeReads=1;MQ=60;set=variant2-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,6:20:99:203,0,555:14,0,6,0 chr1 21220375 . T G 43.74 PASS AC=1;AF=0.726;AN=2;DP=362;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant33-variant34-variant35-variant36-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,6:11:99:196,0,108:2,3,1,5 chr1 21267707 . GCAA G 9823.5 PASS AC=1;AF=0.5;AN=2;DP=1824;MQ=60;set=variant2-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:290,290:580:99:11228,0,11938:155,135,152,138 chr1 21295864 . C T 398.36 PASS AC=1;AF=0.7;AN=2;DP=960;MQ=60;set=variant-variant2-variant3-variant6-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant24-variant25-variant27-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,22:44:99:491,0,524:14,8,14,8 chr1 21307743 . AT A,ATT 128.4 PASS AC=1,0;AF=0.469,0.031;AN=2;DP=1055;set=filterInvariant4-filterInvariant9-filterInvariant15-filterInvariant20-filterInvariant22-filterInvariant23-filterInvariant25-variant29-filterInvariant30-filterInvariant32-filterInvariant33-filterInvariant35-filterInvariant36-filterInvariant39-filterInvariant40-filterInvariant43 GT:DP:GQ:SB 0/1:55:99:15,28,7,5 chr1 21324191 . A C 881.28 PASS AC=1;AF=0.5;AN=2;DP=102;MQ=60;set=variant2-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,10:26:99:244,0,464:7,9,4,6 chr1 21325360 . C A 573.79 PASS AC=1;AF=0.7;AN=2;DP=1485;MQ=60;set=variant-variant2-variant3-variant6-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant24-variant25-variant27-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,13:46:99:278,0,984:18,15,7,6 chr1 21327637 . C T 3232.64 PASS AC=2;AF=1;AN=2;DP=5018;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,125:125:99:3847,375,0:0,0,72,53 chr1 21329128 . T C 709.94 PASS AC=1;AF=0.5;AN=2;DP=221;FS=0;MQ=60;set=variant2-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,31:64:99:848,0,919:24,9,23,8 chr1 21377314 . C T 945.78 PASS AC=2;AF=0.989;AN=2;DP=1148;MQ=60;MQRankSum=0.106;ReadPosRankSum=-1.936;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1112,102,0:0,0,25,9 chr1 21494634 . C T 519.84 PASS AC=1;AF=0.7;AN=2;DP=614;set=variant-variant2-variant3-variant6-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant24-variant25-variant27-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,10:26:99:291,0,435:5,11,2,8 chr1 21501095 . C A 84.57 PASS AC=1;AF=0.683;AN=2;DP=737;MQ=60;set=variant-variant2-variant3-variant6-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant24-variant25-variant27-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,8:23:99:169,0,441:11,4,5,3 chr1 21502496 . G A 389.19 PASS AC=1;AF=0.5;AN=2;DP=94;FractionInformativeReads=1;MQ=60;set=variant2-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,17:34:99:510,0,453:11,6,13,4 chr1 21553933 . T C 36.15 PASS AC=1;AF=0.603;AN=2;DP=316;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant9-variant11-variant12-variant13-variant14-variant16-variant19-variant21-variant22-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,2:6:64:64,0,152:0,4,0,2 chr1 21554319 . A G 481.36 PASS AC=2;AF=0.977;AN=2;DP=1230;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:991,78,0:0,0,19,7 chr1 21560253 . G C 679.55 PASS AC=1;AF=0.583;AN=2;DP=1055;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant6-variant9-variant10-variant11-variant14-variant16-variant21-variant22-variant24-variant25-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,25:56:99:629,0,740:12,19,8,17 chr1 21571601 . G A 1371.71 PASS AC=1;AF=0.591;AN=2;DP=2284;set=variant2-variant3-variant9-variant10-variant14-variant16-variant21-variant22-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,70:112:99:1708,0,1046:12,30,26,44 chr1 21573603 . C T 82.65 PASS AC=1;AF=0.5;AN=2;DP=119;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant8-variant13-variant16-variant17-variant23-variant35 GT:AD:DP:GQ:PL:SB 0/1:8,10:18:99:363,0,252:6,2,10,0 chr1 21573722 . G A 1355.39 PASS AC=1;AF=0.591;AN=2;DP=2427;MQ=60;set=variant2-variant3-variant9-variant10-variant12-variant14-variant16-variant21-variant22-variant24-variant25-variant26-variant28-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,62:111:99:1656,0,1232:28,21,39,23 chr1 21582348 . T C 481.81 PASS AC=1;AF=0.565;AN=2;DP=514;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant9-variant10-variant12-variant14-variant16-variant21-variant22-variant24-variant25-variant26-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,15:31:99:520,0,552:13,3,13,2 chr1 21582425 . C T 1380.05 PASS AC=1;AF=0.5;AN=2;DP=1011;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant8-variant16-variant17-variant23-variant28-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:55,56:111:99:1398,0,1544:41,14,35,21 chr1 21583925 . C T 730.93 PASS AC=1;AF=0.565;AN=2;DP=1327;MQ=60;set=variant2-variant3-variant9-variant10-variant12-variant14-variant16-variant21-variant22-variant24-variant25-variant26-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,23:56:99:626,0,995:24,9,14,9 chr1 21583973 . A G 1196.57 PASS AC=1;AF=0.565;AN=2;DP=2336;MQ=60;set=variant2-variant3-variant9-variant10-variant12-variant14-variant16-variant21-variant22-variant24-variant25-variant26-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,39:96:99:1119,0,1421:35,22,26,13 chr1 21584941 . T C 355.13 PASS AC=2;AF=0.766;AN=2;DP=371;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant11-variant12-variant13-variant14-variant16-variant19-variant20-variant21-variant22-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:402,33,0:0,0,7,4 chr1 21585014 . C T 264.83 PASS AC=1;AF=0.5;AN=2;DP=207;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant8-variant16-variant17-variant23-variant28-variant34-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:8,8:16:99:231,0,254:8,0,5,3 chr1 21751142 . A G 1146.87 PASS AC=2;AF=0.547;AN=2;DP=2856;set=filterInvariant-variant2-filterInvariant3-filterInvariant4-filterInvariant5-variant6-filterInvariant7-variant8-variant10-filterInvariant11-filterInvariant12-variant13-filterInvariant14-variant15-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-variant26-filterInvariant27-filterInvariant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant32-variant33-filterInvariant34-variant35-variant36-filterInvariant37-filterInvariant38-filterInvariant39-filterInvariant40-filterInvariant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:1410,144,0:0,0,35,13 chr1 21751214 . G A 3577.5 PASS AC=2;AF=0.535;AN=2;DP=9497;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-filterInvariant14-variant15-variant16-filterInvariant17-filterInvariant18-variant19-filterInvariant20-variant21-variant22-variant23-variant24-variant25-variant26-filterInvariant27-filterInvariant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-filterInvariant39-filterInvariant40-filterInvariant41-filterInvariant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 1/1:0,144:144:99:4314,432,0:0,0,96,48 chr1 21751325 . G C 2306.01 PASS AC=1;AF=0.5;AN=2;DP=1131;FractionInformativeReads=1;set=variant5-variant15-variant21-variant28-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:95,81:176:99:1889,0,2021:43,52,32,49 chr1 21753562 . A C 190.1 PASS AC=2;AF=0.824;AN=2;DP=1102;set=filterInvariant-variant2-variant4-variant5-filterInvariant6-variant7-variant10-variant11-variant12-variant13-filterInvariant15-variant16-filterInvariant17-filterInvariant18-filterInvariant19-variant20-filterInvariant21-variant22-filterInvariant24-variant25-filterInvariant26-variant27-variant28-variant29-filterInvariant30-variant31-variant32-filterInvariant33-filterInvariant35-filterInvariant36-variant37-filterInvariant38-filterInvariant39-filterInvariant40-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:216,21,0:0,0,7,0 chr1 21754993 . A T 1184.41 PASS AC=1;AF=0.5;AN=2;DP=453;set=variant15-variant21-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:71,45:116:99:1093,0,1677:27,44,13,32 chr1 21754996 . C T 3200.4 PASS AC=2;AF=0.989;AN=2;DP=4876;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,112:113:99:3857,327,0:0,1,37,75 chr1 21755055 . C A 1546.59 PASS AC=2;AF=0.826;AN=2;DP=1962;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1364,116,0:0,0,7,32 chr1 21755135 . T G 881.09 PASS AC=1;AF=0.671;AN=2;DP=836;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,9:15:99:324,0,153:6,0,8,1 chr1 21755288 . A ACCGCCGCGACT 2063.77 PASS AC=1;AF=0.5;AN=2;DP=839;set=variant5-variant15-variant21-variant28-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:76,62:138:99:2602,0,2977:41,35,36,26 chr1 21755347 . C T 3292.91 PASS AC=1;AF=0.671;AN=2;DP=6425;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:96,98:194:99:2139,0,2343:40,56,43,55 chr1 21755453 . G A 1047.64 PASS AC=2;AF=0.826;AN=2;DP=2307;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-filterInvariant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1659,129,0:0,0,4,39 chr1 21755539 . C A 379.14 PASS AC=2;AF=0.846;AN=2;DP=696;set=variant-variant2-filterInvariant3-variant4-variant5-variant7-filterInvariant8-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-filterInvariant19-filterInvariant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:295,24,0:0,0,5,3 chr1 21755747 . A G 2596.6 PASS AC=1;AF=0.5;AN=2;DP=991;set=variant15-variant21-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:121,113:234:99:2800,0,2965:77,44,68,45 chr1 21755756 . G C 4868.3 PASS AC=2;AF=0.826;AN=2;DP=10176;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,267:267:99:9682,802,0:0,0,156,111 chr1 21755867 . A G 5568.25 PASS AC=2;AF=0.826;AN=2;DP=10910;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,297:298:99:8904,848,0:1,0,129,168 chr1 21755906 . G A 4328.42 PASS AC=2;AF=0.826;AN=2;DP=8395;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,234:236:99:6841,655,0:1,1,97,137 chr1 21756008 . G T 1587.13 PASS AC=2;AF=0.826;AN=2;DP=3302;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,94:95:99:2894,238,0:0,1,31,63 chr1 21756029 . A T 867.55 PASS AC=1;AF=0.5;AN=2;DP=71;FS=3.483;FractionInformativeReads=1;MQ=53.62;MQRankSum=-0.423;QD=12.22;ReadPosRankSum=2.545;SOR=1.162;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:40,31:71:99:896,0,1099:14,26,8,23 chr1 21756069 . G A 848.77 PASS AC=2;AF=0.826;AN=2;DP=1438;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1253,105,0:0,0,7,28 chr1 21766776 . G C 2136.29 PASS AC=2;AF=0.583;AN=2;DP=3965;MQ=60;set=variant2-variant3-variant4-variant8-variant14-variant15-variant19-variant21-variant23-variant26-variant30-variant31-variant35-variant36-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,243:243:99:7006,727,0:0,0,126,117 chr1 21804815 . T G 1895.64 PASS AC=2;AF=1;AN=2;DP=5808;FS=0;MQRankSum=-0.374;ReadPosRankSum=1.677;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,167:167:99:4960,500,0:0,0,74,93 chr1 21880818 . CAT CATATAT,CATAT,C,CATATATAT 193.4 PASS AC=1,0,0,0;AF=0.638,0.138,0.013,0.025;AN=2;DP=1054;set=variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:9:88:0,2,2,5 chr1 21887290 . C A 317.28 PASS AC=2;AF=0.74;AN=2;DP=975;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant7-variant9-variant10-variant11-variant13-variant17-variant18-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant32-variant33-variant35-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1657,137,0:0,0,6,40 chr1 21889506 . C T 772.24 PASS AC=1;AF=0.559;AN=2;DP=1179;MQ=60;set=variant7-variant8-variant9-variant10-variant13-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant30-variant32-variant33-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,33:77:99:809,0,1077:29,15,23,10 chr1 21889635 . T C 2897.73 PASS AC=2;AF=0.955;AN=2;DP=7280;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,183:183:99:5404,548,0:0,0,91,92 chr1 21889784 . CG C 680.49 PASS AC=1;AF=0.583;AN=2;DP=874;MQ=60;set=variant7-variant9-variant10-variant20-variant21-variant25-variant28-variant30-variant32-variant33-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,41:71:99:1126,0,739:10,20,15,26 chr1 21890464 . A G 772.73 PASS AC=2;AF=1;AN=2;DP=1472;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1226,99,0:0,0,28,5 chr1 21890673 . C T 1666 PASS AC=1;AF=0.5;AN=2;DP=129;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.208;QD=12.91;ReadPosRankSum=0.173;SOR=0.754;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:59,70:129:99:1694,0,1295:27,32,31,39 chr1 21896767 . C T 362.83 PASS AC=1;AF=0.563;AN=2;DP=1308;MQ=60;set=variant-variant4-variant5-variant9-variant13-variant17-variant18-variant22-variant24-variant27-variant28-variant32-variant33-variant35-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:37,56:93:99:1282,0,936:19,18,27,29 chr1 21900420 . A G 624.89 PASS AC=1;AF=0.816;AN=2;DP=2362;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,43:83:99:1147,0,970:15,25,15,28 chr1 21900459 . A C 175.65 PASS AC=1;AF=0.583;AN=2;DP=761;MQ=60;set=variant7-variant8-variant9-variant10-variant15-variant20-variant21-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant35-variant37-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,30:59:99:765,0,816:8,21,10,20 chr1 21900891 . G A 1014.58 PASS AC=2;AF=0.966;AN=2;DP=963;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:959,75,0:0,0,22,3 chr1 21901277 . A G 236.88 PASS AC=2;AF=0.932;AN=2;DP=1313;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:1001,78,0:0,0,6,20 chr1 21904131 . T C 3278.06 PASS AC=1;AF=0.5;AN=2;DP=1335;MQ=60;set=variant3-variant4-variant18-variant24-variant28-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:108,112:220:99:2866,0,2644:34,74,38,74 chr1 21904267 . A G 689.61 PASS AC=1;AF=0.798;AN=2;DP=2516;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,23:57:99:484,0,927:15,19,10,13 chr1 21904374 . A C 840.21 PASS AC=1;AF=0.55;AN=2;DP=564;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant6-variant18-variant23-variant24-variant27-variant28-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:34,37:71:99:944,0,812:15,19,23,14 chr1 21904529 . C T 512.25 PASS AC=1;AF=0.529;AN=2;DP=1165;MQ=60;set=variant-variant4-variant5-variant9-variant13-variant17-variant20-variant21-variant22-variant27-variant28-variant30-variant32-variant35-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,46:82:99:1070,0,905:14,22,26,20 chr1 21925108 . T C 135.29 PASS AC=2;AF=0.952;AN=2;DP=456;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:279,24,0:0,0,4,4 chr1 21928344 . C G 902.31 PASS AC=1;AF=0.558;AN=2;DP=1675;MQ=60;set=variant2-variant3-variant8-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,32:73:99:915,0,1221:11,30,7,25 chr1 21929260 . A G 4055.81 PASS AC=2;AF=0.932;AN=2;DP=6285;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,163:163:99:4975,489,0:0,0,88,75 chr1 21929456 . GC G 434.58 PASS AC=1;AF=0.763;AN=2;DP=1747;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,22:30:99:583,0,149:2,6,4,18 chr1 21932530 . C A 2269.11 PASS AC=1;AF=0.807;AN=2;DP=3315;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:41,52:93:99:1367,0,999:28,13,34,18 chr1 21934693 . T C 1436.34 PASS AC=1;AF=0.5;AN=2;DP=804;FractionInformativeReads=1;MQ=60;set=variant4-variant16-variant18-variant21-variant24-variant27-variant28-variant31-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:50,46:96:99:1044,0,1381:30,20,20,26 chr1 21935467 . G A 840.87 PASS AC=1;AF=0.5;AN=2;DP=988;FractionInformativeReads=1;MQ=60;set=variant4-variant13-variant16-variant18-variant21-variant24-variant27-variant28-variant31-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:61,50:111:99:1118,0,1599:25,36,19,31 chr1 21935884 . GA G 92.4 PASS AC=1;AF=0.574;AN=2;DP=579;MQ=60;set=variant2-variant4-variant5-variant6-variant8-variant9-variant11-variant13-variant17-variant20-variant21-variant22-variant23-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,12:23:99:231,0,171:10,1,10,2 chr1 21939741 . G C 1893.76 PASS AC=2;AF=0.633;AN=2;DP=3661;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant33-variant35-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,160:160:99:4633,479,0:0,0,66,94 chr1 21943820 . G A 119.33 PASS AC=1;AF=0.583;AN=2;DP=1690;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant17-variant20-variant21-variant22-variant23-variant24-variant28-variant29-variant30-variant35-variant37-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,41:79:99:1028,0,943:22,16,24,17 chr1 21945389 . C T 824.53 PASS AC=1;AF=0.5;AN=2;DP=838;MQ=60;set=variant4-variant8-variant10-variant11-variant16-variant18-variant21-variant26-variant31-variant33-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:33,30:63:99:728,0,809:21,12,19,11 chr1 21946396 . T C 164.69 PASS AC=2;AF=0.577;AN=2;DP=426;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant8-variant9-variant10-variant11-variant13-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant26-variant30-variant31-variant33-variant34-variant35-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:937,75,0:0,0,21,4 chr1 21946415 . G A 543.84 PASS AC=2;AF=0.837;AN=2;DP=1156;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:1154,87,0:0,0,25,4 chr1 21948936 . G C 66.22 PASS AC=2;AF=0.892;AN=2;DP=374;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:311,33,0:0,0,4,7 chr1 21952884 . G A 834.98 PASS AC=1;AF=0.5;AN=2;DP=263;MQ=60;set=variant4-variant30-variant35 GT:AD:DP:GQ:PL:SB 0/1:49,41:90:99:918,0,1190:24,25,19,22 chr1 21953304 . G A 1033.21 PASS AC=1;AF=0.5;AN=2;DP=2536;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant12-variant14-variant17-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:50,85:135:99:2069,0,1307:33,17,47,38 chr1 21953436 . A G 2890.98 PASS AC=2;AF=0.852;AN=2;DP=6396;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,141:141:99:4377,422,0:0,0,60,81 chr1 21961339 . A T 1434.36 PASS AC=2;AF=1;AN=2;DP=3863;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,98:98:99:2927,294,0:0,0,44,54 chr1 21975923 . G T 290.68 PASS AC=2;AF=0.821;AN=2;DP=472;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:517,48,0:0,0,9,7 chr1 22005667 . T TC 184.09 PASS AC=1;AF=0.5;AN=2;DP=37;FS=89.214;FractionInformativeReads=0.946;MQ=60;MQRankSum=0.017;QD=4.98;ReadPosRankSum=-2.45;SOR=5.13;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:23,12:35:99:221,0,2195:0,23,12,0 chr1 22005671 . A C 162.72 PASS AC=1;AF=0.5;AN=2;DP=359;MQ=60;set=variant14-variant16-filterInvariant26-filterInvariant29-filterInvariant35-filterInvariant39-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:24,12:36:99:212,0,2370:0,24,12,0 chr1 22005675 . A C 55.32 PASS AC=1;AF=0.5;AN=2;DP=192;MQ=60;set=filterInvariant14-filterInvariant29-variant35-filterInvariant39 GT:AD:DP:GQ:PL:SB 0/1:26,8:34:99:203,0,2451:5,21,8,0 chr1 22005678 . A C 154.21 PASS AC=1;AF=0.5;AN=2;DP=120;MQ=60;set=variant14-filterInvariant16-variant35 GT:AD:DP:GQ:PL:SB 0/1:28,8:36:99:170,0,2493:7,21,8,0 chr1 22013561 . C A 275.25 PASS AC=2;AF=0.808;AN=2;DP=592;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:47:484,47,0:0,0,11,5 chr1 22013771 . G A 601.14 PASS AC=2;AF=0.633;AN=2;DP=1786;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant20-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1221,123,0:0,0,17,24 chr1 22016678 . TA TAA,T 96.22 PASS AC=2,0;AF=0.579,0.053;AN=2;DP=180;MQ=60;set=variant3-variant5-variant7-variant9-variant10-variant19-variant20-variant23-variant25-variant26-variant28-variant30-variant31-variant32-variant35-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:5:15:0,0,0,5 chr1 22032472 . A AT 283.32 PASS AC=2;AF=1;AN=2;DP=459;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:214,18,0:0,0,4,2 chr1 22032570 . T G 797.03 PASS AC=1;AF=0.587;AN=2;DP=1035;MQ=60;set=variant3-variant5-variant6-variant7-variant9-variant11-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant31-variant33-variant35-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:25,26:51:99:612,0,604:17,8,17,9 chr1 22050649 . C A 880.68 PASS AC=2;AF=0.775;AN=2;DP=4313;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,159:159:99:5059,477,0:0,0,76,83 chr1 22054427 . C A 3968.56 PASS AC=2;AF=0.729;AN=2;DP=11447;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,330:330:99:10070,988,0:0,0,191,139 chr1 22063149 . G A 818.23 PASS AC=2;AF=0.729;AN=2;DP=2204;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,73:73:99:2317,219,0:0,0,26,47 chr1 22082923 . G A 144.4 PASS AC=2;AF=0.75;AN=2;DP=430;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:497,39,0:0,0,11,2 chr1 22082967 . CAA CA,C,CAAA 238.1 PASS AC=2,0,0;AF=0.397,0.256,0.013;AN=2;DP=1222;set=variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-filterInvariant43-variant44 GT:DP:GQ:SB 1/1:20:27:0,2,14,4 chr1 22084201 . A G 849.17 PASS AC=1;AF=0.5;AN=2;DP=94;FS=0.779;FractionInformativeReads=1;MQ=60;MQRankSum=-1.854;QD=9.03;ReadPosRankSum=-0.837;SOR=0.82;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:54,40:94:99:877,0,1292:26,28,18,22 chr1 22109370 . G A 1397.3 PASS AC=2;AF=0.588;AN=2;DP=2383;MQ=60;set=variant-variant2-variant4-variant5-variant9-variant10-variant11-variant12-variant16-variant20-variant26-variant27-variant29-variant32-variant33-variant35-variant39 GT:AD:DP:GQ:PL:SB 1/1:0,176:176:99:5153,525,0:0,0,86,90 chr1 22110072 . A G 879.57 PASS AC=2;AF=1;AN=2;DP=2118;FS=0;MQ=60;MQRankSum=1.511;ReadPosRankSum=1.659;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,52:52:99:1729,156,0:0,0,20,32 chr1 22141206 . A C 4000.14 PASS AC=2;AF=0.789;AN=2;DP=4317;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,129:129:99:4181,387,0:0,0,59,70 chr1 22149935 . T C 4455.8 PASS AC=2;AF=0.807;AN=2;DP=15828;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,406:406:99:11666,1215,0:0,0,203,203 chr1 22150257 . C T 982.87 PASS AC=2;AF=0.653;AN=2;DP=5143;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:2,172:174:99:5374,500,0:1,1,81,91 chr1 22155723 . T C 247.06 PASS AC=2;AF=0.807;AN=2;DP=965;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:1128,84,0:0,0,23,5 chr1 22155824 . G C 1685.62 PASS AC=1;AF=0.5;AN=2;DP=121;FS=6.057;FractionInformativeReads=1;MQ=60;MQRankSum=-0.206;QD=13.93;ReadPosRankSum=-0.591;SOR=0.335;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:55,66:121:99:1714,0,1469:40,15,41,25 chr1 22157689 . G A 3397.03 PASS AC=2;AF=0.807;AN=2;DP=14812;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,393:393:99:11851,1172,0:0,0,195,198 chr1 22158157 . A G 3492.17 PASS AC=1;AF=0.5;AN=2;DP=1054;FractionInformativeReads=1;MQ=60;set=variant24-variant35-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:144,149:293:99:3460,0,3838:72,72,75,74 chr1 22158363 . G A 896.55 PASS AC=2;AF=0.657;AN=2;DP=2491;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,84:84:99:2447,249,0:0,0,28,56 chr1 22160148 . C T 580.97 PASS AC=2;AF=0.653;AN=2;DP=2424;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,87:87:99:2911,261,0:0,0,26,61 chr1 22165901 . A G 2609.28 PASS AC=1;AF=0.5;AN=2;DP=3968;MQ=60;set=variant7-variant8-variant12-variant17-variant18-variant20-variant24-variant25-variant26-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:123,140:263:99:3344,0,3030:72,51,79,61 chr1 22168216 . C T 805.83 PASS AC=2;AF=0.789;AN=2;DP=3101;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,89:89:99:2835,265,0:0,0,32,57 chr1 22172458 . T C 47.19 PASS AC=2;AF=0.821;AN=2;DP=686;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:586,54,0:0,0,12,6 chr1 22174600 . A G 1466.15 PASS AC=2;AF=0.807;AN=2;DP=5238;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,147:147:99:4746,441,0:0,0,52,95 chr1 22177119 . A G 266.75 PASS AC=2;AF=0.657;AN=2;DP=944;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:926,72,0:0,0,2,22 chr1 22179673 . T C 1294.29 PASS AC=2;AF=0.653;AN=2;DP=4103;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,141:141:99:4914,423,0:0,0,37,104 chr1 22180548 . T C 752.16 PASS AC=2;AF=0.814;AN=2;DP=4441;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,104:104:99:3218,311,0:0,0,49,55 chr1 22183471 . A C 516.4 PASS AC=2;AF=0.807;AN=2;DP=3047;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:1857,194,0:0,0,41,24 chr1 22183739 . A G 2671.26 PASS AC=2;AF=0.708;AN=2;DP=8784;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,245:245:99:7420,735,0:0,0,128,117 chr1 22186234 . A G 1635.47 PASS AC=2;AF=0.977;AN=2;DP=2092;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1527,129,0:0,0,24,19 chr1 22191454 . G A 2395.87 PASS AC=2;AF=0.762;AN=2;DP=9068;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,245:245:99:7743,733,0:0,0,110,135 chr1 22199081 . A T 1974.59 PASS AC=2;AF=1;AN=2;DP=3900;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,108:108:99:3578,323,0:0,0,62,46 chr1 22199245 . C T 1730.45 PASS AC=2;AF=0.743;AN=2;DP=4772;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant35-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,145:145:99:4562,434,0:0,0,69,76 chr1 22199821 . G A 1308.45 PASS AC=2;AF=0.872;AN=2;DP=2495;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,67:67:99:2005,200,0:0,0,41,26 chr1 22200067 . A G 491.86 PASS AC=2;AF=0.7;AN=2;DP=2685;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,72:73:99:2348,209,0:0,1,33,39 chr1 22200082 . T C 1176.21 PASS AC=2;AF=1;AN=2;DP=2486;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,64:64:99:2009,192,0:0,0,26,38 chr1 22200835 . C G 946.74 PASS AC=2;AF=1;AN=2;DP=1369;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:1004,90,0:0,0,15,15 chr1 22202109 . C T 2571.24 PASS AC=2;AF=1;AN=2;DP=3957;FS=0;MQ=60;MQRankSum=1.447;ReadPosRankSum=0.925;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,103:103:99:3273,309,0:0,0,65,38 chr1 22203259 . A G 111 PASS AC=2;AF=0.731;AN=2;DP=1306;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1248,114,0:0,0,13,25 chr1 22205408 . T C 230.25 PASS AC=2;AF=1;AN=2;DP=595;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:444,36,0:0,0,10,2 chr1 22205466 . T C 340.68 PASS AC=2;AF=1;AN=2;DP=1188;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1330,131,0:0,0,29,15 chr1 22206649 . T C 3462.23 PASS AC=2;AF=1;AN=2;DP=5477;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,165:165:99:5444,495,0:0,0,93,72 chr1 22206942 . G A 6380.41 PASS AC=2;AF=1;AN=2;DP=11056;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:2,292:294:99:8902,828,0:1,1,136,156 chr1 22207235 . T C 2383.37 PASS AC=2;AF=1;AN=2;DP=4546;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,122:122:99:3983,365,0:0,0,54,68 chr1 22207804 . ACCCAGGGTGGCAG A 4260.86 PASS AC=2;AF=1;AN=2;DP=6434;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,172:172:99:7674,521,0:0,0,95,77 chr1 22208030 . C T 1463.69 PASS AC=2;AF=0.989;AN=2;DP=2241;FS=0;MQ=60;MQRankSum=0.974;ReadPosRankSum=2.15;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:1911,176,0:0,0,18,41 chr1 22211222 . T C 6222.06 PASS AC=2;AF=0.886;AN=2;DP=8824;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,230:230:99:6741,687,0:0,0,131,99 chr1 22215088 . T C 4137.26 PASS AC=2;AF=1;AN=2;DP=5899;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,141:141:99:4274,422,0:0,0,91,50 chr1 22216574 . C A 652.52 PASS AC=2;AF=0.731;AN=2;DP=4047;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,122:122:99:3895,364,0:0,0,55,67 chr1 22216604 . C G 573.46 PASS AC=2;AF=0.731;AN=2;DP=3376;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,97:97:99:3181,291,0:0,0,40,57 chr1 22217108 . G A 3996.52 PASS AC=2;AF=1;AN=2;DP=8719;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,207:207:99:6186,618,0:0,0,93,114 chr1 22299656 . T G 2090.29 PASS AC=2;AF=0.737;AN=2;DP=1831;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1189,102,0:0,0,25,9 chr1 22304428 . C G 411.52 PASS AC=2;AF=1;AN=2;DP=666;FS=0;FractionInformativeReads=1;set=variant-filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant6-variant7-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant13-filterInvariant14-variant15-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant20-variant22-filterInvariant23-filterInvariant24-variant25-filterInvariant26-filterInvariant29-variant30-variant31-filterInvariant32-filterInvariant33-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant38-filterInvariant40-variant41-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:474,33,0:0,0,8,3 chr1 22304429 . C T 411.52 PASS AC=2;AF=1;AN=2;DP=675;FS=0;FractionInformativeReads=1;set=variant-filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant6-variant7-filterInvariant8-filterInvariant9-variant10-filterInvariant11-filterInvariant12-filterInvariant13-filterInvariant14-variant15-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant20-variant22-filterInvariant23-filterInvariant24-variant25-filterInvariant26-filterInvariant29-variant30-variant31-filterInvariant32-filterInvariant33-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant38-filterInvariant40-variant41-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:33:474,33,0:0,0,7,3 chr1 22304463 . A G 632.54 PASS AC=2;AF=0.939;AN=2;DP=803;FractionInformativeReads=1;set=variant-variant2-filterInvariant3-variant4-filterInvariant6-variant7-filterInvariant8-variant9-filterInvariant10-variant11-variant12-variant14-variant15-variant17-filterInvariant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant40-variant41-filterInvariant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:1033,87,0:0,0,23,6 chr1 22304712 . A G 1569.01 PASS AC=2;AF=0.793;AN=2;DP=1636;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,64:64:99:2370,192,0:0,0,26,38 chr1 22307340 . C T 1079.65 PASS AC=2;AF=0.966;AN=2;DP=1454;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1366,114,0:0,0,30,8 chr1 22307358 . C G 1413.84 PASS AC=2;AF=0.966;AN=2;DP=2313;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2321,210,0:0,0,48,22 chr1 22307538 . C T 3489.79 PASS AC=2;AF=0.989;AN=2;DP=6013;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,169:170:99:4989,462,0:0,1,68,101 chr1 22310139 . T G 5088.23 PASS AC=2;AF=0.966;AN=2;DP=5715;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,133:133:99:6104,415,0:0,0,100,33 chr1 22310145 . C T 5286.66 PASS AC=2;AF=0.966;AN=2;DP=6223;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,146:146:99:6382,442,0:0,0,108,38 chr1 22310262 . G C 9192.96 PASS AC=2;AF=0.966;AN=2;DP=19163;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,497:497:99:14233,1490,0:0,0,250,247 chr1 22310411 . A G 2301.01 PASS AC=2;AF=0.943;AN=2;DP=3931;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,90:90:99:4061,274,0:0,0,23,67 chr1 22310413 . A G 2301.01 PASS AC=2;AF=0.884;AN=2;DP=3747;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,90:90:99:4061,274,0:0,0,24,66 chr1 22310662 . G T 8422.62 PASS AC=2;AF=0.932;AN=2;DP=18598;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,444:445:99:12712,1318,0:1,0,209,235 chr1 22310674 . C T 8334.33 PASS AC=2;AF=0.966;AN=2;DP=17648;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,426:427:99:12550,1266,0:1,0,192,234 chr1 22310725 . G C 5771.42 PASS AC=2;AF=0.932;AN=2;DP=11307;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,285:285:99:8752,853,0:0,0,100,185 chr1 22310824 . T C 982.03 PASS AC=2;AF=0.989;AN=2;DP=1615;MQRankSum=0.147;ReadPosRankSum=1.292;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1642,117,0:0,0,1,38 chr1 22313161 . T C 2287.51 PASS AC=2;AF=0.966;AN=2;DP=7176;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,194:194:99:5747,581,0:0,0,77,117 chr1 22313197 . C A 1227.56 PASS AC=2;AF=0.845;AN=2;DP=4251;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,123:123:99:4081,369,0:0,0,34,89 chr1 22315738 . C T 207.04 PASS AC=2;AF=0.851;AN=2;DP=331;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:185,21,0:0,0,3,4 chr1 22325061 . G A 286.77 PASS AC=2;AF=0.786;AN=2;DP=315;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:542,45,0:0,0,3,12 chr1 22327961 . C G 121.67 PASS AC=1;AF=0.5;AN=2;DP=413;FractionInformativeReads=1;set=variant-variant2-variant8-variant9-variant14-variant15-variant18-variant22-variant29-variant33-variant35-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,21:36:99:867,0,1099:13,2,18,3 chr1 22327963 . A G 121.67 PASS AC=1;AF=0.5;AN=2;DP=288;FractionInformativeReads=1;set=variant-variant2-variant9-variant14-variant15-variant18-variant22-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:16,22:38:99:867,0,1099:14,2,19,3 chr1 22329062 . C G 3049.13 PASS AC=1;AF=0.5;AN=2;DP=13932;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:205,137:342:99:5079,0,11146:140,65,72,65 chr1 22329063 . C T 3049.13 PASS AC=1;AF=0.5;AN=2;DP=14150;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:208,138:346:99:5079,0,11146:141,67,72,66 chr1 22329414 . G A 2395.51 PASS AC=2;AF=0.756;AN=2;DP=2956;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,92:92:99:2949,275,0:0,0,50,42 chr1 22332319 . G A 1058.79 PASS AC=1;AF=0.5;AN=2;DP=4189;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:65,42:107:99:1607,0,3274:31,34,26,16 chr1 22332332 . T C 1217.72 PASS AC=1;AF=0.5;AN=2;DP=4438;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:68,49:117:99:1847,0,3442:31,37,28,21 chr1 22332333 . G A 1223.74 PASS AC=1;AF=0.5;AN=2;DP=4459;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:68,49:117:99:1847,0,3442:31,37,28,21 chr1 22332411 . A G 842.63 PASS AC=1;AF=0.5;AN=2;DP=4695;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:49,69:118:99:1609,0,1179:21,28,30,39 chr1 22333595 . G A 2130.01 PASS AC=2;AF=0.731;AN=2;DP=4186;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,121:121:99:4403,363,0:0,0,32,89 chr1 22336277 . C G 3553.56 PASS AC=2;AF=0.977;AN=2;DP=8843;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,224:224:99:6633,671,0:0,0,102,122 chr1 22336371 . C A 1465.68 PASS AC=2;AF=0.793;AN=2;DP=3942;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,101:102:99:3273,296,0:1,0,30,71 chr1 22336810 . C CA 479.74 PASS AC=2;AF=0.731;AN=2;DP=1719;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:3,50:53:75:1357,75,0:1,2,18,32 chr1 22379088 . G A 1237.64 PASS AC=1;AF=0.775;AN=2;DP=2919;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,52:98:99:1171,0,1147:30,16,31,21 chr1 22405379 . CTT C,CT,CTTT 297.03 PASS AC=1,1,0;AF=0.135,0.554,0.054;AN=2;DP=961;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant17-variant18-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/2:15:95:0,0,3,12 chr1 22408106 . G A 3488.62 PASS AC=2;AF=0.919;AN=2;DP=4751;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,150:150:99:4275,449,0:0,0,76,74 chr1 22447148 . G C 1209.43 PASS AC=2;AF=0.919;AN=2;DP=1095;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:496,39,0:0,0,2,11 chr1 22447645 . C CTG 178.89 PASS AC=2;AF=0.826;AN=2;DP=975;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:893,60,0:0,0,18,2 chr1 22778239 . G GC 100.07 PASS AC=2;AF=0.632;AN=2;DP=273;MQ=60;set=variant4-variant6-filterInvariant7-variant12-variant22-variant24-variant27-variant28-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:566,54,0:0,0,12,6 chr1 22778456 . C A 593.71 PASS AC=2;AF=0.619;AN=2;DP=1301;MQ=60;set=variant4-variant6-variant7-variant9-variant12-variant14-variant18-variant22-variant24-variant27-variant28-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1182,128,0:0,0,19,24 chr1 22816233 . C T 92.16 PASS AC=2;AF=0.625;AN=2;DP=229;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant9-variant12-variant14-variant18-variant22-variant24-variant27-variant28-variant31-variant32-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:457,48,0:0,0,10,6 chr1 22816262 . T C 137.93 PASS AC=2;AF=0.736;AN=2;DP=708;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant14-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:739,72,0:0,0,16,8 chr1 22827931 . C T 803.09 PASS AC=2;AF=0.619;AN=2;DP=1595;MQ=60;set=variant4-variant6-variant7-variant9-variant12-variant14-variant18-variant22-variant24-variant27-variant28-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:1976,226,0:0,0,44,33 chr1 22832743 . A T 287.71 PASS AC=2;AF=0.736;AN=2;DP=1081;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant14-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,26:27:45:881,45,0:1,0,7,19 chr1 22835677 . A G 1891.77 PASS AC=2;AF=0.795;AN=2;DP=4320;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,107:107:99:3291,321,0:0,0,42,65 chr1 22835781 . A T 474.54 PASS AC=1;AF=0.5;AN=2;DP=25;FS=3.128;FractionInformativeReads=1;MQ=60;MQRankSum=-0.739;QD=18.98;ReadPosRankSum=-0.465;SOR=0.123;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:11,14:25:99:503,0,408:0,11,2,12 chr1 22837849 . C T 745.56 PASS AC=2;AF=0.667;AN=2;DP=591;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant16-variant18-variant22-variant24-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:823,69,0:0,0,6,17 chr1 22846452 . C G 515.5 PASS AC=2;AF=0.673;AN=2;DP=791;MQ=60;set=variant2-variant4-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant16-variant18-variant22-variant24-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1347,111,0:0,0,29,8 chr1 22846709 . G A 917.45 PASS AC=2;AF=1;AN=2;DP=2483;FS=0;MQ=60;MQRankSum=1.253;ReadPosRankSum=1.253;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1754,159,0:0,0,18,35 chr1 22848972 . A C 2081.05 PASS AC=2;AF=0.6;AN=2;DP=1006;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant9-variant11-variant13-variant14-variant16-variant22-variant28-variant30-variant32-variant35-variant36-variant38-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:2174,204,0:0,0,25,43 chr1 22854927 . AAAAC A 4819.36 PASS AC=2;AF=0.673;AN=2;DP=2691;set=variant2-variant4-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant16-variant18-variant22-variant24-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,86:86:99:3830,259,0:0,0,42,44 chr1 22855441 . C T 2370.8 PASS AC=2;AF=0.64;AN=2;DP=1692;MQ=60;set=variant2-variant4-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant16-variant18-variant22-variant24-variant27-variant28-variant30-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,101:101:99:3181,303,0:0,0,49,52 chr1 22912819 . T C 605.81 PASS AC=2;AF=0.989;AN=2;DP=951;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.506;ReadPosRankSum=-0.985;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1043,102,0:0,0,17,17 chr1 22925292 . C G 4989.23 PASS AC=2;AF=1;AN=2;DP=7907;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,187:187:99:5757,560,0:0,0,118,69 chr1 22966262 . T C 100.16 PASS AC=1;AF=0.5;AN=2;DP=19;FS=0;FractionInformativeReads=1;MQ=60;set=variant11-variant35 GT:AD:DP:GQ:PL:SB 0/1:6,6:12:99:153,0,154:2,4,2,4 chr1 22970642 . C T 1833.49 PASS AC=1;AF=0.55;AN=2;DP=2972;MQ=60;set=variant2-variant3-variant5-variant7-variant11-variant12-variant13-variant14-variant17-variant22-variant23-variant28-variant29-variant30-variant35-variant36-variant37-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:86,94:180:99:2114,0,2086:44,42,52,42 chr1 22970828 . G T 483.84 PASS AC=1;AF=0.656;AN=2;DP=2147;MQ=60;set=variant2-variant3-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant16-variant17-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,45:95:99:1115,0,1394:15,35,17,28 chr1 22970925 . T C 178.74 PASS AC=1;AF=0.586;AN=2;DP=670;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant7-variant9-variant11-variant12-variant13-variant14-variant16-variant17-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,10:23:99:312,0,281:5,8,2,8 chr1 22973699 . C G 365.63 PASS AC=1;AF=0.5;AN=2;DP=212;FractionInformativeReads=1;MQ=60;set=variant2-variant11-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:26,29:55:99:793,0,670:13,13,19,10 chr1 22974297 . C A 706.44 PASS AC=1;AF=0.607;AN=2;DP=2568;MQ=60;set=variant2-variant3-variant5-variant7-variant9-variant11-variant12-variant14-variant16-variant17-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,36:89:99:870,0,1400:18,35,11,25 chr1 22974379 . CCCACCAGATGGACTTCT C 647.68 PASS AC=1;AF=0.596;AN=2;DP=1349;MQ=60;set=variant2-variant3-variant5-variant7-variant11-variant12-variant13-variant14-variant16-variant17-variant22-variant23-variant26-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,15:50:99:408,0,1402:14,21,5,10 chr1 22974533 . CTT CT,C,CTTT 127.82 PASS AC=0,1,0;AF=0.202,0.405,0.012;AN=2;DP=4096;set=filterInvariant-variant2-variant3-filterInvariant4-variant5-variant6-variant7-variant8-variant9-filterInvariant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-filterInvariant18-filterInvariant20-filterInvariant21-variant22-variant23-variant24-variant25-variant26-filterInvariant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:DP:GQ:SB 0/2:103:99:24,20,31,28 chr1 22979655 . T G 750.67 PASS AC=1;AF=0.656;AN=2;DP=1545;MQ=60;set=variant2-variant3-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant16-variant17-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,35:74:99:732,0,967:22,17,16,19 chr1 22979899 . T C 143.78 PASS AC=1;AF=0.667;AN=2;DP=305;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant16-variant17-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,9:10:6:331,0,6:0,1,2,7 chr1 22985785 . AGATGGATGGATGGATGGATGGATGGATGGATGGATGCAGATGGAGGAATAGAGAGATGGATG AGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGCAGATGGAGGAATAGAGAGATGGATG,AGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGCAGATGGAGGAATAGAGAGATGGATG,AGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGCAGATGGAGGAATAGAGAGATGGATG,AGATGGATGGATGGATGGATGGATGGATGGATGCAGATGGAGGAATAGAGAGATGGATG,A 223.28 PASS AC=0,0,0,0,1;AF=0.333,0.03,0.121,0.121,0.03;AN=2;DP=588;set=variant2-variant3-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:DP:GQ:SB 0/5:35:99:16,10,7,2 chr1 22987958 . A G 2213.71 PASS AC=2;AF=0.989;AN=2;DP=3965;MQ=60;MQRankSum=-1.324;ReadPosRankSum=1.276;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,73:73:99:2438,219,0:0,0,33,40 chr1 23101688 . T G 1033.4 PASS AC=2;AF=0.849;AN=2;DP=3059;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2184,210,0:0,0,41,29 chr1 23107811 . TAA TA,T 289.15 PASS AC=2,0;AF=0.512,0.256;AN=2;DP=1450;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:36:31:2,2,24,8 chr1 23108089 . A G 52.74 PASS AC=2;AF=0.829;AN=2;DP=554;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:633,54,0:0,0,3,15 chr1 23191746 . G T 286.03 PASS AC=1;AF=0.542;AN=2;DP=1070;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant7-variant8-variant10-variant17-variant21-variant27-variant33-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:54,45:99:99:1180,0,1581:14,40,12,33 chr1 23216712 . T C 1179.27 PASS AC=2;AF=0.656;AN=2;DP=1388;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1555,153,0:0,0,24,27 chr1 23219187 . C T 1368.17 PASS AC=2;AF=0.65;AN=2;DP=1194;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant19-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,52:52:99:1774,156,0:0,0,39,13 chr1 23219493 . T C 6536.6 PASS AC=2;AF=1;AN=2;DP=13927;FS=0;MQ=60;MQRankSum=1.569;ReadPosRankSum=1.002;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,336:336:99:10213,1006,0:0,0,177,159 chr1 23223116 . C T 827.84 PASS AC=2;AF=0.65;AN=2;DP=1846;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant19-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,63:64:99:2256,182,0:0,1,14,49 chr1 23232400 . C T 827.77 PASS AC=2;AF=0.667;AN=2;DP=941;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1417,116,0:0,0,34,5 chr1 23236826 . C T 1400.29 PASS AC=1;AF=0.652;AN=2;DP=2109;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:26,44:70:99:1185,0,678:16,10,27,17 chr1 23279651 . A T 6374.21 PASS AC=1;AF=0.5;AN=2;DP=988;FractionInformativeReads=1;MQ=60;set=variant19-variant35 GT:AD:DP:GQ:PL:SB 0/1:215,248:463:99:6166,0,5022:109,106,126,122 chr1 23280424 . G T 2069.59 PASS AC=1;AF=0.591;AN=2;DP=4370;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:133,103:236:99:2589,0,3139:65,68,43,60 chr1 23285678 . A G 61.77 PASS AC=2;AF=0.932;AN=2;DP=302;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:321,27,0:0,0,2,7 chr1 23289568 . T C 1809.34 PASS AC=1;AF=0.7;AN=2;DP=2842;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,40:89:99:1096,0,1184:25,24,24,16 chr1 23291582 . G A 535.27 PASS AC=1;AF=0.7;AN=2;DP=1101;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:22,15:37:99:347,0,546:13,9,10,5 chr1 23342362 . A G 1759.42 PASS AC=2;AF=0.813;AN=2;DP=2327;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,52:52:99:1571,156,0:0,0,27,25 chr1 23346225 . G A 1656.6 PASS AC=1;AF=0.5;AN=2;DP=222;MQ=60;set=variant17-variant35 GT:AD:DP:GQ:PL:SB 0/1:45,47:92:99:1315,0,1475:22,23,25,22 chr1 23380198 . A G 1049.64 PASS AC=2;AF=0.805;AN=2;DP=1016;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:708,51,0:0,0,15,2 chr1 23385826 . CTT C 1881.64 PASS AC=1;AF=0.655;AN=2;DP=2407;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:44,41:85:99:1541,0,1950:25,19,20,21 chr1 23399932 . C T 2627.96 PASS AC=2;AF=0.805;AN=2;DP=2674;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:1869,174,0:0,0,22,36 chr1 23405794 . A C 1835.22 PASS AC=2;AF=0.786;AN=2;DP=2365;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:1660,162,0:0,0,27,27 chr1 23405865 . A C 478.77 PASS AC=1;AF=0.5;AN=2;DP=262;MQ=60;set=variant3-variant14-variant35-variant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:34,21:55:99:600,0,904:15,19,12,9 chr1 23409538 . G A 516.04 PASS AC=1;AF=0.563;AN=2;DP=758;MQ=60;set=variant-variant2-variant3-variant4-variant8-variant9-variant11-variant14-variant16-variant18-variant19-variant20-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant37-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:15,11:26:99:328,0,508:13,2,8,3 chr1 23410137 . T TG 1236.49 PASS AC=1;AF=0.5;AN=2;DP=2631;set=variant7-variant10-variant16-variant17-variant23-variant25-variant26-variant27-variant32-variant33-variant35-variant36-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:94,67:161:99:1185,0,2104:52,42,38,29 chr1 23410138 . T G 4461.2 PASS AC=1;AF=0.684;AN=2;DP=7276;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:76,88:164:99:1829,0,1567:42,34,49,39 chr1 23410140 . G T 3821.42 PASS AC=2;AF=0.805;AN=2;DP=7845;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:11,156:167:99:3961,198,0:6,5,88,68 chr1 23410469 . C CTT 32.26 PASS AC=1;AF=0.619;AN=2;DP=239;MQ=60;set=variant-variant2-variant3-variant4-variant8-variant11-variant14-variant16-variant18-variant19-variant20-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:6,5:11:99:182,0,225:3,3,5,0 chr1 23410721 . A T 1190.34 PASS AC=2;AF=0.817;AN=2;DP=1474;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1294,117,0:0,0,19,20 chr1 23410742 . A C 1124.85 PASS AC=2;AF=0.817;AN=2;DP=1483;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1189,105,0:0,0,19,16 chr1 23411225 . T TC 17027.1 PASS AC=1;AF=0.78;AN=2;DP=20363;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:252,232:484:99:5587,0,8814:118,134,115,117 chr1 23411233 . T C 6226.1 PASS AC=1;AF=0.5;AN=2;DP=1053;MQ=60;set=variant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:239,267:506:99:6110,0,7968:119,120,121,146 chr1 23413027 . T C 880.17 PASS AC=2;AF=0.805;AN=2;DP=1647;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1282,120,0:0,0,20,20 chr1 23413458 . T G 869.67 PASS AC=2;AF=0.805;AN=2;DP=1924;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1766,159,0:0,0,30,23 chr1 23413707 . T C 580.87 PASS AC=2;AF=0.793;AN=2;DP=1385;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1283,132,0:0,0,16,28 chr1 23415102 . T C 863.91 PASS AC=2;AF=0.805;AN=2;DP=1442;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1193,123,0:0,0,23,18 chr1 23418153 . C T 7204.82 PASS AC=2;AF=0.817;AN=2;DP=8265;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,250:250:99:7593,747,0:0,0,108,142 chr1 23419260 . C CACTCTCCACATTTCCCTTCA 1601.83 PASS AC=1;AF=0.5;AN=2;DP=130;FS=2.52;FractionInformativeReads=0.869;MQ=60;MQRankSum=-1.086;QD=12.32;ReadPosRankSum=-3.642;SOR=0.471;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:69,44:113:99:1639,0,2671:27,42,20,24 chr1 23419261 . G A,GTCCA 3863.21 PASS AC=1,1;AF=0.714,0.071;AN=2;DP=965;MQ=60;set=variant35-variant37-variant38-variant39-variant40-variant41-variant43 GT:DP:GQ:SB 1/2:105:99:0,1,43,61 chr1 23419374 . G T 3057.47 PASS AC=2;AF=0.805;AN=2;DP=4812;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,121:121:99:5317,364,0:0,0,70,51 chr1 23419383 . C T 3092.39 PASS AC=2;AF=0.805;AN=2;DP=4950;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,128:128:99:5622,391,0:0,0,73,55 chr1 23419855 . T C 4142.99 PASS AC=2;AF=0.817;AN=2;DP=5140;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,131:131:99:4235,392,0:0,0,60,71 chr1 23435669 . T C 203.67 PASS AC=1;AF=0.5;AN=2;DP=173;MQ=60;set=variant7-variant10-variant16-variant17-variant23-variant25-variant26-variant27-variant32-variant33-variant34-variant35-variant36-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:2,10:12:13:252,0,13:1,1,4,6 chr1 23518524 . T C 447.93 PASS AC=1;AF=0.661;AN=2;DP=981;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,14:27:99:417,0,357:8,5,10,4 chr1 23519508 . T TA 193.12 PASS AC=1;AF=0.629;AN=2;DP=728;MQ=60;set=variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,7:23:99:116,0,346:12,4,5,2 chr1 23631625 . A G 3745.98 PASS AC=1;AF=0.531;AN=2;DP=5997;set=variant5-variant8-variant10-variant12-variant14-variant15-variant16-variant18-variant25-variant26-variant27-variant33-variant34-variant35-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:198,183:381:99:4679,0,5083:105,93,95,88 chr1 23632206 . ACT A 5857.38 PASS AC=1;AF=0.5;AN=2;DP=2084;MQ=60;set=variant5-variant12-variant14-variant15-variant26-variant35 GT:AD:DP:GQ:PL:SB 0/1:156,184:340:99:7213,0,6018:97,59,120,64 chr1 23632626 . G C 5920.58 PASS AC=2;AF=0.864;AN=2;DP=6704;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,158:158:99:4766,473,0:0,0,80,78 chr1 23633278 . G A 4604.01 PASS AC=2;AF=0.989;AN=2;DP=5728;MQRankSum=-1.335;ReadPosRankSum=-2.619;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,104:104:99:3409,311,0:0,0,76,28 chr1 23634406 . TA T 1281.83 PASS AC=1;AF=0.524;AN=2;DP=2443;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant10-variant12-variant13-variant17-variant18-variant22-filterInvariant25-variant27-variant30-variant31-variant33-variant34-variant35-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:52,53:105:99:1068,0,1044:22,30,25,28 chr1 23636015 . GTT GT,G 1784.03 PASS AC=1,1;AF=0.761,0.216;AN=2;DP=4309;set=Intersection GT:DP:GQ:SB 2/1:82:99:1,1,35,45 chr1 23664511 . T G 722.18 PASS AC=1;AF=0.731;AN=2;DP=789;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,10:18:99:295,0,171:3,5,2,8 chr1 23670801 . CT C 1343.92 PASS AC=1;AF=0.568;AN=2;DP=2334;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant12-variant13-variant17-variant20-variant22-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:49,43:92:99:1437,0,1769:21,28,19,24 chr1 23670803 . G C 1713.65 PASS AC=1;AF=0.529;AN=2;DP=1639;MQ=60;set=variant5-variant8-variant10-variant12-variant14-variant15-variant16-variant18-variant25-variant26-variant27-variant33-variant34-variant35-variant36-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:43,49:92:99:1149,0,1640:19,24,21,28 chr1 23685968 . T C 126.36 PASS AC=1;AF=0.583;AN=2;DP=73;FractionInformativeReads=1;MQ=60;set=variant5-variant14-variant15-variant26-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:3,11:14:3:292,0,3:2,1,7,4 chr1 23686246 . C T 1413.87 PASS AC=2;AF=0.86;AN=2;DP=2163;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:1856,185,0:0,0,30,32 chr1 23687827 . T C 175.14 PASS AC=1;AF=0.531;AN=2;DP=376;MQ=60;set=variant5-variant8-variant10-variant12-variant14-variant15-variant16-variant18-variant25-variant26-variant27-variant33-variant35-variant36-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:10,6:16:99:178,0,279:4,6,3,3 chr1 23688178 . A G 469.38 PASS AC=2;AF=0.872;AN=2;DP=1593;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1282,110,0:0,0,16,21 chr1 23688933 . A G 6123.78 PASS AC=1;AF=0.75;AN=2;DP=8301;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:124,120:244:99:2932,0,3013:66,58,65,55 chr1 23689083 . G A 2317.09 PASS AC=1;AF=0.5;AN=2;DP=1155;FractionInformativeReads=1;MQ=60;set=variant5-variant12-variant14-variant15-variant26-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:66,75:141:99:2115,0,1843:25,41,34,41 chr1 23689786 . AT A 63.81 PASS AC=1;AF=0.583;AN=2;DP=218;MQ=60;set=variant5-variant8-variant10-variant12-variant15-variant16-variant18-variant26-variant27-variant33-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,7:13:99:144,0,117:1,5,1,6 chr1 23693385 . T C 963.62 PASS AC=1;AF=0.531;AN=2;DP=1053;MQ=60;set=variant5-variant8-variant10-variant12-variant14-variant15-variant16-variant18-variant25-variant26-variant27-variant33-variant35-variant36-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:29,34:63:99:871,0,733:20,9,23,11 chr1 23693422 . T C 3436.51 PASS AC=1;AF=0.744;AN=2;DP=3432;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,49:92:99:1267,0,1078:26,17,32,17 chr1 23694238 . C A 290.43 PASS AC=1;AF=0.5;AN=2;DP=29;FractionInformativeReads=1;MQ=60;set=variant14-variant35 GT:AD:DP:GQ:PL:SB 0/1:7,11:18:99:385,0,266:6,1,11,0 chr1 23696152 . G A 1910.81 PASS AC=2;AF=0.86;AN=2;DP=3368;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,84:84:99:2630,252,0:0,0,32,52 chr1 23697617 . T C 577.9 PASS AC=1;AF=0.531;AN=2;DP=740;MQ=60;set=variant5-variant8-variant10-variant12-variant14-variant15-variant16-variant18-variant25-variant26-variant27-variant33-variant35-variant36-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:29,26:55:99:884,0,843:14,15,16,10 chr1 23698120 . C G 1336.32 PASS AC=1;AF=0.5;AN=2;DP=621;FractionInformativeReads=1;MQ=60;set=variant5-variant12-variant14-variant15-variant26-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:45,49:94:99:1343,0,1328:15,30,22,27 chr1 23707692 . A G 845.93 PASS AC=2;AF=0.872;AN=2;DP=909;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1024,108,0:0,0,22,14 chr1 23710805 . A G 2808.84 PASS AC=2;AF=0.86;AN=2;DP=4647;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,114:114:99:3527,342,0:0,0,67,47 chr1 23713952 . T G 3230.05 PASS AC=2;AF=0.86;AN=2;DP=5710;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,130:130:99:4203,390,0:0,0,57,73 chr1 23720260 . T G 874.87 PASS AC=2;AF=0.875;AN=2;DP=1271;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:1207,87,0:0,0,27,2 chr1 23724183 . C T 1031.36 PASS AC=1;AF=0.711;AN=2;DP=1764;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,30:56:99:772,0,798:9,17,17,13 chr1 23730504 . C A 1170.73 PASS AC=1;AF=0.5;AN=2;DP=158;FractionInformativeReads=1;MQ=60;set=variant17-variant35 GT:AD:DP:GQ:PL:SB 0/1:37,36:73:99:1057,0,1039:19,18,17,19 chr1 23735241 . G T 1693.89 PASS AC=2;AF=0.837;AN=2;DP=3760;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:2288,225,0:0,0,36,39 chr1 23743581 . C G 1449.24 PASS AC=2;AF=0.738;AN=2;DP=2089;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:2367,212,0:0,0,52,19 chr1 23751140 . G T 13006.5 PASS AC=1;AF=0.667;AN=2;DP=16369;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:291,250:541:99:5047,0,6929:118,173,104,146 chr1 23755513 . T C 2326.93 PASS AC=2;AF=0.841;AN=2;DP=3690;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,78:78:99:2506,234,0:0,0,41,37 chr1 23755716 . T C 1468.01 PASS AC=2;AF=0.841;AN=2;DP=2175;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:2065,195,0:0,0,35,30 chr1 23756155 . T C 958.14 PASS AC=2;AF=0.841;AN=2;DP=2165;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1508,147,0:0,0,24,25 chr1 23756695 . A G 905.77 PASS AC=2;AF=0.791;AN=2;DP=841;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:881,81,0:0,0,10,17 chr1 23758134 . A G 2505.25 PASS AC=2;AF=0.841;AN=2;DP=3842;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:2306,213,0:0,0,36,35 chr1 23758498 . T TA 711.22 PASS AC=1;AF=0.533;AN=2;DP=409;MQ=60;set=variant4-variant5-variant6-variant7-variant23-variant24-filterInvariant29-filterInvariant31-variant34-variant35-filterInvariant37-filterInvariant39-filterInvariant40-variant41-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:4,7:11:72:112,0,72:0,4,1,6 chr1 23762679 . A G 292.45 PASS AC=2;AF=0.738;AN=2;DP=855;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:764,66,0:0,0,6,16 chr1 23765472 . A G 1280.56 PASS AC=2;AF=0.841;AN=2;DP=2030;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:1840,171,0:0,0,23,34 chr1 23769359 . T C 733.04 PASS AC=2;AF=0.784;AN=2;DP=1354;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1096,108,0:0,0,12,24 chr1 23810658 . G A 1954.68 PASS AC=1;AF=0.689;AN=2;DP=2594;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,28:65:99:607,0,865:16,21,10,18 chr1 23833599 . A AT 307.94 PASS AC=1;AF=0.583;AN=2;DP=887;MQ=60;set=variant-variant4-variant5-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,18:39:99:431,0,523:9,12,7,11 chr1 23833611 . G T 349.56 PASS AC=1;AF=0.583;AN=2;DP=823;MQ=60;set=variant-variant4-variant5-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-filterInvariant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,15:35:99:442,0,513:8,12,5,10 chr1 23834486 . G A 457.01 PASS AC=1;AF=0.552;AN=2;DP=1490;MQ=60;set=variant-variant4-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,17:56:99:335,0,1074:19,20,8,9 chr1 23835794 . A G 268.56 PASS AC=1;AF=0.581;AN=2;DP=1421;MQ=60;set=variant-variant4-variant5-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,33:72:99:729,0,913:18,21,17,16 chr1 23836364 . A G 1398.86 PASS AC=1;AF=0.583;AN=2;DP=3622;MQ=60;set=variant-variant4-variant5-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:78,65:143:99:1614,0,2085:42,36,34,31 chr1 23847464 . C A 462.85 PASS AC=1;AF=0.581;AN=2;DP=2194;MQ=60;set=variant-variant4-variant5-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,48:78:99:1324,0,790:14,16,22,26 chr1 23847583 . C T 756.26 PASS AC=1;AF=0.5;AN=2;DP=134;FractionInformativeReads=1;MQ=60;set=variant22-variant35 GT:AD:DP:GQ:PL:SB 0/1:25,41:66:99:975,0,577:13,12,17,24 chr1 23847709 . C G 213.93 PASS AC=1;AF=0.621;AN=2;DP=949;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,19:35:99:454,0,394:4,12,9,10 chr1 23857742 . CT CTT,C 75.53 PASS AC=0,1;AF=0.048,0.452;AN=2;DP=841;MQ=60;set=variant-filterInvariant2-variant6-variant8-variant10-variant11-filterInvariant12-variant14-variant17-variant20-filterInvariant21-variant22-filterInvariant25-variant27-filterInvariant28-variant30-variant33-variant35-variant36-variant39-variant41 GT:DP:GQ:SB 0/2:35:99:6,17,4,8 chr1 23884333 . C G 1126.45 PASS AC=2;AF=0.538;AN=2;DP=1208;FractionInformativeReads=1;MQ=60;set=variant9-variant13-variant17-variant19-variant20-variant21-variant22-variant28-variant29-variant31-variant32-variant33-variant35 GT:AD:DP:GQ:PL:SB 1/1:0,78:78:99:2396,234,0:0,0,44,34 chr1 23884661 . G A 3845.45 PASS AC=2;AF=0.821;AN=2;DP=5801;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,145:145:99:4618,434,0:0,0,65,80 chr1 23885498 . T C 2838.85 PASS AC=2;AF=0.929;AN=2;DP=6591;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,174:174:99:5325,522,0:0,0,100,74 chr1 23886073 . T C 1596.56 PASS AC=2;AF=0.656;AN=2;DP=1863;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:1766,162,0:0,0,23,31 chr1 23954126 . T TAC,TACAC 822.98 PASS AC=2,0;AF=0.622,0.041;AN=2;DP=2361;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant41-variant42-variant43 GT:DP:GQ:SB 1/1:70:99:0,0,34,36 chr1 23955186 . T TTTATTATTATTA,TTTATTATTATTATTATTA,TTTATTATTATTATTATTATTATTATTA,TTTATTATTATTATTA,TTTATTATTATTATTATTATTATTA,TTTATTATTATTATTATTATTA 183.39 PASS AC=0,0,0,2,0,0;AF=0.214,0.071,0.071,0.286,0.107,0.179;AN=2;DP=295;set=variant5-variant7-variant8-variant13-variant17-variant19-variant22-variant23-variant35-variant36-variant38-variant39-variant40-variant44 GT:DP:GQ:SB 4/4:4:9:0,0,1,3 chr1 23967159 . G A 3101.88 PASS AC=2;AF=0.694;AN=2;DP=7779;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,196:196:99:5743,585,0:0,0,83,113 chr1 24018277 . C G 1292.27 PASS AC=2;AF=1;AN=2;DP=4094;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2161,210,0:0,0,36,34 chr1 24021843 . C A 914.45 PASS AC=2;AF=1;AN=2;DP=1578;FS=0;MQ=60;MQRankSum=-0.247;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1151,110,0:0,0,15,22 chr1 24022437 . A G 1645.19 PASS AC=1;AF=0.692;AN=2;DP=4402;MQ=60;set=variant-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant19-variant20-variant22-variant24-variant26-variant28-variant29-variant30-variant32-variant33-variant35-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:90,81:171:99:1798,0,2035:45,45,35,46 chr1 24069637 . G C 211.61 PASS AC=1;AF=0.676;AN=2;DP=1037;MQ=60;set=variant-variant2-variant4-variant5-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-filterInvariant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,18:37:99:403,0,533:12,7,10,8 chr1 24077206 . ATCT A 310.59 PASS AC=1;AF=0.5;AN=2;DP=42;FractionInformativeReads=1;MQ=60;set=variant9-variant35 GT:AD:DP:GQ:PL:SB 0/1:15,8:23:99:291,0,699:10,5,8,0 chr1 24082269 . CA C,CAA,CAAA 49.52 PASS AC=1,0,0;AF=0.421,0.053,0.026;AN=2;DP=562;MQ=60;set=variant-filterInvariant2-variant4-filterInvariant13-filterInvariant15-variant17-variant18-variant19-variant20-variant23-variant27-variant29-variant35-variant36-variant37-variant39-filterInvariant40-variant43-variant44 GT:DP:GQ:SB 0/1:25:93:12,6,7,0 chr1 24082285 . AT A 101.4 PASS AC=1;AF=0.5;AN=2;DP=249;MQ=60;set=variant3-filterInvariant8-filterInvariant10-filterInvariant13-filterInvariant18-variant35 GT:AD:DP:GQ:PL:SB 0/1:21,21:42:99:432,0,567:16,5,14,7 chr1 24083494 . C T 187.39 PASS AC=1;AF=0.558;AN=2;DP=612;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant18-variant22-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:24,24:48:99:558,0,776:21,3,16,8 chr1 24088128 . G A 1076.93 PASS AC=1;AF=0.536;AN=2;DP=1016;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant9-variant16-variant23-variant28-variant30-variant33-variant35-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,49:88:99:1377,0,1158:10,29,16,33 chr1 24106510 . A AT 1140.85 PASS AC=2;AF=0.932;AN=2;DP=1536;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1322,123,0:0,0,9,32 chr1 24114129 . G A 421.61 PASS AC=1;AF=0.681;AN=2;DP=2466;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,25:57:99:606,0,905:13,19,9,16 chr1 24117835 . G A 236.7 PASS AC=2;AF=1;AN=2;DP=75;FS=0;MQ=60;MQRankSum=0.747;ReadPosRankSum=0.747;set=variant2-variant3-variant4-variant11-variant16-variant17-variant21-variant24-variant25-variant27-variant29-variant33-variant34-variant35-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:159,15,0:0,0,2,3 chr1 24122986 . C T 224.06 PASS AC=1;AF=0.696;AN=2;DP=365;MQ=60;set=variant2-variant7-variant9-variant11-variant14-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,5:10:92:140,0,92:5,0,5,0 chr1 24128467 . C T 1490.3 PASS AC=2;AF=0.932;AN=2;DP=2589;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,61:61:99:2228,183,0:0,0,37,24 chr1 24129126 . A G 1504.08 PASS AC=1;AF=0.586;AN=2;DP=4321;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant22-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:78,76:154:99:1840,0,1996:32,46,27,49 chr1 24133612 . G A 847.83 PASS AC=1;AF=0.697;AN=2;DP=3450;set=variant-variant2-variant4-variant5-variant7-variant9-variant11-variant14-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,56:116:99:1121,0,1442:31,29,28,28 chr1 24134462 . C T 274.58 PASS AC=2;AF=0.942;AN=2;DP=549;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:641,51,0:0,0,15,2 chr1 24134721 . T C 4199.35 PASS AC=2;AF=0.932;AN=2;DP=5979;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,134:134:99:4210,402,0:0,0,65,69 chr1 24143932 . A G 1183.69 PASS AC=2;AF=0.932;AN=2;DP=2179;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:1593,162,0:0,0,28,26 chr1 24151996 . C A 502.23 PASS AC=1;AF=0.661;AN=2;DP=1091;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:15,14:29:99:333,0,385:3,12,0,14 chr1 24171543 . C G 1055.42 PASS AC=1;AF=0.645;AN=2;DP=1304;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:16,14:30:99:378,0,503:13,3,9,5 chr1 24180962 . T C 1899.89 PASS AC=1;AF=0.586;AN=2;DP=3635;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant22-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:63,65:128:99:1592,0,1445:30,33,31,34 chr1 24192200 . A G 745.79 PASS AC=1;AF=0.645;AN=2;DP=2226;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:41,26:67:99:616,0,1108:16,25,10,16 chr1 24196957 . C G 1441.02 PASS AC=1;AF=0.7;AN=2;DP=3140;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,44:93:99:1068,0,1397:34,15,29,15 chr1 24197408 . T C 732.76 PASS AC=2;AF=1;AN=2;DP=689;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:819,69,0:0,0,4,19 chr1 24197644 . CAAAA CAAA,CA,CAA,C 439.71 PASS AC=0,1,0,0;AF=0.258,0.177,0.097,0.048;AN=2;DP=1762;set=variant2-variant4-variant5-variant7-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:56:99:12,11,27,6 chr1 24197696 . A G 2688.7 PASS AC=1;AF=0.7;AN=2;DP=5202;set=variant-variant2-variant4-variant5-variant7-variant9-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:81,74:155:99:1942,0,2336:51,30,45,29 chr1 24197898 . C G 3717.73 PASS AC=1;AF=0.7;AN=2;DP=9726;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:140,138:278:99:3371,0,3478:68,72,61,77 chr1 24198622 . CAA CAAA,C,CAAAA,CAAAAA 69.82 PASS AC=0,0,2,0;AF=0.125,0.125,0.25,0.125;AN=2;DP=37;FS=0;set=variant3-variant26-variant35-variant37 GT:DP:GQ:SB 3/3:5:15:0,0,5,0 chr1 24198804 . T C 1222.79 PASS AC=1;AF=0.7;AN=2;DP=2760;set=variant-variant2-variant4-variant5-variant7-variant9-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,39:73:99:1050,0,864:23,11,25,14 chr1 24198840 . C G 2177.87 PASS AC=1;AF=0.7;AN=2;DP=4360;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,58:106:99:1523,0,1247:30,18,35,23 chr1 24199026 . A C 5231.98 PASS AC=1;AF=0.7;AN=2;DP=7730;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:141,121:262:99:3080,0,3910:69,72,58,63 chr1 24199041 . T C 4860.41 PASS AC=1;AF=0.7;AN=2;DP=7500;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:135,112:247:99:2969,0,3837:64,71,53,59 chr1 24199137 . G A 2498.03 PASS AC=1;AF=0.5;AN=2;DP=244;FS=1.011;FractionInformativeReads=1;MQ=60;MQRankSum=0.521;QD=10.24;ReadPosRankSum=-2.62;SOR=0.62;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:151,93:244:99:2526,0,4269:84,67,50,43 chr1 24199182 . T C 4225.3 PASS AC=1;AF=0.7;AN=2;DP=9327;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:164,117:281:99:3092,0,4294:82,82,64,53 chr1 24199290 . T C 2802.7 PASS AC=1;AF=0.7;AN=2;DP=7292;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:122,119:241:99:2944,0,3352:52,70,55,64 chr1 24199339 . A C 2137.62 PASS AC=1;AF=0.7;AN=2;DP=5578;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:112,83:195:99:2146,0,2820:49,63,38,45 chr1 24199363 . T C 2300.43 PASS AC=1;AF=0.7;AN=2;DP=4746;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:93,72:165:99:1818,0,3775:42,51,33,39 chr1 24199364 . G A 2300.43 PASS AC=1;AF=0.7;AN=2;DP=4703;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:92,72:164:99:2702,0,3722:42,50,34,38 chr1 24199642 . G A 1797.37 PASS AC=1;AF=0.7;AN=2;DP=5536;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:85,87:172:99:2051,0,1827:39,46,38,49 chr1 24199738 . A AT 577.63 PASS AC=1;AF=0.7;AN=2;DP=1363;set=variant-variant2-variant4-variant5-variant7-variant9-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,19:33:99:691,0,875:1,13,4,15 chr1 24199750 . C CAG 581.19 PASS AC=1;AF=0.7;AN=2;DP=924;FractionInformativeReads=1;set=variant-variant2-variant4-variant5-variant7-variant9-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,19:33:99:694,0,854:0,14,4,15 chr1 24200158 . T C 364.75 PASS AC=1;AF=0.706;AN=2;DP=836;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,5:12:99:128,0,141:3,4,2,3 chr1 24200524 . C T 890.54 PASS AC=1;AF=0.7;AN=2;DP=2206;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,26:51:99:632,0,626:16,9,13,13 chr1 24200606 . A G 1366.51 PASS AC=1;AF=0.7;AN=2;DP=3755;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,49:101:99:1246,0,1350:30,22,30,19 chr1 24200772 . C G 680.76 PASS AC=1;AF=0.7;AN=2;DP=3848;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:72,48:120:99:1090,0,1883:37,35,18,30 chr1 24200800 . T C 542.26 PASS AC=1;AF=0.7;AN=2;DP=3123;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:77,36:113:99:833,0,2051:41,36,14,22 chr1 24200903 . G C 1005.21 PASS AC=1;AF=0.706;AN=2;DP=2065;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,21:86:99:679,0,2961:27,38,14,7 chr1 24200921 . T C 942.56 PASS AC=1;AF=0.7;AN=2;DP=2262;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,27:84:99:857,0,2735:25,32,18,9 chr1 24200969 . T C 1247.54 PASS AC=1;AF=0.7;AN=2;DP=3120;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,36:95:99:1360,0,2926:26,33,20,16 chr1 24200983 . C T 1268.8 PASS AC=1;AF=0.7;AN=2;DP=3353;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,44:105:99:1553,0,2954:30,31,25,19 chr1 24201094 . G C 1741.11 PASS AC=1;AF=0.7;AN=2;DP=4698;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:81,69:150:99:1716,0,2072:46,35,35,34 chr1 24201109 . C T 1618.9 PASS AC=1;AF=0.7;AN=2;DP=4786;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:83,78:161:99:1896,0,2073:46,37,39,39 chr1 24201262 . A G 487.54 PASS AC=1;AF=0.7;AN=2;DP=6177;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:112,84:196:99:1970,0,2773:57,55,42,42 chr1 24201357 . A G 398.49 PASS AC=1;AF=0.7;AN=2;DP=4028;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:74,49:123:99:1358,0,2062:32,42,22,27 chr1 24201448 . C T 660.11 PASS AC=1;AF=0.7;AN=2;DP=3587;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,67:125:99:1736,0,1482:28,30,33,34 chr1 24201643 . G A 549.69 PASS AC=1;AF=0.7;AN=2;DP=2817;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,41:88:99:1117,0,1245:20,27,19,22 chr1 24201919 . T C 1695.89 PASS AC=1;AF=0.7;AN=2;DP=5804;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:94,106:200:99:4113,0,4957:48,46,50,56 chr1 24201920 . T C 1695.89 PASS AC=1;AF=0.7;AN=2;DP=5790;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:94,105:199:99:4113,0,4957:48,46,49,56 chr1 24239588 . C CGGAGGT 187.73 PASS AC=2;AF=0.984;AN=2;DP=115;FS=0;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:89,6,0:0,0,1,1 chr1 24239719 . C G 525.13 PASS AC=2;AF=1;AN=2;DP=753;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0;ReadPosRankSum=0.29;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:651,63,0:0,0,12,9 chr1 24286300 . C T 491.27 PASS AC=2;AF=0.989;AN=2;DP=669;FractionInformativeReads=1;MQRankSum=-0.113;ReadPosRankSum=-0.453;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:751,63,0:0,0,16,5 chr1 24287227 . C T 160.68 PASS AC=2;AF=1;AN=2;DP=330;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:498,42,0:0,0,11,3 chr1 24287780 . GCTT G 424.79 PASS AC=1;AF=0.662;AN=2;DP=421;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,6:7:38:249,0,38:0,1,3,3 chr1 24289891 . ATGAATG A 1225.53 PASS AC=1;AF=0.639;AN=2;DP=3304;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:72,33:105:99:1169,0,5576:33,39,15,18 chr1 24291597 . G C 5111.05 PASS AC=2;AF=0.989;AN=2;DP=6710;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,128:128:99:4615,383,0:0,0,60,68 chr1 24292140 . G A 11913.1 PASS AC=2;AF=0.989;AN=2;DP=14896;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,335:335:99:10456,1004,0:0,0,163,172 chr1 24292830 . A G 2250.91 PASS AC=2;AF=0.989;AN=2;DP=3331;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,66:66:99:2147,198,0:0,0,27,39 chr1 24292854 . T C 683.43 PASS AC=1;AF=0.681;AN=2;DP=2277;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,23:54:99:566,0,838:13,18,8,15 chr1 24294249 . C T 3760.37 PASS AC=2;AF=0.989;AN=2;DP=5335;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,107:107:99:3049,320,0:0,0,60,47 chr1 24294362 . A T 1547.22 PASS AC=1;AF=0.639;AN=2;DP=3912;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,62:112:99:1462,0,1298:26,24,29,33 chr1 24294450 . CAA CA,CAAA,C 646.13 PASS AC=1,0,0;AF=0.489,0.159,0.057;AN=2;DP=3360;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-filterInvariant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:63:99:18,14,13,18 chr1 24294587 . G A 129.94 PASS AC=1;AF=0.596;AN=2;DP=1083;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant11-variant13-variant17-variant18-variant20-variant23-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,17:35:99:554,0,477:6,12,3,14 chr1 24294627 . C T 253.62 PASS AC=1;AF=0.681;AN=2;DP=896;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,10:17:99:277,0,252:1,6,4,6 chr1 24296853 . G GTTT,GTTTT,GT,GTT,GTTTTT,GTTTTTT 85.54 PASS AC=0,1,1,0,0,0;AF=0.105,0.197,0.289,0.118,0.079,0.013;AN=2;DP=703;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 3/2:15:97:0,2,2,11 chr1 24298263 . T C 499.34 PASS AC=1;AF=0.681;AN=2;DP=940;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,6:15:99:109,0,283:7,2,3,3 chr1 24301685 . C A 356.17 PASS AC=1;AF=0.639;AN=2;DP=1176;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,22:34:99:551,0,262:3,9,9,13 chr1 24301721 . T C 287.99 PASS AC=2;AF=0.989;AN=2;DP=759;FS=0;MQ=60;MQRankSum=0.362;ReadPosRankSum=1.359;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:649,57,0:0,0,5,14 chr1 24305397 . T C 494.21 PASS AC=1;AF=0.596;AN=2;DP=1006;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant11-variant13-variant17-variant18-variant20-variant23-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,25:42:99:587,0,358:8,9,10,15 chr1 24382484 . C A 607.64 PASS AC=1;AF=0.786;AN=2;DP=3296;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,45:88:99:1013,0,1127:29,14,26,19 chr1 24383819 . T C 847.5 PASS AC=1;AF=0.786;AN=2;DP=4113;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:76,46:122:99:1122,0,2150:31,45,22,24 chr1 24388371 . T C 3011.56 PASS AC=2;AF=0.932;AN=2;DP=3846;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,109:109:99:3393,327,0:0,0,71,38 chr1 24389509 . GAA G 240.28 PASS AC=1;AF=0.726;AN=2;DP=836;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,14:22:99:564,0,313:7,1,9,5 chr1 24390731 . C T 684.97 PASS AC=1;AF=0.581;AN=2;DP=1761;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant9-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,28:60:99:845,0,789:12,20,9,19 chr1 24393656 . G A 727.22 PASS AC=1;AF=0.581;AN=2;DP=3419;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant9-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,91:156:99:2147,0,1500:32,33,36,55 chr1 24393729 . G A 427.26 PASS AC=1;AF=0.645;AN=2;DP=1554;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,32:64:99:969,0,897:10,22,6,26 chr1 24393773 . C CCTTT 154.5 PASS AC=1;AF=0.65;AN=2;DP=169;set=variant-variant6-variant14-variant27-variant28-variant30-variant35-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:15,5:20:99:165,0,558:2,13,0,5 chr1 24395003 . T G 398.5 PASS AC=1;AF=0.667;AN=2;DP=367;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,8:10:52:230,0,52:0,2,2,6 chr1 24397473 . G GC 412.02 PASS AC=1;AF=0.542;AN=2;DP=206;MQ=60;set=variant3-variant7-variant8-variant9-variant13-variant16-variant17-variant23-variant32-variant35-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,4:13:99:110,0,298:8,1,3,1 chr1 24400584 . G C 4777.94 PASS AC=2;AF=1;AN=2;DP=6643;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,155:155:99:4600,462,0:0,0,91,64 chr1 24400633 . C G 6102.71 PASS AC=2;AF=1;AN=2;DP=8369;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,196:196:99:5792,586,0:0,0,100,96 chr1 24406535 . G A 2666.39 PASS AC=1;AF=0.538;AN=2;DP=2246;MQ=60;set=variant3-variant7-variant8-variant9-variant13-variant16-variant17-variant22-variant23-variant32-variant35-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:80,87:167:99:2073,0,1865:45,35,48,39 chr1 24406647 . G A 1594.7 PASS AC=1;AF=0.591;AN=2;DP=6402;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant9-variant11-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:108,91:199:99:2040,0,2581:51,57,40,51 chr1 24408015 . C G 927.76 PASS AC=1;AF=0.591;AN=2;DP=2535;set=variant-variant3-variant4-variant6-variant7-variant9-variant11-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,34:79:99:810,0,1023:24,21,14,20 chr1 24408765 . T C 198.06 PASS AC=1;AF=0.591;AN=2;DP=803;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant9-variant11-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,16:26:99:381,0,294:1,9,6,10 chr1 24409191 . C T 1194.45 PASS AC=1;AF=0.581;AN=2;DP=4172;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant9-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,76:135:99:1978,0,1477:31,28,37,39 chr1 24410751 . T C 418.74 PASS AC=1;AF=0.591;AN=2;DP=1182;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant9-variant11-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,20:52:99:446,0,701:16,16,9,11 chr1 24413159 . T C 1221.83 PASS AC=1;AF=0.591;AN=2;DP=4408;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant9-variant11-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,70:134:99:1767,0,1670:42,22,41,29 chr1 24413427 . T G 227.51 PASS AC=1;AF=0.576;AN=2;DP=800;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant9-variant11-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,13:28:99:331,0,536:0,15,6,7 chr1 24416059 . T C 2719.91 PASS AC=2;AF=1;AN=2;DP=3838;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,121:121:99:3601,363,0:0,0,70,51 chr1 24416070 . G C 701.16 PASS AC=1;AF=0.622;AN=2;DP=3625;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:79,51:130:99:1107,0,1996:47,32,28,23 chr1 24418768 . T C 905.93 PASS AC=1;AF=0.661;AN=2;DP=3066;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant9-variant11-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,52:112:99:1226,0,1304:25,35,23,29 chr1 24419496 . A G 1503.9 PASS AC=1;AF=0.682;AN=2;DP=6169;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant9-variant11-variant12-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:106,123:229:99:2997,0,2548:61,45,73,50 chr1 24421334 . G T 775.5 PASS AC=1;AF=0.597;AN=2;DP=2504;MQ=60;set=variant-variant3-variant6-variant7-variant9-variant11-variant12-variant15-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,37:82:99:1015,0,1046:24,21,24,13 chr1 24421474 . G A 1108.67 PASS AC=1;AF=0.656;AN=2;DP=4499;MQ=60;set=variant-variant3-variant6-variant7-variant9-variant11-variant12-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:76,76:152:99:1823,0,1793:36,40,36,40 chr1 24421643 . T C 68.12 PASS AC=1;AF=0.667;AN=2;DP=542;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant9-variant11-variant12-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,8:22:99:233,0,409:4,10,2,6 chr1 24421875 . C T 282.7 PASS AC=1;AF=0.597;AN=2;DP=1190;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant6-variant7-variant9-variant11-variant12-variant15-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,15:38:99:507,0,711:18,5,14,1 chr1 24421950 . C G 966.47 PASS AC=1;AF=0.682;AN=2;DP=3376;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant9-variant11-variant12-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,68:120:99:1614,0,1212:29,23,40,28 chr1 24434595 . T C 1324.17 PASS AC=2;AF=0.694;AN=2;DP=6127;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,182:182:99:5660,545,0:0,0,73,109 chr1 24447116 . C T 1226.77 PASS AC=1;AF=0.63;AN=2;DP=2647;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant25-variant27-variant31-variant32-variant35-variant36-variant37-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,55:105:99:1342,0,1288:27,23,29,26 chr1 24447214 . G A 890.6 PASS AC=2;AF=0.765;AN=2;DP=2890;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant27-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,98:98:99:3156,293,0:0,0,45,53 chr1 24447468 . G C 1721.12 PASS AC=1;AF=0.63;AN=2;DP=3432;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant25-variant27-variant31-variant32-variant35-variant36-variant37-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:89,78:167:99:1693,0,2286:51,38,42,36 chr1 24454902 . C T 404.65 PASS AC=1;AF=0.5;AN=2;DP=313;MQ=60;set=variant5-variant9-variant22-variant27-variant35-variant36-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:25,24:49:99:586,0,657:8,17,8,16 chr1 24460797 . T G 2986.92 PASS AC=1;AF=0.73;AN=2;DP=4244;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,54:119:99:1299,0,1634:28,37,23,31 chr1 24464006 . CT CTT,CTTT,C 121.01 PASS AC=1,0,1;AF=0.375,0.036,0.25;AN=2;DP=627;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant27-variant34-variant35-variant36-filterInvariant37-variant38-variant40-variant43-variant44 GT:DP:GQ:SB 3/1:18:99:0,0,5,13 chr1 24465113 . C T 1292.73 PASS AC=1;AF=0.648;AN=2;DP=2993;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant27-variant31-variant34-variant35-variant36-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,50:104:99:1215,0,1401:26,28,22,28 chr1 24480612 . CA C 667.84 PASS AC=2;AF=0.909;AN=2;DP=1066;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:761,81,0:0,0,20,7 chr1 24480864 . G A 6907.81 PASS AC=1;AF=0.731;AN=2;DP=8215;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:134,113:247:99:2522,0,3391:69,65,55,58 chr1 24480905 . C T 6189.69 PASS AC=1;AF=0.725;AN=2;DP=7348;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:117,96:213:99:2391,0,3171:56,61,45,51 chr1 24481349 . T C 106.77 PASS AC=1;AF=0.815;AN=2;DP=145;FractionInformativeReads=1;set=variant-variant2-variant3-variant5-variant6-variant7-variant10-variant11-variant12-variant14-variant15-variant18-variant19-variant20-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:2,2:4:78:78,0,354:2,0,1,1 chr1 24481351 . T C 141.01 PASS AC=1;AF=0.804;AN=2;DP=152;FractionInformativeReads=1;set=variant-variant2-variant3-variant5-variant6-variant7-variant10-variant11-variant12-variant14-variant15-variant18-variant19-variant20-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:2,2:4:78:78,0,354:2,0,1,1 chr1 24481376 . A C 96.01 PASS AC=1;AF=0.781;AN=2;DP=228;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,2:5:75:75,0,443:3,0,1,1 chr1 24481390 . C T 105.52 PASS AC=1;AF=0.779;AN=2;DP=288;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,2:6:72:72,0,450:4,0,1,1 chr1 24481706 . ATG A 2085.19 PASS AC=2;AF=0.909;AN=2;DP=3531;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:2162,169,0:0,0,33,23 chr1 24481828 . G A 1808.17 PASS AC=1;AF=0.725;AN=2;DP=3238;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,29:68:99:738,0,1047:22,17,10,19 chr1 24481940 . G A 1132.14 PASS AC=2;AF=0.817;AN=2;DP=2115;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1513,147,0:0,0,19,30 chr1 24482004 . G A 783.25 PASS AC=1;AF=0.5;AN=2;DP=373;FractionInformativeReads=1;MQ=60;set=variant5-variant9-variant19-variant22-variant27-variant35-variant36-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:10,21:31:99:669,0,254:4,6,10,11 chr1 24482059 . C T 886.95 PASS AC=1;AF=0.725;AN=2;DP=1487;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,20:48:99:429,0,736:15,13,11,9 chr1 24482474 . G A 1963.17 PASS AC=1;AF=0.579;AN=2;DP=1269;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant8-variant9-variant16-variant19-variant22-variant23-variant24-variant27-variant28-variant33-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,37:79:99:993,0,1122:25,17,22,15 chr1 24482748 . T G 1935.99 PASS AC=2;AF=1;AN=2;DP=3147;FS=0;MQ=60;MQRankSum=-0.279;ReadPosRankSum=0.335;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,83:83:99:2518,249,0:0,0,45,38 chr1 24482992 . C G 1393.01 PASS AC=2;AF=0.881;AN=2;DP=2741;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,101:101:99:3028,302,0:0,0,53,48 chr1 24483455 . G A 1719.73 PASS AC=2;AF=1;AN=2;DP=2686;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,81:81:99:2500,242,0:0,0,45,36 chr1 24483491 . A G 1452.54 PASS AC=2;AF=1;AN=2;DP=2705;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2253,210,0:0,0,39,31 chr1 24484441 . A G 2048.28 PASS AC=2;AF=1;AN=2;DP=3484;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,108:108:99:3147,324,0:0,0,56,52 chr1 24485518 . T C 1309.03 PASS AC=2;AF=1;AN=2;DP=2561;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:1916,174,0:0,0,39,19 chr1 24485813 . T C 1071.74 PASS AC=2;AF=1;AN=2;DP=1731;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.139;ReadPosRankSum=0.346;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1685,138,0:0,0,20,26 chr1 24485941 . T C 2916.41 PASS AC=2;AF=0.829;AN=2;DP=4107;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,125:126:99:3967,332,0:0,1,79,46 chr1 24486216 . GT G,GTTTTTTTTTTTTTGTTTT,GTTTTGTTTTTTTTGTTTT,GTTTT 162.83 PASS AC=1,0,0,0;AF=0.716,0.011,0.102,0.011;AN=2;DP=1234;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-filterInvariant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:16:4:0,2,1,13 chr1 24487760 . T C 1137.31 PASS AC=2;AF=1;AN=2;DP=1459;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1103,105,0:0,0,23,12 chr1 24513613 . C A 132.14 PASS AC=2;AF=0.667;AN=2;DP=82;FractionInformativeReads=1;MQ=60;set=variant6-variant10-variant26-variant32-variant35-variant36 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:463,39,0:0,0,7,6 chr1 24513784 . C T 351.96 PASS AC=1;AF=0.5;AN=2;DP=40;FS=2.795;FractionInformativeReads=1;MQ=60;MQRankSum=0.693;QD=8.8;ReadPosRankSum=0.449;SOR=0.695;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:22,18:40:99:380,0,566:13,9,8,10 chr1 24513924 . AGGG AG,AGG,A 229.11 PASS AC=0,2,0;AF=0.45,0.175,0.175;AN=2;DP=203;MQ=60;set=variant-variant2-variant5-variant6-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant21-variant26-variant30-variant32-variant35-variant36-variant37 GT:DP:GQ:SB 2/2:11:11:0,1,3,7 chr1 24645737 . A C 377.19 PASS AC=1;AF=0.5;AN=2;DP=900;MQ=60;set=variant-variant2-variant4-filterInvariant7-variant10-variant12-variant13-variant14-variant17-variant20-variant22-variant23-variant24-filterInvariant25-filterInvariant27-variant29-variant31-filterInvariant32-variant33-filterInvariant34-filterInvariant35-variant37-filterInvariant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,11:42:64:64,0,1509:10,21,11,0 chr1 24645743 . T C 207.6 PASS AC=1;AF=0.5;AN=2;DP=1004;MQ=60;set=variant-variant5-variant10-variant11-filterInvariant12-variant14-variant16-filterInvariant17-filterInvariant20-variant22-variant23-variant24-variant25-variant27-variant28-variant29-filterInvariant31-variant33-variant35-variant37-variant38-variant40-filterInvariant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,12:42:99:275,0,1171:6,24,12,0 chr1 24645745 . A C 206.67 PASS AC=1;AF=0.5;AN=2;DP=787;MQ=60;set=variant-variant5-filterInvariant12-variant14-variant16-variant17-filterInvariant20-filterInvariant24-filterInvariant25-variant27-variant29-filterInvariant31-variant33-variant34-filterInvariant35-variant37-filterInvariant38-filterInvariant41-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:34,9:43:80:80,0,1517:10,24,9,0 chr1 24649416 . C T 283.54 PASS AC=1;AF=0.5;AN=2;DP=189;MQ=60;set=variant4-variant16-variant20-variant24-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:19,8:27:99:194,0,499:13,6,6,2 chr1 24657860 . A G 653.25 PASS AC=1;AF=0.5;AN=2;DP=1076;MQ=60;set=variant3-variant4-variant16-variant19-variant20-variant24-variant29-variant31-variant34-variant35-variant36-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:29,36:65:99:889,0,940:23,6,24,12 chr1 24658063 . C G 1342.05 PASS AC=1;AF=0.5;AN=2;DP=835;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant16-variant19-variant20-variant24-variant29-variant31-variant35-variant36-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:30,31:61:99:830,0,879:9,21,11,20 chr1 24662903 . G C 888.48 PASS AC=1;AF=0.5;AN=2;DP=416;MQ=60;set=variant4-variant9-variant10-variant13-variant20-variant24-variant30-variant31-variant33-variant34-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:23,18:41:99:571,0,749:18,5,15,3 chr1 24663184 . T C 2939.21 PASS AC=1;AF=0.5;AN=2;DP=735;MQ=60;set=variant7-variant19-variant35 GT:AD:DP:GQ:PL:SB 0/1:141,128:269:99:3231,0,3562:75,66,64,64 chr1 24668667 . C G 2066.06 PASS AC=1;AF=0.55;AN=2;DP=2723;MQ=60;set=variant3-variant4-variant8-variant9-variant10-variant11-variant12-variant15-variant19-variant20-variant23-variant24-variant26-variant28-variant31-variant34-variant35-variant36-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,80:148:99:2010,0,1646:31,37,40,40 chr1 24671418 . A G 708.71 PASS AC=1;AF=0.5;AN=2;DP=147;FractionInformativeReads=1;MQ=60;set=variant7-variant19-variant35 GT:AD:DP:GQ:PL:SB 0/1:17,31:48:99:929,0,473:3,14,7,24 chr1 24927561 . T C 2783.8 PASS AC=1;AF=0.735;AN=2;DP=3925;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:50,66:116:99:1563,0,1107:24,26,32,34 chr1 24927727 . C T 64.47 PASS AC=1;AF=0.643;AN=2;DP=382;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant19-variant20-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,9:15:99:351,0,392:1,5,1,8 chr1 24927731 . G A 34.68 PASS AC=1;AF=0.636;AN=2;DP=367;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant19-variant20-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,8:14:99:318,0,395:1,5,1,7 chr1 24932733 . A G 636.27 PASS AC=1;AF=0.636;AN=2;DP=943;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant14-variant19-variant20-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:24,22:46:99:571,0,812:14,10,11,11 chr1 24932942 . T C 2431.66 PASS AC=1;AF=0.729;AN=2;DP=2546;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:25,32:57:99:798,0,620:9,16,15,17 chr1 24933194 . C T 264.68 PASS AC=1;AF=0.625;AN=2;DP=390;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant14-variant19-variant20-variant26-variant27-variant28-variant30-variant32-variant33-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,11:17:99:241,0,161:2,4,5,6 chr1 24933757 . G A 830.71 PASS AC=1;AF=0.636;AN=2;DP=982;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant14-variant19-variant20-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:20,35:55:99:860,0,434:11,9,19,16 chr1 24933977 . T TA 2547.7 PASS AC=1;AF=0.625;AN=2;DP=2487;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant14-variant19-variant20-variant26-variant27-variant28-variant30-variant32-variant33-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:64,68:132:99:2023,0,1886:30,34,32,36 chr1 24989762 . G T 1344.11 PASS AC=2;AF=0.977;AN=2;DP=2280;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1788,168,0:0,0,21,35 chr1 25098245 . T C 810.95 PASS AC=2;AF=0.744;AN=2;DP=1534;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,31:31:93:1081,93,0:0,0,22,9 chr1 25098335 . CA C 1832.41 PASS AC=1;AF=0.5;AN=2;DP=397;MQ=60;set=variant4-variant22-variant35 GT:AD:DP:GQ:PL:SB 0/1:82,67:149:99:2036,0,2646:53,29,35,32 chr1 25098341 . C T 2107.84 PASS AC=2;AF=0.744;AN=2;DP=5614;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,154:156:99:5697,413,0:2,0,88,66 chr1 25153692 . G A 3006.5 PASS AC=2;AF=0.989;AN=2;DP=5343;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,122:122:99:3489,365,0:0,0,60,62 chr1 25168124 . G C 2181.68 PASS AC=2;AF=0.731;AN=2;DP=4256;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,129:129:99:4248,387,0:0,0,80,49 chr1 25169875 . C A 12039.8 PASS AC=2;AF=0.977;AN=2;DP=15793;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,351:351:99:11218,1054,0:0,0,149,202 chr1 25227519 . G T 88.71 PASS AC=1;AF=0.5;AN=2;DP=6;FS=3.979;FractionInformativeReads=1;MQ=57.15;MQRankSum=0.406;QD=14.78;ReadPosRankSum=-0.988;SOR=2.8;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:99:117,0,106:2,1,0,3 chr1 25234062 . T G 169.45 PASS AC=1;AF=0.611;AN=2;DP=336;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant6-variant7-variant9-variant10-variant12-variant15-variant16-variant17-variant19-variant20-variant23-variant25-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,6:19:99:213,0,412:3,10,0,6 chr1 25254317 . C T 434.65 PASS AC=2;AF=0.705;AN=2;DP=1141;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1534,126,0:0,0,8,34 chr1 25255982 . C T 1853.32 PASS AC=1;AF=0.5;AN=2;DP=291;MQ=60;set=variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:82,76:158:99:1882,0,2082:36,46,28,48 chr1 25256444 . G A 1345.61 PASS AC=2;AF=0.692;AN=2;DP=2778;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,86:86:99:2636,255,0:0,0,28,58 chr1 25291010 . A T 1359.61 PASS AC=1;AF=0.632;AN=2;DP=2526;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,52:79:99:1419,0,573:14,13,33,19 chr1 25558970 . T C 1595.6 PASS AC=1;AF=0.5;AN=2;DP=149;FS=1.299;FractionInformativeReads=0.993;MQ=60;MQRankSum=-0.063;QD=10.71;ReadPosRankSum=-0.117;SOR=0.585;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:80,68:148:99:1624,0,1782:47,33,38,30 chr1 25570081 . T C 952.02 PASS AC=2;AF=0.579;AN=2;DP=1506;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant6-variant10-variant11-variant14-variant16-variant17-variant18-variant19-variant23-variant27-variant29-variant30-variant35-variant36-variant37-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:2,92:94:99:2445,231,0:1,1,48,44 chr1 25570550 . A AT 123.85 PASS AC=2;AF=0.92;AN=2;DP=735;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,24:25:48:607,48,0:1,0,15,9 chr1 25611035 . G C 1660.85 PASS AC=2;AF=0.938;AN=2;DP=6571;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,336:336:99:10214,1006,0:0,0,197,139 chr1 25655728 . GTTTT G,GTTTTTT,GTTTTT 40.36 PASS AC=0,0,1;AF=0.125,0.125,0.375;AN=2;DP=76;set=variant13-variant28-variant35-variant44 GT:DP:GQ:SB 0/3:23:2:1,4,9,9 chr1 25678002 . TA T 83.48 PASS AC=2;AF=0.942;AN=2;DP=734;FS=0;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,22:24:29:501,29,0:2,0,17,5 chr1 25678238 . T A 2114.48 PASS AC=2;AF=1;AN=2;DP=3192;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,74:74:99:2264,222,0:0,0,28,46 chr1 25687901 . T C 2784.52 PASS AC=2;AF=0.667;AN=2;DP=2265;set=variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant37-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,88:88:99:2711,264,0:0,0,43,45 chr1 25780668 . C T 409.24 PASS AC=2;AF=0.677;AN=2;DP=1468;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant37-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1385,120,0:0,0,28,12 chr1 25780889 . A ATG 479.1 PASS AC=2;AF=0.679;AN=2;DP=571;set=variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant35-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,22:23:59:926,59,0:1,0,1,21 chr1 25780893 . A G 488.16 PASS AC=2;AF=0.683;AN=2;DP=544;FractionInformativeReads=1;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,21:22:59:927,59,0:1,0,0,21 chr1 25780929 . ATGTG ATG,A 61.68 PASS AC=0,2;AF=0.333,0.667;AN=2;DP=52;FS=0;MQRankSum=0.736;ReadPosRankSum=0.736;set=variant15-variant16-variant24-variant28-variant32-variant35 GT:DP:GQ:SB 2/2:3:9:0,0,0,3 chr1 25785451 . A G 279.28 PASS AC=2;AF=0.677;AN=2;DP=1316;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant37-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1350,108,0:0,0,7,29 chr1 25825781 . G A 787.32 PASS AC=2;AF=0.677;AN=2;DP=1698;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant37-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:2034,171,0:0,0,21,36 chr1 25825950 . G T 810.97 PASS AC=2;AF=0.682;AN=2;DP=2020;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:4,61:65:68:1547,68,0:2,2,32,29 chr1 25825956 . T C 364.6 PASS AC=2;AF=0.677;AN=2;DP=2088;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant37-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,78:80:99:3111,175,0:1,1,42,36 chr1 25826328 . G A 1996.74 PASS AC=2;AF=0.677;AN=2;DP=5662;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant37-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,186:187:99:5558,550,0:1,0,114,72 chr1 25826502 . A G 3986.17 PASS AC=2;AF=0.677;AN=2;DP=10764;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant37-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,311:311:99:9533,932,0:0,0,165,146 chr1 25870018 . C G 972.02 PASS AC=2;AF=0.966;AN=2;DP=776;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:531,42,0:0,0,11,3 chr1 25880194 . A G 172.61 PASS AC=1;AF=0.5;AN=2;DP=25;FractionInformativeReads=1;MQ=60;set=variant35-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:6,6:12:99:201,0,192:4,2,4,2 chr1 25880261 . CAA C,CA 44.75 PASS AC=0,1;AF=0.2,0.35;AN=2;DP=355;set=variant-variant2-variant5-variant11-variant13-variant14-variant15-variant16-variant19-variant24-variant25-variant26-variant29-variant30-variant33-variant35-variant38-variant41-variant42-variant43 GT:DP:GQ:SB 0/2:27:99:9,4,13,1 chr1 25883780 . G T 1326.62 PASS AC=1;AF=0.5;AN=2;DP=404;MQ=60;set=variant10-variant13-variant34-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:55,31:86:99:967,0,1495:19,36,6,25 chr1 25889342 . CAG C 838.25 PASS AC=2;AF=0.667;AN=2;DP=2793;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant17-variant18-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:3226,217,0:0,0,31,41 chr1 25889422 . C T 622.27 PASS AC=2;AF=0.667;AN=2;DP=2299;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant17-variant18-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:2472,224,0:0,0,37,38 chr1 25889632 . T C 632.25 PASS AC=2;AF=0.667;AN=2;DP=1749;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant17-variant18-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1820,153,0:0,0,19,32 chr1 25889633 . C A 617.73 PASS AC=1;AF=0.5;AN=2;DP=100;FS=0;FractionInformativeReads=1;MQ=60;set=variant10-variant35 GT:AD:DP:GQ:PL:SB 0/1:30,21:51:99:488,0,744:11,19,8,13 chr1 25889672 . G A 306.28 PASS AC=2;AF=0.639;AN=2;DP=1086;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant17-variant18-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,31:31:92:1005,92,0:0,0,8,23 chr1 25890050 . A G 511.51 PASS AC=2;AF=0.681;AN=2;DP=2647;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant17-variant18-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:2778,230,0:0,0,64,13 chr1 25890189 . A G 1597.92 PASS AC=2;AF=0.697;AN=2;DP=9765;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant17-variant18-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,303:303:99:9195,907,0:0,0,165,138 chr1 25893961 . C T 791.48 PASS AC=1;AF=0.5;AN=2;DP=130;MQ=60;set=variant10-variant35 GT:AD:DP:GQ:PL:SB 0/1:29,40:69:99:1066,0,807:13,16,16,24 chr1 25894468 . C CTG 2363.07 PASS AC=2;AF=0.989;AN=2;DP=2864;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,82:82:99:3672,247,0:0,0,33,49 chr1 25895277 . G A 442.93 PASS AC=1;AF=0.5;AN=2;DP=482;FractionInformativeReads=1;MQ=60;set=variant9-variant20-variant26-variant31-variant35-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:32,26:58:99:736,0,804:11,21,7,19 chr1 25944741 . T C 826.72 PASS AC=1;AF=0.5;AN=2;DP=537;MQ=60;set=variant10-variant13-variant34-variant35-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:66,40:106:99:779,0,1601:31,35,21,19 chr1 25944849 . C T 769.75 PASS AC=1;AF=0.5;AN=2;DP=342;FractionInformativeReads=1;MQ=60;set=variant10-variant13-variant34-variant35-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:27,24:51:99:608,0,753:11,16,11,13 chr1 26085048 . AG A 1214.14 PASS AC=2;AF=0.886;AN=2;DP=2798;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,64:64:99:2038,193,0:0,0,47,17 chr1 26089977 . CAAAAAA CAA,CAAAAAAA,CAAAA,CAAA,CA,CAAAAAAAA,C,CAAAAA 346.26 PASS AC=0,1,0,0,0,0,0,0;AF=0.021,0.25,0.042,0.063,0.021,0.042,0.021,0.063;AN=2;DP=829;set=variant-variant2-variant4-variant6-variant8-variant9-variant10-variant12-variant13-variant19-variant20-variant21-variant23-variant24-variant29-variant30-variant31-variant33-variant35-variant36-variant40-variant41-variant42-variant44 GT:DP:GQ:SB 0/2:31:74:10,1,12,8 chr1 26090072 . A G 2651.58 PASS AC=2;AF=0.886;AN=2;DP=4375;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,115:115:99:3577,345,0:0,0,52,63 chr1 26098107 . G A 1547.39 PASS AC=2;AF=0.797;AN=2;DP=2280;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,84:84:99:2581,252,0:0,0,53,31 chr1 26098333 . G A 1034.2 PASS AC=2;AF=0.875;AN=2;DP=2090;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,64:64:99:1940,190,0:0,0,21,43 chr1 26107321 . A C 324.19 PASS AC=2;AF=0.864;AN=2;DP=701;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:522,51,0:0,0,10,7 chr1 26107688 . C A 1416.13 PASS AC=2;AF=0.852;AN=2;DP=3836;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,97:97:99:3171,290,0:0,0,48,49 chr1 26109237 . A G 2457.78 PASS AC=2;AF=0.763;AN=2;DP=3450;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,105:105:99:3248,315,0:0,0,35,70 chr1 26110065 . A G 1723.91 PASS AC=2;AF=0.757;AN=2;DP=2534;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,74:74:99:2413,221,0:0,0,51,23 chr1 26110143 . G A 3728.27 PASS AC=2;AF=0.763;AN=2;DP=5097;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,123:123:99:3732,366,0:0,0,64,59 chr1 26111715 . CTT C,CT 82.86 PASS AC=0,2;AF=0.03,0.833;AN=2;DP=331;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant37-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 2/2:13:39:0,0,3,10 chr1 26111743 . G A 359.75 PASS AC=2;AF=0.855;AN=2;DP=209;set=variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:399,33,0:0,0,2,9 chr1 26112414 . CA CAAA,C,CAA,CAAAA 518.21 PASS AC=0,0,1,0;AF=0.016,0.097,0.435,0.016;AN=2;DP=2485;set=variant3-variant7-variant9-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-filterInvariant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:DP:GQ:SB 0/3:69:99:31,7,20,11 chr1 26127020 . G A 635.57 PASS AC=2;AF=0.86;AN=2;DP=704;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:50:598,50,0:0,0,11,6 chr1 26128307 . C T 636.35 PASS AC=2;AF=0.881;AN=2;DP=710;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:619,51,0:0,0,13,4 chr1 26128484 . CT C,CTT 120.94 PASS AC=1,0;AF=0.48,0.02;AN=2;DP=1325;MQ=60;set=variant2-variant4-variant5-filterInvariant6-filterInvariant8-filterInvariant9-variant10-filterInvariant11-filterInvariant14-filterInvariant15-filterInvariant19-variant22-variant24-variant26-variant27-filterInvariant28-filterInvariant32-variant33-variant35-variant36-filterInvariant37-variant39-variant40-variant43-filterInvariant44 GT:DP:GQ:SB 0/1:38:99:13,12,5,8 chr1 26131654 . G A 582.1 PASS AC=2;AF=0.837;AN=2;DP=1764;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1788,159,0:0,0,36,17 chr1 26135741 . C G 1796.85 PASS AC=2;AF=0.708;AN=2;DP=1922;MQ=60;set=variant3-variant4-variant5-variant9-variant11-variant13-variant16-variant17-variant18-variant19-variant23-variant24-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,93:93:99:3084,279,0:0,0,27,66 chr1 26138136 . C A 2464.28 PASS AC=2;AF=0.833;AN=2;DP=11682;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,311:311:99:9118,928,0:0,0,174,137 chr1 26138262 . T C 4947.17 PASS AC=2;AF=0.869;AN=2;DP=7058;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,205:205:99:6221,616,0:0,0,77,128 chr1 26139055 . AACACACACACACAC AACACAC,AACACACACACACACACACACACACAC,AACACACAC,AACACACACACACACACAC,AACACACACACAC,AACACACACACACACAC,AACACACACACACACACACAC,AACACACACACACACACACACAC,A 340.57 PASS AC=2,0,0,0,0,0,0,0,0;AF=0.383,0.017,0.033,0.1,0.067,0.033,0.167,0.033,0.05;AN=2;DP=303;set=variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43 GT:DP:GQ:SB 1/1:6:18:0,0,4,2 chr1 26139137 . C T 759.64 PASS AC=2;AF=0.821;AN=2;DP=1390;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1308,111,0:0,0,25,12 chr1 26139392 . A G 899.66 PASS AC=2;AF=0.857;AN=2;DP=1594;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1288,123,0:0,0,17,24 chr1 26139444 . G A 248.06 PASS AC=2;AF=0.817;AN=2;DP=764;MQ=60;set=variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:891,78,0:0,0,6,20 chr1 26139879 . C G 510.58 PASS AC=2;AF=0.845;AN=2;DP=800;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:899,75,0:0,0,20,5 chr1 26139919 . C T 973.17 PASS AC=2;AF=0.845;AN=2;DP=1522;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1264,110,0:0,0,26,11 chr1 26140573 . C A 1896.39 PASS AC=2;AF=0.821;AN=2;DP=4988;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,114:116:99:3423,296,0:1,1,52,62 chr1 26142710 . G A 1054.52 PASS AC=1;AF=0.5;AN=2;DP=196;MQ=60;set=variant23-variant35 GT:AD:DP:GQ:PL:SB 0/1:56,53:109:99:1266,0,1505:33,23,31,22 chr1 26143704 . A ATTTTG 591.25 PASS AC=2;AF=0.857;AN=2;DP=1100;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:1203,81,0:0,0,13,14 chr1 26143931 . T C 337.32 PASS AC=2;AF=0.872;AN=2;DP=346;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:279,24,0:0,0,6,2 chr1 26144437 . TC T 941.05 PASS AC=2;AF=0.833;AN=2;DP=2024;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:1436,141,0:0,0,23,24 chr1 26144674 . G A 336.08 PASS AC=2;AF=0.69;AN=2;DP=594;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant9-variant11-variant13-variant16-variant17-variant18-variant19-variant23-variant24-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:937,87,0:0,0,12,17 chr1 26146392 . C G 834.75 PASS AC=2;AF=0.857;AN=2;DP=1338;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:790,78,0:0,0,16,10 chr1 26146449 . C T 513.86 PASS AC=2;AF=0.717;AN=2;DP=1178;MQ=60;set=variant3-variant4-variant5-variant9-variant11-variant13-variant16-variant17-variant18-variant19-variant23-variant24-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1047,109,0:0,0,20,17 chr1 26146539 . A C 2182.45 PASS AC=2;AF=0.845;AN=2;DP=2763;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,67:67:99:2279,201,0:0,0,42,25 chr1 26146884 . C G 4132.53 PASS AC=2;AF=0.845;AN=2;DP=4544;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,132:132:99:4510,396,0:0,0,41,91 chr1 26148011 . G A 1035.48 PASS AC=2;AF=0.845;AN=2;DP=1711;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1299,116,0:0,0,25,14 chr1 26148941 . T C 391.35 PASS AC=2;AF=0.872;AN=2;DP=498;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:377,33,0:0,0,5,6 chr1 26149257 . TC T 139.45 PASS AC=2;AF=0.727;AN=2;DP=317;set=variant3-variant4-variant5-variant9-variant11-variant13-variant16-variant17-variant18-variant19-variant23-variant24-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:482,39,0:0,0,10,3 chr1 26149356 . GCT G 807.4 PASS AC=2;AF=0.845;AN=2;DP=1918;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:2439,165,0:0,0,32,23 chr1 26150023 . C T 2652.05 PASS AC=2;AF=0.833;AN=2;DP=3847;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,105:105:99:3588,314,0:0,0,59,46 chr1 26152666 . T C 2329.75 PASS AC=2;AF=0.845;AN=2;DP=2235;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,57:58:99:1860,164,0:1,0,40,17 chr1 26152758 . A G 5017.82 PASS AC=2;AF=0.845;AN=2;DP=6391;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,163:163:99:5001,488,0:0,0,85,78 chr1 26158900 . A ACT 1379.27 PASS AC=2;AF=0.845;AN=2;DP=1837;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:2353,162,0:0,0,27,26 chr1 26158962 . A G 1255.14 PASS AC=2;AF=0.845;AN=2;DP=2013;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,52:52:99:1656,156,0:0,0,25,27 chr1 26161037 . G C 222.07 PASS AC=2;AF=0.926;AN=2;DP=185;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:82,6,0:0,0,2,0 chr1 26161086 . A G 182.78 PASS AC=2;AF=0.903;AN=2;DP=262;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:249,18,0:0,0,6,0 chr1 26161106 . CAAAA CAA,CAAA,CA,C 287.93 PASS AC=1,0,0,0;AF=0.574,0.093,0.093,0.019;AN=2;DP=339;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant11-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:8:7:1,0,6,1 chr1 26187778 . G C 2575.44 PASS AC=2;AF=0.989;AN=2;DP=3997;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,73:73:99:2207,219,0:0,0,45,28 chr1 26190129 . G T 4766.88 PASS AC=1;AF=0.5;AN=2;DP=252;FS=0.976;FractionInformativeReads=1;MQ=60;MQRankSum=0.304;QD=18.92;ReadPosRankSum=2.626;SOR=0.606;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:127,125:252:99:4795,0,7449:75,52,71,54 chr1 26190130 . C A 4766.88 PASS AC=1;AF=0.5;AN=2;DP=252;FS=1.533;FractionInformativeReads=1;MQ=60;MQRankSum=-1.451;QD=18.92;ReadPosRankSum=2.759;SOR=0.574;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:126,126:252:99:4795,0,7449:74,52,70,56 chr1 26232739 . G C 143.97 PASS AC=1;AF=0.5;AN=2;DP=316;MQ=60;set=variant2-variant7-variant9-variant10-variant11-variant13-variant17-variant18-variant23-variant24-variant26-variant27-variant28-variant31-variant32-variant34-variant35-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,8:24:99:211,0,764:6,10,8,0 chr1 26232742 . CACCAA C 44.5 PASS AC=1;AF=0.5;AN=2;DP=58;FractionInformativeReads=1;MQ=60;set=variant23-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,8:28:99:202,0,899:10,10,8,0 chr1 26286840 . G A 721.08 PASS AC=1;AF=0.614;AN=2;DP=2074;MQ=60;set=variant-variant3-variant4-variant5-variant9-variant11-variant13-variant16-variant17-variant19-variant21-variant24-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,45:100:99:1206,0,1305:25,30,19,26 chr1 26287300 . CT C,CTTT 496.49 PASS AC=2,0;AF=0.838,0.013;AN=2;DP=975;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:DP:GQ:SB 1/1:16:48:0,0,4,12 chr1 26287563 . T C 256.96 PASS AC=2;AF=0.893;AN=2;DP=465;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:504,39,0:0,0,8,5 chr1 26310213 . T C 388.48 PASS AC=1;AF=0.742;AN=2;DP=1228;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:35,15:50:99:341,0,859:19,16,11,4 chr1 26310394 . A G 1793.04 PASS AC=1;AF=0.742;AN=2;DP=3019;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:57,56:113:99:1355,0,1479:32,25,31,25 chr1 26310836 . G T 656.26 PASS AC=1;AF=0.742;AN=2;DP=1295;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:20,26:46:99:660,0,495:12,8,15,11 chr1 26314564 . T C 574.28 PASS AC=2;AF=0.875;AN=2;DP=852;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:775,69,0:0,0,17,6 chr1 26317383 . G A 2416.3 PASS AC=1;AF=0.646;AN=2;DP=2740;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant9-variant11-variant13-variant16-variant17-variant19-variant21-variant22-variant24-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,66:119:99:1799,0,1393:26,27,25,41 chr1 26324520 . T C 200.02 PASS AC=1;AF=0.75;AN=2;DP=657;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,9:21:99:248,0,303:8,4,5,4 chr1 26324582 . T G 251.34 PASS AC=2;AF=1;AN=2;DP=1141;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:794,81,0:0,0,16,11 chr1 26348474 . A G 2956.43 PASS AC=2;AF=0.864;AN=2;DP=4345;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,125:126:99:3635,339,0:1,0,58,67 chr1 26349967 . C T 647.02 PASS AC=2;AF=0.661;AN=2;DP=2636;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,84:84:99:2742,252,0:0,0,28,56 chr1 26357656 . C A 2577.79 PASS AC=2;AF=0.656;AN=2;DP=6765;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,256:257:99:7412,757,0:0,1,123,133 chr1 26357855 . A G 1378.46 PASS AC=2;AF=1;AN=2;DP=2855;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,67:67:99:2146,201,0:0,0,41,26 chr1 26358030 . G A 1674.27 PASS AC=1;AF=0.5;AN=2;DP=131;FS=6.519;FractionInformativeReads=1;MQ=60;MQRankSum=-0.062;QD=12.78;ReadPosRankSum=-1.292;SOR=0.869;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:64,67:131:99:1703,0,1589:29,35,38,29 chr1 26358752 . T TA 2235.08 PASS AC=2;AF=0.864;AN=2;DP=3728;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,93:93:99:3451,295,0:0,0,65,28 chr1 26362194 . T C 1135.36 PASS AC=2;AF=0.647;AN=2;DP=3964;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,179:179:99:5669,535,0:0,0,84,95 chr1 26364249 . C T 441.26 PASS AC=2;AF=0.652;AN=2;DP=1569;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1479,149,0:0,0,28,22 chr1 26364371 . T C 410.54 PASS AC=2;AF=0.65;AN=2;DP=1649;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant18-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:2014,176,0:0,0,34,25 chr1 26365374 . T G 2206.39 PASS AC=2;AF=0.65;AN=2;DP=4905;set=variant2-variant3-variant4-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant18-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,183:183:99:5264,548,0:0,0,94,89 chr1 26365549 . C T 972.83 PASS AC=2;AF=0.652;AN=2;DP=2998;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,82:82:99:2615,245,0:0,0,43,39 chr1 26368787 . C T 49.76 PASS AC=2;AF=0.712;AN=2;DP=198;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant20-variant21-variant22-variant25-variant28-variant29-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:488,36,0:0,0,11,1 chr1 26372144 . A G 850.02 PASS AC=2;AF=0.864;AN=2;DP=2025;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1775,168,0:0,0,37,19 chr1 26372605 . G C 254.91 PASS AC=2;AF=0.872;AN=2;DP=877;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1065,99,0:0,0,12,21 chr1 26377880 . G A 436.85 PASS AC=2;AF=0.617;AN=2;DP=1495;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1236,126,0:0,0,25,17 chr1 26378002 . C T 1344.39 PASS AC=2;AF=0.621;AN=2;DP=2398;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant18-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,88:88:99:2956,263,0:0,0,59,29 chr1 26387625 . A C 365.67 PASS AC=1;AF=0.615;AN=2;DP=1177;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant9-variant10-variant11-variant12-variant13-variant16-variant17-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,31:55:99:760,0,816:19,5,21,10 chr1 26392535 . C T 187.57 PASS AC=1;AF=0.667;AN=2;DP=170;MQ=60;set=variant5-variant9-variant10-variant11-variant12-variant13-variant16-variant17-variant21-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,6:13:99:150,0,161:4,3,4,2 chr1 26438455 . T C 758.65 PASS AC=1;AF=0.615;AN=2;DP=2062;MQ=60;set=variant-variant2-variant3-variant5-variant9-variant10-variant11-variant12-variant13-variant16-variant17-variant18-variant21-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,61:109:99:1407,0,1091:20,28,29,32 chr1 26438498 . G C 358.87 PASS AC=1;AF=0.6;AN=2;DP=1127;MQ=60;set=variant-variant2-variant3-variant5-variant9-variant10-variant11-variant12-variant13-variant16-variant17-variant21-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,47:80:99:1134,0,755:13,20,20,27 chr1 26438933 . T C 353.62 PASS AC=1;AF=0.6;AN=2;DP=667;MQ=60;set=variant-variant2-variant3-variant5-variant9-variant10-variant11-filterInvariant12-variant13-variant16-variant17-variant21-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,6:20:99:166,0,335:7,7,5,1 chr1 26439226 . C T 200.64 PASS AC=1;AF=0.706;AN=2;DP=118;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant9-variant10-variant12-variant13-variant16-variant17-variant18-variant24-variant27-variant29-variant31-variant32-variant33-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:3,4:7:74:138,0,74:1,2,0,4 chr1 26440718 . A T 364.65 PASS AC=1;AF=0.6;AN=2;DP=928;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant9-variant10-variant11-variant12-variant13-variant16-variant17-variant21-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,18:33:99:447,0,445:11,4,13,5 chr1 26448447 . A G 855.76 PASS AC=1;AF=0.6;AN=2;DP=2766;MQ=60;set=variant-variant2-variant3-variant5-variant9-variant10-variant11-variant12-variant13-variant16-variant17-variant21-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,71:136:99:1839,0,1589:34,31,34,37 chr1 26448849 . T C 1584.26 PASS AC=1;AF=0.6;AN=2;DP=2915;set=variant-variant2-variant3-variant5-variant9-variant10-variant11-variant12-variant13-variant16-variant17-variant21-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,65:113:99:1709,0,1228:22,26,30,35 chr1 26449327 . A G 3634.57 PASS AC=1;AF=0.6;AN=2;DP=3908;MQ=60;set=variant-variant2-variant3-variant5-variant9-variant10-variant11-variant12-variant13-variant16-variant17-variant21-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:96,65:161:99:2448,0,5218:45,51,33,32 chr1 26449337 . A G 3667.43 PASS AC=1;AF=0.6;AN=2;DP=4044;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant9-variant10-variant11-variant12-variant13-variant16-variant17-variant21-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:100,69:169:99:2467,0,5233:48,52,35,34 chr1 26449595 . G A 1587.8 PASS AC=1;AF=0.6;AN=2;DP=3433;MQ=60;set=variant-variant2-variant3-variant5-variant9-variant10-variant11-variant12-variant13-variant16-variant17-variant21-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:62,60:122:99:1545,0,1583:25,37,25,35 chr1 26449667 . GT GTT,G 122.97 PASS AC=0,1;AF=0.067,0.433;AN=2;DP=1073;MQ=60;set=filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant8-variant10-filterInvariant11-filterInvariant15-filterInvariant16-filterInvariant21-variant34-filterInvariant35-filterInvariant39-filterInvariant40-filterInvariant43 GT:DP:GQ:SB 0/2:45:99:15,19,5,6 chr1 26450009 . C T 4773.6 PASS AC=1;AF=0.6;AN=2;DP=9028;MQ=60;set=variant-variant2-variant3-variant5-variant9-variant10-variant11-variant12-variant13-variant16-variant17-variant21-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:230,159:389:99:4079,0,5767:117,113,76,83 chr1 26450101 . A G 4423.59 PASS AC=1;AF=0.6;AN=2;DP=7936;MQ=60;set=variant-variant2-variant3-variant5-variant9-variant10-variant11-variant12-variant13-variant16-variant17-variant21-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:140,142:282:99:3707,0,3805:62,78,74,68 chr1 26452024 . C CAA 503.27 PASS AC=1;AF=0.604;AN=2;DP=680;MQ=60;set=variant-variant2-variant3-variant5-variant9-variant10-variant11-variant12-variant13-variant16-variant17-variant21-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant35-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,10:19:99:311,0,287:3,6,4,6 chr1 26488947 . C T 537.72 PASS AC=1;AF=0.577;AN=2;DP=920;MQ=60;set=variant-variant2-variant3-variant5-variant9-variant10-variant12-variant13-variant16-variant17-variant18-variant21-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,19:35:99:458,0,479:5,11,10,9 chr1 26496370 . C T 2103.9 PASS AC=1;AF=0.55;AN=2;DP=2867;MQ=60;set=variant4-variant6-variant7-variant11-variant13-variant14-variant18-variant19-variant20-variant23-variant24-variant26-variant27-variant29-variant30-variant32-variant34-variant35-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:97,86:183:99:2136,0,2536:56,41,47,39 chr1 26496651 . T C 1331.43 PASS AC=1;AF=0.629;AN=2;DP=3554;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,73:129:99:1891,0,1343:21,35,26,47 chr1 26496870 . A G 628.08 PASS AC=1;AF=0.65;AN=2;DP=1769;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,41:77:99:1157,0,881:23,13,30,11 chr1 26497340 . A C 1664.21 PASS AC=1;AF=0.866;AN=2;DP=3441;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,51:85:99:1336,0,825:17,17,25,26 chr1 26497626 . C G 979.02 PASS AC=1;AF=0.629;AN=2;DP=2948;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,51:102:99:1248,0,1278:23,28,28,23 chr1 26498196 . G T 841.76 PASS AC=1;AF=0.633;AN=2;DP=2764;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,64:125:99:1692,0,1560:29,32,28,36 chr1 26498570 . T C 200.36 PASS AC=1;AF=0.633;AN=2;DP=411;MQ=60;set=variant-variant2-variant4-variant5-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,6:12:99:190,0,235:1,5,1,5 chr1 26504036 . G A 1794.29 PASS AC=1;AF=0.583;AN=2;DP=5012;MQ=60;set=variant-variant2-variant3-variant5-variant9-variant10-variant12-variant13-variant16-variant17-variant21-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:117,104:221:99:2389,0,2825:63,54,58,46 chr1 26504196 . C G 522.37 PASS AC=1;AF=0.629;AN=2;DP=1177;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,20:42:99:622,0,783:5,17,3,17 chr1 26514111 . CTTT CTT,CTTTT,C,CTTTTT,CT 162.37 PASS AC=1,0,0,0,0;AF=0.323,0.081,0.048,0.032,0.097;AN=2;DP=1430;set=variant-variant4-variant6-filterInvariant7-variant9-filterInvariant10-variant11-variant12-variant14-variant16-variant17-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant28-variant29-filterInvariant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-filterInvariant43-variant44 GT:DP:GQ:SB 0/1:26:98:2,14,1,9 chr1 26517267 . A G 1099.04 PASS AC=1;AF=0.565;AN=2;DP=2599;set=variant-variant2-variant3-variant5-variant9-variant10-variant12-variant16-variant17-variant21-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,50:111:99:1042,0,1334:28,33,25,25 chr1 26517667 . T C 111.6 PASS AC=1;AF=0.629;AN=2;DP=1333;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant16-variant17-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,35:64:99:890,0,560:16,13,21,14 chr1 26517773 . T C 372.41 PASS AC=1;AF=0.563;AN=2;DP=2179;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant9-variant10-variant12-variant16-variant17-variant21-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,55:123:99:2096,0,3153:35,33,27,28 chr1 26517794 . A G 453.34 PASS AC=1;AF=0.565;AN=2;DP=2259;MQ=60;set=variant-variant2-variant3-variant5-variant9-variant10-variant12-variant16-variant17-variant21-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,56:123:99:2076,0,3132:33,34,29,27 chr1 26517891 . C T 442.65 PASS AC=1;AF=0.565;AN=2;DP=1699;MQ=60;set=variant-variant2-variant3-variant5-variant9-variant10-variant12-variant16-variant17-variant21-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,43:94:99:1024,0,1283:21,30,17,26 chr1 26524401 . A G 238.06 PASS AC=1;AF=0.565;AN=2;DP=841;MQ=60;set=variant-variant2-variant3-variant5-variant9-variant10-variant12-variant16-variant17-variant21-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,20:49:99:626,0,790:16,13,15,5 chr1 26524706 . A G 4831.54 PASS AC=2;AF=0.875;AN=2;DP=6289;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,148:148:99:4805,444,0:0,0,75,73 chr1 26526348 . G C 642.73 PASS AC=1;AF=0.56;AN=2;DP=1115;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant9-variant10-variant12-variant16-variant17-variant19-variant21-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,16:51:99:397,0,931:22,13,12,4 chr1 26526439 . A G 1607.11 PASS AC=1;AF=0.56;AN=2;DP=3261;MQ=60;set=variant-variant2-variant3-variant5-variant9-variant10-variant12-variant16-variant17-variant19-variant21-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:66,53:119:99:1440,0,1759:39,27,37,16 chr1 26526554 . G A 1246.39 PASS AC=1;AF=0.633;AN=2;DP=2362;MQ=60;set=variant5-variant6-variant7-variant10-variant13-variant14-variant18-variant23-variant27-variant29-variant34-variant35-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:80,66:146:99:1630,0,1916:36,44,30,36 chr1 26527304 . T C 694.47 PASS AC=1;AF=0.625;AN=2;DP=371;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant7-variant10-variant13-variant14-variant18-variant23-variant24-variant27-variant29-variant34-variant35-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:16,19:35:99:777,0,1110:14,2,18,1 chr1 26527310 . C G 723.17 PASS AC=1;AF=0.625;AN=2;DP=408;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant7-variant10-variant13-variant14-variant18-variant23-variant24-variant27-variant29-variant34-variant35-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:20,20:40:99:764,0,1197:16,4,19,1 chr1 26527809 . A C 892.97 PASS AC=1;AF=0.632;AN=2;DP=514;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant7-variant10-variant11-variant13-variant14-variant18-variant23-variant24-variant27-variant29-variant33-variant34-variant35-variant36-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:7,12:19:99:483,0,485:7,0,10,2 chr1 26527810 . G A 892.97 PASS AC=1;AF=0.632;AN=2;DP=531;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant7-variant10-variant11-variant13-variant14-variant18-variant23-variant24-variant27-variant29-variant33-variant34-variant35-variant36-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:7,12:19:99:483,0,485:7,0,10,2 chr1 26527951 . G A 2093.01 PASS AC=1;AF=0.611;AN=2;DP=2595;MQ=60;set=variant4-variant6-variant7-variant10-variant13-variant14-variant18-variant23-variant24-variant27-variant29-variant33-variant34-variant35-variant36-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:76,96:172:99:2317,0,1779:44,32,54,42 chr1 26528181 . CTT C,CTTTT,CTTTTT,CTTT,CT,CTTTTTTT,CTTTTTTTT 148.88 PASS AC=1,0,0,0,0,0,0;AF=0.3,0.171,0.014,0.143,0.014,0.014,0.014;AN=2;DP=632;set=variant-variant2-variant3-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:DP:GQ:SB 0/1:22:99:3,12,0,7 chr1 26528922 . C G 1365.54 PASS AC=1;AF=0.619;AN=2;DP=1989;MQ=60;set=variant4-variant6-variant7-variant8-variant10-variant12-variant14-variant16-variant18-variant20-variant23-variant24-variant26-variant29-variant30-variant34-variant35-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:59,67:126:99:1620,0,1361:36,23,39,28 chr1 26560945 . C G 587.59 PASS AC=2;AF=0.919;AN=2;DP=864;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:667,51,0:0,0,1,16 chr1 26560962 . C T 197.71 PASS AC=1;AF=0.533;AN=2;DP=217;FractionInformativeReads=1;MQ=60;set=variant6-variant13-variant14-variant18-variant20-variant22-variant23-variant28-variant29-variant30-variant34-variant35-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:4,7:11:99:279,0,147:0,4,0,7 chr1 26570482 . CAAAAAAAAAAA C,CA,CAA,CAAAAAAAAAAAAA 458.96 PASS AC=1,0,0,0;AF=0.743,0.027,0.014,0.014;AN=2;DP=541;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:14:99:3,1,9,1 chr1 26596080 . G A 604.25 PASS AC=1;AF=0.531;AN=2;DP=922;MQ=60;set=variant6-variant13-variant14-variant18-variant20-variant22-variant23-variant25-variant28-variant29-variant30-variant34-variant35-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:43,25:68:99:505,0,1162:19,24,10,15 chr1 26597189 . G A 49.73 PASS AC=1;AF=0.567;AN=2;DP=119;FractionInformativeReads=1;MQ=60;set=variant6-variant13-variant14-variant18-variant20-variant22-variant25-variant28-variant29-variant30-variant34-variant35-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:5,4:9:99:150,0,202:5,0,4,0 chr1 26597435 . G A 3720.03 PASS AC=2;AF=0.919;AN=2;DP=5917;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,137:137:99:4132,410,0:0,0,77,60 chr1 26597673 . G A 464.72 PASS AC=1;AF=0.667;AN=2;DP=1184;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant13-variant14-variant15-variant18-variant19-variant20-variant22-variant23-variant25-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,14:37:99:337,0,639:9,14,5,9 chr1 26597781 . C T 125.44 PASS AC=1;AF=0.545;AN=2;DP=107;FractionInformativeReads=1;MQ=60;set=variant6-variant18-variant25-variant28-variant29-variant30-variant34-variant35-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:6,4:10:99:109,0,241:0,6,1,3 chr1 26601385 . G A 2357.09 PASS AC=1;AF=0.757;AN=2;DP=2599;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,37:59:99:897,0,578:14,8,20,17 chr1 26601570 . A G 1106.42 PASS AC=1;AF=0.563;AN=2;DP=1013;FractionInformativeReads=1;MQ=60;set=variant6-variant13-variant14-variant18-variant20-variant22-variant23-variant25-variant28-variant29-variant30-variant34-variant35-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:30,38:68:99:1120,0,702:12,18,14,24 chr1 26603883 . G GAA 1569.91 PASS AC=1;AF=0.531;AN=2;DP=1239;MQ=60;set=variant6-variant13-variant14-variant18-variant20-variant22-variant23-variant25-variant28-variant29-variant30-variant34-variant35-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:50,51:101:99:1991,0,2113:26,24,27,24 chr1 26603993 . A C 2305.86 PASS AC=2;AF=0.919;AN=2;DP=3157;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,89:89:99:2654,266,0:0,0,38,51 chr1 26604071 . T G 890.69 PASS AC=1;AF=0.531;AN=2;DP=899;MQ=60;set=variant6-variant13-variant14-variant18-variant20-variant22-variant23-variant25-variant28-variant29-variant30-variant34-variant35-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:27,26:53:99:751,0,704:12,15,14,12 chr1 26605069 . T C 673.14 PASS AC=1;AF=0.531;AN=2;DP=647;FractionInformativeReads=1;set=variant6-variant13-variant14-variant18-variant20-variant22-variant23-variant25-variant28-variant29-variant30-variant34-variant35-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:23,21:44:99:592,0,584:13,10,9,12 chr1 26606029 . G GA 1186.3 PASS AC=1;AF=0.531;AN=2;DP=1346;MQ=60;set=variant6-variant13-variant14-variant18-variant20-variant22-variant23-variant25-variant28-variant29-variant30-variant34-variant35-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:62,37:99:99:932,0,1697:32,30,15,22 chr1 26606174 . A C 1479.42 PASS AC=1;AF=0.531;AN=2;DP=1775;MQ=60;set=variant6-variant13-variant14-variant18-variant20-variant22-variant23-variant25-variant28-variant29-variant30-variant34-variant35-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:49,65:114:99:1631,0,1281:24,25,34,31 chr1 26607726 . T G 1133.46 PASS AC=1;AF=0.531;AN=2;DP=1737;MQ=60;set=variant6-variant13-variant14-variant18-variant20-variant22-variant23-variant25-variant28-variant29-variant30-variant34-variant35-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:54,54:108:99:1562,0,1373:26,28,32,22 chr1 26608761 . C T 1570.61 PASS AC=1;AF=0.5;AN=2;DP=1589;set=variant6-variant13-variant14-variant18-variant20-variant22-variant23-variant25-variant28-variant29-variant30-variant34-variant35-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:74,51:125:99:1379,0,2157:38,36,24,27 chr1 26608811 . TCCAGGACAGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA T 1374.15 PASS AC=1;AF=0.5;AN=2;DP=5812;set=variant-variant2-variant3-variant4-variant5-filterInvariant6-filterInvariant7-filterInvariant8-variant9-variant10-variant12-filterInvariant14-variant15-variant16-variant17-filterInvariant18-variant19-filterInvariant21-variant24-variant26-filterInvariant29-variant31-filterInvariant32-variant33-filterInvariant35-variant36-variant37-variant38-filterInvariant40-filterInvariant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:179,25:204:99:357,0,7198:111,68,7,18 chr1 26608814 . A G 1616 PASS AC=1;AF=0.57;AN=2;DP=4216;set=variant-variant2-filterInvariant3-filterInvariant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,83:108:99:3569,0,623:7,18,52,31 chr1 26608825 . TGGGGCCG T 1848.41 PASS AC=1;AF=0.5;AN=2;DP=4076;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:75,48:123:99:1605,0,2728:35,40,32,16 chr1 26608835 . ACCGGGACCGGGACTGGG A 1849.13 PASS AC=1;AF=0.5;AN=2;DP=4218;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:86,49:135:99:1572,0,3230:44,42,33,16 chr1 26608848 . CTGGGGCCGGG C 2167.02 PASS AC=1;AF=0.531;AN=2;DP=1603;set=variant6-variant13-variant14-variant18-variant20-variant22-variant23-variant25-variant28-variant29-variant30-variant34-variant35-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:76,56:132:99:2096,0,2976:42,34,33,23 chr1 26608859 . ACCGGGACC A 2187.94 PASS AC=1;AF=0.531;AN=2;DP=1652;set=variant6-variant13-variant14-variant18-variant20-variant22-variant23-variant25-variant28-variant29-variant30-variant34-variant35-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:84,56:140:99:2195,0,3369:47,37,33,23 chr1 26608877 . GCCGGGA G 2246.68 PASS AC=1;AF=0.531;AN=2;DP=1812;set=variant6-variant13-variant14-variant18-variant20-variant22-variant23-variant25-variant28-variant29-variant30-variant34-variant35-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:93,66:159:99:2401,0,3573:55,38,40,26 chr1 26609259 . C T 8341.48 PASS AC=1;AF=0.757;AN=2;DP=11310;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:143,222:365:99:5564,0,3398:69,74,113,109 chr1 26609307 . G T 7500.24 PASS AC=2;AF=0.919;AN=2;DP=11153;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,301:303:99:9076,886,0:2,0,135,166 chr1 26610891 . A C 4571.87 PASS AC=2;AF=0.919;AN=2;DP=6580;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,228:228:99:6891,683,0:0,0,111,117 chr1 26612042 . A G 1725.4 PASS AC=2;AF=0.919;AN=2;DP=2265;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1313,135,0:0,0,19,26 chr1 26612297 . C A 1170.35 PASS AC=1;AF=0.5;AN=2;DP=1144;MQ=60;set=variant6-variant13-variant14-variant18-variant20-variant22-variant23-variant25-variant28-variant29-variant30-variant34-variant35-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:50,40:90:99:1037,0,1399:32,18,29,11 chr1 26612460 . G A 1838.98 PASS AC=1;AF=0.531;AN=2;DP=2597;MQ=60;set=variant6-variant13-variant14-variant18-variant20-variant22-variant23-variant25-variant28-variant29-variant30-variant34-variant35-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:107,93:200:99:2126,0,2609:45,62,42,51 chr1 26620846 . C CA 796.1 PASS AC=2;AF=0.919;AN=2;DP=2493;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:2627,204,0:0,0,24,44 chr1 26623641 . C T 510.53 PASS AC=1;AF=0.531;AN=2;DP=523;MQ=60;set=variant6-variant13-variant14-variant18-variant20-variant22-variant23-variant25-variant28-variant29-variant30-variant34-variant35-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:8,21:29:99:633,0,223:3,5,5,16 chr1 26627478 . T C 2730.53 PASS AC=1;AF=0.795;AN=2;DP=8380;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:113,121:234:99:2835,0,2560:57,56,60,61 chr1 26629465 . G C 1703.75 PASS AC=1;AF=0.795;AN=2;DP=2787;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,50:81:99:1248,0,747:12,19,22,28 chr1 26629532 . A G 699.63 PASS AC=1;AF=0.5;AN=2;DP=64;FS=3.469;FractionInformativeReads=1;MQ=60;MQRankSum=-1.211;QD=10.93;ReadPosRankSum=-0.413;SOR=0.354;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:36,28:64:99:728,0,999:14,22,14,14 chr1 26644399 . C T 746.2 PASS AC=1;AF=0.531;AN=2;DP=668;FractionInformativeReads=1;MQ=60;set=variant6-variant13-variant14-variant18-variant20-variant22-variant23-variant25-variant28-variant29-variant30-variant34-variant35-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:20,25:45:99:649,0,645:16,4,17,8 chr1 26644698 . C T 1219.24 PASS AC=1;AF=0.531;AN=2;DP=1915;FractionInformativeReads=1;MQ=60;set=variant6-variant13-variant14-variant18-variant20-variant22-variant23-variant25-variant28-variant29-variant30-variant34-variant35-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:59,85:144:99:2069,0,1435:28,31,39,46 chr1 26646726 . A G 4324.34 PASS AC=1;AF=0.795;AN=2;DP=6308;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:111,88:199:99:3319,0,5056:52,59,44,44 chr1 26646730 . A G 4288.42 PASS AC=1;AF=0.795;AN=2;DP=6240;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:109,88:197:99:3338,0,5075:51,58,43,45 chr1 26648381 . C T 1354.39 PASS AC=1;AF=0.563;AN=2;DP=1185;MQ=60;set=variant6-variant13-variant14-variant18-variant20-variant22-variant23-variant25-variant28-variant29-variant30-variant34-variant35-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:36,40:76:99:1012,0,848:24,12,28,12 chr1 26648551 . G C 5256.84 PASS AC=1;AF=0.803;AN=2;DP=9150;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:122,124:246:99:3037,0,2850:62,60,68,56 chr1 26648838 . G T 658.67 PASS AC=1;AF=0.533;AN=2;DP=667;FractionInformativeReads=1;MQ=60;set=variant13-variant14-variant18-variant20-variant22-variant23-variant25-variant28-variant29-variant30-variant34-variant35-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:27,29:56:99:653,0,857:4,23,11,18 chr1 26650550 . C A 281.52 PASS AC=2;AF=0.705;AN=2;DP=2646;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,87:88:99:2840,253,0:0,1,61,26 chr1 26654937 . G C 1222.36 PASS AC=2;AF=0.845;AN=2;DP=2685;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,89:89:99:2775,267,0:0,0,29,60 chr1 26655208 . C T 189.7 PASS AC=2;AF=0.692;AN=2;DP=1089;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,34:35:95:1168,95,0:1,0,27,7 chr1 26655462 . C T 161.9 PASS AC=2;AF=0.692;AN=2;DP=831;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:505,45,0:0,0,4,11 chr1 26655507 . C A 90.15 PASS AC=2;AF=0.681;AN=2;DP=375;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:17:196,17,0:0,0,0,6 chr1 26662774 . C T 2688.6 PASS AC=2;AF=0.845;AN=2;DP=5165;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,118:118:99:3606,352,0:0,0,63,55 chr1 26663362 . C T 1806.38 PASS AC=2;AF=0.692;AN=2;DP=5850;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,184:184:99:5577,549,0:0,0,92,92 chr1 26664968 . C T 1004.89 PASS AC=2;AF=0.667;AN=2;DP=3819;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,132:134:99:3811,351,0:1,1,64,68 chr1 26671522 . GAAATGAGGCATCA G 2611.52 PASS AC=1;AF=0.628;AN=2;DP=8105;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-filterInvariant22-variant23-variant24-variant25-variant26-filterInvariant27-variant28-variant29-variant30-variant31-filterInvariant32-variant33-variant34-variant35-filterInvariant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,71:84:99:2535,0,103:7,6,41,30 chr1 26671538 . AGCAC A 2388.33 PASS AC=1;AF=0.634;AN=2;DP=8148;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant12-filterInvariant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-filterInvariant22-variant23-variant24-variant25-variant26-filterInvariant27-variant28-variant29-variant30-variant31-filterInvariant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-filterInvariant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,79:91:63:2941,0,63:6,6,43,36 chr1 26671544 . GGGGCCCTTCACGACCTCTTTCCAGGTGGGGAACA G 2283.09 PASS AC=1;AF=0.641;AN=2;DP=8518;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-filterInvariant22-variant23-variant24-variant25-variant26-filterInvariant27-variant28-variant29-variant30-variant31-filterInvariant32-variant33-filterInvariant34-variant35-filterInvariant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,86:98:61:2943,0,61:6,6,49,37 chr1 26694245 . T C 4717.53 PASS AC=1;AF=0.604;AN=2;DP=2714;MQ=60;set=variant4-variant6-variant7-variant11-variant12-variant13-variant14-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant33-variant35-variant36-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:60,86:146:99:3391,0,3083:35,25,36,50 chr1 26694260 . T C 1780.58 PASS AC=1;AF=0.611;AN=2;DP=2048;MQ=60;set=variant4-variant11-variant13-variant18-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant30-variant33-variant35-variant36-variant37-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:52,84:136:99:3344,0,3001:30,22,37,47 chr1 26698884 . T C 1827.5 PASS AC=1;AF=0.611;AN=2;DP=2011;MQ=60;set=variant4-variant11-variant13-variant18-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant30-variant33-variant35-variant36-variant37-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:58,60:118:99:1522,0,1538:33,25,32,28 chr1 26698938 . A G 4492.65 PASS AC=1;AF=0.604;AN=2;DP=3441;MQ=60;set=variant4-variant6-variant7-variant11-variant12-variant13-variant14-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant33-variant35-variant36-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:66,78:144:99:1716,0,1722:34,32,42,36 chr1 26699103 . T C 3517.74 PASS AC=1;AF=0.614;AN=2;DP=2286;set=variant4-variant6-variant7-variant11-variant12-variant13-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant33-variant35-variant36-variant37-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:53,40:93:99:872,0,1432:20,33,15,25 chr1 26699157 . T C 1659.83 PASS AC=1;AF=0.604;AN=2;DP=1175;set=variant4-variant6-variant7-variant11-variant12-variant13-variant14-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant33-variant35-variant36-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:30,15:45:99:368,0,772:9,21,5,10 chr1 26700631 . A G 518.7 PASS AC=1;AF=0.536;AN=2;DP=597;MQ=60;set=variant4-variant11-variant13-variant21-variant22-variant23-variant27-variant28-variant33-variant35-variant36-variant37-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:36,17:53:99:363,0,704:21,15,9,8 chr1 26700795 . T C 815.51 PASS AC=2;AF=1;AN=2;DP=2736;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,64:64:99:1913,192,0:0,0,33,31 chr1 26752992 . T C 1120.14 PASS AC=2;AF=0.83;AN=2;DP=3614;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,110:110:99:3113,329,0:0,0,49,61 chr1 26753942 . T C 173.13 PASS AC=2;AF=0.652;AN=2;DP=489;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,24:25:29:725,29,0:0,1,12,12 chr1 26758748 . G A 714.49 PASS AC=2;AF=0.83;AN=2;DP=1279;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:909,87,0:0,0,19,10 chr1 26769543 . C CTTTTTT 417.36 PASS AC=2;AF=0.854;AN=2;DP=486;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:672,45,0:0,0,3,12 chr1 26796806 . CT C,CTT,CTTT 326.62 PASS AC=1,0,0;AF=0.257,0.108,0.149;AN=2;DP=2100;set=variant2-variant3-filterInvariant4-variant5-variant6-variant7-filterInvariant8-variant9-variant10-variant11-variant12-variant13-filterInvariant14-variant16-variant17-variant19-variant20-variant21-filterInvariant22-variant23-filterInvariant24-filterInvariant25-variant26-variant28-variant30-variant31-variant32-filterInvariant33-filterInvariant34-variant35-variant36-variant38-filterInvariant39-variant40-filterInvariant41-variant42-variant43 GT:DP:GQ:SB 0/1:33:99:9,10,5,9 chr1 26797654 . C T 431.59 PASS AC=2;AF=0.543;AN=2;DP=880;MQ=60;set=variant-variant2-variant4-variant8-variant12-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant31-variant34-variant35-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1299,129,0:0,0,18,25 chr1 26801229 . C A 853.87 PASS AC=2;AF=0.543;AN=2;DP=2180;MQ=60;set=variant-variant2-variant4-variant8-variant12-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant31-variant34-variant35-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,98:98:99:2852,293,0:0,0,38,60 chr1 26856462 . T G 1105.23 PASS AC=2;AF=0.943;AN=2;DP=1542;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1436,138,0:0,0,23,23 chr1 26857954 . T A 420.52 PASS AC=2;AF=0.943;AN=2;DP=684;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:498,45,0:0,0,3,12 chr1 26869610 . G A 1236.93 PASS AC=2;AF=0.756;AN=2;DP=4245;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,107:107:99:3214,321,0:0,0,62,45 chr1 26879792 . T C 329.76 PASS AC=2;AF=0.756;AN=2;DP=742;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:378,33,0:0,0,9,2 chr1 26879920 . T C 1073.75 PASS AC=2;AF=1;AN=2;DP=3067;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:2375,228,0:0,0,45,31 chr1 26881565 . AG A 202.38 PASS AC=2;AF=0.563;AN=2;DP=764;MQ=60;set=variant-variant2-variant4-variant8-variant12-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant31-variant34-variant35-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1274,111,0:0,0,26,11 chr1 26900735 . C G 3020.31 PASS AC=2;AF=0.761;AN=2;DP=5136;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,121:121:99:3671,363,0:0,0,49,72 chr1 26901090 . C T 2008.95 PASS AC=2;AF=0.705;AN=2;DP=2563;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:2201,185,0:0,0,37,25 chr1 27088546 . A T 145.68 PASS AC=1;AF=0.5;AN=2;DP=127;FractionInformativeReads=1;MQ=60;set=variant6-variant19-variant26-variant33-variant35-variant36-variant40 GT:AD:DP:GQ:PL:SB 0/1:17,7:24:99:196,0,530:14,3,6,1 chr1 27094156 . A G 43.71 PASS AC=1;AF=0.538;AN=2;DP=131;FractionInformativeReads=1;MQ=60;set=variant6-variant7-variant19-variant20-variant23-variant26-variant29-variant33-variant34-variant35-variant36-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:99:117,0,115:3,0,3,0 chr1 27097515 . A G 750.1 PASS AC=1;AF=0.5;AN=2;DP=260;FractionInformativeReads=1;MQ=60;set=variant6-variant19-variant26-variant33-variant34-variant35-variant36-variant40 GT:AD:DP:GQ:PL:SB 0/1:13,15:28:99:532,0,460:12,1,13,2 chr1 27107650 . TAA TA,T,TAAAA 499.27 PASS AC=1,0,0;AF=0.431,0.056,0.014;AN=2;DP=2808;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:67:99:16,9,29,13 chr1 27114479 . A C 310.48 PASS AC=1;AF=0.5;AN=2;DP=285;FractionInformativeReads=1;MQ=60;set=variant6-variant19-variant33-variant34-variant35-variant36-variant40 GT:AD:DP:GQ:PL:SB 0/1:28,16:44:99:334,0,693:16,12,11,5 chr1 27153703 . A G 554.21 PASS AC=1;AF=0.5;AN=2;DP=199;FractionInformativeReads=1;MQ=60;set=variant6-variant19-variant26-variant33-variant34-variant35-variant36-variant40 GT:AD:DP:GQ:PL:SB 0/1:7,18:25:99:517,0,234:0,7,5,13 chr1 27158844 . G T 166.45 PASS AC=1;AF=0.538;AN=2;DP=327;MQ=60;set=variant6-variant7-variant19-variant20-variant23-variant26-variant29-variant33-variant34-variant35-variant36-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:15,22:37:99:518,0,386:10,5,16,6 chr1 27174976 . C G 263.85 PASS AC=1;AF=0.5;AN=2;DP=159;FractionInformativeReads=1;MQ=60;set=variant6-variant19-variant26-variant33-variant34-variant35-variant36-variant40 GT:AD:DP:GQ:PL:SB 0/1:9,16:25:99:544,0,320:9,0,15,1 chr1 27180829 . A C 1174.44 PASS AC=1;AF=0.638;AN=2;DP=1568;MQ=60;set=variant3-variant6-variant7-variant8-variant11-variant13-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,26:56:99:555,0,790:11,19,13,13 chr1 27182261 . A G 130.62 PASS AC=1;AF=0.545;AN=2;DP=98;FractionInformativeReads=1;MQ=60;set=variant6-variant19-variant23-variant26-variant29-variant33-variant34-variant35-variant36-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:6,8:14:99:234,0,134:2,4,3,5 chr1 27190821 . GGTGTGTGTGT GGTGTGTGT,GGTGTGT,G,GGTGTGTGTGTGT,GGTGTGTGTGTGTGTGTGTGTGTGT,GGTGTGTGTGTGTGT,GGTGTGTGTGTGTGTGT,GGTGTGTGTGTGTGTGTGT,GGTGT 1301.51 PASS AC=0,0,0,1,0,0,0,0,0;AF=0.063,0.25,0.013,0.2,0.013,0.063,0.013,0.025,0.025;AN=2;DP=2542;set=variant3-filterInvariant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-filterInvariant31-variant32-variant33-variant34-variant35-filterInvariant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/4:40:99:11,16,7,6 chr1 27190855 . T C 595.04 PASS AC=1;AF=0.5;AN=2;DP=185;MQ=60;set=variant25-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:26,28:54:99:693,0,799:12,14,15,13 chr1 27210721 . T C 3406.38 PASS AC=1;AF=0.795;AN=2;DP=4056;MQ=60;set=variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:76,47:123:99:1009,0,1978:39,37,27,20 chr1 27215378 . A T 1112.27 PASS AC=1;AF=0.5;AN=2;DP=77;FS=0.949;FractionInformativeReads=1;MQ=60;MQRankSum=0.821;QD=14.45;ReadPosRankSum=0.627;SOR=0.941;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:37,40:77:99:1141,0,917:25,12,29,11 chr1 27220625 . T C 461.45 PASS AC=1;AF=0.5;AN=2;DP=298;FractionInformativeReads=1;MQ=60;set=variant6-variant26-variant33-variant34-variant35-variant36-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:17,14:31:99:381,0,374:11,6,9,5 chr1 27238150 . A G 1278.77 PASS AC=2;AF=0.8;AN=2;DP=2720;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:2238,216,0:0,0,38,34 chr1 27238235 . G C 591.08 PASS AC=1;AF=0.5;AN=2;DP=514;MQ=60;set=variant6-variant26-variant33-variant34-variant35-variant36-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:31,46:77:99:1359,0,735:18,13,25,21 chr1 27238689 . C T 914.75 PASS AC=1;AF=0.5;AN=2;DP=284;MQ=60;set=variant6-variant26-variant33-variant34-variant35-variant36-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:8,26:34:99:728,0,166:3,5,11,15 chr1 27248273 . C A 1499.61 PASS AC=1;AF=0.5;AN=2;DP=798;MQ=60;set=variant6-variant26-variant33-variant34-variant35-variant36-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:51,66:117:99:1683,0,1460:34,17,38,28 chr1 27248645 . A G 238.64 PASS AC=1;AF=0.536;AN=2;DP=221;FractionInformativeReads=1;MQ=60;set=variant6-variant7-variant20-variant23-variant26-variant29-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:10,12:22:99:441,0,346:1,9,1,11 chr1 27277725 . G A 263.69 PASS AC=1;AF=0.5;AN=2;DP=35;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.017;QD=7.53;ReadPosRankSum=-0.295;SOR=0.665;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:23,12:35:99:292,0,763:17,6,9,3 chr1 27320356 . T C 1808.25 PASS AC=2;AF=1;AN=2;DP=3028;FS=0;MQ=60;MQRankSum=0.544;ReadPosRankSum=1.336;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:2417,230,0:0,0,40,37 chr1 27426219 . A G 717.44 PASS AC=1;AF=0.571;AN=2;DP=1348;MQ=60;set=variant4-variant6-variant8-variant9-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant32-variant34-variant35-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:48,27:75:99:547,0,1270:27,21,14,13 chr1 27426796 . T C 3762.4 PASS AC=2;AF=0.989;AN=2;DP=6150;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,134:134:99:4048,402,0:0,0,68,66 chr1 27427041 . T C 2085.08 PASS AC=2;AF=0.989;AN=2;DP=6458;MQ=60;MQRankSum=-0.886;ReadPosRankSum=1.358;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,169:169:99:5204,507,0:0,0,72,97 chr1 27428321 . T C 1356.95 PASS AC=1;AF=0.571;AN=2;DP=2037;MQ=60;set=variant4-variant6-variant8-variant9-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant32-variant34-variant35-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:65,59:124:99:1614,0,1449:32,33,26,33 chr1 27435976 . C G 1099.63 PASS AC=1;AF=0.571;AN=2;DP=1225;MQ=60;set=variant4-variant6-variant8-variant9-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant32-variant34-variant35-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:38,45:83:99:1108,0,831:22,16,29,16 chr1 27480757 . A G 1317.27 PASS AC=1;AF=0.545;AN=2;DP=2397;MQ=60;set=variant4-variant8-variant9-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant32-variant33-variant34-variant35-variant36-variant38 GT:AD:DP:GQ:PL:SB 0/1:66,70:136:99:1819,0,1642:33,33,36,34 chr1 27561359 . T C 859.65 PASS AC=2;AF=0.989;AN=2;DP=1243;FractionInformativeReads=1;MQ=60;MQRankSum=-0.411;ReadPosRankSum=3.388;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:874,81,0:0,0,15,12 chr1 27609980 . T G 2588.78 PASS AC=2;AF=0.989;AN=2;DP=5532;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,105:105:99:3006,314,0:0,0,51,54 chr1 27610069 . C T 2268.43 PASS AC=2;AF=0.802;AN=2;DP=3091;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:2362,213,0:0,0,29,42 chr1 27679692 . A G 1885.48 PASS AC=1;AF=0.732;AN=2;DP=2464;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,27:50:99:784,0,571:16,7,20,7 chr1 27679797 . A G 5478.71 PASS AC=1;AF=0.732;AN=2;DP=8804;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:95,122:217:99:2968,0,2171:52,43,72,50 chr1 27680292 . A G 1753.76 PASS AC=1;AF=0.775;AN=2;DP=3691;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,49:116:99:996,0,1648:37,30,26,23 chr1 27682440 . T TG 868.77 PASS AC=1;AF=0.607;AN=2;DP=2631;set=variant-variant2-variant3-variant5-variant6-variant8-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant24-variant25-variant27-variant29-variant30-variant31-variant34-variant35-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,43:93:99:1467,0,1724:22,28,22,21 chr1 27682481 . G A 620.47 PASS AC=1;AF=0.587;AN=2;DP=2295;set=variant-variant3-variant5-variant6-variant8-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant21-variant24-variant27-variant29-variant30-variant31-variant35-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,52:105:99:1351,0,1316:24,29,22,30 chr1 27684396 . G A 524.46 PASS AC=1;AF=0.536;AN=2;DP=451;MQ=60;set=variant3-variant4-variant5-variant7-variant12-variant13-variant23-variant26-variant29-variant32-variant33-variant35-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:19,22:41:99:693,0,606:5,14,6,16 chr1 27685108 . G A 1727.12 PASS AC=1;AF=0.5;AN=2;DP=571;MQ=60;set=variant7-variant13-variant29-variant35 GT:AD:DP:GQ:PL:SB 0/1:80,71:151:99:1727,0,1935:38,42,36,35 chr1 27686063 . G C 3024.46 PASS AC=2;AF=0.977;AN=2;DP=4652;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,101:101:99:3323,303,0:0,0,44,57 chr1 27687466 . G T 1292.5 PASS AC=1;AF=0.523;AN=2;DP=1974;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant6-variant8-variant11-variant13-variant14-variant15-variant17-variant18-variant21-variant24-variant27-variant29-variant30-variant31-variant35-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,67:111:99:1730,0,1068:19,25,27,40 chr1 27689763 . C T 465.36 PASS AC=1;AF=0.543;AN=2;DP=876;MQ=60;set=variant-variant3-variant5-variant6-variant8-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant21-variant24-variant27-variant29-variant30-variant31-variant35-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,33:50:99:1070,0,433:9,8,24,9 chr1 27690359 . T C 368.95 PASS AC=1;AF=0.56;AN=2;DP=1302;MQ=60;set=variant-variant3-variant5-variant6-variant8-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant24-variant27-variant29-variant30-variant31-variant34-variant35-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,23:46:99:498,0,578:13,10,15,8 chr1 27690644 . A G 1562.28 PASS AC=1;AF=0.611;AN=2;DP=3983;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant24-variant27-variant29-variant30-variant31-variant34-variant35-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:83,81:164:99:1974,0,2273:37,46,44,37 chr1 27696011 . C T 2709.81 PASS AC=2;AF=1;AN=2;DP=3693;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,124:124:99:4296,372,0:0,0,28,96 chr1 27696837 . G T 98.73 PASS AC=1;AF=0.55;AN=2;DP=339;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant8-variant10-variant11-variant13-variant15-variant17-variant18-variant21-variant24-variant27-variant29-variant30-variant35-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,13:22:99:316,0,244:7,2,6,7 chr1 27755511 . CTT C,CT 1246.27 PASS AC=0,1;AF=0.045,0.455;AN=2;DP=10847;set=Intersection GT:DP:GQ:SB 0/2:169:99:31,51,30,57 chr1 27860770 . T G 1183.95 PASS AC=1;AF=0.583;AN=2;DP=285;set=variant2-variant4-variant9-variant10-variant19-variant35 GT:AD:DP:GQ:PL:SB 0/1:27,14:41:99:326,0,1011:16,11,7,7 chr1 27860771 . TG T 920.16 PASS AC=1;AF=0.583;AN=2;DP=291;set=variant2-variant4-variant9-variant10-variant19-variant35 GT:AD:DP:GQ:PL:SB 0/1:27,14:41:99:326,0,1011:16,11,7,7 chr1 27860907 . G GA 1099.65 PASS AC=1;AF=0.5;AN=2;DP=145;FS=4.179;FractionInformativeReads=0.945;MQ=60;MQRankSum=-1.148;QD=7.58;ReadPosRankSum=-1.359;SOR=1.065;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:82,55:137:99:1137,0,1939:44,38,34,21 chr1 27875824 . C T 8603.46 PASS AC=2;AF=1;AN=2;DP=12884;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,276:276:99:8414,825,0:0,0,144,132 chr1 27876482 . C A 2158.5 PASS AC=2;AF=0.743;AN=2;DP=6213;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,182:182:99:5535,544,0:0,0,81,101 chr1 27877418 . G A 11131.7 PASS AC=1;AF=0.583;AN=2;DP=2150;MQ=60;set=variant2-variant4-variant9-variant10-variant19-variant35 GT:AD:DP:GQ:PL:SB 0/1:161,188:349:99:4910,0,4036:79,82,104,84 chr1 27878162 . C T 8991.47 PASS AC=1;AF=0.583;AN=2;DP=1947;MQ=60;set=variant2-variant4-variant9-variant10-variant19-variant35 GT:AD:DP:GQ:PL:SB 0/1:186,169:355:99:3849,0,5019:106,80,93,76 chr1 27944000 . T A 1371.95 PASS AC=2;AF=0.898;AN=2;DP=2144;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1524,132,0:0,0,12,32 chr1 27992800 . CA CAAAAA,CAAA,CAA,CAAAA,C 476.74 PASS AC=0,1,0,0,0;AF=0.041,0.324,0.108,0.095,0.014;AN=2;DP=811;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43 GT:DP:GQ:SB 0/2:8:20:2,0,5,1 chr1 27995077 . G T 1730.33 PASS AC=2;AF=0.92;AN=2;DP=3689;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,74:74:99:2270,220,0:0,0,30,44 chr1 28086955 . C A 2117.16 PASS AC=1;AF=0.93;AN=2;DP=2867;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,34:74:99:782,0,1031:24,16,21,13 chr1 28087457 . GTTT GTT,GT,G,GTTTT 35.19 PASS AC=0,0,0,1;AF=0.35,0.05,0.05,0.1;AN=2;DP=99;MQ=60;set=variant2-variant5-variant15-variant20-variant22-variant23-variant29-variant35-variant42-variant43 GT:DP:GQ:SB 0/4:11:46:3,2,3,3 chr1 28087772 . GA G 6782.42 PASS AC=2;AF=0.966;AN=2;DP=8450;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,189:189:99:5645,568,0:0,0,108,81 chr1 28177859 . C T 3707.12 PASS AC=1;AF=0.5;AN=2;DP=275;FS=0.441;FractionInformativeReads=1;MQ=60;MQRankSum=1.299;QD=13.48;ReadPosRankSum=1.296;SOR=0.744;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:130,145:275:99:3735,0,3363:59,71,64,81 chr1 28206588 . T C 1105.36 PASS AC=1;AF=0.589;AN=2;DP=3630;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant30-variant32-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:80,62:142:99:1525,0,2111:24,56,21,41 chr1 28209305 . A G 682.54 PASS AC=1;AF=0.675;AN=2;DP=3972;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,44:101:99:1066,0,1422:30,27,28,16 chr1 28209362 . T C 837.94 PASS AC=1;AF=0.675;AN=2;DP=4190;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,58:117:99:2255,0,2930:28,31,29,29 chr1 28209366 . A G 837.94 PASS AC=1;AF=0.675;AN=2;DP=4186;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,59:120:99:2242,0,2976:30,31,30,29 chr1 28211650 . T C 603.72 PASS AC=1;AF=0.571;AN=2;DP=813;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant34-variant35-variant36-variant37-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:22,17:39:99:450,0,607:17,5,11,6 chr1 28212272 . G A 473.97 PASS AC=1;AF=0.571;AN=2;DP=1286;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:27,18:45:99:588,0,623:16,11,15,3 chr1 28212975 . C T 904.07 PASS AC=1;AF=0.574;AN=2;DP=1642;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant34-variant35-variant36-variant37-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:39,21:60:99:518,0,1141:23,16,12,9 chr1 28213032 . AG A 1769.3 PASS AC=1;AF=0.571;AN=2;DP=2651;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:51,40:91:99:1205,0,1629:27,24,21,19 chr1 28213157 . T C 1404.2 PASS AC=1;AF=0.574;AN=2;DP=3361;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant34-variant35-variant36-variant37-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:62,64:126:99:1460,0,1403:27,35,29,35 chr1 28213213 . A G 950.48 PASS AC=1;AF=0.574;AN=2;DP=1888;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant34-variant35-variant36-variant37-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:30,37:67:99:898,0,813:10,20,13,24 chr1 28218100 . T C 1984.12 PASS AC=1;AF=0.571;AN=2;DP=4704;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant34-variant35-variant36-variant37-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:91,96:187:99:2196,0,2087:50,41,53,43 chr1 28220484 . C A 898.82 PASS AC=1;AF=0.526;AN=2;DP=1387;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant12-variant13-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant35-variant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:45,23:68:99:576,0,1186:24,21,12,11 chr1 28223981 . TAA TA,T 163.71 PASS AC=1,0;AF=0.54,0.04;AN=2;DP=350;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant11-variant13-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43 GT:DP:GQ:SB 0/1:23:99:7,3,9,4 chr1 28224312 . C T 457.98 PASS AC=1;AF=0.571;AN=2;DP=537;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,9:18:99:252,0,298:1,8,2,7 chr1 28268573 . C T 566.33 PASS AC=1;AF=0.756;AN=2;DP=1255;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,8:25:99:159,0,493:10,7,6,2 chr1 28268829 . T TC 713.2 PASS AC=1;AF=0.526;AN=2;DP=1098;MQ=60;set=variant-variant3-variant4-variant11-variant15-variant16-variant17-variant19-variant20-variant22-variant24-variant27-variant31-variant32-variant35-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,39:79:99:1495,0,2095:19,21,16,23 chr1 28268835 . A C 722.29 PASS AC=1;AF=0.756;AN=2;DP=2116;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,38:78:99:1495,0,2095:19,21,16,22 chr1 28280012 . G C 308.96 PASS AC=1;AF=0.528;AN=2;DP=436;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant11-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant27-variant31-variant32-variant35-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,15:31:99:434,0,504:5,11,4,11 chr1 28282292 . T C 1712.75 PASS AC=1;AF=0.583;AN=2;DP=2517;MQ=60;set=variant2-variant4-variant5-variant9-variant11-variant13-variant14-variant20-variant21-variant23-variant25-variant26-variant28-variant35-variant36-variant37-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:85,76:161:99:1772,0,1982:50,35,43,33 chr1 28282819 . T C 2643.43 PASS AC=2;AF=0.955;AN=2;DP=5526;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,131:131:99:4009,393,0:0,0,61,70 chr1 28285534 . T C 4698.08 PASS AC=2;AF=0.955;AN=2;DP=8355;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,218:218:99:6870,653,0:0,0,130,88 chr1 28285632 . A T 8723.34 PASS AC=2;AF=0.955;AN=2;DP=14084;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,332:332:99:9958,994,0:0,0,156,176 chr1 28290231 . C G 1293.23 PASS AC=2;AF=0.943;AN=2;DP=2323;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1473,149,0:0,0,19,31 chr1 28300079 . T A 608.24 PASS AC=1;AF=0.633;AN=2;DP=1285;MQ=60;set=variant3-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant21-variant23-variant25-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,13:30:99:312,0,438:9,8,6,7 chr1 28305197 . G A 92.22 PASS AC=1;AF=0.5;AN=2;DP=43;FractionInformativeReads=1;MQ=60;set=variant16-variant18-variant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:3,2:5:62:62,0,76:1,2,0,2 chr1 28323718 . TG T 274.95 PASS AC=1;AF=0.526;AN=2;DP=514;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant8-variant9-variant11-variant13-variant14-variant20-variant21-variant24-variant25-variant26-variant28-variant35-variant36-variant37-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:16,14:30:99:474,0,555:13,3,10,4 chr1 28369279 . G A 1049.83 PASS AC=1;AF=0.694;AN=2;DP=787;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,10:22:99:303,0,474:1,11,2,8 chr1 28422847 . C T 5050.94 PASS AC=1;AF=0.694;AN=2;DP=6538;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:110,99:209:99:2465,0,2830:59,51,55,44 chr1 28422967 . C CT 1525.75 PASS AC=1;AF=0.531;AN=2;DP=2799;set=variant2-variant4-variant5-variant8-variant9-variant11-variant14-variant20-variant21-variant24-variant26-variant35-variant36-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:86,90:176:99:1874,0,1854:32,54,33,57 chr1 28520161 . C T 177.99 PASS AC=1;AF=0.611;AN=2;DP=469;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant7-variant8-variant9-variant10-variant13-variant15-variant16-variant20-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,4:10:99:147,0,174:3,3,4,0 chr1 28527011 . A G 830.33 PASS AC=1;AF=0.607;AN=2;DP=2416;MQ=60;set=variant-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant15-variant16-variant20-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,36:77:99:783,0,981:21,20,18,18 chr1 28527888 . A T 757.65 PASS AC=1;AF=0.5;AN=2;DP=252;MQ=60;set=variant3-variant9-variant19-variant22-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:22,20:42:99:414,0,574:11,11,10,10 chr1 28536707 . T C 384.87 PASS AC=1;AF=0.5;AN=2;DP=313;MQ=60;set=variant6-variant9-variant15-variant16-variant25-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:32,14:46:99:272,0,831:11,21,4,10 chr1 28537245 . C T 863.16 PASS AC=1;AF=0.5;AN=2;DP=673;FractionInformativeReads=1;MQ=60;set=variant6-variant9-variant15-variant16-variant25-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:38,45:83:99:1096,0,876:14,24,16,29 chr1 28555426 . G A 160.39 PASS AC=1;AF=0.636;AN=2;DP=251;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant8-variant10-variant13-variant15-variant16-variant20-variant23-variant26-variant27-variant28-variant31-variant32-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,8:12:99:306,0,129:4,0,8,0 chr1 28563759 . G A 725.94 PASS AC=1;AF=0.5;AN=2;DP=585;FractionInformativeReads=1;MQ=60;set=variant6-variant9-variant15-variant16-variant25-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:37,37:74:99:982,0,966:18,19,17,20 chr1 28564252 . A G 978.19 PASS AC=1;AF=0.607;AN=2;DP=2109;MQ=60;set=variant-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant15-variant16-variant20-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,56:106:99:1397,0,1145:26,24,34,22 chr1 28564654 . A C 1115.26 PASS AC=1;AF=0.5;AN=2;DP=619;MQ=60;set=variant6-variant9-variant15-variant16-variant25-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:36,53:89:99:1533,0,989:10,26,14,39 chr1 28573423 . C CGATT 81.87 PASS AC=1;AF=0.5;AN=2;DP=177;MQ=60;set=variant6-variant9-variant15-variant16-variant25-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,4:9:99:152,0,241:0,5,1,3 chr1 28608721 . G A 859.44 PASS AC=1;AF=0.5;AN=2;DP=467;MQ=60;set=variant4-variant6-variant8-variant9-variant16-variant25-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:30,30:60:99:797,0,925:11,19,10,20 chr1 28696091 . C A 456.51 PASS AC=2;AF=0.565;AN=2;DP=1080;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant11-variant13-variant15-variant16-variant20-variant22-variant24-variant25-variant29-variant30-variant31-variant35-variant37-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:1738,179,0:0,0,38,22 chr1 28696392 . C G 2552.91 PASS AC=2;AF=0.565;AN=2;DP=5796;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant11-variant13-variant15-variant16-variant20-variant22-variant24-variant25-variant29-variant30-variant31-variant35-variant37-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,258:258:99:7654,772,0:0,0,112,146 chr1 28733775 . A AG 188.38 PASS AC=2;AF=0.591;AN=2;DP=103;FS=0;MQ=60;set=variant-variant6-variant8-variant9-variant11-variant16-variant25-variant29-variant30-variant35-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:223,18,0:0,0,6,0 chr1 28733993 . G T 2106.9 PASS AC=2;AF=0.565;AN=2;DP=2667;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant11-variant13-variant15-variant16-variant20-variant22-variant24-variant25-variant29-variant30-variant31-variant35-variant37-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,108:108:99:3014,322,0:0,0,48,60 chr1 28764551 . C CA 90.28 PASS AC=2;AF=0.615;AN=2;DP=120;FS=0;FractionInformativeReads=1;set=variant4-variant6-variant9-variant13-variant15-variant16-variant22-variant24-variant25-variant31-variant35-variant40-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:590,45,0:0,0,12,3 chr1 28800380 . C A 1056.08 PASS AC=2;AF=0.55;AN=2;DP=2324;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant11-variant16-variant20-variant22-variant24-variant25-variant29-variant30-variant31-variant35-variant37-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,133:133:99:4340,398,0:0,0,54,79 chr1 28817597 . A G 574.99 PASS AC=2;AF=0.565;AN=2;DP=1438;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant11-variant13-variant15-variant16-variant20-variant22-variant24-variant25-variant29-variant30-variant31-variant35-variant37-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:2004,203,0:0,0,25,43 chr1 28823671 . T C 1118.82 PASS AC=2;AF=0.55;AN=2;DP=2073;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant11-variant16-variant20-variant22-variant24-variant25-variant29-variant30-variant31-variant35-variant37-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,100:100:99:3102,300,0:0,0,42,58 chr1 28826587 . G A 4230.01 PASS AC=2;AF=0.565;AN=2;DP=4026;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant11-variant13-variant15-variant16-variant20-variant22-variant24-variant25-variant29-variant30-variant31-variant35-variant37-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,222:223:99:6886,619,0:1,0,105,117 chr1 28834112 . CTTTTT CTT,CTTT,C,CT 61.28 PASS AC=0,0,0,1;AF=0.136,0.364,0.091,0.091;AN=2;DP=112;FS=0;MQ=60;set=variant3-variant6-variant8-variant9-variant13-variant14-variant15-variant19-variant24-variant30-variant35 GT:DP:GQ:SB 0/4:5:53:1,1,0,3 chr1 28843318 . A G 1183.89 PASS AC=1;AF=0.5;AN=2;DP=1275;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant6-variant8-variant9-variant16-variant24-variant25-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:71,57:128:99:1251,0,1583:35,36,24,33 chr1 28844612 . TGGCCAAGGGCTCCCCCAGCCC T,TGGCCAAGGGCTCCCCCAGCCCGGCCAAGGGCTCCCCCAGCCC 1169.66 PASS AC=0,1;AF=0.143,0.357;AN=2;DP=235;MQ=60;set=variant3-variant4-variant6-variant9-variant16-variant21-variant35 GT:DP:GQ:SB 0/2:19:99:5,6,7,1 chr1 28856677 . A C 136.72 PASS AC=1;AF=0.556;AN=2;DP=45;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant8-variant16-variant22-variant25-variant30-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:3,2:5:75:75,0,512:3,0,1,1 chr1 28856679 . A C 136.82 PASS AC=1;AF=0.556;AN=2;DP=45;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant8-variant16-variant22-variant25-variant30-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:3,2:5:75:75,0,512:3,0,1,1 chr1 28861636 . G A 727.96 PASS AC=1;AF=0.545;AN=2;DP=2796;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant11-variant13-variant16-variant22-variant24-variant25-variant29-variant30-variant31-variant32-variant35-variant37-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:70,75:145:99:1978,0,1975:37,33,44,31 chr1 28863075 . A G 556.91 PASS AC=1;AF=0.545;AN=2;DP=1078;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant11-variant13-variant16-variant22-variant24-variant25-variant29-variant30-variant31-variant32-variant35-variant37-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:32,20:52:99:518,0,784:15,17,6,14 chr1 28865710 . A G 2970.08 PASS AC=1;AF=0.563;AN=2;DP=3904;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant11-variant13-variant15-variant16-variant22-variant24-variant25-variant29-variant30-variant31-variant32-variant35-variant37-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:96,88:184:99:2108,0,2345:49,47,43,45 chr1 28865812 . A AT 606.24 PASS AC=1;AF=0.523;AN=2;DP=1601;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant11-variant13-variant16-variant22-variant24-variant25-variant29-variant30-variant31-variant32-variant35-variant37-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:33,30:63:99:589,0,680:10,23,12,18 chr1 28887031 . A G 98.72 PASS AC=1;AF=0.58;AN=2;DP=354;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant22-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant35-variant37-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,12:18:99:361,0,212:6,0,8,4 chr1 28893572 . G A 180.34 PASS AC=1;AF=0.5;AN=2;DP=261;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant6-variant8-variant9-variant12-variant16-variant24-variant25-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,8:16:99:271,0,267:7,1,6,2 chr1 28904895 . G GACTT 490.29 PASS AC=1;AF=0.543;AN=2;DP=659;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant13-variant16-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant35-variant37-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:15,8:23:99:291,0,816:5,10,3,5 chr1 28906940 . C T 896.97 PASS AC=1;AF=0.5;AN=2;DP=189;FractionInformativeReads=1;MQ=60;set=variant12-variant14-variant35 GT:AD:DP:GQ:PL:SB 0/1:40,38:78:99:1067,0,1141:29,11,28,10 chr1 28918992 . C G 580.97 PASS AC=1;AF=0.619;AN=2;DP=896;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant8-variant9-variant11-variant12-variant13-variant16-variant25-variant29-variant30-variant31-variant32-variant35-variant37-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:18,20:38:99:479,0,544:11,7,11,9 chr1 28919261 . G A 1431.96 PASS AC=1;AF=0.5;AN=2;DP=379;FractionInformativeReads=1;MQ=60;set=variant4-variant9-variant16-variant35 GT:AD:DP:GQ:PL:SB 0/1:58,46:104:99:1059,0,1540:28,30,23,23 chr1 28931625 . T G 517.17 PASS AC=1;AF=0.595;AN=2;DP=872;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant8-variant9-variant11-variant12-variant13-variant16-variant25-variant29-variant30-variant31-variant32-variant35-variant37-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:20,31:51:99:742,0,399:12,8,17,14 chr1 28969314 . A G 2749.76 PASS AC=2;AF=1;AN=2;DP=5094;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,149:149:99:4638,445,0:0,0,84,65 chr1 29016715 . GT GTTT,GTT,G 71.38 PASS AC=0,1,0;AF=0.125,0.275,0.125;AN=2;DP=1093;set=filterInvariant-filterInvariant4-variant5-variant8-variant9-filterInvariant10-variant11-variant14-filterInvariant16-variant19-variant22-filterInvariant24-variant25-filterInvariant26-filterInvariant28-variant32-filterInvariant33-filterInvariant35-filterInvariant38-filterInvariant41 GT:DP:GQ:SB 0/2:44:96:14,17,2,11 chr1 29016737 . G T 51.39 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=77;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:33,12:45:99:122,0,1323:4,29,12,0 chr1 29016739 . C T 93.46 PASS AC=1;AF=0.5;AN=2;DP=40;FS=59.278;FractionInformativeReads=1;MQ=60;MQRankSum=0.765;QD=2.34;ReadPosRankSum=-3.17;SOR=4.796;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:30,10:40:99:122,0,1323:4,26,10,0 chr1 29016740 . A T 102.33 PASS AC=1;AF=0.5;AN=2;DP=39;FS=54.719;FractionInformativeReads=1;MQ=60;MQRankSum=0.183;QD=2.62;ReadPosRankSum=-2.883;SOR=4.606;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:30,9:39:99:131,0,1245:4,26,9,0 chr1 29018316 . TTTTATTTATTTATTTA TTTTATTTATTTA,T 124.34 PASS AC=1,0;AF=0.733,0.033;AN=2;DP=379;FS=0;MQ=60;set=variant2-variant3-variant13-variant14-variant16-variant17-variant20-variant23-variant26-variant29-variant31-variant33-variant35-variant36-variant39 GT:DP:GQ:SB 0/1:9:23:0,1,2,6 chr1 29043253 . TG T,TGG 2116.51 PASS AC=2,0;AF=0.667,0.028;AN=2;DP=3797;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:109:99:7,0,75,27 chr1 29044612 . T C 725.88 PASS AC=1;AF=0.5;AN=2;DP=207;FractionInformativeReads=1;MQ=60;set=variant12-variant14-variant35 GT:AD:DP:GQ:PL:SB 0/1:30,42:72:99:1163,0,732:13,17,17,25 chr1 29063559 . A C 4158.68 PASS AC=2;AF=0.989;AN=2;DP=5445;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,136:136:99:4265,408,0:0,0,69,67 chr1 29064036 . C T 948.1 PASS AC=1;AF=0.548;AN=2;DP=1989;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant15-variant16-variant20-variant21-variant25-variant26-variant28-variant32-variant35-variant37-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:69,39:108:99:829,0,1847:44,25,23,16 chr1 29138975 . G T 1492.59 PASS AC=2;AF=0.875;AN=2;DP=5370;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,135:135:99:4359,403,0:0,0,89,46 chr1 29139202 . G T 1939.83 PASS AC=1;AF=0.5;AN=2;DP=714;FractionInformativeReads=1;MQ=60;set=variant14-variant29-variant34-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:75,70:145:99:1776,0,2163:26,49,27,43 chr1 29139385 . C CCTTGCTT 1026.91 PASS AC=1;AF=0.5;AN=2;DP=123;MQ=60;set=variant14-variant29-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:17,17:34:99:621,0,1419:7,10,7,10 chr1 29189597 . C T 3214.03 PASS AC=1;AF=0.676;AN=2;DP=12381;MQ=60;set=variant-variant2-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:251,207:458:99:4621,0,6212:130,121,106,101 chr1 29190138 . G A 538.22 PASS AC=1;AF=0.621;AN=2;DP=1794;MQ=60;set=variant-variant2-variant6-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:23,25:48:99:562,0,633:12,11,11,14 chr1 29213316 . A C,T 150.89 PASS AC=1,0;AF=0.769,0.013;AN=2;DP=776;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:15:99:6,3,4,2 chr1 29220178 . G A 561.61 PASS AC=1;AF=0.725;AN=2;DP=1874;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,37:62:99:989,0,601:13,12,24,13 chr1 29220270 . A C 1485.99 PASS AC=1;AF=0.725;AN=2;DP=4302;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:76,65:141:99:1471,0,1883:43,33,34,31 chr1 29320013 . G A 1778.16 PASS AC=1;AF=0.5;AN=2;DP=586;FractionInformativeReads=1;MQ=60;set=variant4-variant15-variant21-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:66,43:109:99:884,0,1497:31,35,18,25 chr1 29342090 . G GA 71.47 PASS AC=1;AF=0.639;AN=2;DP=283;set=variant4-variant5-variant9-variant10-variant11-variant12-variant14-variant15-variant18-variant20-variant23-variant27-variant32-variant35-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,6:18:99:103,0,242:9,3,4,2 chr1 29345009 . C CTT 1348.62 PASS AC=1;AF=0.875;AN=2;DP=1360;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:12,13:25:99:510,0,488:3,9,3,10 chr1 29345027 . T G 349.49 PASS AC=1;AF=0.786;AN=2;DP=831;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,7:14:99:270,0,227:2,5,0,7 chr1 29379992 . G A 187.64 PASS AC=1;AF=0.604;AN=2;DP=390;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant23-variant26-variant27-variant29-variant32-variant35-variant36-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,4:15:99:135,0,416:1,10,0,4 chr1 29385486 . G C 697.96 PASS AC=1;AF=0.604;AN=2;DP=1571;FractionInformativeReads=1;set=variant4-variant5-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant23-variant26-variant27-variant29-variant32-variant35-variant36-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,29:77:99:743,0,1226:19,29,7,22 chr1 29443675 . T C 3071 PASS AC=1;AF=0.756;AN=2;DP=3523;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,48:98:99:1371,0,1312:18,32,17,31 chr1 29443723 . A G 2433.82 PASS AC=1;AF=0.802;AN=2;DP=3682;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,38:80:99:1012,0,1173:19,23,20,18 chr1 29445038 . G A 443.82 PASS AC=1;AF=0.5;AN=2;DP=59;FS=5.952;FractionInformativeReads=1;MQ=60;MQRankSum=0.965;QD=7.52;ReadPosRankSum=-0.592;SOR=1.661;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:40,19:59:99:472,0,976:22,18,14,5 chr1 29445227 . T C 739.07 PASS AC=1;AF=0.538;AN=2;DP=747;MQ=60;set=variant3-variant4-variant6-variant15-variant17-variant21-variant23-variant28-variant30-variant35-variant38-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,34:66:99:790,0,829:15,17,14,20 chr1 29445514 . C A 348.87 PASS AC=1;AF=0.703;AN=2;DP=2233;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant13-variant15-variant16-variant17-variant19-variant21-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,54:96:99:1116,0,985:18,24,29,25 chr1 29445598 . A G 700.89 PASS AC=1;AF=0.553;AN=2;DP=1526;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant15-variant17-variant21-variant28-variant29-variant30-variant33-variant35-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,45:84:99:1248,0,1019:16,23,21,24 chr1 29446332 . AT A 2770.69 PASS AC=1;AF=0.774;AN=2;DP=4149;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,61:109:99:1508,0,1109:28,20,36,25 chr1 29446811 . A G 1791.3 PASS AC=1;AF=0.774;AN=2;DP=3199;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,56:88:99:1456,0,704:12,20,27,29 chr1 29450284 . CGAGG C,CGAGGGAGG 1036.72 PASS AC=1,0;AF=0.756,0.035;AN=2;DP=1205;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:36:99:7,10,11,8 chr1 29475341 . C T 911.79 PASS AC=1;AF=0.695;AN=2;DP=1442;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,22:35:99:675,0,391:6,7,9,13 chr1 29475394 . C G 1227.74 PASS AC=1;AF=0.695;AN=2;DP=1854;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,31:55:99:861,0,671:15,9,18,13 chr1 29475648 . T G 3770.6 PASS AC=1;AF=0.814;AN=2;DP=4790;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,60:125:99:1508,0,1556:28,37,22,38 chr1 29508350 . C T 1327.45 PASS AC=1;AF=0.559;AN=2;DP=1966;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant15-variant21-variant28-variant29-variant30-variant33-variant35-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:79,55:134:99:1471,0,2303:35,44,20,35 chr1 29519778 . T G 2197.51 PASS AC=1;AF=0.814;AN=2;DP=3741;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,52:102:99:1303,0,1270:29,21,29,23 chr1 29529699 . T C 2043.81 PASS AC=1;AF=0.826;AN=2;DP=5634;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,59:120:99:1395,0,1468:36,25,37,22 chr1 29533080 . A G 239.84 PASS AC=1;AF=0.568;AN=2;DP=534;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant11-variant12-variant15-variant17-variant21-variant28-variant29-variant30-variant32-variant33-variant35-variant37-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,14:29:99:364,0,409:11,4,10,4 chr1 29542435 . C G 1934.37 PASS AC=2;AF=0.943;AN=2;DP=3296;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:2040,195,0:0,0,44,21 chr1 29542559 . G A 1701.22 PASS AC=1;AF=0.5;AN=2;DP=176;FS=0.56;FractionInformativeReads=1;MQ=60;MQRankSum=0.675;QD=9.67;ReadPosRankSum=-2.43;SOR=0.755;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:97,79:176:99:1729,0,2424:55,42,46,33 chr1 29542637 . A G 3414.79 PASS AC=1;AF=0.814;AN=2;DP=7207;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:96,82:178:99:1988,0,2400:49,47,36,46 chr1 29542926 . A T 372.99 PASS AC=1;AF=0.821;AN=2;DP=504;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,4:11:99:147,0,227:5,2,3,1 chr1 29557224 . C T 4152.55 PASS AC=1;AF=0.762;AN=2;DP=8714;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:140,103:243:99:2148,0,3463:73,67,55,48 chr1 29563015 . G C 236.5 PASS AC=2;AF=1;AN=2;DP=909;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,25:25:74:782,74,0:0,0,18,7 chr1 29616318 . C A 1493.17 PASS AC=1;AF=0.5;AN=2;DP=2939;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant20-variant22-variant26-variant27-variant33-variant34-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:108,90:198:99:2254,0,2797:40,68,31,59 chr1 29630455 . C T 580.95 PASS AC=1;AF=0.563;AN=2;DP=1593;MQ=60;set=variant5-variant6-variant11-variant13-variant21-variant23-variant24-variant29-variant31-variant35-variant36-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:73,61:134:99:1482,0,1827:29,44,22,39 chr1 29631236 . C CTA 1225.24 PASS AC=1;AF=0.603;AN=2;DP=6590;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant26-variant27-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:137,100:237:99:3766,0,5665:68,69,51,49 chr1 29633491 . T TCAGCC 544.33 PASS AC=1;AF=0.558;AN=2;DP=631;MQ=60;set=variant3-variant5-variant6-variant7-variant10-variant12-variant13-variant15-variant16-variant17-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:21,11:32:99:399,0,1313:15,6,8,3 chr1 29637136 . T C 474.13 PASS AC=1;AF=0.65;AN=2;DP=985;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant10-variant12-variant13-variant15-variant16-variant17-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:21,19:40:99:657,0,524:14,7,16,3 chr1 29649874 . T C 834.42 PASS AC=1;AF=0.571;AN=2;DP=1561;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant10-variant12-variant13-variant16-variant17-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:41,35:76:99:948,0,1021:25,16,24,11 chr1 29652068 . T C 866.58 PASS AC=1;AF=0.571;AN=2;DP=2842;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant10-variant12-variant13-variant16-variant17-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:53,46:99:99:1132,0,1225:29,24,25,21 chr1 29674996 . C T 96.68 PASS AC=1;AF=0.705;AN=2;DP=174;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant17-variant21-variant22-variant23-variant26-variant27-variant29-variant33-variant35-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:6,3:9:68:68,0,113:3,3,2,1 chr1 29675102 . CTTTT C 142.97 PASS AC=1;AF=0.667;AN=2;DP=300;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant14-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant33-variant34-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:6,12:18:99:451,0,279:3,3,6,6 chr1 29842261 . A T 637.02 PASS AC=2;AF=0.989;AN=2;DP=1318;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1136,110,0:0,0,20,17 chr1 29842282 . TCTC T 577.94 PASS AC=1;AF=0.5;AN=2;DP=75;set=variant14-variant35 GT:AD:DP:GQ:PL:SB 0/1:13,14:27:99:466,0,504:7,6,5,9 chr1 29845223 . C A 338.82 PASS AC=1;AF=0.5;AN=2;DP=223;set=variant4-variant11-variant15-variant17-variant23-variant29-variant35 GT:AD:DP:GQ:PL:SB 0/1:10,13:23:99:399,0,264:4,6,1,12 chr1 29863096 . ACTTTTT A 97.73 PASS AC=2;AF=0.833;AN=2;DP=120;FS=0;set=variant4-variant9-variant10-variant11-variant14-variant15-variant17-variant20-variant29-variant34-variant35-variant39 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:900,60,0:0,0,10,10 chr1 29863140 . CTCCCTCCCTCCCTCCCTCCCTCCCTCCTTCCCTCCCTCCCTCCCTCCT C 204.88 PASS AC=1;AF=0.6;AN=2;DP=124;set=variant9-variant11-variant14-variant15-variant17-variant20-variant23-variant29-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:4,12:16:99:451,0,126:4,0,1,11 chr1 29863141 . T C 90.38 PASS AC=1;AF=0.5;AN=2;DP=19;FS=28.894;FractionInformativeReads=1;MQ=57.61;MQRankSum=-1.25;QD=4.76;ReadPosRankSum=-0.95;SOR=3.22;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:15,4:19:99:119,0,584:1,14,4,0 chr1 29863405 . G A 295.68 PASS AC=2;AF=0.611;AN=2;DP=135;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant8-variant9-variant10-variant11-variant14-variant15-variant20-variant21-variant23-variant24-variant29-variant32-variant34-variant35-variant39-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:180,12,0:0,0,0,4 chr1 31184218 . C A 1185.53 PASS AC=1;AF=0.667;AN=2;DP=2467;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant16-variant17-variant18-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,35:89:99:855,0,1312:29,25,19,16 chr1 31184368 . G A 565.45 PASS AC=1;AF=0.667;AN=2;DP=1390;FractionInformativeReads=1;set=variant-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant16-variant17-variant18-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,37:70:99:957,0,902:17,16,19,18 chr1 31184529 . G A 834.14 PASS AC=1;AF=0.667;AN=2;DP=1976;MQ=60;set=variant-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant16-variant17-variant18-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,57:102:99:1340,0,1047:21,24,28,29 chr1 31184552 . C T 809.58 PASS AC=1;AF=0.667;AN=2;DP=1805;MQ=60;set=variant-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant16-variant17-variant18-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,51:94:99:1235,0,927:19,24,24,27 chr1 31184749 . C G 1342.79 PASS AC=1;AF=0.5;AN=2;DP=728;FractionInformativeReads=1;MQ=60;set=variant6-variant8-variant14-variant16-variant17-variant18-variant27-variant28-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:37,49:86:99:2009,0,1376:24,13,27,22 chr1 31184763 . G A 1321.99 PASS AC=1;AF=0.667;AN=2;DP=2054;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant16-variant17-variant18-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,54:93:99:2179,0,1525:24,15,31,23 chr1 31184779 . T C 1550.17 PASS AC=1;AF=0.667;AN=2;DP=2378;MQ=60;set=variant-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant16-variant17-variant18-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,57:102:99:2176,0,1629:23,22,33,24 chr1 31184857 . T G 2452.68 PASS AC=1;AF=0.667;AN=2;DP=3500;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant16-variant17-variant18-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,68:128:99:2495,0,2193:27,33,35,33 chr1 31184878 . A G 2409.9 PASS AC=1;AF=0.667;AN=2;DP=3533;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant16-variant17-variant18-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:63,65:128:99:2474,0,2343:27,36,31,34 chr1 31185106 . C T 669.24 PASS AC=1;AF=0.667;AN=2;DP=1651;MQ=60;set=variant-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant16-variant17-variant18-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,35:69:99:887,0,1030:17,17,20,15 chr1 31185125 . G A 622.21 PASS AC=1;AF=0.667;AN=2;DP=1717;MQ=60;set=variant-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant16-variant17-variant18-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,36:71:99:951,0,981:17,18,20,16 chr1 31185551 . TC T 825.57 PASS AC=1;AF=0.667;AN=2;DP=2430;MQ=60;set=variant-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant16-variant17-variant18-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,53:97:99:1328,0,1049:20,24,26,27 chr1 31186224 . GCACA GCA,G 1105.4 PASS AC=0,1;AF=0.527,0.054;AN=2;DP=4066;set=variant-filterInvariant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant14-filterInvariant15-variant16-variant17-variant18-filterInvariant19-variant20-filterInvariant21-variant22-filterInvariant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-filterInvariant32-variant33-variant34-variant35-variant36-filterInvariant38-variant40-filterInvariant41-variant42-variant43-filterInvariant44 GT:DP:GQ:SB 0/2:85:99:22,27,24,12 chr1 31186254 . A G 1158.03 PASS AC=1;AF=0.667;AN=2;DP=2493;set=variant-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant16-variant17-variant18-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,46:101:99:1302,0,1558:27,28,28,18 chr1 31186387 . C T 1375.37 PASS AC=1;AF=0.5;AN=2;DP=1393;MQ=60;set=variant6-variant8-variant14-variant16-variant17-variant18-variant27-variant28-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:96,70:166:99:1816,0,2334:43,53,32,38 chr1 31188901 . A G 1179.06 PASS AC=1;AF=0.667;AN=2;DP=4075;MQ=60;set=variant-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant16-variant17-variant18-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:97,87:184:99:2355,0,2589:42,55,37,50 chr1 31205796 . T C 972.05 PASS AC=1;AF=0.661;AN=2;DP=3155;MQ=60;set=variant-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:63,71:134:99:1850,0,1666:35,28,33,38 chr1 31207781 . C T 267.74 PASS AC=1;AF=0.743;AN=2;DP=788;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,6:22:99:191,0,547:14,2,6,0 chr1 31212898 . C T 347.08 PASS AC=1;AF=0.5;AN=2;DP=44;FS=7.695;FractionInformativeReads=1;MQ=60;MQRankSum=-1.121;QD=7.89;ReadPosRankSum=0.743;SOR=2.049;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:30,14:44:99:375,0,829:11,19,2,12 chr1 31215364 . T C 1315.92 PASS AC=2;AF=0.672;AN=2;DP=3822;MQ=60;set=variant2-variant3-variant5-variant7-variant9-variant10-variant11-variant14-variant15-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,142:142:99:4056,425,0:0,0,75,67 chr1 31230195 . T C 274.74 PASS AC=2;AF=0.721;AN=2;DP=508;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:790,72,0:0,0,16,8 chr1 31230668 . C T 952.58 PASS AC=1;AF=0.531;AN=2;DP=1641;set=variant-variant7-variant9-variant13-variant14-variant16-variant18-variant25-variant28-variant30-variant33-variant34-variant35-variant38-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:38,63:101:99:1598,0,1011:14,24,24,39 chr1 31342367 . TA T 110.98 PASS AC=2;AF=0.929;AN=2;DP=135;set=variant2-variant3-variant4-variant7-variant9-variant12-variant16-variant17-variant21-variant22-variant25-variant26-variant28-variant30-variant32-variant33-variant35-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:90,6,0:0,0,1,1 chr1 31342383 . CAAAAAAAA CAAAAAAA,C,CAAAA,CAAAAAA 97.7 PASS AC=2,0,0,0;AF=0.654,0.038,0.038,0.038;AN=2;DP=96;set=variant2-variant4-variant7-variant10-variant11-variant12-variant21-variant22-variant28-variant29-variant35-variant36-variant39 GT:DP:GQ:SB 1/1:3:9:0,0,2,1 chr1 31342388 . A C 48.71 PASS AC=2;AF=0.75;AN=2;DP=40;FS=0;set=variant4-variant21-variant25-variant35-variant36-variant39 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:90,6,0:0,0,1,1 chr1 31342403 . A C,AC 175.96 PASS AC=2,0;AF=0.854,0.083;AN=2;DP=214;set=variant4-variant7-variant9-variant10-variant11-variant12-variant3-variant16-variant17-variant21-variant25-variant26-variant2-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant39-variant40-variant42-variant44 GT:DP:GQ:SB 1/1:5:15:0,0,3,2 chr1 31344952 . C T 633.11 PASS AC=2;AF=0.688;AN=2;DP=2428;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant17-variant21-variant22-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,95:95:99:2841,284,0:0,0,46,49 chr1 31350566 . T C 296.34 PASS AC=1;AF=0.7;AN=2;DP=1692;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,27:45:99:644,0,432:11,7,14,13 chr1 31405507 . TA T 531.55 PASS AC=1;AF=0.75;AN=2;DP=25;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.354;ReadPosRankSum=0.118;set=variant11-variant35 GT:AD:DP:GQ:PL:SB 0/1:2,9:11:16:300,0,16:1,1,6,3 chr1 31405509 . TATA TTA,T 204.24 PASS AC=1,0;AF=0.607,0.036;AN=2;DP=185;MQ=60;set=variant2-variant5-variant8-variant9-variant11-variant13-variant15-variant20-variant22-variant23-variant32-variant35-variant36-variant44 GT:DP:GQ:SB 0/1:11:50:1,1,6,3 chr1 31405512 . A T 113.29 PASS AC=2;AF=0.55;AN=2;DP=165;MQ=60;set=variant3-variant4-variant11-variant14-variant26-variant27-variant29-variant31-variant35-variant41 GT:AD:DP:GQ:PL:SB 1/1:1,11:12:1:419,1,0:1,0,7,4 chr1 31406286 . TACACACACACAC TACACACACAC,TACACACACACACACAC,TACACACAC,TACACACACACACAC,TACACACACACACACACACAC,T,TACACAC,TACACACACACACACACACACACAC 173.04 PASS AC=2,0,0,0,0,0,0,0;AF=0.306,0.048,0.048,0.113,0.032,0.016,0.032,0.016;AN=2;DP=1152;set=variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-filterInvariant12-variant18-variant19-variant20-filterInvariant21-filterInvariant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-filterInvariant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43 GT:DP:GQ:SB 1/1:16:48:0,0,3,13 chr1 31409726 . CCT C 766.44 PASS AC=1;AF=0.542;AN=2;DP=1453;MQ=60;set=variant-variant2-variant3-variant8-variant9-variant14-variant15-variant17-variant20-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,36:67:99:1398,0,1331:12,19,15,21 chr1 31409898 . C T 136.72 PASS AC=1;AF=0.6;AN=2;DP=33;FS=0;MQ=60;set=variant4-variant13-variant26-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:3,5:8:99:157,0,105:1,2,1,4 chr1 31415040 . A T 475.42 PASS AC=1;AF=0.639;AN=2;DP=171;FractionInformativeReads=1;MQ=60;set=variant3-variant12-variant14-variant15-variant17-variant18-variant23-variant25-variant27-variant28-variant29-variant32-variant35-variant36-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:73:73,0,105:0,3,1,2 chr1 31418119 . C T 517.51 PASS AC=1;AF=0.542;AN=2;DP=778;MQ=60;set=variant-variant2-variant3-variant8-variant9-variant14-variant15-variant17-variant20-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,8:27:99:195,0,612:15,4,6,2 chr1 31422799 . C T 353.22 PASS AC=1;AF=0.556;AN=2;DP=315;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant11-variant13-variant25-variant26-variant30-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:16,26:42:99:713,0,421:12,4,17,9 chr1 31426815 . A G 454.72 PASS AC=1;AF=0.574;AN=2;DP=1124;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant8-variant9-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,21:43:99:579,0,621:6,16,7,14 chr1 31440921 . G A 76.67 PASS AC=2;AF=0.756;AN=2;DP=412;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:429,30,0:0,0,10,0 chr1 31445932 . C G 558.91 PASS AC=2;AF=0.621;AN=2;DP=1052;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-filterInvariant30-variant31-variant32-variant34-variant35-variant36-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:823,75,0:0,0,17,8 chr1 31446069 . TG T 535.35 PASS AC=1;AF=0.542;AN=2;DP=1048;MQ=60;set=variant-variant2-variant3-variant8-variant9-variant14-variant15-variant17-variant20-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,17:34:99:605,0,659:8,9,7,10 chr1 31446071 . T A 544.38 PASS AC=1;AF=0.542;AN=2;DP=1037;MQ=60;set=variant-variant2-variant3-variant8-variant9-variant14-variant15-variant17-variant20-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,18:36:99:605,0,660:8,10,7,11 chr1 31478638 . AAGAGAGAGAG AAGAG,A,AAG,AAGAGAGAGAGAGAG 806.46 PASS AC=1,1,0,0;AF=0.605,0.116,0.012,0.012;AN=2;DP=3408;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 2/1:82:99:1,0,54,27 chr1 31479005 . C T 369 PASS AC=1;AF=0.542;AN=2;DP=1301;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant8-variant9-variant14-variant15-variant17-variant20-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,48:77:99:1222,0,696:9,20,19,29 chr1 31501755 . T C 636.97 PASS AC=1;AF=0.542;AN=2;DP=1051;set=variant-variant2-variant3-variant8-variant9-variant14-variant15-variant17-variant20-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,19:42:99:580,0,600:8,15,4,15 chr1 31661148 . C T 187.5 PASS AC=1;AF=0.5;AN=2;DP=60;MQ=60;set=variant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:17,12:29:99:295,0,454:4,13,3,9 chr1 31732390 . G A 6090.03 PASS AC=2;AF=0.989;AN=2;DP=7980;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,176:176:99:5085,525,0:0,0,111,65 chr1 31732602 . CAA C,CA,CAAA 1669.9 PASS AC=0,1,0;AF=0.209,0.523,0.012;AN=2;DP=3715;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:61:99:7,19,14,21 chr1 31732892 . G A 2369.46 PASS AC=1;AF=0.5;AN=2;DP=1728;MQ=60;set=variant4-variant6-variant13-variant18-variant20-variant21-variant22-variant32-variant34-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:84,94:178:99:2338,0,2124:41,43,40,54 chr1 31733721 . A AAAG 359.21 PASS AC=1;AF=0.833;AN=2;DP=545;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant20-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,11:18:91:431,0,91:3,4,8,3 chr1 31733782 . T A 1562.19 PASS AC=1;AF=0.824;AN=2;DP=2133;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,38:59:99:1026,0,585:14,7,23,15 chr1 31733926 . A G 1475.35 PASS AC=2;AF=0.837;AN=2;DP=4773;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,111:111:99:3173,332,0:0,0,47,64 chr1 31734033 . CA C 66.27 PASS AC=1;AF=0.809;AN=2;DP=525;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,8:15:99:147,0,129:3,4,2,6 chr1 31740668 . C T 2034.3 PASS AC=1;AF=0.833;AN=2;DP=1990;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,29:54:99:709,0,699:18,7,19,10 chr1 31744168 . G A 787.66 PASS AC=1;AF=0.833;AN=2;DP=987;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,16:32:99:383,0,426:9,7,9,7 chr1 31744505 . A AT 159.63 PASS AC=2;AF=0.878;AN=2;DP=595;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:399,45,0:0,0,5,10 chr1 31754367 . T C 1592.52 PASS AC=1;AF=0.5;AN=2;DP=1597;FractionInformativeReads=1;set=variant4-variant6-variant13-variant18-variant20-variant21-variant22-variant32-variant34-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:70,80:150:99:1971,0,1648:34,36,37,43 chr1 31754463 . A G 763.5 PASS AC=1;AF=0.5;AN=2;DP=282;MQ=60;set=variant6-variant18-variant21-variant35 GT:AD:DP:GQ:PL:SB 0/1:42,33:75:99:857,0,1122:15,27,9,24 chr1 31754511 . G C 991.02 PASS AC=1;AF=0.824;AN=2;DP=914;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,20:36:99:561,0,504:2,14,6,14 chr1 31761989 . G A 1529.35 PASS AC=2;AF=1;AN=2;DP=2885;FS=0;MQ=60;MQRankSum=1.175;ReadPosRankSum=-0.212;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:2174,186,0:0,0,47,15 chr1 31762374 . C T 2043.82 PASS AC=2;AF=0.837;AN=2;DP=2876;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:2469,231,0:0,0,36,41 chr1 31764693 . G A 1245.9 PASS AC=1;AF=0.833;AN=2;DP=975;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,18:40:99:522,0,692:18,4,15,3 chr1 31764713 . C CAAG 2086.43 PASS AC=1;AF=0.824;AN=2;DP=1427;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,22:50:99:915,0,1225:23,5,16,6 chr1 31764930 . T C 1590.86 PASS AC=2;AF=1;AN=2;DP=2245;FS=0;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:2367,225,0:0,0,24,51 chr1 31765968 . C T 2075.56 PASS AC=1;AF=0.833;AN=2;DP=1804;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,15:49:99:343,0,831:18,16,9,6 chr1 31792141 . A G 707.71 PASS AC=1;AF=0.838;AN=2;DP=819;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant20-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,10:17:99:349,0,181:2,5,2,8 chr1 31819407 . A C 283.46 PASS AC=1;AF=0.5;AN=2;DP=121;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant13-variant20-variant21-variant22-variant32-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:5,4:9:99:143,0,160:3,2,3,1 chr1 31821932 . TA T 278.57 PASS AC=1;AF=0.5;AN=2;DP=334;MQ=60;set=variant4-variant6-variant13-variant18-variant20-variant21-variant22-variant32-variant34-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:19,23:42:99:736,0,584:3,16,7,16 chr1 31837089 . T C 2190.97 PASS AC=1;AF=0.5;AN=2;DP=1194;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant18-variant20-variant21-variant22-variant32-variant34-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:62,57:119:99:1400,0,1634:28,34,26,31 chr1 31837320 . T C 1953.24 PASS AC=1;AF=0.811;AN=2;DP=2890;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,46:97:99:1226,0,1315:24,27,26,20 chr1 31838551 . TAA TA,TAAA,T 121.43 PASS AC=0,1,0;AF=0.306,0.181,0.014;AN=2;DP=1051;set=variant2-variant3-variant4-variant5-variant6-variant7-filterInvariant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant28-filterInvariant29-variant31-filterInvariant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:32:99:18,3,11,0 chr1 31840426 . C G 1268.5 PASS AC=1;AF=0.811;AN=2;DP=1510;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,13:29:99:417,0,595:2,14,3,10 chr1 31882330 . T G 1606.86 PASS AC=2;AF=1;AN=2;DP=1404;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:947,81,0:0,0,19,8 chr1 31882582 . G GGCCTCA 3609.73 PASS AC=1;AF=0.688;AN=2;DP=2016;MQ=60;set=variant3-variant4-variant6-variant10-variant12-variant13-variant14-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant30-variant32-variant34-variant35-variant37-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:45,31:76:99:1207,0,3480:24,21,15,16 chr1 31883295 . T C 2306.77 PASS AC=1;AF=0.688;AN=2;DP=1329;MQ=60;set=variant3-variant4-variant6-variant10-variant12-variant13-variant14-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant30-variant32-variant34-variant35-variant37-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:28,32:60:99:807,0,655:10,18,12,20 chr1 31885859 . A G 291.9 PASS AC=1;AF=0.75;AN=2;DP=175;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant10-variant13-filterInvariant14-variant18-variant19-variant20-variant21-variant22-variant23-variant30-variant32-variant34-variant35-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,6:15:99:125,0,169:4,5,3,3 chr1 31886004 . GCGGGGCCGGGGCGGGGC G 271.5 PASS AC=1;AF=0.5;AN=2;DP=38;MQ=60;set=variant10-variant14-variant35 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:99:157,0,604:2,2,3,1 chr1 31886564 . C G 526.47 PASS AC=1;AF=0.696;AN=2;DP=331;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant6-variant10-variant12-variant13-variant14-variant18-variant19-variant20-variant21-variant22-variant24-variant27-variant28-variant30-variant32-variant34-variant35-variant37-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,10:22:99:246,0,334:8,4,8,2 chr1 31886833 . T C 4918.01 PASS AC=1;AF=0.688;AN=2;DP=3367;MQ=60;set=variant3-variant4-variant6-variant10-variant12-variant13-variant14-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant30-variant32-variant34-variant35-variant37-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:92,81:173:99:2035,0,2281:45,47,39,42 chr1 31897493 . A G 2264.94 PASS AC=2;AF=1;AN=2;DP=2939;FS=0;MQ=60;MQRankSum=-0.027;ReadPosRankSum=0.247;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:2358,227,0:0,0,50,26 chr1 31897587 . G A 2251.97 PASS AC=1;AF=0.5;AN=2;DP=989;MQ=60;set=variant6-variant18-variant21-variant35 GT:AD:DP:GQ:PL:SB 0/1:113,120:233:99:2676,0,2768:62,51,66,54 chr1 31898132 . T C 1242.86 PASS AC=1;AF=0.794;AN=2;DP=3658;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant20-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:62,47:109:99:1060,0,1587:36,26,29,18 chr1 31898162 . C T 1358.92 PASS AC=1;AF=0.794;AN=2;DP=4633;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant20-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:89,57:146:99:1337,0,2246:52,37,33,24 chr1 31898234 . T C 1660.16 PASS AC=1;AF=0.794;AN=2;DP=4574;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant20-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:76,64:140:99:1630,0,1913:39,37,29,35 chr1 31898279 . A C 1194.2 PASS AC=1;AF=0.794;AN=2;DP=3226;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant20-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,48:97:99:1058,0,1215:20,29,22,26 chr1 31898463 . C T 470.35 PASS AC=1;AF=0.794;AN=2;DP=810;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant20-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,14:27:99:401,0,342:8,5,7,7 chr1 31898536 . C T 1323.18 PASS AC=1;AF=0.794;AN=2;DP=1732;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant20-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,33:60:99:826,0,679:17,10,20,13 chr1 31898687 . C T 1718.77 PASS AC=1;AF=0.5;AN=2;DP=530;FractionInformativeReads=1;MQ=60;set=variant11-variant35-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:84,75:159:99:1844,0,2227:47,37,42,33 chr1 31899684 . A T 382.42 PASS AC=2;AF=1;AN=2;DP=1838;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1650,152,0:0,0,15,36 chr1 31899704 . C T 281.14 PASS AC=1;AF=0.864;AN=2;DP=1335;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:16,17:33:99:596,0,387:5,11,1,16 chr1 31902418 . A G 3880.27 PASS AC=1;AF=0.727;AN=2;DP=2005;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant6-variant10-variant13-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant30-variant32-variant34-variant35-variant37-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:42,34:76:99:935,0,1112:17,25,12,22 chr1 31905889 . A ACAG 6543.73 PASS AC=2;AF=0.907;AN=2;DP=7555;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,167:167:99:7569,517,0:0,0,107,60 chr1 31906882 . A G 2731.08 PASS AC=1;AF=0.943;AN=2;DP=5034;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:69,58:127:99:1533,0,1663:37,32,30,28 chr1 31907102 . A G 1558.64 PASS AC=1;AF=0.909;AN=2;DP=3034;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:23,56:79:99:1426,0,543:9,14,23,33 chr1 31907457 . A C,G 1863.63 PASS AC=1,0;AF=0.67,0.273;AN=2;DP=2053;MQ=60;set=Intersection GT:DP:GQ:SB 0/1:57:99:11,16,9,21 chr1 31971684 . C G 467.98 PASS AC=1;AF=0.735;AN=2;DP=785;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,16:28:99:526,0,381:11,1,14,2 chr1 31973122 . GTGGAGTCTGTC G 1942.9 PASS AC=1;AF=0.77;AN=2;DP=3659;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:84,44:128:99:1609,0,3350:45,39,22,22 chr1 31973138 . T C 2026.96 PASS AC=1;AF=0.77;AN=2;DP=3608;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:80,45:125:99:1655,0,3220:42,38,23,22 chr1 31973215 . G A 1249.58 PASS AC=1;AF=0.77;AN=2;DP=3068;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,49:113:99:1163,0,1723:32,32,26,23 chr1 31973266 . G A 1337.43 PASS AC=1;AF=0.75;AN=2;DP=2579;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,46:91:99:1261,0,1136:21,24,26,20 chr1 31973348 . A C 1429.07 PASS AC=1;AF=0.77;AN=2;DP=3443;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,54:110:99:1369,0,1302:23,33,27,27 chr1 31973409 . G A 1766.36 PASS AC=1;AF=0.77;AN=2;DP=3885;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:69,73:142:99:1780,0,1688:34,35,36,37 chr1 31973440 . G A 1964.47 PASS AC=1;AF=0.77;AN=2;DP=3575;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,61:121:99:1509,0,1417:33,27,29,32 chr1 31973481 . C T 1548.72 PASS AC=1;AF=0.75;AN=2;DP=2695;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,53:105:99:1243,0,1212:27,25,23,30 chr1 31973703 . T C 247.44 PASS AC=1;AF=0.75;AN=2;DP=470;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,11:19:99:252,0,216:3,5,5,6 chr1 32042540 . G A 239.89 PASS AC=2;AF=0.618;AN=2;DP=813;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:863,72,0:0,0,18,6 chr1 32044641 . G GTTTAATTTCAGTGAGAGCTGGTGTGTCTGTGTGTGTGTGTGTGATGTCTTCAGTTATAA,GTTTAATTTCAGTGAGAGCTGGTGTGTCTATGTGTGTGTGTGTGTGATGTCTTCAGTTATAA,GTTTAATTTCAGTGAGAGCTGTTGTGTCTATGTGTGTGTGTGTGTGATGTCTTCAGTTATAA 1710.94 PASS AC=2,0,0;AF=0.452,0.238,0.31;AN=2;DP=517;FS=0;MQRankSum=0.474;ReadPosRankSum=0.474;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:DP:GQ:SB 1/1:15:99:0,0,13,2 chr1 32045814 . G C 69.95 PASS AC=1;AF=0.75;AN=2;DP=76;set=variant-variant6-variant10-variant15-variant28-variant31-variant33-variant35-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,4:5:1:66,0,1:1,0,1,3 chr1 32052923 . CT C,CTT 122.75 PASS AC=1,0;AF=0.458,0.042;AN=2;DP=665;set=variant3-variant5-filterInvariant7-variant8-variant9-variant10-variant12-variant13-filterInvariant14-filterInvariant15-variant20-variant21-filterInvariant23-filterInvariant25-variant28-filterInvariant30-variant34-filterInvariant35-variant38-variant39-variant40-variant42-filterInvariant43-filterInvariant44 GT:DP:GQ:SB 0/1:23:79:7,10,2,4 chr1 32084904 . C T 3627.23 PASS AC=2;AF=0.649;AN=2;DP=6067;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,192:192:99:5591,574,0:0,0,102,90 chr1 32085485 . G A 698.09 PASS AC=2;AF=0.725;AN=2;DP=1909;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1231,99,0:0,0,14,19 chr1 32086912 . A C 784.51 PASS AC=2;AF=0.762;AN=2;DP=1255;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1398,117,0:0,0,30,9 chr1 32092525 . A G 1211.83 PASS AC=2;AF=0.725;AN=2;DP=2952;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,78:79:99:2582,227,0:0,1,34,44 chr1 32092735 . T G 3818.38 PASS AC=2;AF=0.649;AN=2;DP=4726;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,120:120:99:3999,360,0:0,0,65,55 chr1 32092918 . T TTCC 10334.2 PASS AC=2;AF=0.649;AN=2;DP=7843;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,194:196:99:8554,478,0:1,1,88,106 chr1 32096265 . A G 1132.19 PASS AC=2;AF=0.649;AN=2;DP=1959;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:1832,174,0:0,0,35,23 chr1 32096746 . T C 184.75 PASS AC=2;AF=0.731;AN=2;DP=475;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:392,30,0:0,0,1,9 chr1 32100551 . GA G 1888.77 PASS AC=2;AF=0.768;AN=2;DP=2878;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,85:85:99:2793,256,0:0,0,35,50 chr1 32118160 . C A 5080.92 PASS AC=2;AF=0.737;AN=2;DP=8785;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:18,200:218:99:4592,129,0:8,10,121,79 chr1 32119347 . AACAC A,AAC,AACACAC 1301.37 PASS AC=2,0,0;AF=0.615,0.013,0.064;AN=2;DP=1754;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:DP:GQ:SB 1/1:29:87:0,0,13,16 chr1 32119431 . T C 979.49 PASS AC=2;AF=0.658;AN=2;DP=2100;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1683,150,0:0,0,26,24 chr1 32122164 . A G 127.02 PASS AC=2;AF=0.784;AN=2;DP=327;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:484,51,0:0,0,9,8 chr1 32128283 . C G,A 264.39 PASS AC=0,1;AF=0.583,0.05;AN=2;DP=426;MQ=60;set=variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant18-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant32-variant33-filterInvariant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:12:99:0,3,0,9 chr1 32131163 . C G 4379.47 PASS AC=2;AF=0.632;AN=2;DP=8171;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,219:219:99:6694,656,0:0,0,98,121 chr1 32134491 . C G 194.63 PASS AC=2;AF=0.738;AN=2;DP=803;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,25:26:68:742,68,0:0,1,9,16 chr1 32136168 . G C,T 4014.62 PASS AC=2,0;AF=0.693,0.273;AN=2;DP=5182;MQ=60;set=Intersection GT:DP:GQ:SB 1/1:150:99:2,2,83,63 chr1 32136398 . G A 1422.96 PASS AC=2;AF=0.667;AN=2;DP=1979;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:1145,96,0:0,0,8,24 chr1 32140733 . C T 2998.67 PASS AC=2;AF=0.671;AN=2;DP=4603;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,104:104:99:3324,311,0:0,0,43,61 chr1 32145009 . C T 2358.43 PASS AC=2;AF=0.977;AN=2;DP=4059;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,90:90:99:2710,270,0:0,0,46,44 chr1 32146425 . C T 833.04 PASS AC=2;AF=0.659;AN=2;DP=1507;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,31:31:93:942,93,0:0,0,19,12 chr1 32148571 . A G 1533.83 PASS AC=2;AF=1;AN=2;DP=4261;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,108:108:99:3444,323,0:0,0,64,44 chr1 32149982 . A T 207.09 PASS AC=2;AF=0.565;AN=2;DP=765;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant14-variant16-variant17-variant19-variant20-variant21-variant23-variant25-variant28-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1222,119,0:0,0,21,19 chr1 32155284 . T C 2509.12 PASS AC=2;AF=0.675;AN=2;DP=5037;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,152:152:99:4871,456,0:0,0,78,74 chr1 32155911 . G T 1200.06 PASS AC=2;AF=0.679;AN=2;DP=1335;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1519,102,0:0,0,22,11 chr1 32155929 . G A 1571.09 PASS AC=2;AF=0.632;AN=2;DP=1712;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,42:44:83:1749,83,0:1,1,28,14 chr1 32156722 . G A 1723.01 PASS AC=2;AF=0.645;AN=2;DP=2943;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,81:81:99:2499,240,0:0,0,57,24 chr1 32156869 . A T 5436.3 PASS AC=2;AF=1;AN=2;DP=11181;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,292:292:99:8794,872,0:0,0,155,137 chr1 32157531 . T C 4876.69 PASS AC=2;AF=0.645;AN=2;DP=6947;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,226:226:99:6549,676,0:0,0,127,99 chr1 32158374 . T C 4550.5 PASS AC=2;AF=0.726;AN=2;DP=8314;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,214:214:99:6915,641,0:0,0,82,132 chr1 32159588 . A C 4324.85 PASS AC=2;AF=0.726;AN=2;DP=7077;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,179:179:99:5321,536,0:0,0,101,78 chr1 32160918 . A G 1287.35 PASS AC=2;AF=0.738;AN=2;DP=2971;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,66:66:99:2154,198,0:0,0,22,44 chr1 32163950 . G C 1121.4 PASS AC=2;AF=0.784;AN=2;DP=1347;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:1098,81,0:0,0,16,11 chr1 32164206 . T G 2865.37 PASS AC=2;AF=0.803;AN=2;DP=3847;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,103:103:99:3209,309,0:0,0,41,62 chr1 32165495 . G T 1509.2 PASS AC=2;AF=0.8;AN=2;DP=3419;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,104:105:99:3292,304,0:1,0,69,35 chr1 32167526 . G C 2488.75 PASS AC=2;AF=1;AN=2;DP=4467;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,116:117:99:3675,326,0:0,1,69,47 chr1 32193647 . T C 2223.2 PASS AC=2;AF=0.829;AN=2;DP=3373;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,91:91:99:2809,272,0:0,0,57,34 chr1 32194404 . A AACAC,AACACACACACACACACACAC,AAC,AACACACAC,AACACACACACAC,AACACAC,AACACACACACACACACACACAC,AACACACACACACACACACACACACAC 240.87 PASS AC=2,0,0,0,0,0,0,0;AF=0.45,0.033,0.267,0.067,0.033,0.067,0.033,0.033;AN=2;DP=445;FS=0;MQRankSum=-0.198;ReadPosRankSum=-0.922;set=variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant29-variant32-variant33-variant34-variant35-variant39-variant40-variant41-variant42-variant43 GT:DP:GQ:SB 1/1:5:22:0,0,2,3 chr1 32196889 . G A 2881.07 PASS AC=1;AF=0.5;AN=2;DP=1115;FractionInformativeReads=1;MQ=60;set=variant6-variant18-variant20-variant35 GT:AD:DP:GQ:PL:SB 0/1:137,120:257:99:2761,0,3220:71,66,64,56 chr1 32256086 . T C 1780.85 PASS AC=2;AF=0.854;AN=2;DP=2594;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,64:64:99:2032,192,0:0,0,40,24 chr1 32260034 . A G 145.3 PASS AC=1;AF=0.714;AN=2;DP=85;FS=0;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant8-variant9-variant16-variant17-variant19-variant22-variant23-variant25-variant34-variant35-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:76:76,0,77:1,2,1,2 chr1 32266026 . A G 6099.17 PASS AC=2;AF=0.86;AN=2;DP=9136;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,255:255:99:7538,763,0:0,0,144,111 chr1 32279629 . G A 336.29 PASS AC=1;AF=0.55;AN=2;DP=2164;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:45,47:92:99:1015,0,1019:24,21,24,23 chr1 32280610 . T C 1753.14 PASS AC=1;AF=0.762;AN=2;DP=3585;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,65:99:99:1817,0,757:19,15,28,37 chr1 32372356 . TACAC TAC,T 47.89 PASS AC=1,1;AF=0.566,0.118;AN=2;DP=1724;set=filterInvariant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant35-variant37-variant38-filterInvariant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 2/1:46:99:4,4,27,11 chr1 32638096 . CTTTT CTTT,CT,C 605.04 PASS AC=1,0,0;AF=0.455,0.034,0.011;AN=2;DP=6856;set=variant-variant2-variant3-variant4-variant5-variant6-filterInvariant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-filterInvariant44 GT:DP:GQ:SB 0/1:143:99:50,46,22,25 chr1 32639057 . G C 1216.37 PASS AC=1;AF=0.533;AN=2;DP=526;FractionInformativeReads=1;MQ=60;set=variant6-variant10-variant12-variant16-variant18-variant20-variant26-variant27-variant30-variant31-variant35-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,24:41:99:542,0,432:9,8,12,12 chr1 32639637 . C T 451.16 PASS AC=1;AF=0.5;AN=2;DP=84;FractionInformativeReads=1;MQ=60;set=variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:27,21:48:99:479,0,705:14,13,11,10 chr1 32645476 . CG C 662.83 PASS AC=1;AF=0.5;AN=2;DP=376;MQ=60;set=variant18-variant35-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,39:85:99:1016,0,1242:17,29,17,22 chr1 32658062 . G GGT 456.93 PASS AC=1;AF=0.671;AN=2;DP=1870;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,37:53:99:1451,0,545:5,11,13,24 chr1 32661600 . CT C,CTT 86.68 PASS AC=0,1;AF=0.5,0.125;AN=2;DP=50;MQ=60;set=variant20-variant31-variant35-variant39 GT:DP:GQ:SB 0/2:9:46:1,2,4,2 chr1 32683402 . G A 932.87 PASS AC=1;AF=0.5;AN=2;DP=81;FS=2.952;FractionInformativeReads=1;MQ=60;MQRankSum=0.855;QD=11.52;ReadPosRankSum=-3.594;SOR=1.075;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:40,41:81:99:961,0,1051:20,20,17,24 chr1 32768050 . CT CTT,C 49.63 PASS AC=0,1;AF=0.182,0.318;AN=2;DP=307;set=filterInvariant-filterInvariant3-variant5-filterInvariant7-filterInvariant15-variant18-filterInvariant27-variant32-variant34-variant35-variant42 GT:DP:GQ:SB 0/2:30:99:19,3,7,1 chr1 32831543 . C T 604.22 PASS AC=1;AF=0.872;AN=2;DP=1578;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:21,23:44:99:632,0,488:10,11,10,13 chr1 32860161 . T C 510.01 PASS AC=2;AF=1;AN=2;DP=1665;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1620,129,0:0,0,7,36 chr1 33065947 . G C 6646.82 PASS AC=2;AF=1;AN=2;DP=7987;FS=0;MQ=60;MQRankSum=0.5;ReadPosRankSum=1.578;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,153:153:99:5059,458,0:0,0,79,74 chr1 33086999 . CA C,CAA 191.64 PASS AC=1,0;AF=0.476,0.024;AN=2;DP=1848;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-filterInvariant8-variant9-variant10-variant11-filterInvariant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-filterInvariant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-filterInvariant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:56:99:22,15,13,6 chr1 33116623 . T G 103.12 PASS AC=2;AF=0.952;AN=2;DP=507;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:672,60,0:0,0,13,7 chr1 33117071 . T G 2278.51 PASS AC=2;AF=1;AN=2;DP=4479;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,93:93:99:2948,278,0:0,0,36,57 chr1 33127730 . T C 661.89 PASS AC=2;AF=1;AN=2;DP=1013;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:636,57,0:0,0,14,5 chr1 33133968 . T C 3710.16 PASS AC=2;AF=1;AN=2;DP=3568;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,92:92:99:2664,276,0:0,0,47,45 chr1 33134774 . A C 760.02 PASS AC=2;AF=0.774;AN=2;DP=3468;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,92:92:99:2706,276,0:0,0,45,47 chr1 33134989 . A G 341.76 PASS AC=2;AF=0.943;AN=2;DP=2056;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1703,168,0:0,0,22,34 chr1 33138516 . A C 4661.04 PASS AC=2;AF=1;AN=2;DP=5344;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,110:110:99:3171,328,0:0,0,55,55 chr1 33138605 . T C 790 PASS AC=2;AF=0.955;AN=2;DP=3373;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:1817,177,0:0,0,21,38 chr1 33139043 . C T,CT 1355.01 PASS AC=2,0;AF=0.955,0.034;AN=2;DP=1669;MQ=60;set=Intersection GT:DP:GQ:SB 1/1:38:99:0,0,18,20 chr1 33139044 . T TC 321.06 PASS AC=2;AF=0.932;AN=2;DP=1659;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1710,114,0:0,0,18,20 chr1 33146501 . A G 1260.66 PASS AC=2;AF=0.955;AN=2;DP=3823;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:2397,228,0:0,0,48,28 chr1 33147143 . C T 2546.19 PASS AC=2;AF=1;AN=2;DP=3499;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,78:78:99:2897,234,0:0,0,33,45 chr1 33160878 . C T 1197.31 PASS AC=2;AF=0.955;AN=2;DP=7415;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,165:165:99:5218,495,0:0,0,98,67 chr1 33161212 . T C 1306.49 PASS AC=2;AF=0.955;AN=2;DP=9321;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,242:242:99:7564,725,0:0,0,123,119 chr1 33231380 . T G 3469.03 PASS AC=1;AF=0.531;AN=2;DP=4374;MQ=60;set=variant5-variant8-variant11-variant12-variant17-variant22-variant23-variant28-variant29-variant31-variant33-variant35-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:176,147:323:99:5314,0,7404:90,86,73,74 chr1 33231403 . G T 3244.81 PASS AC=1;AF=0.531;AN=2;DP=4110;MQ=60;set=variant5-variant8-variant11-variant12-variant17-variant22-variant23-variant28-variant29-variant31-variant33-variant35-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:169,143:312:99:5224,0,7251:86,83,71,72 chr1 33233323 . A G 1596.92 PASS AC=2;AF=1;AN=2;DP=2309;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:1719,140,0:0,0,36,11 chr1 33234128 . G A 513.76 PASS AC=1;AF=0.533;AN=2;DP=353;FractionInformativeReads=1;set=variant5-variant8-variant12-variant17-variant22-variant23-variant28-variant29-variant31-variant33-variant35-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,9:25:99:205,0,398:10,6,6,3 chr1 33234136 . T C 729.13 PASS AC=2;AF=1;AN=2;DP=1188;FS=0;MQ=60;MQRankSum=0.8;ReadPosRankSum=0.933;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:863,75,0:0,0,15,10 chr1 33234153 . G A 766.61 PASS AC=1;AF=0.676;AN=2;DP=1197;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:14,15:29:99:333,0,329:9,5,9,6 chr1 33236554 . A C 389.54 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=1395;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:74,23:97:99:303,0,1326:13,61,23,0 chr1 33236558 . T C 383.51 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=2336;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:80,18:98:72:72,0,2917:20,60,18,0 chr1 33237892 . T C 163.37 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=2826;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:97,23:120:99:246,0,4431:15,82,23,0 chr1 33237898 . A C 549.82 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=940;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:102,18:120:99:241,0,4473:18,84,18,0 chr1 33240185 . G C 460.09 PASS AC=1;AF=0.531;AN=2;DP=633;MQ=60;set=variant5-variant8-variant11-variant12-variant17-variant22-variant23-variant28-variant29-variant31-variant33-variant35-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,12:35:99:364,0,512:11,12,6,6 chr1 33240596 . G T 106.39 PASS AC=1;AF=0.531;AN=2;DP=224;FractionInformativeReads=1;MQ=60;set=variant5-variant8-variant11-variant12-variant17-variant22-variant23-variant28-variant29-variant31-variant33-variant35-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,10:14:99:246,0,99:2,2,6,4 chr1 33246440 . T C 605.75 PASS AC=1;AF=0.531;AN=2;DP=491;FractionInformativeReads=1;MQ=60;set=variant5-variant8-variant11-variant12-variant17-variant22-variant23-variant28-variant29-variant31-variant33-variant35-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,24:38:99:664,0,312:9,5,17,7 chr1 33252099 . TCACATGCATGACTATTCCTAGCC T 772.34 PASS AC=1;AF=0.531;AN=2;DP=1310;MQ=60;set=variant5-variant8-variant11-variant12-variant17-variant22-variant23-variant28-variant29-variant31-variant33-variant35-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,15:59:99:473,0,9013:14,30,4,11 chr1 33256884 . C A 1258.31 PASS AC=1;AF=0.538;AN=2;DP=3359;MQ=60;set=variant2-variant5-variant6-variant8-variant11-variant12-variant15-variant17-variant18-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,78:139:99:2098,0,1564:22,39,30,48 chr1 33275981 . T C 199.4 PASS AC=1;AF=0.591;AN=2;DP=88;FractionInformativeReads=1;MQ=60;set=variant8-variant11-variant12-variant17-variant28-variant29-variant31-variant35-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,2:4:75:78,0,75:2,0,2,0 chr1 33276424 . G A 3536.51 PASS AC=2;AF=1;AN=2;DP=4721;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,111:111:99:3431,332,0:0,0,60,51 chr1 33283583 . G C 1254.06 PASS AC=1;AF=0.531;AN=2;DP=1656;MQ=60;set=variant5-variant8-variant11-variant12-variant17-variant22-variant23-variant28-variant29-variant31-variant33-variant35-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,71:129:99:1736,0,1392:26,32,37,34 chr1 33293748 . T C 365.93 PASS AC=2;AF=1;AN=2;DP=489;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:461,36,0:0,0,0,12 chr1 33299816 . A T 1024.59 PASS AC=2;AF=1;AN=2;DP=1056;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:689,60,0:0,0,5,15 chr1 33318561 . T C 1955.23 PASS AC=2;AF=1;AN=2;DP=2106;FS=0;MQ=60;MQRankSum=-0.139;ReadPosRankSum=1.455;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,63:63:99:2251,189,0:0,0,48,15 chr1 33318634 . G A 4633.44 PASS AC=2;AF=1;AN=2;DP=5130;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,146:147:99:4518,429,0:1,0,93,53 chr1 33321796 . G A 5894.55 PASS AC=1;AF=0.5;AN=2;DP=3373;MQ=60;set=variant11-variant16-variant32-variant34-variant35-variant36-variant38 GT:AD:DP:GQ:PL:SB 0/1:283,228:511:99:5127,0,6821:147,136,120,108 chr1 33322690 . C CT 813.67 PASS AC=1;AF=0.533;AN=2;DP=783;MQ=60;set=variant5-variant8-variant11-variant12-variant17-variant22-variant23-variant28-variant29-variant31-variant33-variant35-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,23:62:99:526,0,1034:18,21,10,13 chr1 33322919 . CT C 77.46 PASS AC=1;AF=0.794;AN=2;DP=288;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:3,4:7:65:94,0,65:1,2,0,4 chr1 33324088 . C G 5273.94 PASS AC=1;AF=0.533;AN=2;DP=5837;MQ=60;set=variant5-variant8-variant11-variant12-variant17-variant22-variant23-variant28-variant29-variant31-variant33-variant35-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:227,194:421:99:4747,0,5674:119,108,102,92 chr1 33324136 . T C 16821.5 PASS AC=1;AF=0.762;AN=2;DP=19320;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:220,226:446:99:5525,0,5314:118,102,109,117 chr1 33328165 . G A 1880.76 PASS AC=1;AF=0.724;AN=2;DP=2381;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:25,42:67:99:1074,0,686:13,12,23,19 chr1 33330432 . A G 1922.4 PASS AC=2;AF=1;AN=2;DP=3901;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,106:106:99:3360,317,0:0,0,40,66 chr1 33402334 . GA G,GAA 1451.02 PASS AC=1,0;AF=0.432,0.068;AN=2;DP=11913;set=Intersection GT:DP:GQ:SB 0/1:280:99:101,80,55,44 chr1 33430102 . T G 309.99 PASS AC=2;AF=1;AN=2;DP=421;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:357,24,0:0,0,7,1 chr1 33430121 . G T 154.62 PASS AC=1;AF=0.5;AN=2;DP=17;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.83;QD=9.1;ReadPosRankSum=-0.537;SOR=0.368;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:10,7:17:99:183,0,315:8,2,5,2 chr1 33485789 . AACACACAC AACACACACACACACAC,AACAC,AACACACACACACAC,A,AACACAC,AACACACACAC,AAC,AACACACACACAC,AACACACACACACACACACACAC 238.02 PASS AC=0,1,0,0,0,0,0,0,0;AF=0.024,0.146,0.183,0.28,0.061,0.049,0.024,0.012,0.024;AN=2;DP=777;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-filterInvariant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:9:68:0,3,0,6 chr1 33497070 . G A 1328.84 PASS AC=2;AF=0.966;AN=2;DP=2043;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1471,129,0:0,0,32,11 chr1 33546860 . G C 1041.97 PASS AC=1;AF=0.5;AN=2;DP=745;FractionInformativeReads=1;MQ=60;set=variant8-variant18-variant24-variant35-variant36-variant38 GT:AD:DP:GQ:PL:SB 0/1:73,54:127:99:1190,0,1812:35,38,27,27 chr1 33560338 . A G 688.67 PASS AC=2;AF=0.977;AN=2;DP=2478;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:1836,177,0:0,0,23,36 chr1 33611890 . C T 421.53 PASS AC=2;AF=0.756;AN=2;DP=2663;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,85:85:99:2448,254,0:0,0,50,35 chr1 33641932 . A G 962.34 PASS AC=2;AF=1;AN=2;DP=3118;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.231;ReadPosRankSum=1.675;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,83:83:99:2374,248,0:0,0,44,39 chr1 33642152 . C T 633.93 PASS AC=2;AF=0.763;AN=2;DP=3524;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,84:84:99:2550,252,0:0,0,32,52 chr1 33646950 . A G 2440.87 PASS AC=2;AF=0.763;AN=2;DP=8114;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,274:274:99:9235,822,0:0,0,125,149 chr1 33741787 . G A 1885.73 PASS AC=1;AF=0.526;AN=2;DP=3752;MQ=60;set=variant2-variant3-variant5-variant11-variant12-variant16-variant17-variant19-variant20-variant23-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant38 GT:AD:DP:GQ:PL:SB 0/1:101,93:194:99:2184,0,2642:47,54,46,47 chr1 33741895 . G A 1038.31 PASS AC=1;AF=0.526;AN=2;DP=2557;MQ=60;set=variant2-variant3-variant5-variant11-variant12-variant16-variant17-variant19-variant20-variant23-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant38 GT:AD:DP:GQ:PL:SB 0/1:74,77:151:99:1817,0,2040:41,33,36,41 chr1 33742228 . T C 538.68 PASS AC=2;AF=1;AN=2;DP=1225;FS=0;MQ=60;MQRankSum=1.22;ReadPosRankSum=1.348;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1273,121,0:0,0,16,25 chr1 33746163 . T C 516.56 PASS AC=2;AF=1;AN=2;DP=1414;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,31:31:93:1137,93,0:0,0,6,25 chr1 33760743 . T C 1421.22 PASS AC=1;AF=0.821;AN=2;DP=5737;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:86,82:168:99:1857,0,1959:51,35,50,32 chr1 33764935 . GT GTTT,G 280.84 PASS AC=1,1;AF=0.476,0.256;AN=2;DP=1721;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 2/1:37:99:0,0,16,21 chr1 33765272 . A G 917.57 PASS AC=1;AF=0.629;AN=2;DP=2221;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,42:95:99:1319,0,1421:33,20,29,13 chr1 33766410 . TGGAGAA T 163.89 PASS AC=1;AF=0.66;AN=2;DP=196;MQ=60;set=variant3-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant18-variant21-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant34-variant35-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,3:9:99:108,0,416:1,5,0,3 chr1 33777524 . T C 75.37 PASS AC=2;AF=0.75;AN=2;DP=1285;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1456,123,0:0,0,32,9 chr1 33778226 . G A 388.61 PASS AC=1;AF=0.607;AN=2;DP=708;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant18-variant21-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,10:28:99:325,0,554:8,10,4,6 chr1 33778591 . T C 384.67 PASS AC=2;AF=0.75;AN=2;DP=1794;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:919,84,0:0,0,12,16 chr1 33789382 . C T 448.16 PASS AC=1;AF=0.607;AN=2;DP=1675;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant18-variant21-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,30:45:99:798,0,321:9,6,14,16 chr1 33789520 . C A 1231.22 PASS AC=2;AF=0.75;AN=2;DP=4407;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,116:117:99:3385,338,0:1,0,67,49 chr1 33789588 . T C 1333.45 PASS AC=2;AF=0.75;AN=2;DP=5298;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,135:135:99:4125,405,0:0,0,65,70 chr1 33789670 . G A 1306.07 PASS AC=1;AF=0.579;AN=2;DP=2180;MQ=60;set=variant2-variant3-variant5-variant11-variant12-variant16-variant17-variant19-variant20-variant23-variant26-variant28-variant29-variant31-variant33-variant35-variant36-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:57,67:124:99:1701,0,1379:26,31,30,37 chr1 33790496 . G A 616.03 PASS AC=1;AF=0.605;AN=2;DP=1347;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant11-variant12-variant16-variant17-variant19-variant20-variant23-variant26-variant28-variant29-variant31-variant33-variant35-variant36-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:38,42:80:99:1168,0,952:24,14,29,13 chr1 33799548 . C T 78.22 PASS AC=1;AF=0.588;AN=2;DP=239;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant11-variant12-variant16-variant17-variant19-variant23-variant26-variant28-variant29-variant31-variant33-variant35-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,6:17:99:206,0,326:8,3,6,0 chr1 33799900 . G A 929.55 PASS AC=1;AF=0.579;AN=2;DP=1245;MQ=60;set=variant2-variant3-variant5-variant11-variant12-variant16-variant17-variant19-variant20-variant23-variant26-variant28-variant29-variant31-variant33-variant35-variant36-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:37,34:71:99:891,0,1098:9,28,9,25 chr1 33820134 . C T 655.38 PASS AC=1;AF=0.579;AN=2;DP=1730;MQ=60;set=variant2-variant3-variant5-variant11-variant12-variant16-variant17-variant19-variant20-variant23-variant26-variant28-variant29-variant31-variant33-variant35-variant36-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:67,49:116:99:1222,0,1760:33,34,28,21 chr1 33832865 . A G 1772.12 PASS AC=2;AF=0.75;AN=2;DP=8098;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,249:249:99:7253,744,0:0,0,119,130 chr1 33834416 . T C 380.31 PASS AC=1;AF=0.531;AN=2;DP=458;MQ=60;set=variant7-variant9-variant10-variant14-variant15-variant21-variant25-variant26-variant27-variant30-variant31-variant35-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,19:34:99:528,0,443:3,12,6,13 chr1 33834455 . A G 104.25 PASS AC=2;AF=0.732;AN=2;DP=499;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:587,45,0:0,0,4,11 chr1 33836796 . C G 921.4 PASS AC=2;AF=0.75;AN=2;DP=2659;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,87:87:99:2725,259,0:0,0,28,59 chr1 33840795 . T G 1136.96 PASS AC=1;AF=0.553;AN=2;DP=1334;MQ=60;set=variant3-variant7-variant9-variant10-variant12-variant14-variant15-variant21-variant24-variant25-variant26-variant27-variant30-variant31-variant35-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,41:77:99:1033,0,879:23,13,22,19 chr1 33944993 . A G 2460.84 PASS AC=1;AF=0.5;AN=2;DP=737;FractionInformativeReads=1;MQ=60;set=variant26-variant31-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:114,103:217:99:2362,0,2967:62,52,48,55 chr1 33954469 . AG A 823.73 PASS AC=2;AF=0.821;AN=2;DP=965;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:1064,87,0:0,0,22,7 chr1 33954805 . C T 697.04 PASS AC=1;AF=0.6;AN=2;DP=606;FractionInformativeReads=1;MQ=60;set=variant5-variant6-variant7-variant12-variant19-variant35-variant36-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:31,24:55:99:752,0,890:8,23,5,19 chr1 33957152 . T G 2173.7 PASS AC=2;AF=1;AN=2;DP=4276;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,69:69:99:2203,207,0:0,0,39,30 chr1 33957773 . T C 4857.69 PASS AC=2;AF=0.821;AN=2;DP=7140;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,164:164:99:5034,492,0:0,0,76,88 chr1 33957878 . T C 3389.63 PASS AC=2;AF=0.821;AN=2;DP=3832;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,94:94:99:3184,282,0:0,0,46,48 chr1 33960062 . A G 3237.3 PASS AC=2;AF=0.821;AN=2;DP=4272;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,106:106:99:3189,318,0:0,0,56,50 chr1 33961147 . T G 7819.59 PASS AC=2;AF=0.821;AN=2;DP=7875;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,187:187:99:5952,561,0:0,0,111,76 chr1 33961722 . C T 1351.01 PASS AC=2;AF=0.821;AN=2;DP=2512;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,85:85:99:2605,255,0:0,0,48,37 chr1 33985353 . C G 5604.24 PASS AC=2;AF=0.743;AN=2;DP=7293;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant31-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,251:251:99:7894,753,0:0,0,117,134 chr1 33999174 . GT G 969.96 PASS AC=2;AF=0.704;AN=2;DP=1570;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant22-variant23-variant28-variant30-variant31-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1688,159,0:0,0,37,16 chr1 33999809 . G A 255.31 PASS AC=2;AF=0.828;AN=2;DP=197;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant6-variant7-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant23-variant24-variant26-variant27-variant28-variant30-variant31-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:87,6,0:0,0,1,1 chr1 34003368 . G A 197.39 PASS AC=2;AF=0.704;AN=2;DP=812;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant22-variant23-variant28-variant30-variant31-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,31:31:93:1129,93,0:0,0,11,20 chr1 34033512 . G C 1928.26 PASS AC=1;AF=0.6;AN=2;DP=1547;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant6-variant7-variant9-variant12-variant16-variant17-variant18-variant19-variant20-variant27-variant29-variant31-variant35-variant36-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:47,40:87:99:962,0,1199:20,27,19,21 chr1 34033636 . G A 1555.97 PASS AC=1;AF=0.6;AN=2;DP=1131;MQ=60;set=variant-variant5-variant6-variant7-variant9-variant12-variant16-variant17-variant18-variant19-variant20-variant27-variant29-variant31-variant35-variant36-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:27,39:66:99:861,0,561:12,15,20,19 chr1 34033737 . A C 331.77 PASS AC=1;AF=0.625;AN=2;DP=182;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant6-variant9-variant12-variant16-variant17-variant19-variant20-variant27-variant35-variant36-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:4,7:11:99:273,0,165:1,3,0,7 chr1 34033756 . G A 318.49 PASS AC=1;AF=0.643;AN=2;DP=126;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant6-variant9-variant12-variant16-variant17-variant19-variant35-variant36-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:2,2:4:78:78,0,127:0,2,0,2 chr1 34038214 . T C 585.58 PASS AC=1;AF=0.686;AN=2;DP=2343;MQ=60;set=variant2-variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,38:81:99:841,0,960:25,18,20,18 chr1 34038413 . A C 144.36 PASS AC=1;AF=0.671;AN=2;DP=822;MQ=60;set=variant2-variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,11:16:99:334,0,170:1,4,1,10 chr1 34038464 . CT C 118.68 PASS AC=1;AF=0.688;AN=2;DP=289;FS=0;MQ=60;set=variant2-variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,2:7:69:69,0,198:1,4,0,2 chr1 34038468 . T C 127.71 PASS AC=1;AF=0.688;AN=2;DP=265;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,2:7:69:69,0,198:1,4,0,2 chr1 34043169 . TC T 1515 PASS AC=2;AF=1;AN=2;DP=3060;FS=0;MQ=60;MQRankSum=1.347;ReadPosRankSum=1.54;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:1926,187,0:0,0,25,37 chr1 34052605 . A G 129.16 PASS AC=1;AF=0.737;AN=2;DP=573;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,9:23:99:256,0,319:10,4,6,3 chr1 34057453 . A C 743.51 PASS AC=1;AF=0.591;AN=2;DP=1569;MQ=60;set=variant6-variant8-variant13-variant14-variant15-variant16-variant21-variant22-variant24-variant25-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,37:74:99:1063,0,996:21,16,21,16 chr1 34070826 . G A 196.77 PASS AC=1;AF=0.703;AN=2;DP=437;MQ=60;set=variant-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,10:15:99:326,0,163:5,0,9,1 chr1 34071434 . C T 1063.14 PASS AC=1;AF=0.697;AN=2;DP=2048;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,38:76:99:885,0,919:23,15,19,19 chr1 34071525 . C T 1635.83 PASS AC=1;AF=0.703;AN=2;DP=2506;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,44:89:99:1123,0,1187:24,21,25,19 chr1 34112467 . A C 58.07 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=142;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:54,17:71:88:88,0,2455:7,47,17,0 chr1 34112469 . T C 59.85 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=68;FS=126.269;FractionInformativeReads=0.956;MQ=60;MQRankSum=-0.129;QD=0.88;ReadPosRankSum=-5.718;SOR=5.666;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:49,16:65:88:88,0,2455:2,47,16,0 chr1 34158472 . C T 1521.65 PASS AC=1;AF=0.625;AN=2;DP=3201;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant21-variant26-variant27-variant28-variant29-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:68,53:121:99:2007,0,3676:40,28,33,20 chr1 34158482 . C T 1684.95 PASS AC=1;AF=0.625;AN=2;DP=3529;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant21-variant26-variant27-variant28-variant29-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:74,57:131:99:2067,0,3810:43,31,34,23 chr1 34189552 . C T 659.35 PASS AC=1;AF=0.659;AN=2;DP=333;FractionInformativeReads=1;MQ=60;set=variant6-variant10-variant11-variant12-variant13-variant15-variant18-variant23-variant24-variant26-variant27-variant28-variant30-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,9:16:99:350,0,272:7,0,9,0 chr1 34189917 . C T 783.59 PASS AC=2;AF=0.716;AN=2;DP=3535;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,81:81:99:2426,241,0:0,0,31,50 chr1 34189957 . AG A 1142.46 PASS AC=2;AF=1;AN=2;DP=2574;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1481,129,0:0,0,13,30 chr1 34205134 . C T 232.71 PASS AC=1;AF=0.757;AN=2;DP=495;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,6:18:99:201,0,445:2,10,0,6 chr1 34254108 . CAA CAAA,CA,CAAAA,C 127.75 PASS AC=1,0,0,0;AF=0.333,0.185,0.019,0.019;AN=2;DP=898;set=variant2-variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant18-variant21-variant23-variant24-variant25-variant27-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:25:99:12,0,8,5 chr1 34270498 . G A 3640.94 PASS AC=2;AF=0.791;AN=2;DP=4748;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,112:113:99:3288,326,0:0,1,43,69 chr1 34278533 . C T 257.39 PASS AC=2;AF=0.75;AN=2;DP=660;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:539,51,0:0,0,11,6 chr1 34278562 . A G 594.52 PASS AC=2;AF=0.791;AN=2;DP=1123;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:856,81,0:0,0,16,11 chr1 34279526 . T C 238.54 PASS AC=1;AF=0.571;AN=2;DP=69;FractionInformativeReads=1;MQ=60;set=variant2-variant11-variant18-variant23-variant27-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,8:10:48:249,0,48:2,0,6,2 chr1 34279742 . A T 1110.14 PASS AC=2;AF=0.791;AN=2;DP=1831;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1597,159,0:0,0,25,28 chr1 34279849 . T C 394.48 PASS AC=1;AF=0.571;AN=2;DP=135;FractionInformativeReads=1;MQ=60;set=variant2-variant11-variant18-variant27-variant35-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,10:27:99:276,0,434:6,11,3,7 chr1 34285342 . G A 254.26 PASS AC=1;AF=0.671;AN=2;DP=1505;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:39,21:60:99:454,0,925:19,20,15,6 chr1 34285381 . C T 431.94 PASS AC=1;AF=0.671;AN=2;DP=2278;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:40,38:78:99:941,0,1025:20,20,22,16 chr1 34285995 . G A 256.07 PASS AC=1;AF=0.681;AN=2;DP=1068;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:11,12:23:99:234,0,315:6,5,6,6 chr1 34286166 . CAAAA CA,CAA,C,CAAA 223.94 PASS AC=0,2,0,0;AF=0.117,0.183,0.033,0.283;AN=2;DP=893;set=variant-filterInvariant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-filterInvariant18-variant19-variant20-variant22-filterInvariant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant41-filterInvariant42-variant43 GT:DP:GQ:SB 2/2:26:1:3,3,10,10 chr1 34286189 . A C 266.27 PASS AC=2;AF=0.744;AN=2;DP=955;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-filterInvariant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,28:29:68:975,68,0:1,0,14,14 chr1 34326062 . C T 558.67 PASS AC=2;AF=0.818;AN=2;DP=1142;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:583,54,0:0,0,13,5 chr1 34326409 . T C 4113.99 PASS AC=2;AF=1;AN=2;DP=4407;FS=0;MQ=60;MQRankSum=0.874;ReadPosRankSum=0.478;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,102:102:99:3474,306,0:0,0,30,72 chr1 34327944 . CTGTGTGTGTGTGTGTGTGTG CTGTGTGTGTGTGTGTGTGTGTGTGTG,CTGTGTGTGTGTGTGTGTG,CTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG,CTGTGTGTGTGTGTGTGTGTGTGTG,C,CTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG,CTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG,CTGTGTGTGTGTGTGTGTGTGTG,CTGTGTGTGTGTG,CTGTGTGTGTGTGTGTGTGTGTGTGTGTG,CTGTGTGTGTGTGTG,CTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG,CTGTGTGTGTGTGTGTG 206.16 PASS AC=0,0,0,0,0,0,0,0,0,0,0,2,0;AF=0.094,0.094,0.063,0.219,0.031,0.031,0.063,0.063,0.063,0.031,0.063,0.063,0.031;AN=2;DP=122;FS=0;set=variant2-variant4-variant5-variant7-variant12-variant13-variant14-variant19-variant23-variant29-variant30-variant35-variant37-variant40-variant41-variant43 GT:DP:GQ:SB 12/12:1:9:0,0,1,0 chr1 34328552 . G A 189.51 PASS AC=2;AF=0.703;AN=2;DP=1916;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-filterInvariant38-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1258,111,0:0,0,25,12 chr1 34329897 . T C 2501.99 PASS AC=2;AF=0.943;AN=2;DP=4212;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:2490,231,0:0,0,51,26 chr1 34330067 . A C 3194.7 PASS AC=2;AF=0.818;AN=2;DP=7171;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,203:203:99:6216,608,0:0,0,105,98 chr1 34330537 . G GGGA 508.82 PASS AC=1;AF=0.622;AN=2;DP=376;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,3:5:75:116,0,75:2,0,0,3 chr1 34330549 . G A 135.15 PASS AC=1;AF=0.5;AN=2;DP=98;FractionInformativeReads=1;set=variant2-variant4-variant5-variant10-variant19-variant20-variant24-variant29-variant30-variant31-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:1,3:4:33:120,0,33:0,1,3,0 chr1 34383554 . T C 942.33 PASS AC=1;AF=0.542;AN=2;DP=689;FractionInformativeReads=1;MQ=60;set=variant10-variant11-variant12-variant14-variant17-variant18-variant20-variant23-variant33-variant35-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:31,19:50:99:459,0,908:24,7,10,9 chr1 34684463 . G A 516.91 PASS AC=2;AF=0.842;AN=2;DP=2695;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,86:86:99:2751,258,0:0,0,45,41 chr1 34684571 . CACACAT C 696.71 PASS AC=2;AF=0.7;AN=2;DP=2275;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:2508,171,0:0,0,21,36 chr1 34684621 . A G 611.18 PASS AC=2;AF=0.829;AN=2;DP=2457;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1366,120,0:0,0,14,26 chr1 35183838 . A C 1416.85 PASS AC=1;AF=0.762;AN=2;DP=2267;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,21:34:99:518,0,325:10,3,13,8 chr1 35184033 . C T 1697.02 PASS AC=1;AF=0.756;AN=2;DP=2197;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,24:59:99:650,0,894:14,21,10,14 chr1 35184084 . C T 720 PASS AC=1;AF=0.75;AN=2;DP=1121;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,12:29:99:315,0,545:4,13,5,7 chr1 35228604 . C T 611.15 PASS AC=1;AF=0.587;AN=2;DP=1428;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant9-variant11-variant13-variant15-variant16-variant18-variant21-variant23-variant25-variant26-variant29-variant32-variant34-variant35-variant36-variant37-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:33,30:63:99:799,0,914:14,19,11,19 chr1 35228693 . C A 1524.79 PASS AC=1;AF=0.6;AN=2;DP=288;FractionInformativeReads=1;MQ=60;set=variant4-variant13-variant15-variant16-variant35 GT:AD:DP:GQ:PL:SB 0/1:35,29:64:99:697,0,962:18,17,17,12 chr1 35246653 . T C 207.7 PASS AC=1;AF=0.625;AN=2;DP=768;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,12:31:99:355,0,539:14,5,9,3 chr1 35251161 . C T 1110.92 PASS AC=1;AF=0.538;AN=2;DP=1434;MQ=60;set=variant-variant2-variant6-variant7-variant9-variant11-variant18-variant21-variant23-variant26-variant29-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:52,86:138:99:2121,0,1164:22,30,37,49 chr1 35251229 . G A 852.07 PASS AC=1;AF=0.714;AN=2;DP=2227;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant34-variant35-variant36-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:35,33:68:99:969,0,1055:10,25,10,23 chr1 35259961 . A G 1785.36 PASS AC=1;AF=0.773;AN=2;DP=10179;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:132,107:239:99:2808,0,3584:68,64,53,54 chr1 35260769 . C T 1197.38 PASS AC=1;AF=0.633;AN=2;DP=4207;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant34-variant35-variant36-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:61,86:147:99:2175,0,1669:20,41,31,55 chr1 35260929 . G A 232.42 PASS AC=1;AF=0.773;AN=2;DP=1827;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:14,19:33:99:532,0,474:7,7,9,10 chr1 35318269 . A ATT,AT,ATTT 94.03 PASS AC=2,0,0;AF=0.614,0.029,0.014;AN=2;DP=728;set=variant-variant2-variant4-variant5-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:19:57:0,0,14,5 chr1 35318368 . A G 1522.15 PASS AC=2;AF=0.966;AN=2;DP=3200;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:2409,216,0:0,0,43,29 chr1 35318439 . A G 2212.03 PASS AC=2;AF=0.966;AN=2;DP=5013;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,117:117:99:3665,351,0:0,0,66,51 chr1 35319323 . C T 5725.13 PASS AC=2;AF=0.966;AN=2;DP=5201;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,131:131:99:4605,393,0:0,0,27,104 chr1 35321242 . A C 2967.06 PASS AC=1;AF=0.5;AN=2;DP=1296;FractionInformativeReads=1;MQ=60;set=variant2-variant12-variant19-variant35-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:122,126:248:99:3159,0,2949:66,56,68,58 chr1 35321684 . A AT,ATT 54.25 PASS AC=1,1;AF=0.535,0.081;AN=2;DP=1664;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-filterInvariant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/2:25:99:0,3,3,19 chr1 35324786 . C T 95.06 PASS AC=1;AF=0.75;AN=2;DP=10;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.937;ReadPosRankSum=0.937;set=variant2-variant35 GT:AD:DP:GQ:PL:SB 0/1:3,4:7:74:110,0,74:1,2,1,3 chr1 35332926 . G C 598.97 PASS AC=1;AF=0.531;AN=2;DP=559;MQ=60;set=variant5-variant6-variant10-variant11-variant12-variant15-variant20-variant23-variant29-variant30-variant31-variant35-variant37-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,15:35:99:454,0,627:10,10,10,5 chr1 35333126 . T C 1910.77 PASS AC=1;AF=0.583;AN=2;DP=1450;MQ=60;set=variant2-variant12-variant19-variant35-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:159,128:287:99:2911,0,3829:85,74,67,61 chr1 35350573 . CT C 1108.21 PASS AC=1;AF=0.5;AN=2;DP=1097;MQ=60;set=variant6-variant11-variant19-variant20-variant29-variant30-variant31-variant35-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,49:100:99:1449,0,1499:31,20,24,25 chr1 35449179 . CA C,CAAAAAAAAA 72.08 PASS AC=2,0;AF=0.5,0.167;AN=2;DP=25;set=variant3-variant35-variant42 GT:DP:GQ:SB 1/1:6:17:0,0,5,1 chr1 35545022 . G GGC 3281.24 PASS AC=2;AF=1;AN=2;DP=2472;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:2428,165,0:0,0,29,26 chr1 35561510 . G A 3367.07 PASS AC=2;AF=0.942;AN=2;DP=3429;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,63:63:99:1841,189,0:0,0,30,33 chr1 35562965 . G A 3735.23 PASS AC=2;AF=0.955;AN=2;DP=4613;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,109:109:99:3444,327,0:0,0,65,44 chr1 35563206 . C G 2115.8 PASS AC=2;AF=0.943;AN=2;DP=2308;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:2128,174,0:0,0,13,45 chr1 35576145 . C T 106.77 PASS AC=2;AF=0.973;AN=2;DP=213;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:218,18,0:0,0,3,3 chr1 35581295 . GT G 12076.8 PASS AC=2;AF=0.955;AN=2;DP=14809;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,294:294:99:10479,885,0:0,0,151,143 chr1 35879852 . C G 235.95 PASS AC=1;AF=0.5;AN=2;DP=12;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.831;QD=19.66;ReadPosRankSum=0.831;SOR=1.022;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:5,7:12:99:264,0,189:0,5,0,7 chr1 35899684 . CTTT CT,CTT,C,CTTTT 158.79 PASS AC=1,0,0,0;AF=0.227,0.227,0.045,0.023;AN=2;DP=712;set=variant2-variant4-variant5-filterInvariant6-filterInvariant9-variant10-variant11-filterInvariant12-variant18-variant19-variant23-variant24-variant26-filterInvariant27-filterInvariant29-filterInvariant30-variant31-variant35-variant37-variant39-filterInvariant40-filterInvariant43 GT:DP:GQ:SB 0/1:13:84:3,6,1,3 chr1 35919051 . C G 228.13 PASS AC=1;AF=0.5;AN=2;DP=14;FS=2.963;FractionInformativeReads=1;MQ=60;MQRankSum=-1.733;QD=16.3;ReadPosRankSum=-1.6;SOR=0.18;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:5,9:14:99:256,0,165:5,0,7,2 chr1 35925861 . C A 2372.01 PASS AC=2;AF=0.932;AN=2;DP=3065;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:1740,170,0:0,0,36,21 chr1 36107250 . G C 1661.38 PASS AC=2;AF=1;AN=2;DP=3713;FS=0;MQ=60;MQRankSum=0.709;ReadPosRankSum=0.312;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,82:82:99:2709,246,0:0,0,31,51 chr1 36107510 . C A 334.14 PASS AC=2;AF=0.875;AN=2;DP=931;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:555,57,0:0,0,9,10 chr1 36184975 . G A 4341.45 PASS AC=2;AF=1;AN=2;DP=6049;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,143:143:99:4190,426,0:0,0,62,81 chr1 36205166 . A G 1435.19 PASS AC=2;AF=0.884;AN=2;DP=1731;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1359,126,0:0,0,13,29 chr1 36213712 . G T 1094.11 PASS AC=2;AF=1;AN=2;DP=1659;FS=0;MQ=60;MQRankSum=1.639;ReadPosRankSum=1.639;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1575,135,0:0,0,14,31 chr1 36214421 . CTTTTTTTTTTT CTTTTTTTTTT,CTTTTTTTTTTTT,C,CTTTTTTTTT,CTTTTTTTT,CTT 172.83 PASS AC=0,0,0,0,1,0;AF=0.25,0.036,0.107,0.071,0.036,0.036;AN=2;DP=452;set=variant2-variant8-variant11-filterInvariant14-filterInvariant16-variant18-filterInvariant19-variant27-variant34-filterInvariant35-variant36-variant37-variant41-variant42 GT:DP:GQ:SB 0/5:17:69:4,9,0,4 chr1 36216835 . C T 537.75 PASS AC=2;AF=0.884;AN=2;DP=1002;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:508,42,0:0,0,11,3 chr1 36282399 . CAAAAAAAAAAAAA CAAAAAAAAAAAA,C 50.57 PASS AC=1,0;AF=0.438,0.094;AN=2;DP=386;set=filterInvariant7-variant11-variant12-filterInvariant19-variant23-variant25-filterInvariant27-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant41-filterInvariant43 GT:DP:GQ:SB 0/1:22:91:12,3,7,0 chr1 36282417 . A G,AG 1115.19 PASS AC=2,0;AF=0.854,0.012;AN=2;DP=1359;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:44:99:0,1,34,9 chr1 36288635 . G A 955.18 PASS AC=1;AF=0.5;AN=2;DP=153;FractionInformativeReads=1;MQ=60;set=variant20-variant35 GT:AD:DP:GQ:PL:SB 0/1:38,40:78:99:991,0,988:11,27,14,26 chr1 36307412 . CATAT C,CAT 212.59 PASS AC=0,2;AF=0.139,0.639;AN=2;DP=653;FS=0;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-filterInvariant27-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-filterInvariant42-variant43-variant44 GT:DP:GQ:SB 2/2:11:33:0,0,3,8 chr1 36316418 . C CA 1332.99 PASS AC=2;AF=1;AN=2;DP=2394;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:899,96,0:0,0,23,9 chr1 36316571 . A C 3902.99 PASS AC=2;AF=0.872;AN=2;DP=6545;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,180:180:99:5065,537,0:0,0,94,86 chr1 36321253 . CTT CT,CTTT,C 241.93 PASS AC=1,0,0;AF=0.487,0.013,0.013;AN=2;DP=3886;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-filterInvariant12-filterInvariant13-variant14-variant15-variant16-filterInvariant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-filterInvariant28-variant29-filterInvariant30-variant32-variant33-filterInvariant34-variant35-variant36-variant37-variant38-variant39-filterInvariant40-variant41-variant42-filterInvariant43-variant44 GT:DP:GQ:SB 0/1:67:99:17,23,6,21 chr1 36322431 . AGG A 111.85 PASS AC=2;AF=0.974;AN=2;DP=322;FS=0;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:191,15,0:0,0,5,0 chr1 36372409 . GA G,GAA 72.76 PASS AC=1,0;AF=0.467,0.033;AN=2;DP=1101;set=filterInvariant-variant3-variant4-variant5-variant6-variant7-filterInvariant9-variant10-variant12-variant15-filterInvariant16-filterInvariant17-variant18-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant31-filterInvariant33-filterInvariant34-variant35-variant36-variant37-variant38-variant41-variant43-variant44 GT:DP:GQ:SB 0/1:30:99:15,4,8,3 chr1 36393158 . A G 327.84 PASS AC=2;AF=0.966;AN=2;DP=1484;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:917,75,0:0,0,8,17 chr1 36520795 . C T 340.57 PASS AC=1;AF=0.5;AN=2;DP=15;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.718;QD=22.7;ReadPosRankSum=1.11;SOR=0.368;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:4,11:15:99:369,0,138:0,4,2,9 chr1 36549664 . G A 902.26 PASS AC=2;AF=0.845;AN=2;DP=957;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,21:21:62:710,62,0:0,0,18,3 chr1 36551895 . A G 103.54 PASS AC=2;AF=1;AN=2;DP=171;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:378,36,0:0,0,5,7 chr1 36553673 . A G 2389.27 PASS AC=2;AF=0.943;AN=2;DP=5525;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,179:179:99:5393,536,0:0,0,88,91 chr1 36554442 . G C 4840.92 PASS AC=2;AF=0.907;AN=2;DP=7906;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,189:190:99:5739,557,0:1,0,107,82 chr1 36563158 . C A 2210.69 PASS AC=2;AF=0.884;AN=2;DP=3166;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,91:91:99:2728,272,0:0,0,44,47 chr1 36565584 . C G 996.82 PASS AC=2;AF=0.898;AN=2;DP=1750;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1695,150,0:0,0,34,16 chr1 36565617 . G A 1364.48 PASS AC=2;AF=0.829;AN=2;DP=2638;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,85:86:99:2291,245,0:0,1,48,37 chr1 36602943 . C T 1029.85 PASS AC=2;AF=0.825;AN=2;DP=2480;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:2191,212,0:0,0,21,50 chr1 36603290 . C T 404.99 PASS AC=2;AF=0.8;AN=2;DP=791;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:940,81,0:0,0,20,7 chr1 36614664 . GT G 638.06 PASS AC=2;AF=0.825;AN=2;DP=1859;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1893,153,0:0,0,35,16 chr1 36614713 . C G 1216.68 PASS AC=2;AF=0.825;AN=2;DP=3026;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,93:93:99:3336,279,0:0,0,68,25 chr1 36641729 . C T 96.7 PASS AC=2;AF=0.686;AN=2;DP=781;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1288,135,0:0,0,25,20 chr1 36642420 . T C 298.53 PASS AC=2;AF=0.714;AN=2;DP=1286;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:1500,141,0:0,0,15,32 chr1 36752433 . C T 346.48 PASS AC=2;AF=0.841;AN=2;DP=4587;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,104:104:99:3405,311,0:0,0,51,53 chr1 36754467 . G C 1463.1 PASS AC=2;AF=0.977;AN=2;DP=1534;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:1747,162,0:0,0,37,17 chr1 36754522 . C A 3232.31 PASS AC=2;AF=0.977;AN=2;DP=3525;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,89:89:99:2699,267,0:0,0,53,36 chr1 36762396 . C T 1486.61 PASS AC=2;AF=0.977;AN=2;DP=2544;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:1784,186,0:0,0,31,31 chr1 36766975 . G C 299.53 PASS AC=2;AF=0.841;AN=2;DP=758;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:934,75,0:0,0,15,10 chr1 36767400 . C T 537.71 PASS AC=2;AF=0.841;AN=2;DP=1788;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:1549,144,0:0,0,16,32 chr1 36770806 . C G 2595.29 PASS AC=2;AF=0.989;AN=2;DP=2225;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:2550,186,0:0,0,59,3 chr1 36773405 . T G 490.74 PASS AC=2;AF=0.621;AN=2;DP=3286;MQ=60;set=variant-variant3-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant33-variant35-variant36-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,123:123:99:3820,368,0:0,0,52,71 chr1 36773819 . C G 1846.8 PASS AC=2;AF=0.977;AN=2;DP=3814;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,90:90:99:2826,270,0:0,0,46,44 chr1 36785270 . C T 585.14 PASS AC=1;AF=0.55;AN=2;DP=1463;MQ=60;set=variant-variant3-variant6-variant9-variant10-variant15-variant16-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant33-variant35-variant36-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:26,33:59:99:854,0,715:9,17,14,19 chr1 36788356 . A G 1917.97 PASS AC=2;AF=0.989;AN=2;DP=2857;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:2093,195,0:0,0,27,38 chr1 36809698 . A C 959.69 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=9236;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:141,87:228:99:1218,0,1944:16,125,86,1 chr1 36809705 . G C 77.77 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=4240;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:166,57:223:99:229,0,5753:30,136,57,0 chr1 36824321 . C T 882.57 PASS AC=1;AF=0.5;AN=2;DP=445;MQ=60;set=variant7-variant11-variant12-variant13-variant19-variant20-variant28-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:31,21:52:99:537,0,814:18,13,14,7 chr1 36858917 . C T 175.73 PASS AC=1;AF=0.684;AN=2;DP=188;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant6-variant7-variant9-variant11-variant13-variant20-variant21-variant24-variant26-variant28-variant29-variant30-variant34-variant35-variant36-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:12,3:15:82:82,0,390:8,4,3,0 chr1 36863523 . A G 2392.03 PASS AC=2;AF=0.955;AN=2;DP=3865;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,102:102:99:3093,306,0:0,0,44,58 chr1 36863654 . T C 201.45 PASS AC=1;AF=0.607;AN=2;DP=474;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant16-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:10,7:17:99:214,0,318:2,8,2,5 chr1 36883946 . T C 949.86 PASS AC=1;AF=0.615;AN=2;DP=2440;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:43,64:107:99:1811,0,1113:15,28,21,43 chr1 36884473 . A G 146.54 PASS AC=1;AF=0.62;AN=2;DP=456;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant33-variant34-variant35-variant36-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:8,7:15:99:270,0,283:8,0,7,0 chr1 36884527 . C CA 84.2 PASS AC=1;AF=0.5;AN=2;DP=453;set=filterInvariant-variant6-variant7-filterInvariant8-variant13-variant20-filterInvariant30-variant35-variant38-filterInvariant40 GT:AD:DP:GQ:PL:SB 0/1:29,15:44:99:204,0,1076:22,7,14,1 chr1 36884530 . G A 807.71 PASS AC=1;AF=0.559;AN=2;DP=934;set=variant-variant6-variant7-variant8-variant11-variant13-variant20-variant21-variant22-variant27-variant28-variant29-variant30-variant34-variant35-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:24,27:51:99:879,0,532:18,6,21,6 chr1 36886117 . C T 1043.16 PASS AC=1;AF=0.583;AN=2;DP=1592;MQ=60;set=variant-variant6-variant7-variant8-variant11-variant13-variant20-variant21-variant22-variant27-variant28-variant29-variant30-variant34-variant35-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:44,54:98:99:1497,0,1066:25,19,32,22 chr1 36886364 . C G 937.28 PASS AC=1;AF=0.757;AN=2;DP=950;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,15:27:99:364,0,270:3,9,5,10 chr1 36887702 . C T 2791 PASS AC=1;AF=0.757;AN=2;DP=2326;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:45,30:75:99:859,0,1184:30,15,21,9 chr1 36889197 . T C 238.97 PASS AC=1;AF=0.797;AN=2;DP=297;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,7:19:99:211,0,353:4,8,1,6 chr1 36898067 . T C 1238.58 PASS AC=1;AF=0.588;AN=2;DP=1476;MQ=60;set=variant-variant6-variant7-variant8-variant11-variant13-variant20-variant21-variant22-variant27-variant28-variant29-variant30-variant34-variant35-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:40,52:92:99:1441,0,1022:29,11,34,18 chr1 36898332 . C T 618.53 PASS AC=1;AF=0.588;AN=2;DP=746;MQ=60;set=variant-variant6-variant7-variant8-variant11-variant13-variant20-variant21-variant22-variant27-variant28-variant29-variant30-variant34-variant35-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:16,24:40:99:614,0,540:2,14,10,14 chr1 36921371 . G T 1202.27 PASS AC=1;AF=0.646;AN=2;DP=2757;MQ=60;set=variant2-variant9-variant12-variant15-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:79,75:154:99:1676,0,1895:43,36,43,32 chr1 36921812 . C T 669.89 PASS AC=1;AF=0.5;AN=2;DP=64;FS=0.993;FractionInformativeReads=1;MQ=60;MQRankSum=0.521;QD=10.47;ReadPosRankSum=-0.413;SOR=0.859;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:36,28:64:99:698,0,877:23,13,19,9 chr1 36926445 . C T 990.03 PASS AC=1;AF=0.648;AN=2;DP=2756;MQ=60;set=variant2-variant4-variant6-variant9-variant12-variant15-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,46:96:99:1036,0,1150:21,29,20,26 chr1 36927733 . G A 2819.16 PASS AC=2;AF=0.989;AN=2;DP=3266;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,96:96:99:2756,287,0:0,0,53,43 chr1 36929673 . C T 1502.59 PASS AC=1;AF=0.559;AN=2;DP=2888;MQ=60;set=variant-variant6-variant7-variant8-variant11-variant13-variant20-variant21-variant22-variant27-variant28-variant29-variant30-variant34-variant35-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:81,118:199:99:2806,0,1960:38,43,63,55 chr1 36937059 . A G 3488.27 PASS AC=1;AF=0.726;AN=2;DP=4225;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:95,77:172:99:1710,0,2273:50,45,39,38 chr1 37324683 . A C 1843.91 PASS AC=1;AF=0.583;AN=2;DP=1752;MQ=60;set=variant-variant8-variant9-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:27,32:59:99:989,0,696:20,7,26,6 chr1 37324935 . T C 1738.02 PASS AC=1;AF=0.583;AN=2;DP=2260;FractionInformativeReads=1;MQ=60;set=variant-variant8-variant9-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:59,49:108:99:1308,0,1626:17,42,13,36 chr1 37325477 . A C 1058.73 PASS AC=1;AF=0.6;AN=2;DP=1685;MQ=60;set=variant-variant8-variant9-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:40,41:81:99:1144,0,960:27,13,29,12 chr1 37325723 . C T 426.64 PASS AC=1;AF=0.583;AN=2;DP=335;MQ=60;set=variant15-variant20-variant25-variant27-variant28-variant35 GT:AD:DP:GQ:PL:SB 0/1:30,35:65:99:969,0,779:9,21,9,26 chr1 37335458 . A G 2444.71 PASS AC=1;AF=0.898;AN=2;DP=4368;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:65,57:122:99:1412,0,1622:22,43,20,37 chr1 37335485 . A G 1982.53 PASS AC=1;AF=0.898;AN=2;DP=2813;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:45,37:82:99:1306,0,2347:9,36,10,27 chr1 37335494 . G T 1681.77 PASS AC=1;AF=0.898;AN=2;DP=2417;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:42,31:73:99:1154,0,2266:7,35,8,23 chr1 37626981 . T C 88.71 PASS AC=1;AF=0.72;AN=2;DP=655;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,5:16:99:136,0,390:10,1,4,1 chr1 37940175 . A G 206.9 PASS AC=2;AF=0.989;AN=2;DP=720;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:423,39,0:0,0,7,6 chr1 37941662 . G A 656.53 PASS AC=1;AF=0.5;AN=2;DP=434;FractionInformativeReads=1;MQ=60;set=variant22-variant23-variant24-variant35-variant36-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:45,25:70:99:652,0,1125:18,27,9,16 chr1 37948912 . C T 2365.54 PASS AC=1;AF=0.542;AN=2;DP=2526;MQ=60;set=variant2-variant6-variant14-variant16-variant23-variant25-variant28-variant30-variant35-variant36-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:134,113:247:99:2725,0,3416:66,68,61,52 chr1 37958161 . CAA CA,C,CAAA,CAAAA,CAAAAA 607.33 PASS AC=0,1,0,0,0;AF=0.2,0.1,0.157,0.1,0.014;AN=2;DP=3764;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant33-filterInvariant34-variant35-variant36-variant37-variant39-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:89:99:42,21,24,2 chr1 37959450 . T C 1809.26 PASS AC=2;AF=0.864;AN=2;DP=6578;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,147:147:99:6112,442,0:0,0,69,78 chr1 37959470 . C G 1692.8 PASS AC=2;AF=0.864;AN=2;DP=5570;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,122:122:99:5411,376,0:0,0,52,70 chr1 37959499 . G C 1665.97 PASS AC=2;AF=0.568;AN=2;DP=2107;MQ=60;set=variant3-variant6-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant24-variant25-variant29-variant32-variant33-variant35-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,92:92:99:2858,276,0:0,0,36,56 chr1 37961297 . AC A 527.91 PASS AC=2;AF=0.577;AN=2;DP=350;set=variant11-variant14-variant15-variant18-variant19-filterInvariant21-variant23-variant24-variant29-variant33-variant35-variant36-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:60:810,60,0:0,0,14,4 chr1 37961317 . A C 916.5 PASS AC=2;AF=0.548;AN=2;DP=944;set=variant3-variant6-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant24-variant25-variant29-variant32-variant33-variant35-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,31:31:93:1190,93,0:0,0,25,6 chr1 37967707 . ATTGACAGAGAAGATACATG A 201.29 PASS AC=2;AF=0.89;AN=2;DP=1537;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-filterInvariant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:60:797,60,0:0,0,3,15 chr1 37967774 . C A 233.18 PASS AC=2;AF=0.864;AN=2;DP=695;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:843,63,0:0,0,3,18 chr1 37975279 . C T 227.1 PASS AC=2;AF=0.898;AN=2;DP=2200;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:1733,162,0:0,0,19,35 chr1 37975312 . T C 467.75 PASS AC=2;AF=0.881;AN=2;DP=1497;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1290,126,0:0,0,15,27 chr1 37978897 . G A 889.57 PASS AC=2;AF=0.568;AN=2;DP=1774;MQ=60;set=variant3-variant6-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant24-variant25-variant29-variant32-variant33-variant35-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,78:78:99:2530,234,0:0,0,51,27 chr1 38002068 . C T 936.08 PASS AC=2;AF=0.571;AN=2;DP=955;MQ=60;set=variant3-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant24-variant25-variant29-variant32-variant33-variant35-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1228,108,0:0,0,27,9 chr1 38003233 . G A 763.33 PASS AC=1;AF=0.5;AN=2;DP=74;FS=1.971;FractionInformativeReads=1;MQ=60;MQRankSum=-1.806;QD=10.32;ReadPosRankSum=-2.908;SOR=1.034;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:42,32:74:99:792,0,1044:23,19,20,12 chr1 38006359 . A G 74.91 PASS AC=2;AF=0.881;AN=2;DP=2261;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:1787,171,0:0,0,21,36 chr1 38023316 . C T 2209.05 PASS AC=2;AF=0.565;AN=2;DP=4602;MQ=60;set=variant3-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant24-variant25-variant29-variant32-variant33-variant35-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,207:207:99:6019,618,0:0,0,108,99 chr1 38046920 . G T 661.79 PASS AC=2;AF=0.864;AN=2;DP=2854;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:2446,228,0:0,0,50,26 chr1 38049552 . C G 718.11 PASS AC=2;AF=0.872;AN=2;DP=2661;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,72:73:99:2260,177,0:0,1,24,48 chr1 38061572 . G T 448.21 PASS AC=2;AF=0.864;AN=2;DP=2466;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,63:63:99:2058,189,0:0,0,19,44 chr1 38077067 . A G 480.5 PASS AC=2;AF=0.872;AN=2;DP=2213;FractionInformativeReads=1;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:1868,170,0:0,0,41,16 chr1 38077349 . CTTATCCCCATACTAGTTATTATCGAAACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCGTACGCCTA C 396.34 PASS AC=2;AF=0.864;AN=2;DP=2035;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1490,113,0:0,0,14,20 chr1 38078171 . G GGT,GGTGT,GGTGTGTGT 285.14 PASS AC=1,1,0;AF=0.535,0.267,0.023;AN=2;DP=2203;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:DP:GQ:SB 1/2:58:99:0,0,32,26 chr1 38078630 . A T 821 PASS AC=2;AF=0.563;AN=2;DP=1684;MQ=60;set=variant3-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant24-variant25-variant29-variant32-variant33-variant35-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,88:88:99:2833,264,0:0,0,32,56 chr1 38082122 . G A 1061.47 PASS AC=2;AF=0.563;AN=2;DP=808;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant24-variant25-variant29-variant32-variant33-variant35-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:1260,84,0:0,0,19,9 chr1 38082123 . C T 1061.47 PASS AC=2;AF=0.563;AN=2;DP=822;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant24-variant25-variant29-variant32-variant33-variant35-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:1260,84,0:0,0,19,9 chr1 38098035 . C G 395.38 PASS AC=2;AF=0.595;AN=2;DP=798;MQ=60;set=variant3-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant21-variant24-variant25-variant29-variant32-variant33-variant35-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1500,149,0:0,0,18,32 chr1 38098129 . T G 201.21 PASS AC=2;AF=0.989;AN=2;DP=496;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:411,33,0:0,0,1,10 chr1 38098177 . CA C 79.49 PASS AC=2;AF=0.974;AN=2;DP=189;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:79,6,0:0,0,1,1 chr1 38147606 . T A 1165.44 PASS AC=2;AF=0.667;AN=2;DP=506;FractionInformativeReads=1;MQ=60;set=variant-variant9-variant12-variant14-variant18-variant23-variant24-variant35-variant38 GT:AD:DP:GQ:PL:SB 1/1:0,67:67:99:2137,201,0:0,0,34,33 chr1 38148765 . A G 873.98 PASS AC=2;AF=0.846;AN=2;DP=2924;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:2316,213,0:0,0,27,44 chr1 38155699 . T G 43.74 PASS AC=2;AF=0.65;AN=2;DP=119;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant9-variant12-variant14-variant18-variant23-variant24-variant35-variant38 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:366,30,0:0,0,1,9 chr1 38158211 . C T 2756.73 PASS AC=2;AF=0.65;AN=2;DP=1929;MQ=60;set=variant-variant2-variant9-variant12-variant14-variant18-variant23-variant24-variant35-variant38 GT:AD:DP:GQ:PL:SB 1/1:0,211:211:99:6525,632,0:0,0,108,103 chr1 38161694 . A G 1188.44 PASS AC=2;AF=0.648;AN=2;DP=2454;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant35-variant37-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,112:113:99:3391,308,0:1,0,48,64 chr1 38164438 . GC G 165.15 PASS AC=2;AF=0.7;AN=2;DP=36;FractionInformativeReads=1;MQ=60;set=variant-variant9-variant12-variant24-variant35 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:202,15,0:0,0,4,1 chr1 38164724 . C G 1363.87 PASS AC=2;AF=0.648;AN=2;DP=2639;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant35-variant37-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,95:95:99:2957,285,0:0,0,31,64 chr1 38166022 . T C 751.21 PASS AC=2;AF=0.648;AN=2;DP=1576;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant35-variant37-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:1799,175,0:0,0,35,24 chr1 38166327 . A T 677.34 PASS AC=2;AF=0.648;AN=2;DP=1589;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant35-variant37-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,61:62:99:1850,140,0:1,0,28,33 chr1 38167345 . TA TAA,T 253.3 PASS AC=2,0;AF=0.364,0.182;AN=2;DP=323;MQ=60;set=variant2-variant18-filterInvariant22-variant23-variant24-filterInvariant27-filterInvariant29-variant32-variant35-variant38-variant39 GT:DP:GQ:SB 1/1:17:5:2,0,10,5 chr1 38167709 . CT CTT,C 79.19 PASS AC=0,2;AF=0.1,0.7;AN=2;DP=72;FS=0;MQ=60;set=variant16-variant18-variant24-variant31-variant35 GT:DP:GQ:SB 2/2:5:15:0,0,0,5 chr1 38173983 . TTTC T 1978.03 PASS AC=2;AF=0.65;AN=2;DP=1032;MQ=60;set=variant-variant2-variant9-variant12-variant14-variant18-variant23-variant24-variant35-variant38 GT:AD:DP:GQ:PL:SB 1/1:2,85:87:99:2536,201,0:1,1,51,34 chr1 38174185 . G T 1987.39 PASS AC=2;AF=0.648;AN=2;DP=4325;set=variant-variant2-variant3-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant35-variant37-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,151:151:99:4601,450,0:0,0,77,74 chr1 38174366 . G T 753.23 PASS AC=2;AF=0.65;AN=2;DP=891;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant9-variant12-variant14-variant18-variant23-variant24-variant35-variant38 GT:AD:DP:GQ:PL:SB 1/1:0,111:111:99:3358,332,0:0,0,56,55 chr1 38174987 . T C 619.88 PASS AC=2;AF=0.846;AN=2;DP=2501;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,73:73:99:2125,219,0:0,0,34,39 chr1 38182135 . C T 978.38 PASS AC=2;AF=0.65;AN=2;DP=1298;MQ=60;set=variant-variant2-variant9-variant12-variant14-variant18-variant23-variant24-variant35-variant38 GT:AD:DP:GQ:PL:SB 1/1:0,159:159:99:4679,476,0:0,0,87,72 chr1 38188574 . G A 2281.25 PASS AC=2;AF=0.625;AN=2;DP=777;FractionInformativeReads=1;MQ=60;set=variant14-variant18-variant24-variant35 GT:AD:DP:GQ:PL:SB 1/1:0,184:184:99:5513,552,0:0,0,104,80 chr1 38196841 . T C 339.25 PASS AC=1;AF=0.574;AN=2;DP=957;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant6-variant7-variant8-filterInvariant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant25-variant26-variant29-variant35-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,12:21:99:384,0,181:5,4,10,2 chr1 38226761 . T A 611.98 PASS AC=1;AF=0.622;AN=2;DP=1100;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-filterInvariant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,12:17:87:353,0,87:3,2,8,4 chr1 38228797 . A T 106.77 PASS AC=1;AF=0.824;AN=2;DP=231;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,9:13:99:274,0,102:1,3,1,8 chr1 38230983 . T C 1041.23 PASS AC=1;AF=0.875;AN=2;DP=1355;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:23,23:46:99:643,0,503:9,14,5,18 chr1 38268797 . A G 1760.76 PASS AC=1;AF=0.5;AN=2;DP=734;FractionInformativeReads=1;MQ=60;set=variant3-variant10-variant20-variant23-variant25-variant27-variant29-variant32-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:26,43:69:99:1207,0,608:11,15,17,26 chr1 38275802 . T C 465.94 PASS AC=1;AF=0.724;AN=2;DP=1312;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,26:47:99:722,0,578:11,10,12,14 chr1 38276381 . C T 4214.46 PASS AC=2;AF=1;AN=2;DP=5765;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,150:150:99:4417,449,0:0,0,81,69 chr1 38279666 . CTT CT,C,CTTT 749.46 PASS AC=1,0,0;AF=0.488,0.023,0.023;AN=2;DP=12266;set=variant-variant2-filterInvariant3-variant4-variant5-filterInvariant6-variant8-variant9-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant13-variant14-filterInvariant15-filterInvariant16-variant17-variant18-variant19-filterInvariant20-variant21-variant22-filterInvariant23-variant24-variant25-variant26-variant27-filterInvariant28-filterInvariant29-filterInvariant30-variant31-variant32-variant33-variant34-variant35-variant36-filterInvariant37-variant38-filterInvariant39-filterInvariant40-variant41-variant42-variant43-filterInvariant44 GT:DP:GQ:SB 0/1:224:99:62,107,18,37 chr1 38292160 . G A 293.07 PASS AC=1;AF=0.5;AN=2;DP=219;FractionInformativeReads=1;MQ=60;set=variant3-variant10-variant20-variant23-variant25-variant27-variant29-variant32-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:13,8:21:99:203,0,364:9,4,6,2 chr1 38293753 . G A 531.71 PASS AC=1;AF=0.5;AN=2;DP=228;FractionInformativeReads=1;MQ=60;set=variant3-variant10-variant20-variant23-variant25-variant27-filterInvariant29-variant32-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:6,10:16:99:272,0,205:6,0,7,3 chr1 38293992 . C T 1581.8 PASS AC=2;AF=1;AN=2;DP=1652;FS=0;MQRankSum=0.933;ReadPosRankSum=-0.4;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1371,123,0:0,0,17,24 chr1 38294006 . C T 333.02 PASS AC=1;AF=0.5;AN=2;DP=324;FractionInformativeReads=1;MQ=60;set=variant3-variant10-variant20-variant23-variant25-variant27-variant29-variant32-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:19,14:33:99:389,0,466:7,12,4,10 chr1 38301250 . A G 484.25 PASS AC=1;AF=0.692;AN=2;DP=1903;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,25:50:99:661,0,597:16,9,17,8 chr1 38301476 . G A 607.48 PASS AC=1;AF=0.697;AN=2;DP=1718;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,30:51:99:807,0,580:5,16,9,21 chr1 38301478 . CT C 48.95 DRAGENHardINDEL AC=1;AF=0.5;AN=2;DP=83;FS=0;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:29,7:36:87:87,0,666:7,22,2,5 chr1 38306356 . T C 186.07 PASS AC=1;AF=0.5;AN=2;DP=170;FractionInformativeReads=1;MQ=60;set=variant3-variant10-variant20-variant23-variant25-variant27-variant29-variant32-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:9,8:17:99:258,0,346:0,9,1,7 chr1 38325416 . G A,C 93.32 PASS AC=1,0;AF=0.45,0.05;AN=2;DP=113;MQ=60;set=variant10-variant20-variant23-variant25-variant27-variant29-variant32-variant35-variant40-variant41 GT:DP:GQ:SB 0/1:15:91:2,3,4,6 chr1 38326547 . C T 1300.15 PASS AC=1;AF=0.5;AN=2;DP=713;MQ=60;set=variant3-variant10-variant20-variant23-variant25-variant27-variant29-variant32-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:40,28:68:99:810,0,1135:14,26,5,23 chr1 38327982 . G T 1077.17 PASS AC=1;AF=0.692;AN=2;DP=3423;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,40:95:99:969,0,1367:24,31,18,22 chr1 38328154 . GAC G 523.05 PASS AC=1;AF=0.5;AN=2;DP=318;MQ=60;set=variant3-variant10-variant20-variant23-variant25-variant27-variant29-variant32-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:7,16:23:99:610,0,228:3,4,3,13 chr1 38329999 . C G 1499.72 PASS AC=1;AF=0.5;AN=2;DP=934;MQ=60;set=variant3-variant10-variant20-variant23-variant25-variant27-variant29-variant32-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:50,63:113:99:1521,0,1254:25,25,31,32 chr1 38332074 . TCTCTCACA T 404.07 PASS AC=1;AF=0.545;AN=2;DP=1544;set=variant-variant6-variant7-variant10-variant12-variant13-variant15-variant17-variant19-variant20-variant21-variant24-variant28-variant29-variant30-variant35-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,25:51:99:525,0,922:17,9,21,4 chr1 38338795 . A G 1733.34 PASS AC=1;AF=0.692;AN=2;DP=4592;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,82:137:99:2009,0,1385:21,34,35,47 chr1 38345896 . A C 331.48 PASS AC=1;AF=0.697;AN=2;DP=859;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,9:18:99:301,0,218:3,6,3,6 chr1 38348506 . G A 1804.41 PASS AC=1;AF=0.5;AN=2;DP=1419;MQ=60;set=variant3-variant10-variant20-variant23-variant25-variant27-variant29-variant32-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:80,70:150:99:1576,0,1957:47,33,42,28 chr1 38352849 . G C 619.92 PASS AC=1;AF=0.697;AN=2;DP=1631;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,18:47:99:443,0,836:7,22,5,13 chr1 38355520 . A G 498.16 PASS AC=1;AF=0.5;AN=2;DP=225;FractionInformativeReads=1;MQ=60;set=variant3-variant10-variant20-variant23-variant25-variant27-variant29-variant32-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:10,6:16:99:222,0,352:0,10,0,6 chr1 38356899 . C CAA,CA 119.89 PASS AC=0,1;AF=0.125,0.583;AN=2;DP=185;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant16-variant17-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant35-variant38-variant40-variant42 GT:DP:GQ:SB 0/2:8:58:4,0,4,0 chr1 38395410 . T A 514.11 PASS AC=1;AF=0.727;AN=2;DP=266;MQ=60;set=variant2-variant4-variant5-variant6-variant8-variant9-variant16-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant31-variant34-variant35-variant36-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,6:13:99:173,0,178:2,5,1,5 chr1 38395826 . T A 440.83 PASS AC=1;AF=0.5;AN=2;DP=92;FractionInformativeReads=1;MQ=60;set=variant8-variant9-variant22-variant30-variant35-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,3:13:89:89,0,359:9,1,3,0 chr1 38395947 . A T 1574.79 PASS AC=1;AF=0.711;AN=2;DP=5210;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:88,40:128:99:799,0,2196:54,34,24,16 chr1 38396205 . A G 298.83 PASS AC=1;AF=0.5;AN=2;DP=519;FractionInformativeReads=1;MQ=60;set=variant8-variant9-variant22-variant25-variant28-variant30-variant35-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,24:52:99:583,0,807:15,13,12,12 chr1 38397823 . GC G 241.99 PASS AC=1;AF=0.5;AN=2;DP=153;MQ=60;set=variant8-variant9-variant22-variant25-variant28-variant30-variant35-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,10:14:99:367,0,894:0,4,2,8 chr1 38397825 . GCAC G 241.73 PASS AC=1;AF=0.5;AN=2;DP=149;MQ=60;set=variant8-variant9-variant22-variant25-variant28-variant30-variant35-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,10:14:99:367,0,895:0,4,2,8 chr1 38422544 . T C 178.67 PASS AC=1;AF=0.658;AN=2;DP=118;MQ=60;set=variant2-variant10-variant11-variant12-variant13-variant15-variant17-variant19-variant20-variant21-variant24-variant28-variant29-variant33-variant35-variant37-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:3,2:5:75:75,0,120:3,0,1,1 chr1 38422547 . T A 46.72 PASS AC=1;AF=0.5;AN=2;DP=6;FS=0;FractionInformativeReads=0.833;MQ=60;MQRankSum=1.231;QD=7.79;ReadPosRankSum=-0.358;SOR=0.061;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:3,2:5:75:75,0,120:3,0,1,1 chr1 38422571 . T C 606.22 PASS AC=2;AF=0.921;AN=2;DP=340;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:540,36,0:0,0,9,3 chr1 38422593 . T C 66.22 PASS AC=2;AF=1;AN=2;DP=574;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:644,48,0:0,0,10,6 chr1 38423047 . TC T 37.74 PASS AC=2;AF=0.833;AN=2;DP=75;FS=0;set=variant10-variant13-variant15-variant17-variant18-variant35-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:255,18,0:0,0,1,5 chr1 38423059 . C G 265.1 PASS AC=2;AF=0.806;AN=2;DP=198;FS=0;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant22-variant25-variant26-variant27-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:255,18,0:0,0,1,5 chr1 38423061 . C T 240.53 PASS AC=2;AF=0.844;AN=2;DP=189;FS=0;FractionInformativeReads=1;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant22-variant25-variant26-variant27-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:255,18,0:0,0,1,5 chr1 38423588 . G A 587.74 PASS AC=2;AF=0.909;AN=2;DP=1296;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:789,75,0:0,0,11,14 chr1 38423853 . G C 459.74 PASS AC=2;AF=0.909;AN=2;DP=863;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:900,72,0:0,0,20,4 chr1 38425629 . CAAAA CAA,CA,CAAA,C 677 PASS AC=2,0,0,0;AF=0.438,0.263,0.088,0.013;AN=2;DP=1316;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:32:65:0,2,28,2 chr1 38425724 . T C 4173.76 PASS AC=2;AF=0.909;AN=2;DP=5769;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,136:136:99:4089,408,0:0,0,77,59 chr1 38425895 . T C 2299.84 PASS AC=2;AF=0.909;AN=2;DP=3945;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,114:114:99:3590,342,0:0,0,44,70 chr1 38442547 . G A 3662.97 PASS AC=2;AF=0.909;AN=2;DP=3833;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,101:101:99:3220,303,0:0,0,47,54 chr1 38444749 . T C 366.76 PASS AC=2;AF=0.677;AN=2;DP=1188;MQ=60;set=variant-variant2-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant28-variant29-variant30-variant33-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,31:31:93:975,93,0:0,0,13,18 chr1 38446513 . CTTTT CTT,CT,C,CTTT,CTTTTTT 109.94 PASS AC=0,2,0,0,0;AF=0.1,0.2,0.1,0.15,0.025;AN=2;DP=430;set=variant2-filterInvariant3-variant8-variant9-variant10-variant15-variant19-variant21-variant25-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-filterInvariant38-variant43 GT:DP:GQ:SB 2/2:3:9:0,0,0,3 chr1 38447615 . G T 766.07 PASS AC=2;AF=0.886;AN=2;DP=854;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:791,69,0:0,0,7,16 chr1 38449910 . T C 1486.77 PASS AC=1;AF=0.6;AN=2;DP=1924;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant24-variant28-variant29-variant30-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,49:92:99:1280,0,1054:26,17,32,17 chr1 38450367 . A G 2078.22 PASS AC=2;AF=0.909;AN=2;DP=3383;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,63:63:99:1881,189,0:0,0,27,36 chr1 38453576 . A C 673.86 PASS AC=1;AF=0.615;AN=2;DP=2917;MQ=60;set=variant-variant2-variant6-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant24-variant28-variant29-variant30-variant33-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,68:113:99:1775,0,994:21,24,30,38 chr1 38455389 . C T 531.12 PASS AC=2;AF=0.898;AN=2;DP=1311;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1137,105,0:0,0,12,23 chr1 38456028 . TGAG T 1777.13 PASS AC=1;AF=0.5;AN=2;DP=668;MQ=60;set=variant8-variant9-variant22-variant25-variant28-variant30-variant35-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,46:94:99:1752,0,1837:21,27,16,30 chr1 38456106 . G A 334.35 PASS AC=2;AF=0.677;AN=2;DP=1002;MQ=60;set=variant-variant2-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant28-variant29-variant30-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1229,105,0:0,0,10,25 chr1 38462898 . T A 1165.33 PASS AC=2;AF=0.966;AN=2;DP=1648;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1854,126,0:0,0,29,13 chr1 38462905 . C G 1088.54 PASS AC=2;AF=0.966;AN=2;DP=1703;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1931,135,0:0,0,29,16 chr1 38463504 . C T 1385.34 PASS AC=2;AF=0.667;AN=2;DP=5214;set=variant-variant2-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant28-variant29-variant30-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,191:191:99:5960,572,0:0,0,88,103 chr1 38464639 . C G 1488.91 PASS AC=2;AF=1;AN=2;DP=5007;FS=0;MQ=60;MQRankSum=1.272;ReadPosRankSum=1.678;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,115:115:99:3503,344,0:0,0,71,44 chr1 38489889 . G A 1755.94 PASS AC=1;AF=0.5;AN=2;DP=176;FS=5.4;FractionInformativeReads=1;MQ=60;MQRankSum=0.761;QD=9.98;ReadPosRankSum=-1.306;SOR=1.013;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:98,78:176:99:1784,0,2527:48,50,45,33 chr1 39303995 . C T 1542.77 PASS AC=2;AF=0.955;AN=2;DP=1989;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:2018,168,0:0,0,28,28 chr1 39304247 . A G 5356.38 PASS AC=2;AF=0.955;AN=2;DP=6253;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,151:152:99:4496,419,0:1,0,64,87 chr1 39304728 . A G 3094.07 PASS AC=2;AF=0.955;AN=2;DP=4556;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,94:94:99:3330,282,0:0,0,67,27 chr1 39305002 . AT A,ATTT,ATT 624.88 PASS AC=1,0,0;AF=0.464,0.012,0.036;AN=2;DP=6270;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:117:99:26,38,22,31 chr1 39325063 . T C 585.12 PASS AC=2;AF=0.743;AN=2;DP=2390;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,92:92:99:2478,275,0:0,0,45,47 chr1 39332322 . C T 271.67 PASS AC=2;AF=0.655;AN=2;DP=416;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant13-variant16-variant17-variant19-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant35-variant36-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:577,48,0:0,0,13,3 chr1 39339449 . C T 1690.67 PASS AC=2;AF=0.661;AN=2;DP=3798;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant13-variant16-variant17-variant19-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant35-variant36-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,137:137:99:4215,410,0:0,0,73,64 chr1 39339682 . T C 418 PASS AC=2;AF=0.661;AN=2;DP=1049;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant13-variant16-variant17-variant19-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant35-variant36-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1449,131,0:0,0,15,29 chr1 39340001 . T TA 41.76 PASS AC=2;AF=0.696;AN=2;DP=215;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant16-variant21-variant22-variant23-variant25-variant28-variant29-variant31-variant33-variant35-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:9:78,9,0:0,0,1,1 chr1 39340282 . C T 1527.67 PASS AC=2;AF=0.661;AN=2;DP=3712;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant13-variant16-variant17-variant19-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant35-variant36-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,152:152:99:4724,454,0:0,0,83,69 chr1 39351659 . G A 1504.89 PASS AC=2;AF=0.955;AN=2;DP=2462;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,69:70:99:2074,200,0:0,1,25,44 chr1 39352083 . T G 4621.13 PASS AC=2;AF=0.655;AN=2;DP=9652;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant13-variant16-variant17-variant19-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,320:320:99:9216,956,0:0,0,158,162 chr1 39352271 . G T 2721.24 PASS AC=2;AF=0.661;AN=2;DP=7196;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant13-variant16-variant17-variant19-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant35-variant36-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,263:264:99:8185,781,0:0,1,130,133 chr1 39352492 . G A 251.63 PASS AC=2;AF=0.661;AN=2;DP=756;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant13-variant16-variant17-variant19-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant35-variant36-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:1322,96,0:0,0,4,28 chr1 39361615 . G A 683.13 PASS AC=2;AF=0.661;AN=2;DP=1582;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant13-variant16-variant17-variant19-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant35-variant36-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:1422,141,0:0,0,26,21 chr1 39385086 . A C 1198.23 PASS AC=2;AF=0.932;AN=2;DP=2093;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1581,153,0:0,0,17,34 chr1 39391986 . G C 1187.37 PASS AC=2;AF=0.769;AN=2;DP=3716;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,107:107:99:3341,320,0:0,0,63,44 chr1 39457006 . C T 268.86 PASS AC=1;AF=0.625;AN=2;DP=1003;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,20:33:99:467,0,486:8,5,10,10 chr1 39457016 . C T 319.81 PASS AC=1;AF=0.571;AN=2;DP=911;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant13-variant14-variant16-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant29-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:18,14:32:99:324,0,714:9,9,8,6 chr1 39457293 . T C 209.2 PASS AC=1;AF=0.647;AN=2;DP=148;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant9-variant13-variant16-variant21-variant23-variant25-variant26-variant29-variant35-variant36-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,3:7:74:74,0,75:2,2,1,2 chr1 39466626 . A G 380.65 PASS AC=1;AF=0.569;AN=2;DP=1025;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant13-variant14-variant16-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant29-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,19:31:99:586,0,338:10,2,13,6 chr1 39466786 . C G 580.07 PASS AC=1;AF=0.569;AN=2;DP=2778;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant13-variant14-variant16-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant29-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:43,52:95:99:1336,0,1009:20,23,27,25 chr1 39466955 . CTTT CTT,C,CT,CTTTTT 73.48 PASS AC=2,0,0,0;AF=0.326,0.043,0.261,0.022;AN=2;DP=401;set=variant-variant3-variant6-variant8-variant15-variant17-variant18-filterInvariant19-variant20-variant23-variant24-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant43 GT:DP:GQ:SB 1/1:7:20:0,0,1,6 chr1 39470364 . A G 2982.29 PASS AC=1;AF=0.625;AN=2;DP=4808;MQ=60;set=variant2-variant3-variant4-variant8-variant12-variant15-variant17-variant18-variant19-variant20-variant22-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:90,101:191:99:2710,0,2455:33,57,39,62 chr1 39471666 . G C 341.35 PASS AC=1;AF=0.5;AN=2;DP=28;FS=3.372;FractionInformativeReads=1;MQ=60;MQRankSum=1.013;QD=12.19;ReadPosRankSum=-1.981;SOR=1.426;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:15,13:28:99:370,0,338:7,8,4,9 chr1 39471706 . T A 460.53 PASS AC=1;AF=0.571;AN=2;DP=727;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant13-variant14-variant16-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant29-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,11:16:99:244,0,177:1,4,5,6 chr1 39491927 . G C 1370.53 PASS AC=2;AF=0.884;AN=2;DP=1777;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,38:39:99:1245,107,0:1,0,26,12 chr1 39492080 . G T 2869.37 PASS AC=2;AF=0.884;AN=2;DP=5018;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,140:140:99:4042,419,0:0,0,65,75 chr1 39494666 . CT CTT,C 447.36 PASS AC=1,0;AF=0.489,0.023;AN=2;DP=3408;set=variant-variant2-variant3-variant4-filterInvariant5-variant6-filterInvariant7-variant8-variant9-filterInvariant10-variant11-variant12-variant13-variant14-variant15-filterInvariant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-filterInvariant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:64:99:14,20,11,19 chr1 39494687 . G A 1495.35 PASS AC=2;AF=0.895;AN=2;DP=1896;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:2024,155,0:0,0,14,37 chr1 39494760 . G A 505.31 PASS AC=2;AF=0.895;AN=2;DP=529;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:516,39,0:0,0,1,12 chr1 39549146 . T G 72.46 PASS AC=1;AF=0.5;AN=2;DP=65;FractionInformativeReads=1;MQ=60;set=variant11-variant21-variant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:4,6:10:99:184,0,168:2,2,2,4 chr1 39549152 . A C 37.69 PASS AC=1;AF=0.5;AN=2;DP=58;FS=0;FractionInformativeReads=1;MQ=60;set=variant11-variant21-variant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:99:156,0,174:2,2,1,3 chr1 39550210 . C T 449.67 PASS AC=2;AF=0.966;AN=2;DP=829;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:627,42,0:0,0,0,14 chr1 39568249 . A G 661.7 PASS AC=1;AF=0.563;AN=2;DP=265;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant12-variant14-variant16-variant17-variant23-variant25-variant26-variant28-variant30-variant32-variant33-variant34-variant35-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:1,6:7:25:246,0,25:0,1,6,0 chr1 39568765 . T C 14504.3 PASS AC=2;AF=0.692;AN=2;DP=14206;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,350:352:99:10238,1032,0:1,1,185,165 chr1 39571211 . T C 1319.6 PASS AC=2;AF=0.629;AN=2;DP=3407;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant25-variant26-variant29-variant30-variant32-variant34-variant35-variant37-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,120:120:99:3926,360,0:0,0,75,45 chr1 39696718 . C A 371.1 PASS AC=1;AF=0.5;AN=2;DP=14;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.552;QD=26.51;ReadPosRankSum=-1.187;SOR=0.914;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:2,12:14:50:399,0,50:2,0,10,2 chr1 39717566 . T C 1582.63 PASS AC=2;AF=0.989;AN=2;DP=2304;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1773,158,0:0,0,15,38 chr1 39719812 . G A 480.71 PASS AC=1;AF=0.591;AN=2;DP=593;MQ=60;set=variant3-variant7-variant11-variant17-variant18-variant22-variant25-variant29-variant35-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:29,21:50:99:585,0,750:17,12,15,6 chr1 39751172 . CTT CT,CTTT,C 461.92 PASS AC=0,0,1;AF=0.367,0.133,0.033;AN=2;DP=482;set=variant-variant6-filterInvariant11-filterInvariant12-filterInvariant16-variant23-variant25-variant30-variant34-variant35-variant36-variant38-variant39-variant43-variant44 GT:DP:GQ:SB 0/3:26:99:18,3,4,1 chr1 39757799 . G C 527.54 PASS AC=1;AF=0.605;AN=2;DP=1623;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant7-variant8-variant11-variant13-variant15-variant17-variant18-variant20-variant21-variant22-variant25-variant29-variant30-variant35-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,34:74:99:811,0,1047:14,26,16,18 chr1 39758634 . G A 1017.4 PASS AC=1;AF=0.605;AN=2;DP=1688;MQ=60;set=variant2-variant3-variant7-variant8-variant11-variant13-variant15-variant17-variant18-variant20-variant21-variant22-variant25-variant29-variant30-variant35-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,51:93:99:1161,0,1148:12,30,20,31 chr1 39759367 . AGCTTGGGTG A 158.8 PASS AC=1;AF=0.5;AN=2;DP=6;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.736;QD=26.47;ReadPosRankSum=0.736;SOR=2.303;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:1,5:6:95:196,0,95:0,1,0,5 chr1 39766041 . A G 971.27 PASS AC=1;AF=0.605;AN=2;DP=1417;MQ=60;set=variant2-variant3-variant7-variant8-variant11-variant13-variant15-variant17-variant18-variant20-variant21-variant22-variant25-variant29-variant30-variant35-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,48:73:99:1231,0,538:12,13,21,27 chr1 39788761 . C G 581.79 PASS AC=1;AF=0.5;AN=2;DP=29;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.024;QD=20.06;ReadPosRankSum=0.561;SOR=0.673;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:8,21:29:99:610,0,215:2,6,6,15 chr1 39796844 . CTTTTTTTTTTTTTT CT,CTTT,CTT,C,CTTTTTTTTTTTTT,CTTTT,CTTTTTTTTTTT 141.85 PASS AC=0,0,0,0,0,0,1;AF=0.013,0.526,0.145,0.013,0.013,0.013,0.013;AN=2;DP=886;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43 GT:DP:GQ:SB 0/7:11:87:3,2,3,3 chr1 39797055 . A G 1132.81 PASS AC=1;AF=0.605;AN=2;DP=1778;MQ=60;set=variant2-variant3-variant7-variant8-variant11-variant13-variant15-variant17-variant18-variant20-variant21-variant22-variant25-variant29-variant30-variant35-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,31:83:99:804,0,1478:28,24,17,14 chr1 39799912 . C T 1085.77 PASS AC=1;AF=0.5;AN=2;DP=70;FS=0.918;FractionInformativeReads=1;MQ=60;MQRankSum=-0.611;QD=15.51;ReadPosRankSum=2.154;SOR=0.902;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:30,40:70:99:1114,0,810:15,15,22,18 chr1 39801815 . A C 993.19 PASS AC=1;AF=0.605;AN=2;DP=1603;MQ=60;set=variant2-variant3-variant7-variant8-variant11-variant13-variant15-variant17-variant18-variant20-variant21-variant22-variant25-variant29-variant30-variant35-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,43:87:99:1096,0,1280:24,20,19,24 chr1 39806610 . C T 1177.16 PASS AC=2;AF=0.989;AN=2;DP=1861;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:1794,185,0:0,0,22,40 chr1 39812518 . C T 305.57 PASS AC=1;AF=0.605;AN=2;DP=359;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant7-variant8-variant11-variant13-variant15-variant17-variant18-variant20-variant21-variant22-variant25-variant29-variant30-variant35-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,7:14:99:226,0,236:5,2,6,1 chr1 39812620 . G T 2437.41 PASS AC=2;AF=0.989;AN=2;DP=3767;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,71:72:99:2193,205,0:1,0,45,26 chr1 39812822 . C A 4165.75 PASS AC=2;AF=0.989;AN=2;DP=5628;MQ=60;MQRankSum=-0.751;ReadPosRankSum=-1.057;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,115:115:99:3845,345,0:0,0,55,60 chr1 39815143 . T A 2176.33 PASS AC=1;AF=0.605;AN=2;DP=3724;MQ=60;set=variant2-variant3-variant7-variant8-variant11-variant13-variant15-variant17-variant18-variant20-variant21-variant22-variant25-variant29-variant30-variant35-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:113,111:224:99:2465,0,2659:58,55,62,49 chr1 39815344 . G A 144.39 PASS AC=1;AF=0.605;AN=2;DP=799;MQ=60;set=variant2-variant3-variant7-variant8-variant11-variant13-variant15-variant17-variant18-variant20-variant21-variant22-variant25-variant29-variant30-variant35-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,21:51:99:516,0,939:8,22,8,13 chr1 39823032 . A AT 1613.84 PASS AC=1;AF=0.605;AN=2;DP=3204;MQ=60;set=variant2-variant3-variant7-variant8-variant11-variant13-variant15-variant17-variant18-variant20-variant21-variant22-variant25-variant29-variant30-variant35-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:96,63:159:99:1274,0,2222:49,47,30,33 chr1 39824718 . C G 106.42 PASS AC=2;AF=0.6;AN=2;DP=412;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant10-variant11-variant13-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant29-variant30-variant34-variant35-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:1071,84,0:0,0,22,6 chr1 39826391 . A ATTAT 199.07 PASS AC=2;AF=0.786;AN=2;DP=51;FractionInformativeReads=1;MQ=60;set=variant13-variant20-variant23-variant29-variant35-variant38-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:225,15,0:0,0,4,1 chr1 39835817 . A G 696.36 PASS AC=1;AF=0.605;AN=2;DP=1511;MQ=60;set=variant2-variant3-variant7-variant8-variant11-variant13-variant15-variant17-variant18-variant20-variant21-variant22-variant25-variant29-variant30-variant35-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,37:77:99:810,0,936:20,20,20,17 chr1 39838174 . T C 999.85 PASS AC=1;AF=0.5;AN=2;DP=84;FS=2.957;FractionInformativeReads=1;MQ=60;MQRankSum=-0.152;QD=11.9;ReadPosRankSum=0.215;SOR=0.422;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:45,39:84:99:1028,0,1120:29,16,22,17 chr1 39843958 . G A 305.06 PASS AC=2;AF=0.6;AN=2;DP=482;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant10-variant11-variant13-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant29-variant30-variant34-variant35-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:400,30,0:0,0,9,1 chr1 39844028 . C T 461.96 PASS AC=1;AF=0.5;AN=2;DP=39;FS=1.342;FractionInformativeReads=1;MQ=60;MQRankSum=-2.352;QD=11.85;ReadPosRankSum=-0.549;SOR=1.179;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:21,18:39:99:490,0,585:13,8,13,5 chr1 39845296 . T G 243.92 PASS AC=1;AF=0.5;AN=2;DP=14;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.733;QD=17.42;ReadPosRankSum=-2;SOR=0.76;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:5,9:14:99:272,0,136:1,4,2,7 chr1 39851009 . C T 186.48 PASS AC=1;AF=0.5;AN=2;DP=14;FS=2.363;FractionInformativeReads=1;MQ=60;MQRankSum=-1.485;QD=13.32;ReadPosRankSum=2.647;SOR=1.609;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:8,6:14:99:215,0,198:5,3,5,1 chr1 39878815 . A G 1980.64 PASS AC=1;AF=0.5;AN=2;DP=122;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.41;QD=16.23;ReadPosRankSum=-0.368;SOR=0.642;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:47,75:122:99:2009,0,1156:20,27,33,42 chr1 39879366 . T C 408.98 PASS AC=2;AF=0.609;AN=2;DP=996;set=variant-variant2-variant3-variant7-variant8-variant10-variant11-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant29-variant30-variant34-variant35-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1562,122,0:0,0,21,20 chr1 39880274 . A G 2912.96 PASS AC=1;AF=0.5;AN=2;DP=266;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=3.23;QD=10.95;ReadPosRankSum=-0.611;SOR=0.666;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:139,127:266:99:2941,0,3326:68,71,63,64 chr1 39880319 . T G 3493.55 PASS AC=1;AF=0.605;AN=2;DP=5258;MQ=60;set=variant2-variant3-variant7-variant8-variant11-variant13-variant15-variant17-variant18-variant20-variant21-variant22-variant25-variant29-variant30-variant35-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:133,148:281:99:3686,0,3413:69,64,76,72 chr1 39880765 . G A 4697.94 PASS AC=1;AF=0.5;AN=2;DP=409;FS=1.743;FractionInformativeReads=1;MQ=60;MQRankSum=2.155;QD=11.49;ReadPosRankSum=0.995;SOR=0.836;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:220,189:409:99:4726,0,5627:104,116,83,106 chr1 39881040 . G C 1143.65 PASS AC=2;AF=0.6;AN=2;DP=1350;set=variant-variant2-variant3-variant7-variant8-variant10-variant11-variant13-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant29-variant30-variant34-variant35-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:1914,171,0:0,0,14,43 chr1 39881468 . T A 670.85 PASS AC=1;AF=0.605;AN=2;DP=1049;MQ=60;set=variant2-variant3-variant7-variant8-variant11-variant13-variant15-variant17-variant18-variant20-variant21-variant22-variant25-variant29-variant30-variant35-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,25:62:99:683,0,942:20,17,12,13 chr1 39889677 . G A 698.91 PASS AC=2;AF=0.6;AN=2;DP=1051;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant10-variant11-variant13-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant29-variant30-variant34-variant35-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1034,99,0:0,0,23,10 chr1 39893093 . C T 567.85 PASS AC=2;AF=0.604;AN=2;DP=1199;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant10-variant11-variant13-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant29-variant30-variant34-variant35-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:1822,170,0:0,0,37,20 chr1 39894811 . T C 241.68 PASS AC=1;AF=0.5;AN=2;DP=11;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.566;QD=21.97;ReadPosRankSum=-0.978;SOR=0.693;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:3,8:11:99:270,0,99:3,0,7,1 chr1 39894839 . A G 329.56 PASS AC=2;AF=0.779;AN=2;DP=681;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:719,57,0:0,0,16,3 chr1 39895460 . G A 631.1 PASS AC=2;AF=0.6;AN=2;DP=1436;set=variant-variant2-variant3-variant7-variant8-variant10-variant11-variant13-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant29-variant30-variant34-variant35-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:1856,171,0:0,0,36,21 chr1 39900058 . CT C,CTT 102.62 PASS AC=1,0;AF=0.469,0.031;AN=2;DP=1230;set=variant2-filterInvariant3-variant4-filterInvariant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-filterInvariant15-variant16-filterInvariant19-variant20-variant21-filterInvariant23-variant24-variant26-variant29-variant30-variant31-filterInvariant32-filterInvariant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:31:99:14,7,6,4 chr1 39905017 . A C 1180.48 PASS AC=1;AF=0.5;AN=2;DP=82;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.619;QD=14.4;ReadPosRankSum=0.562;SOR=0.709;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:35,47:82:99:1209,0,969:20,15,27,20 chr1 39908506 . G A 404.72 PASS AC=2;AF=0.604;AN=2;DP=1483;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant10-variant11-variant13-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant29-variant30-variant34-variant35-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1325,123,0:0,0,21,20 chr1 39908726 . A G 230.53 PASS AC=2;AF=0.625;AN=2;DP=169;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant7-variant8-variant10-variant11-variant13-variant15-variant20-variant21-variant22-variant23-variant25-variant29-variant30-variant35-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:144,15,0:0,0,2,3 chr1 39913351 . A G 1464 PASS AC=1;AF=0.605;AN=2;DP=2583;MQ=60;set=variant2-variant3-variant7-variant8-variant11-variant13-variant15-variant17-variant18-variant20-variant21-variant22-variant25-variant29-variant30-variant35-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:81,85:166:99:2185,0,2110:45,36,38,47 chr1 39913643 . C G 1833.62 PASS AC=1;AF=0.5;AN=2;DP=157;FS=1.989;FractionInformativeReads=1;MQ=60;MQRankSum=-0.384;QD=11.68;ReadPosRankSum=0.465;SOR=0.535;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:79,78:157:99:1862,0,2130:35,44,38,40 chr1 39914363 . G C 1108.19 PASS AC=2;AF=0.662;AN=2;DP=3940;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,111:111:99:3261,332,0:0,0,57,54 chr1 39917888 . C A 805.6 PASS AC=1;AF=0.5;AN=2;DP=73;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-2.157;QD=11.04;ReadPosRankSum=0.292;SOR=0.651;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:37,36:73:99:834,0,923:23,14,22,14 chr1 39923894 . T A 244.65 PASS AC=1;AF=0.5;AN=2;DP=15;FS=2.796;FractionInformativeReads=1;MQ=60;MQRankSum=0.766;QD=16.31;ReadPosRankSum=-1.12;SOR=2.115;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:6,9:15:99:273,0,142:4,2,8,1 chr1 39927463 . CAAAA C,CAA,CA,CAAA 54.46 PASS AC=0,0,0,2;AF=0.071,0.429,0.071,0.143;AN=2;DP=48;set=variant-variant2-variant9-variant12-variant19-variant22-variant35 GT:DP:GQ:SB 4/4:6:7:0,1,5,0 chr1 39927507 . G A 1786.71 PASS AC=1;AF=0.989;AN=2;DP=1503;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:19,20:39:99:518,0,494:12,7,14,6 chr1 39945749 . T TAGCCTCTGAAAGACTCCAGTGAGGAGAAGAAATAAAAATG 30.05 PASS AC=1;AF=0.5;AN=2;DP=38;FS=0;MQ=60;SOR=1.609;set=filterInvariant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:0,1:1:14:67,0,14:0,0,1,0 chr1 39952822 . T C 1517.75 PASS AC=1;AF=0.909;AN=2;DP=3551;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:53,49:102:99:1184,0,1364:18,35,16,33 chr1 39957669 . C G 1004.74 PASS AC=1;AF=0.5;AN=2;DP=272;MQ=60;set=variant-variant10-variant15-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:42,28:70:99:662,0,1152:22,20,14,14 chr1 39957913 . A G 7354.32 PASS AC=1;AF=0.909;AN=2;DP=20590;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:294,313:607:99:7515,0,6671:163,131,169,144 chr1 39981522 . G A 2548.5 PASS AC=1;AF=0.615;AN=2;DP=1901;set=variant3-variant7-variant11-variant17-variant18-variant22-variant24-variant25-variant29-variant30-variant35-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:87,80:167:99:1915,0,1997:34,53,26,54 chr1 39986904 . A T 236.97 DRAGENHardSNP AC=1;AF=0.722;AN=2;DP=272;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:21,15:36:99:358,0,490:14,7,13,2 chr1 39988145 . T C 673.66 PASS AC=1;AF=0.5;AN=2;DP=1590;set=variant5-variant9-variant23-variant24-variant26-variant27-filterInvariant28-variant29-variant32-filterInvariant35-variant39-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:161,32:193:99:417,0,3905:90,71,20,12 chr1 39988231 . A G 1297.11 PASS AC=1;AF=0.5;AN=2;DP=271;set=variant16-variant35 GT:AD:DP:GQ:PL:SB 0/1:88,77:165:99:1742,0,2218:37,51,33,44 chr1 39988967 . C A 1108.3 PASS AC=1;AF=0.5;AN=2;DP=146;FractionInformativeReads=1;MQ=60;set=variant16-variant35 GT:AD:DP:GQ:PL:SB 0/1:36,24:60:99:625,0,952:13,23,7,17 chr1 39991588 . G T 1433.13 PASS AC=1;AF=0.629;AN=2;DP=5129;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:85,95:180:99:2718,0,2237:37,48,35,60 chr1 40028180 . A G 1531.73 PASS AC=1;AF=0.587;AN=2;DP=3668;MQ=60;set=variant2-variant3-variant7-variant8-variant13-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant33-variant35-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:74,88:162:99:2345,0,1807:28,46,29,59 chr1 40035119 . C T 242.22 PASS AC=1;AF=0.5;AN=2;DP=11;FS=4.393;FractionInformativeReads=1;MQ=60;MQRankSum=-0.278;QD=22.02;ReadPosRankSum=-2.52;SOR=2.833;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:4,7:11:99:270,0,108:3,1,7,0 chr1 40035686 . C T 1135.18 PASS AC=1;AF=0.587;AN=2;DP=1463;MQ=60;set=variant2-variant3-variant7-variant8-variant13-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant33-variant35-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,34:82:99:741,0,1181:22,26,12,22 chr1 40036847 . G C 506.85 PASS AC=1;AF=0.587;AN=2;DP=602;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant7-variant8-variant13-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant33-variant35-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,12:24:99:421,0,454:11,1,10,2 chr1 40036944 . G A 1625.72 PASS AC=1;AF=0.5;AN=2;DP=128;FS=6.863;FractionInformativeReads=1;MQ=60;MQRankSum=-0.867;QD=12.7;ReadPosRankSum=0.055;SOR=0.325;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:56,72:128:99:1654,0,1374:37,19,39,33 chr1 40037354 . C G 255.27 PASS AC=1;AF=0.567;AN=2;DP=338;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant17-variant18-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant35-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,12:24:99:251,0,366:5,7,5,7 chr1 40041371 . G GA 836.36 PASS AC=1;AF=0.587;AN=2;DP=1436;MQ=60;set=variant2-variant3-variant7-variant8-variant13-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant33-variant35-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,36:69:99:1074,0,969:23,10,29,7 chr1 40041699 . T TCGGAGC 669.69 PASS AC=1;AF=0.567;AN=2;DP=346;MQ=60;set=variant3-variant7-variant17-variant18-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant35-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:15,10:25:99:448,0,583:7,8,2,8 chr1 40041714 . G A 82.4 PASS AC=1;AF=0.5;AN=2;DP=47;FractionInformativeReads=1;MQ=60;set=variant16-variant35 GT:AD:DP:GQ:PL:SB 0/1:11,14:25:99:288,0,337:4,7,8,6 chr1 40089945 . A G 1432.26 PASS AC=2;AF=0.652;AN=2;DP=2099;MQ=60;set=variant2-variant4-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,69:71:99:2137,164,0:1,1,42,27 chr1 40090805 . C G 815.41 PASS AC=1;AF=0.5;AN=2;DP=263;FractionInformativeReads=1;MQ=60;set=variant16-variant32-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:34,30:64:99:855,0,975:20,14,18,12 chr1 40091660 . TC T 1535.74 PASS AC=1;AF=0.5;AN=2;DP=319;FractionInformativeReads=1;MQ=60;set=variant16-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:49,50:99:99:1484,0,1419:25,24,25,25 chr1 40092089 . T C 2863.67 PASS AC=2;AF=0.989;AN=2;DP=4372;MQ=60;MQRankSum=-2.503;ReadPosRankSum=0.928;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,120:120:99:3898,359,0:0,0,72,48 chr1 40096053 . T C 606.18 PASS AC=1;AF=0.591;AN=2;DP=960;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant10-variant11-variant12-variant15-variant16-variant18-variant20-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant35-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:23,23:46:99:737,0,765:3,20,3,20 chr1 40098054 . G A 70.94 PASS AC=1;AF=0.568;AN=2;DP=257;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant9-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant23-variant25-variant26-variant29-variant30-variant31-variant35-variant36-variant37-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:7,3:10:99:102,0,263:7,0,2,1 chr1 40098328 . T C 1444.18 PASS AC=2;AF=0.989;AN=2;DP=2433;FractionInformativeReads=1;MQ=60;MQRankSum=0.56;ReadPosRankSum=0.56;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,66:66:99:1817,197,0:0,0,33,33 chr1 40137754 . G A 889.98 PASS AC=1;AF=0.577;AN=2;DP=1089;MQ=60;set=variant2-variant4-variant5-variant9-variant10-variant16-variant21-variant32-variant34-variant35-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:48,57:105:99:1889,0,1613:3,45,5,52 chr1 40144486 . A C 2389.69 PASS AC=1;AF=0.611;AN=2;DP=3398;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,49:107:99:1154,0,1346:27,31,25,24 chr1 40144857 . G GCTTCTTCT 4158.03 PASS AC=1;AF=0.611;AN=2;DP=4140;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,46:96:99:1947,0,4277:22,28,23,23 chr1 40145297 . C T 3525.94 PASS AC=1;AF=0.611;AN=2;DP=3927;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:66,33:99:99:943,0,2086:18,48,12,21 chr1 40146253 . T C 1639.83 PASS AC=1;AF=0.869;AN=2;DP=2816;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,35:75:99:824,0,1041:22,18,18,17 chr1 40146417 . G T 1700.31 PASS AC=1;AF=0.611;AN=2;DP=1968;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,44:78:99:1048,0,859:16,18,25,19 chr1 40147343 . G T 1236.54 PASS AC=1;AF=0.614;AN=2;DP=1687;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,20:39:99:424,0,461:10,9,12,8 chr1 40149515 . A G 1113.36 PASS AC=1;AF=0.869;AN=2;DP=1838;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,20:43:99:536,0,626:16,7,14,6 chr1 40149551 . G C 2772.71 PASS AC=1;AF=0.607;AN=2;DP=2256;MQ=60;set=variant2-variant4-variant5-variant6-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant23-variant25-variant26-variant28-variant29-variant30-variant32-variant35-variant36-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:38,41:79:99:1247,0,1034:27,11,31,10 chr1 40149642 . G T 7388.87 PASS AC=1;AF=0.869;AN=2;DP=10205;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:137,117:254:99:2807,0,3338:79,58,74,43 chr1 40149870 . C G 1773.06 PASS AC=1;AF=0.869;AN=2;DP=2625;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,33:53:99:1138,0,687:1,19,0,33 chr1 40149926 . C CCCCGGGTGCCTCGCCTCCTCCCAT 328.6 PASS AC=1;AF=0.897;AN=2;DP=748;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,6:10:99:259,0,145:0,4,0,6 chr1 40149971 . G A 174 PASS AC=2;AF=0.688;AN=2;DP=219;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant16-variant17-variant19-variant20-variant21-variant23-variant25-variant26-variant31-variant33-variant35-variant36-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:20:190,20,0:0,0,4,3 chr1 40150370 . C T 1365.71 PASS AC=1;AF=0.869;AN=2;DP=1720;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,34:53:99:822,0,459:9,10,19,15 chr1 40157143 . C T 1790.61 PASS AC=1;AF=0.58;AN=2;DP=3391;MQ=60;set=variant2-variant4-variant6-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant23-variant26-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant37-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:70,84:154:99:2085,0,1550:35,35,44,40 chr1 40157260 . C A 1258.07 PASS AC=1;AF=0.58;AN=2;DP=2845;MQ=60;set=variant2-variant4-variant6-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant23-variant26-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant37-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:54,61:115:99:1601,0,1318:24,30,29,32 chr1 40204424 . A T 962.65 PASS AC=1;AF=0.658;AN=2;DP=348;MQ=60;set=variant3-variant12-variant16-variant18-variant20-variant21-variant24-variant25-variant27-variant29-variant31-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:7,5:12:90:90,0,272:7,0,3,2 chr1 40204802 . ACTT A 94.69 PASS AC=1;AF=0.5;AN=2;DP=119;MQ=60;set=variant9-variant23-variant27-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:11,13:24:99:513,0,423:2,9,2,11 chr1 40207169 . T G 973.03 PASS AC=2;AF=0.786;AN=2;DP=2639;MQ=60;set=variant-variant3-variant5-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,83:83:99:2610,249,0:0,0,29,54 chr1 40214525 . T A 2356.85 PASS AC=1;AF=0.65;AN=2;DP=1223;MQ=60;set=variant3-variant12-variant14-variant16-variant18-variant20-variant21-variant24-variant25-variant27-variant29-variant31-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:29,25:54:99:677,0,936:23,6,18,7 chr1 40219065 . C T 4491.72 PASS AC=1;AF=0.658;AN=2;DP=2222;MQ=60;set=variant3-variant12-variant14-variant16-variant18-variant20-variant21-variant24-variant25-variant27-variant29-variant31-variant35-variant36-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:62,55:117:99:1385,0,1679:30,32,29,26 chr1 40219280 . T C 2099.49 PASS AC=2;AF=0.708;AN=2;DP=1178;MQ=60;set=variant3-variant5-variant9-variant12-variant14-variant16-variant18-variant20-variant21-variant23-variant24-variant25-variant27-variant29-variant31-variant32-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,71:73:99:2234,170,0:1,1,34,37 chr1 40223128 . T C 2620.33 PASS AC=1;AF=0.5;AN=2;DP=2299;FractionInformativeReads=1;MQ=60;set=variant5-variant9-variant23-variant24-variant26-variant27-variant28-variant29-variant32-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:106,94:200:99:2409,0,2795:44,62,40,54 chr1 40226046 . G A 8883.22 PASS AC=1;AF=0.658;AN=2;DP=4696;MQ=60;set=variant3-variant12-variant14-variant16-variant18-variant20-variant21-variant24-variant25-variant27-variant29-variant31-variant35-variant36-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:142,152:294:99:3441,0,3461:68,74,75,77 chr1 40229297 . A AC 961.21 PASS AC=2;AF=0.818;AN=2;DP=1598;set=variant-variant3-variant5-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:517,45,0:0,0,10,5 chr1 40229319 . G A 966.62 PASS AC=2;AF=0.783;AN=2;DP=1839;set=variant-variant3-variant5-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant27-variant29-variant31-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:53:555,53,0:0,0,13,5 chr1 40229360 . GA G 754.52 PASS AC=1;AF=0.5;AN=2;DP=21;FS=0;FractionInformativeReads=1;MQ=45.05;MQRankSum=-2.216;QD=31.24;ReadPosRankSum=-0.659;SOR=1.292;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:2,19:21:27:792,0,27:1,1,12,7 chr1 40229368 . A G 1853.31 PASS AC=1;AF=0.763;AN=2;DP=988;set=variant3-variant12-variant14-variant16-variant18-variant20-variant21-variant24-variant25-variant27-variant29-variant31-variant35-variant36-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:2,20:22:24:814,0,24:1,1,12,8 chr1 40230257 . G A 164.9 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=200;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:117,24:141:99:266,0,3003:93,24,19,5 chr1 40230531 . C T 2169.74 DRAGENHardSNP AC=1;AF=0.533;AN=2;DP=6060;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:141,158:299:99:3202,0,2788:56,85,61,97 chr1 40236074 . A C 1147.41 PASS AC=1;AF=0.577;AN=2;DP=5320;set=variant-variant5-variant7-variant9-filterInvariant10-variant11-variant15-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:160,87:247:99:2061,0,3875:85,75,59,28 chr1 40253726 . C T 1507.47 PASS AC=2;AF=0.652;AN=2;DP=3654;set=variant-variant3-variant5-variant7-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,121:121:99:5031,387,0:0,0,102,19 chr1 40253747 . G C 2719.39 PASS AC=1;AF=0.5;AN=2;DP=208;FS=0;FractionInformativeReads=1;MQ=51.2;MQRankSum=0.476;QD=13.07;ReadPosRankSum=1.126;SOR=0.737;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:106,102:208:99:2748,0,2797:77,29,75,27 chr1 40253768 . C CA 5320.45 PASS AC=2;AF=0.712;AN=2;DP=7648;set=variant-variant3-variant5-variant7-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,295:295:99:13804,924,0:0,0,207,88 chr1 40253770 . C T 5363.87 PASS AC=2;AF=0.712;AN=2;DP=7909;set=variant-variant3-variant5-variant7-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,307:307:99:14051,954,0:0,0,215,92 chr1 40253786 . C T 6004.05 PASS AC=2;AF=0.712;AN=2;DP=9935;set=variant-variant3-variant5-variant7-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,401:402:99:16573,1201,0:0,1,254,147 chr1 40254231 . A G 145.15 PASS AC=1;AF=0.7;AN=2;DP=84;FractionInformativeReads=1;MQ=60;set=variant3-variant12-variant16-variant18-variant25-variant27-variant35-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:6,6:12:99:193,0,163:1,5,3,3 chr1 40254522 . G A 417.84 PASS AC=2;AF=0.814;AN=2;DP=2635;MQ=60;set=variant-variant3-variant5-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:2346,226,0:0,0,28,48 chr1 40306865 . C T 412.52 PASS AC=1;AF=0.583;AN=2;DP=544;MQ=60;set=variant4-variant10-variant12-variant21-variant22-variant27-variant29-variant35-variant36-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:33,20:53:99:439,0,842:18,15,13,7 chr1 40306898 . T C 1511.91 PASS AC=1;AF=0.66;AN=2;DP=1205;MQ=60;set=variant4-variant6-variant9-variant10-variant12-variant14-variant15-variant17-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant29-variant30-variant34-variant35-variant36-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,29:65:99:701,0,916:20,16,18,11 chr1 40313849 . T C 883.1 PASS AC=1;AF=0.591;AN=2;DP=676;MQ=60;set=variant4-variant12-variant21-variant22-variant27-variant29-variant35-variant36-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:26,34:60:99:863,0,605:10,16,12,22 chr1 40319587 . A C 2902.21 PASS AC=2;AF=0.667;AN=2;DP=2746;MQ=60;set=variant4-variant5-variant6-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,78:78:99:2331,233,0:0,0,48,30 chr1 40349131 . G A 3786.57 PASS AC=1;AF=0.66;AN=2;DP=2359;MQ=60;set=variant4-variant6-variant9-variant10-variant12-variant14-variant15-variant17-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant29-variant30-variant34-variant35-variant36-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,73:121:99:1744,0,1116:23,25,31,42 chr1 40349333 . G A 538.65 PASS AC=1;AF=0.5;AN=2;DP=154;FractionInformativeReads=1;MQ=60;set=variant5-variant16-variant17-variant18-variant23-variant35 GT:AD:DP:GQ:PL:SB 0/1:13,15:28:99:409,0,317:6,7,5,10 chr1 40349410 . T C 376.77 PASS AC=2;AF=0.761;AN=2;DP=164;MQ=60;set=variant4-variant5-variant6-variant9-variant10-variant12-variant14-variant16-variant17-variant18-variant20-variant21-variant23-variant25-variant27-variant29-variant34-variant35-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:361,27,0:0,0,1,8 chr1 40349428 . G A 68.22 PASS AC=1;AF=0.611;AN=2;DP=72;FractionInformativeReads=1;MQ=60;set=variant4-variant10-variant12-variant21-variant29-variant35-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,4:9:99:141,0,157:1,4,0,4 chr1 40361307 . T TA 2215.92 PASS AC=1;AF=0.5;AN=2;DP=236;FS=1.664;FractionInformativeReads=0.903;MQ=60;MQRankSum=-1.578;QD=9.39;ReadPosRankSum=-1.626;SOR=0.721;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:107,106:213:99:2253,0,2221:52,55,55,51 chr1 40361783 . G C 769.91 PASS AC=1;AF=0.533;AN=2;DP=629;MQ=60;set=variant4-variant5-variant14-variant15-variant16-variant17-variant18-variant23-variant25-variant26-variant27-variant30-variant35-variant36-variant39 GT:AD:DP:GQ:PL:SB 0/1:25,24:49:99:585,0,732:11,14,8,16 chr1 40361843 . A C 130.84 PASS AC=1;AF=0.577;AN=2;DP=330;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant12-variant16-variant21-variant22-variant27-variant29-variant35-variant36-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,14:22:99:418,0,210:4,4,5,9 chr1 40362066 . C A 590.58 PASS AC=1;AF=0.563;AN=2;DP=807;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant9-variant12-variant16-variant17-variant21-variant22-variant27-variant28-variant29-variant35-variant36-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:34,16:50:99:429,0,893:18,16,7,9 chr1 40362461 . T C 1047.38 PASS AC=1;AF=0.577;AN=2;DP=663;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant12-variant16-variant21-variant22-variant27-variant29-variant35-variant36-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:23,34:57:99:843,0,491:14,9,19,15 chr1 40363054 . G C 4297.35 PASS AC=2;AF=0.909;AN=2;DP=5869;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,121:121:99:3853,362,0:0,0,69,52 chr1 40367592 . A G 4027.89 PASS AC=2;AF=0.966;AN=2;DP=4593;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,111:111:99:3483,333,0:0,0,63,48 chr1 40421617 . TG T 156.61 PASS AC=1;AF=0.536;AN=2;DP=178;MQ=60;set=variant4-variant6-variant12-variant16-variant21-variant22-variant25-variant27-variant29-variant30-variant35-variant36-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:4,7:11:99:208,0,101:0,4,0,7 chr1 40433771 . A G 312.81 PASS AC=1;AF=0.641;AN=2;DP=944;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant27-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:14,10:24:99:280,0,386:8,6,5,5 chr1 40435514 . CT C 4380.08 PASS AC=2;AF=0.955;AN=2;DP=5373;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,123:123:99:3675,369,0:0,0,66,57 chr1 40505872 . C T 389.85 PASS AC=2;AF=0.75;AN=2;DP=99;MQ=60;set=variant8-variant12-variant33-variant35 GT:AD:DP:GQ:PL:SB 1/1:1,21:22:55:675,55,0:0,1,16,5 chr1 40505924 . A C 914.1 PASS AC=2;AF=0.75;AN=2;DP=217;FractionInformativeReads=1;MQ=60;set=variant8-variant12-variant33-variant35 GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:1850,162,0:0,0,37,17 chr1 40506534 . G T 605.34 PASS AC=2;AF=0.75;AN=2;DP=158;FractionInformativeReads=1;MQ=60;set=variant8-variant12-variant33-variant35 GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1078,99,0:0,0,9,24 chr1 40526003 . T C 329.95 PASS AC=2;AF=0.857;AN=2;DP=875;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:399,30,0:0,0,2,8 chr1 40533266 . T G 786.22 PASS AC=2;AF=1;AN=2;DP=2070;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2843,213,0:0,0,38,32 chr1 40533287 . T G 761.49 PASS AC=2;AF=1;AN=2;DP=2037;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:2872,214,0:0,0,29,39 chr1 40533315 . T G 816.01 PASS AC=2;AF=1;AN=2;DP=1968;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:2680,181,0:0,0,20,39 chr1 40533320 . T G 861.01 PASS AC=2;AF=1;AN=2;DP=1996;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,64:64:99:2905,196,0:0,0,22,42 chr1 40533326 . T G 1041.01 PASS AC=2;AF=1;AN=2;DP=2034;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:3070,207,0:0,0,21,44 chr1 40533347 . T G 1134.85 PASS AC=2;AF=1;AN=2;DP=2310;FS=0;MQRankSum=1.155;ReadPosRankSum=0.982;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,78:78:99:3279,240,0:0,0,27,51 chr1 40536074 . C CT 7949.73 PASS AC=2;AF=1;AN=2;DP=6552;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,162:162:99:6571,490,0:0,0,81,81 chr1 40548044 . A G 170.1 PASS AC=2;AF=0.75;AN=2;DP=50;FS=0;FractionInformativeReads=1;MQ=60;set=variant8-variant12-variant35-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:492,45,0:0,0,6,9 chr1 40554958 . C CAAAAAAAAAAAAAAA,CAAAAAAAAAAAAAAAA,CAAAAAAAAAAAAAAAAAA,CAAAAAAAAAAAAAAAAA,CAAAAAAAAAAAAAA,CAAAAAAAAAAAAA 74.2 PASS AC=2,0,0,0,0,0;AF=0.328,0.224,0.017,0.224,0.017,0.069;AN=2;DP=217;set=variant-variant3-variant4-variant6-variant8-variant10-variant11-variant12-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant38-variant39-variant40-variant41-variant43-variant44 GT:DP:GQ:SB 1/1:7:39:0,0,6,1 chr1 40556922 . T C 3702.75 PASS AC=2;AF=1;AN=2;DP=4384;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,96:96:99:3010,287,0:0,0,57,39 chr1 40556942 . A T 923.21 PASS AC=2;AF=0.833;AN=2;DP=327;MQ=60;set=variant8-variant12-variant35 GT:AD:DP:GQ:PL:SB 1/1:1,106:107:99:2696,292,0:1,0,60,46 chr1 40558256 . C G 1211.59 PASS AC=2;AF=1;AN=2;DP=1106;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.657;ReadPosRankSum=0.896;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:963,84,0:0,0,6,22 chr1 40562993 . T C 351.79 PASS AC=2;AF=0.86;AN=2;DP=2432;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2241,210,0:0,0,28,42 chr1 40626918 . G T 389.73 PASS AC=2;AF=0.833;AN=2;DP=70;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.386;ReadPosRankSum=0.386;set=variant8-variant12-variant35 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:71:865,71,0:0,0,22,2 chr1 40688132 . C T 284.13 PASS AC=2;AF=0.7;AN=2;DP=55;FractionInformativeReads=1;MQ=60;set=variant8-variant10-variant12-variant35-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:308,24,0:0,0,7,1 chr1 40735817 . T G 573.62 PASS AC=2;AF=0.833;AN=2;DP=188;FractionInformativeReads=1;MQ=60;MQRankSum=-0.16;ReadPosRankSum=0.525;set=variant8-variant12-variant35 GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1983,168,0:0,0,13,43 chr1 40737516 . T G 1086.67 PASS AC=2;AF=1;AN=2;DP=1325;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:1092,96,0:0,0,25,7 chr1 40773123 . G C 706.24 PASS AC=1;AF=0.5;AN=2;DP=312;FractionInformativeReads=1;MQ=60;set=variant8-variant12-variant15-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:40,36:76:99:923,0,1052:28,12,23,13 chr1 40775926 . A G 1058.96 PASS AC=1;AF=0.5;AN=2;DP=454;FractionInformativeReads=1;MQ=60;set=variant15-variant18-variant27-variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,35:99:99:779,0,1600:30,34,16,19 chr1 40777884 . CTT CT,CTTT,C 61.8 PASS AC=0,1,0;AF=0.222,0.259,0.019;AN=2;DP=1398;MQ=60;set=filterInvariant-filterInvariant5-variant6-variant8-filterInvariant9-variant10-filterInvariant11-variant12-variant13-variant14-variant15-filterInvariant16-variant19-filterInvariant23-filterInvariant25-variant26-variant27-variant29-variant30-filterInvariant31-filterInvariant32-variant33-variant35-variant38-filterInvariant39-variant41-variant42 GT:DP:GQ:SB 0/2:42:99:7,13,10,12 chr1 40781185 . A C 669.7 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=2316;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:62,26:88:99:311,0,2354:18,44,26,0 chr1 40781191 . A C 250.02 PASS AC=1;AF=0.5;AN=2;DP=1545;MQ=60;set=filterInvariant2-filterInvariant5-filterInvariant8-filterInvariant14-filterInvariant16-filterInvariant17-filterInvariant20-filterInvariant22-filterInvariant23-filterInvariant28-filterInvariant32-variant34-filterInvariant35-filterInvariant38-filterInvariant39-filterInvariant41-filterInvariant42 GT:AD:DP:GQ:PL:SB 0/1:71,24:95:99:288,0,2553:25,46,24,0 chr1 40840270 . T TGC 233.71 PASS AC=1;AF=0.564;AN=2;DP=1686;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-filterInvariant10-variant11-filterInvariant12-variant13-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-filterInvariant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-filterInvariant35-filterInvariant36-variant37-variant38-variant39-filterInvariant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,7:23:99:107,0,484:10,6,6,1 chr1 40840294 . T A 107.43 PASS AC=1;AF=0.5;AN=2;DP=537;set=variant11-variant12-variant13-variant15-variant27-variant29-variant30-filterInvariant33-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:31,12:43:99:234,0,1000:17,14,10,2 chr1 40840296 . T A,TGA,TGTGA 973.38 PASS AC=2,0,0;AF=0.317,0.329,0.061;AN=2;DP=2299;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant2-variant44 GT:DP:GQ:SB 1/1:53:49:1,2,32,18 chr1 40879636 . T C 460.98 PASS AC=2;AF=0.93;AN=2;DP=555;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:576,45,0:0,0,13,2 chr1 40879808 . G T,C 2011.23 PASS AC=1,1;AF=0.898,0.068;AN=2;DP=3576;MQ=60;set=Intersection GT:DP:GQ:SB 2/1:79:99:0,0,45,34 chr1 40881041 . C G 4550.02 PASS AC=2;AF=0.92;AN=2;DP=6688;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,169:169:99:5122,507,0:0,0,74,95 chr1 40882900 . CTT CT,C,CTTT 594 PASS AC=1,0,0;AF=0.41,0.077,0.026;AN=2;DP=4135;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-filterInvariant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-filterInvariant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-filterInvariant42-variant43 GT:DP:GQ:SB 0/1:64:99:11,17,7,29 chr1 40927882 . G A 368.58 PASS AC=1;AF=0.5;AN=2;DP=356;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant7-variant12-variant14-variant16-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:30,22:52:99:614,0,750:18,12,15,7 chr1 40928067 . A T 1011.95 PASS AC=1;AF=0.5;AN=2;DP=689;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant7-variant12-variant14-variant16-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:41,31:72:99:799,0,967:22,19,15,16 chr1 40943156 . A G 2501.16 PASS AC=2;AF=1;AN=2;DP=2781;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,69:69:99:2196,207,0:0,0,43,26 chr1 40955375 . G C 197.36 PASS AC=1;AF=0.605;AN=2;DP=253;MQ=60;set=variant-variant4-variant6-variant8-variant11-variant15-variant17-variant20-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:6,3:9:64:64,0,206:2,4,1,2 chr1 40974799 . T C 555.96 PASS AC=1;AF=0.694;AN=2;DP=2822;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,47:100:99:1068,0,1270:23,30,17,30 chr1 40975104 . C T 729.86 PASS AC=2;AF=1;AN=2;DP=2078;FS=0;MQ=60;MQRankSum=1.347;ReadPosRankSum=1.027;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,61:61:99:1861,183,0:0,0,34,27 chr1 40975260 . G C 90.71 PASS AC=1;AF=0.694;AN=2;DP=1498;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,25:52:99:606,0,777:15,12,10,15 chr1 40980559 . G A 1643.75 PASS AC=1;AF=0.605;AN=2;DP=1792;MQ=60;set=variant-variant4-variant6-variant8-variant11-variant15-variant17-variant20-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:45,53:98:99:1334,0,1149:24,21,27,26 chr1 40980731 . G T 1297.01 PASS AC=1;AF=0.694;AN=2;DP=3085;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,53:110:99:1361,0,1429:26,31,28,25 chr1 40998811 . A G 999.13 PASS AC=1;AF=0.605;AN=2;DP=1403;MQ=60;set=variant-variant4-variant6-variant8-variant11-variant15-variant17-variant20-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:41,65:106:99:1601,0,838:21,20,30,35 chr1 41007403 . T A 863.5 PASS AC=1;AF=0.605;AN=2;DP=1016;MQ=60;set=variant-variant4-variant6-variant8-variant11-variant15-variant17-variant20-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:38,31:69:99:839,0,1109:10,28,8,23 chr1 41010149 . G A 31.7 PASS AC=1;AF=0.667;AN=2;DP=94;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant8-variant11-variant15-variant17-variant20-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:3,6:9:99:150,0,101:3,0,4,2 chr1 41010378 . C T 2495.12 PASS AC=1;AF=0.605;AN=2;DP=3429;MQ=60;set=variant-variant4-variant6-variant8-variant11-variant15-variant17-variant20-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:114,69:183:99:1510,0,2979:64,50,40,29 chr1 41013260 . C T 369.68 PASS AC=1;AF=0.694;AN=2;DP=1344;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,15:53:99:252,0,974:20,18,8,7 chr1 41087169 . A G 767.62 PASS AC=1;AF=0.542;AN=2;DP=509;MQ=60;set=variant4-variant5-variant10-variant11-variant15-variant22-variant27-variant29-variant30-variant33-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:18,19:37:99:515,0,556:8,10,10,9 chr1 41088205 . G A 616.85 PASS AC=1;AF=0.5;AN=2;DP=471;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant6-variant11-variant15-variant22-variant27-variant29-variant30-variant33-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:18,20:38:99:570,0,506:9,9,11,9 chr1 41088577 . C T 356.98 PASS AC=1;AF=0.5;AN=2;DP=455;MQ=60;set=variant4-variant5-variant6-variant11-variant15-variant22-variant27-variant29-variant30-variant33-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:20,16:36:99:406,0,649:9,11,9,7 chr1 41090250 . A G 438.52 PASS AC=2;AF=0.643;AN=2;DP=1401;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,62:64:99:1903,143,0:1,1,35,27 chr1 41091127 . T C 328.38 PASS AC=2;AF=0.833;AN=2;DP=2308;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:1784,162,0:0,0,31,23 chr1 41092018 . G A 761.97 PASS AC=1;AF=0.5;AN=2;DP=527;MQ=60;set=variant4-variant11-variant15-variant22-variant27-variant29-variant30-variant33-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:27,33:60:99:794,0,677:13,14,16,17 chr1 41094320 . C G 347.24 PASS AC=1;AF=0.537;AN=2;DP=929;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant35-variant36-variant37-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,17:30:99:513,0,356:9,4,9,8 chr1 41095171 . A G 614.5 PASS AC=1;AF=0.537;AN=2;DP=1068;MQ=60;set=variant2-variant3-variant5-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant35-variant36-variant37-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,25:40:99:617,0,392:6,9,9,16 chr1 41101572 . A G 523.55 PASS AC=2;AF=0.833;AN=2;DP=2281;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:1798,177,0:0,0,33,26 chr1 41107360 . T C 2240.71 PASS AC=2;AF=0.821;AN=2;DP=10531;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,282:282:99:8342,845,0:0,0,151,131 chr1 41107612 . C G 1141.8 PASS AC=1;AF=0.526;AN=2;DP=1867;MQ=60;set=variant2-variant3-variant5-variant10-variant12-variant14-variant17-variant18-variant20-variant23-variant25-variant27-variant29-variant32-variant35-variant36-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:63,62:125:99:1506,0,1653:25,38,29,33 chr1 41107699 . C G 599.67 PASS AC=1;AF=0.537;AN=2;DP=1404;MQ=60;set=variant2-variant3-variant5-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant35-variant36-variant37-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,32:64:99:804,0,708:15,17,12,20 chr1 41113490 . A AG 155.07 PASS AC=1;AF=0.571;AN=2;DP=789;MQ=60;set=variant2-variant3-variant5-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,16:30:99:495,0,432:6,8,7,9 chr1 41177943 . T C 1025.65 PASS AC=2;AF=0.814;AN=2;DP=2241;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1672,135,0:0,0,38,7 chr1 41178228 . AT A 540.14 PASS AC=2;AF=0.814;AN=2;DP=2709;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,51:52:99:1411,128,0:0,1,15,36 chr1 41204569 . C T 1167.78 PASS AC=1;AF=0.657;AN=2;DP=3153;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,51:93:99:1206,0,1035:21,21,24,27 chr1 41237388 . A G 722.83 PASS AC=1;AF=0.556;AN=2;DP=964;MQ=60;set=variant-variant2-variant4-variant7-variant9-variant11-variant14-variant15-variant16-variant18-variant19-variant21-variant23-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,17:51:99:482,0,1047:5,29,3,14 chr1 41284366 . G C 980.79 PASS AC=2;AF=0.738;AN=2;DP=3931;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,103:103:99:3221,309,0:0,0,42,61 chr1 41284406 . A G 491.66 PASS AC=2;AF=0.738;AN=2;DP=2540;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,66:66:99:2209,198,0:0,0,24,42 chr1 41284509 . C G 175.7 PASS AC=2;AF=0.75;AN=2;DP=513;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:698,48,0:0,0,6,10 chr1 41284520 . A G 220.7 PASS AC=2;AF=0.75;AN=2;DP=463;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:675,45,0:0,0,7,8 chr1 41284527 . T G 136.72 PASS AC=2;AF=0.756;AN=2;DP=424;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:585,39,0:0,0,7,6 chr1 41285087 . T C 2431.51 PASS AC=2;AF=0.738;AN=2;DP=14026;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,361:361:99:10604,1081,0:0,0,182,179 chr1 41289579 . C T 75.41 PASS AC=1;AF=0.577;AN=2;DP=418;MQ=60;set=variant2-variant3-variant4-variant6-variant12-variant13-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,16:21:82:405,0,82:3,2,9,7 chr1 41298652 . T C 540.87 PASS AC=2;AF=0.75;AN=2;DP=5367;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,139:139:99:4185,416,0:0,0,87,52 chr1 41301019 . T C 125.41 PASS AC=2;AF=0.696;AN=2;DP=328;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant7-variant8-variant9-variant11-variant12-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:601,54,0:0,0,5,13 chr1 41305217 . A T 1659.74 PASS AC=2;AF=0.93;AN=2;DP=2866;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,78:78:99:2380,234,0:0,0,39,39 chr1 41327873 . G C 3065.14 PASS AC=1;AF=0.658;AN=2;DP=3416;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,63:114:99:1655,0,1378:26,25,27,36 chr1 41449291 . CT C,CTT 265.85 PASS AC=2,0;AF=0.521,0.083;AN=2;DP=515;set=variant3-variant4-variant7-variant8-filterInvariant10-variant11-variant12-variant13-variant14-variant15-variant16-filterInvariant18-variant20-variant23-filterInvariant24-filterInvariant26-variant27-variant28-variant29-variant33-variant35-variant36-variant37-filterInvariant40 GT:DP:GQ:SB 1/1:17:4:0,2,0,15 chr1 41453286 . GT G 1902.43 PASS AC=2;AF=0.92;AN=2;DP=1757;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1644,135,0:0,0,15,30 chr1 41454425 . G A 1817.39 PASS AC=1;AF=0.633;AN=2;DP=822;MQ=60;set=variant5-variant7-variant8-variant11-variant13-variant16-variant17-variant18-variant19-variant22-variant26-variant34-variant35-variant36-variant38 GT:AD:DP:GQ:PL:SB 0/1:25,36:61:99:985,0,570:9,16,12,24 chr1 41461513 . G C 810.35 PASS AC=1;AF=0.542;AN=2;DP=258;MQ=60;set=variant3-variant4-variant6-variant12-variant15-variant18-variant20-variant22-variant27-variant35-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:9,12:21:99:358,0,246:7,2,10,2 chr1 41462986 . T C 671.25 PASS AC=1;AF=0.542;AN=2;DP=357;MQ=60;set=variant3-variant4-variant6-variant12-variant15-variant18-variant20-variant22-variant27-variant35-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:17,16:33:99:358,0,563:15,2,10,6 chr1 41466550 . T A 37.74 PASS AC=2;AF=0.72;AN=2;DP=212;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant25-variant34-variant35-variant36-variant37-variant38-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:358,27,0:0,0,7,2 chr1 41466803 . G A 873.3 PASS AC=2;AF=0.677;AN=2;DP=1678;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant25-variant26-variant27-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:1746,171,0:0,0,27,30 chr1 41474400 . C G 3393.2 PASS AC=1;AF=0.542;AN=2;DP=1122;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant6-variant12-variant15-variant18-variant20-variant22-variant27-variant35-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:41,48:89:99:1253,0,1169:17,24,22,26 chr1 41475085 . A G 1910.38 PASS AC=2;AF=0.743;AN=2;DP=2896;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,78:78:99:2483,234,0:0,0,47,31 chr1 41483951 . G C 205.56 PASS AC=1;AF=0.609;AN=2;DP=569;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant7-variant8-variant9-variant11-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant25-variant26-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,14:27:99:430,0,365:3,10,3,11 chr1 41485902 . C G 600.79 PASS AC=1;AF=0.609;AN=2;DP=1516;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant7-variant8-variant9-variant11-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant25-variant26-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:26,31:57:99:795,0,646:16,10,20,11 chr1 41486245 . C T 2151.54 PASS AC=1;AF=0.563;AN=2;DP=2816;MQ=60;set=variant2-variant5-variant8-variant9-variant11-variant12-variant13-variant16-variant17-variant19-variant21-variant30-variant35-variant36-variant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:100,105:205:99:2498,0,2443:48,52,52,53 chr1 41486408 . G A 3412.33 PASS AC=1;AF=0.542;AN=2;DP=905;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant6-variant12-variant15-variant18-variant20-variant22-variant27-variant35-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:35,36:71:99:896,0,1062:14,21,18,18 chr1 41486600 . C CAG 1059.54 PASS AC=2;AF=0.677;AN=2;DP=1869;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant25-variant26-variant27-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,52:52:99:2334,156,0:0,0,22,30 chr1 41487337 . G T 807.94 PASS AC=1;AF=0.531;AN=2;DP=1289;set=variant2-variant5-variant7-variant8-variant9-variant11-variant16-variant17-variant19-variant21-variant26-variant34-variant35-variant36-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:46,35:81:99:879,0,1161:22,24,14,21 chr1 41488168 . G T 5000.68 PASS AC=1;AF=0.542;AN=2;DP=1517;MQ=60;set=variant3-variant4-variant6-variant12-variant15-variant18-variant20-variant22-variant27-variant35-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:75,66:141:99:1366,0,1882:39,36,34,32 chr1 41488904 . G A 1197.49 PASS AC=1;AF=0.542;AN=2;DP=371;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant6-variant12-variant15-variant18-variant20-variant22-variant27-variant35-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:10,8:18:99:256,0,309:2,8,1,7 chr1 41493111 . A G 509.34 PASS AC=2;AF=0.71;AN=2;DP=1652;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant25-variant26-variant27-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:1893,171,0:0,0,28,29 chr1 41493749 . G A 616.53 PASS AC=1;AF=0.531;AN=2;DP=889;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant7-variant8-variant9-variant11-variant16-variant17-variant19-variant21-variant26-variant34-variant35-variant36-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:46,32:78:99:808,0,1248:29,17,19,13 chr1 41493811 . C T 3660.18 PASS AC=1;AF=0.542;AN=2;DP=1284;MQ=60;set=variant3-variant4-variant6-variant12-variant15-variant18-variant20-variant22-variant27-variant35-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:62,69:131:99:1595,0,1421:34,28,37,32 chr1 41494222 . G T 2890.73 PASS AC=2;AF=0.719;AN=2;DP=3505;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant25-variant26-variant27-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,112:112:99:3291,335,0:0,0,66,46 chr1 41540853 . A T 4040.78 PASS AC=1;AF=0.826;AN=2;DP=5169;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:86,55:141:99:2037,0,4697:51,35,31,24 chr1 41540861 . T C 4235.78 PASS AC=1;AF=0.826;AN=2;DP=5668;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:91,59:150:99:2159,0,4715:52,39,33,26 chr1 41582429 . T TA 710.93 PASS AC=1;AF=0.542;AN=2;DP=270;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant6-variant12-variant15-variant18-variant20-variant22-variant27-variant35-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:12,10:22:99:360,0,351:10,2,10,0 chr1 41608389 . A G 948.42 PASS AC=1;AF=0.545;AN=2;DP=173;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant6-variant12-variant15-variant20-variant22-variant27-variant35-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:8,7:15:99:185,0,266:7,1,5,2 chr1 41618442 . A T 1140.11 PASS AC=1;AF=0.826;AN=2;DP=2184;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,24:45:99:621,0,469:9,12,8,16 chr1 41651952 . G A 4561.56 PASS AC=1;AF=0.542;AN=2;DP=1483;MQ=60;set=variant3-variant4-variant6-variant12-variant15-variant18-variant20-variant22-variant27-variant35-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:57,49:106:99:1128,0,1437:21,36,21,28 chr1 41707651 . C A 387.52 PASS AC=1;AF=0.55;AN=2;DP=190;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant6-variant12-variant15-variant20-variant27-variant35-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:9,11:20:99:273,0,210:4,5,7,4 chr1 41707766 . T C 376.08 PASS AC=2;AF=1;AN=2;DP=633;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:369,39,0:0,0,6,7 chr1 41849018 . G C 1445.92 PASS AC=2;AF=1;AN=2;DP=1277;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.116;ReadPosRankSum=1.502;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1520,132,0:0,0,18,26 chr1 41849340 . A C 34.68 PASS AC=1;AF=0.676;AN=2;DP=299;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:2,4:6:73:162,0,73:0,2,0,4 chr1 41949595 . G A 1305.46 PASS AC=2;AF=1;AN=2;DP=2782;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:2345,213,0:0,0,44,27 chr1 41949628 . A C 1569.72 PASS AC=1;AF=0.86;AN=2;DP=3526;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,50:84:99:1335,0,904:23,11,33,17 chr1 41950312 . T C 4189.37 PASS AC=2;AF=0.943;AN=2;DP=5966;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,129:129:99:3936,387,0:0,0,56,73 chr1 41972198 . A T 4969.69 PASS AC=2;AF=0.706;AN=2;DP=11194;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant37-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,339:339:99:10699,1015,0:0,0,184,155 chr1 41972270 . TTTTTG T 2712.91 PASS AC=2;AF=0.706;AN=2;DP=10999;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant37-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:32,244:276:99:4928,113,0:20,12,127,117 chr1 41972283 . C T 3405.85 PASS AC=2;AF=0.778;AN=2;DP=11513;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:13,259:272:99:6081,531,0:8,5,136,123 chr1 41972555 . GTTTCT G 7604.85 PASS AC=2;AF=0.706;AN=2;DP=13202;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant37-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,366:368:99:15915,971,0:1,1,155,211 chr1 41973095 . A G 1768.27 PASS AC=2;AF=0.805;AN=2;DP=3644;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,79:81:99:2408,194,0:1,1,42,37 chr1 41973908 . C T 280.37 PASS AC=2;AF=0.706;AN=2;DP=1202;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant37-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:861,81,0:0,0,13,14 chr1 41974258 . G A 669.6 PASS AC=2;AF=0.765;AN=2;DP=2453;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant37-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,86:86:99:2576,258,0:0,0,45,41 chr1 41975149 . G C 4372.78 PASS AC=2;AF=1;AN=2;DP=6340;FS=0;MQ=60;MQRankSum=1.6;ReadPosRankSum=1.07;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,156:156:99:4402,466,0:0,0,81,75 chr1 41975636 . G A 292.37 PASS AC=1;AF=0.5;AN=2;DP=55;FractionInformativeReads=1;MQ=60;set=variant3-variant35 GT:AD:DP:GQ:PL:SB 0/1:17,5:22:78:78,0,456:10,7,2,3 chr1 41976328 . T C 2949.85 PASS AC=2;AF=0.977;AN=2;DP=3125;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:2,77:79:99:2437,202,0:1,1,44,33 chr1 41978359 . G T 651.9 PASS AC=2;AF=0.977;AN=2;DP=580;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:322,30,0:0,0,8,2 chr1 41978566 . T G 3282.22 PASS AC=2;AF=1;AN=2;DP=4240;FS=0;MQRankSum=1.155;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,110:110:99:3494,329,0:0,0,59,51 chr1 41978825 . C G 8438.49 PASS AC=2;AF=1;AN=2;DP=12233;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,314:314:99:9971,939,0:0,0,188,126 chr1 41983912 . C A 2939.6 PASS AC=2;AF=0.977;AN=2;DP=3551;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,81:81:99:2563,241,0:0,0,51,30 chr1 42041479 . A C 1146.41 PASS AC=2;AF=0.567;AN=2;DP=2712;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,84:84:99:2749,252,0:0,0,38,46 chr1 42045302 . G A 1465.02 PASS AC=2;AF=0.989;AN=2;DP=1363;FS=0;MQ=60;MQRankSum=-0.758;ReadPosRankSum=0.993;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,31:31:93:939,93,0:0,0,18,13 chr1 42046491 . A G 1768.53 PASS AC=1;AF=0.5;AN=2;DP=838;MQ=60;set=variant7-variant14-variant18-variant35 GT:AD:DP:GQ:PL:SB 0/1:107,101:208:99:2592,0,2678:45,62,38,63 chr1 42046812 . C T 800.8 PASS AC=2;AF=0.989;AN=2;DP=2337;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1527,145,0:0,0,27,22 chr1 42048745 . T C 3274.7 PASS AC=2;AF=0.989;AN=2;DP=5723;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,123:123:99:4333,368,0:0,0,57,66 chr1 42049032 . G A 2898.43 PASS AC=2;AF=0.977;AN=2;DP=4313;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,120:120:99:4102,357,0:0,0,73,47 chr1 42049140 . C G 6720.74 PASS AC=2;AF=0.977;AN=2;DP=10044;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,251:251:99:7723,754,0:0,0,148,103 chr1 42619139 . A G 1843.91 PASS AC=2;AF=0.533;AN=2;DP=2401;MQ=60;set=variant4-variant7-variant8-variant9-variant10-variant14-variant17-variant22-variant24-variant29-variant32-variant34-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,148:148:99:4588,444,0:0,0,78,70 chr1 42621170 . G C 1631.05 PASS AC=1;AF=0.5;AN=2;DP=1094;FractionInformativeReads=1;MQ=60;set=variant4-variant7-variant8-variant14-variant17-variant22-variant35 GT:AD:DP:GQ:PL:SB 0/1:91,93:184:99:2200,0,2119:45,46,43,50 chr1 42629040 . A G 3155.44 PASS AC=2;AF=1;AN=2;DP=5914;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,166:166:99:5090,497,0:0,0,90,76 chr1 42629346 . G A 397.35 PASS AC=1;AF=0.5;AN=2;DP=92;FractionInformativeReads=1;MQ=60;set=variant32-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:22,11:33:99:237,0,660:6,16,4,7 chr1 42643535 . A G 3408.83 PASS AC=1;AF=0.5;AN=2;DP=1329;MQ=60;set=variant7-variant8-variant14-variant22-variant35 GT:AD:DP:GQ:PL:SB 0/1:128,173:301:99:4316,0,3105:75,53,99,74 chr1 42644770 . C T 8087.2 PASS AC=1;AF=0.886;AN=2;DP=10135;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:125,107:232:99:2753,0,3184:53,72,36,71 chr1 42647536 . TCACA TCACACA,T,TCA 62.76 PASS AC=1,0,0;AF=0.25,0.25,0.023;AN=2;DP=348;set=variant2-variant4-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant21-variant22-variant25-variant26-variant27-variant35-variant36-variant37-variant39-variant42-variant44 GT:DP:GQ:SB 0/1:14:99:5,2,5,2 chr1 42654364 . G A 463.41 PASS AC=1;AF=0.574;AN=2;DP=1288;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant26-variant27-variant28-variant30-variant35-variant36-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,22:44:99:571,0,643:16,6,15,7 chr1 42656868 . C G 493.33 PASS AC=1;AF=0.574;AN=2;DP=692;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant26-variant27-variant28-variant30-variant35-variant36-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,20:37:99:603,0,526:14,3,16,4 chr1 42693597 . A G 4990.59 PASS AC=2;AF=0.738;AN=2;DP=6510;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,158:158:99:4674,473,0:0,0,76,82 chr1 42730525 . T C 4312.92 PASS AC=2;AF=1;AN=2;DP=5950;FS=0;MQ=60;MQRankSum=1.642;ReadPosRankSum=1.102;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,120:120:99:3857,359,0:0,0,79,41 chr1 42776699 . G GA 220.83 PASS AC=1;AF=0.5;AN=2;DP=305;MQ=60;set=variant4-variant7-variant8-variant14-variant17-variant22-variant35 GT:AD:DP:GQ:PL:SB 0/1:31,18:49:99:336,0,719:17,14,10,8 chr1 42801014 . T C 106.77 PASS AC=1;AF=0.686;AN=2;DP=320;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:2,7:9:55:146,0,55:0,2,4,3 chr1 42801370 . G C 808.42 PASS AC=1;AF=0.671;AN=2;DP=1527;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:23,14:37:99:357,0,673:13,10,7,7 chr1 42801476 . GTCTT G 1403.31 PASS AC=1;AF=0.671;AN=2;DP=1872;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:33,28:61:99:1056,0,1713:16,17,14,14 chr1 42880866 . G A 10470 PASS AC=2;AF=1;AN=2;DP=13308;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,318:319:99:9707,913,0:1,0,137,181 chr1 42898843 . A G 3396.56 PASS AC=1;AF=0.805;AN=2;DP=4210;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,55:102:99:1268,0,1254:30,17,30,25 chr1 42915727 . C G 1531.52 PASS AC=1;AF=0.625;AN=2;DP=3136;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant10-variant14-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant32-variant35-variant37-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:103,75:178:99:1731,0,2631:54,49,39,36 chr1 42915753 . T C 1368.73 PASS AC=1;AF=0.629;AN=2;DP=5324;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:85,62:147:99:1563,0,2223:44,41,26,36 chr1 42921211 . C G 294.08 PASS AC=1;AF=0.636;AN=2;DP=468;FractionInformativeReads=1;set=variant-variant3-variant4-variant5-variant7-variant10-variant11-variant12-variant14-variant15-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,11:25:99:321,0,346:8,6,9,2 chr1 42925688 . T G 6263.37 PASS AC=1;AF=0.629;AN=2;DP=17770;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:219,247:466:99:5628,0,5114:109,110,131,116 chr1 42948585 . C A 258.86 PASS AC=1;AF=0.643;AN=2;DP=571;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,7:15:99:199,0,234:3,5,1,6 chr1 43002744 . G A 797.68 PASS AC=1;AF=0.629;AN=2;DP=2379;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,33:62:99:799,0,764:20,9,20,13 chr1 43011030 . A G 203.25 PASS AC=1;AF=0.639;AN=2;DP=166;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant10-variant20-variant21-variant22-variant23-variant26-variant28-variant32-variant35-variant37-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,7:12:99:220,0,180:5,0,6,1 chr1 43011389 . A G 88.71 PASS AC=1;AF=0.667;AN=2;DP=243;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,5:11:99:148,0,186:2,4,1,4 chr1 43021810 . C T 427.43 PASS AC=1;AF=0.629;AN=2;DP=1443;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,23:36:99:575,0,319:8,5,15,8 chr1 43023713 . G GA 630.78 PASS AC=1;AF=0.625;AN=2;DP=693;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant10-variant14-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant32-variant35-variant37-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,22:34:99:532,0,259:8,4,14,8 chr1 43030190 . A ACCTCAGGTGATCCACCCACCTCGG 211.53 PASS AC=1;AF=0.632;AN=2;DP=764;set=variant-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,7:33:99:340,0,1239:15,11,6,1 chr1 43042703 . C T 952.46 PASS AC=1;AF=0.625;AN=2;DP=2442;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant10-variant14-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant32-variant35-variant37-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:87,57:144:99:1454,0,2162:51,36,38,19 chr1 43047057 . A G 276.7 PASS AC=1;AF=0.625;AN=2;DP=885;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant10-variant14-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant32-variant35-variant37-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,26:45:99:712,0,518:12,7,18,8 chr1 43054909 . T C 91.49 PASS AC=1;AF=0.731;AN=2;DP=82;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant7-variant10-variant22-variant23-variant24-variant26-variant28-variant32-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,5:10:99:154,0,174:5,0,4,1 chr1 43055243 . C G 186.39 PASS AC=1;AF=0.768;AN=2;DP=777;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,4:16:99:129,0,440:2,10,0,4 chr1 43102844 . T C 231.5 PASS AC=1;AF=0.607;AN=2;DP=159;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant6-variant7-variant10-variant14-variant22-variant27-variant28-variant32-variant34-variant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:74:82,0,74:2,1,2,1 chr1 43108188 . G A 826.06 PASS AC=1;AF=0.583;AN=2;DP=1154;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant7-variant10-variant22-variant28-variant32-variant34-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:62,50:112:99:1119,0,1530:34,28,28,22 chr1 43110276 . G A 264.05 PASS AC=1;AF=0.705;AN=2;DP=886;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,14:30:99:452,0,544:14,2,10,4 chr1 43111741 . G A 168.43 PASS AC=1;AF=0.583;AN=2;DP=296;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant7-variant10-variant22-variant28-variant32-variant34-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,10:18:99:274,0,293:7,1,7,3 chr1 43119855 . A C 4483.94 PASS AC=1;AF=0.583;AN=2;DP=3747;MQ=60;set=variant-variant6-variant7-variant10-variant22-variant28-variant32-variant34-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:175,175:350:99:4391,0,4106:92,83,84,91 chr1 43124220 . G A 449.83 PASS AC=1;AF=0.583;AN=2;DP=1285;MQ=60;set=variant-variant6-variant7-variant10-variant22-variant28-variant32-variant34-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:69,72:141:99:1686,0,1710:27,42,31,41 chr1 43124701 . A G 271.42 PASS AC=1;AF=0.711;AN=2;DP=1328;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,17:40:99:486,0,550:6,17,5,12 chr1 43124859 . C T 1263.74 PASS AC=1;AF=0.711;AN=2;DP=3140;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,42:93:99:978,0,1252:32,19,24,18 chr1 43131653 . G A 1555.27 PASS AC=1;AF=0.571;AN=2;DP=1725;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant7-variant8-variant10-variant22-variant28-variant32-variant34-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,52:111:99:1203,0,1421:34,25,30,22 chr1 43162182 . GC GCCC,G,GCC,GCCCC 258.4 PASS AC=0,0,0,1;AF=0.143,0.054,0.375,0.054;AN=2;DP=542;MQ=60;set=variant-variant2-variant3-variant6-variant8-variant11-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant37-variant38-variant40-variant41-variant44 GT:DP:GQ:SB 0/4:16:99:3,10,0,3 chr1 43166409 . GAGA G 1932.47 PASS AC=1;AF=0.571;AN=2;DP=1838;MQ=60;set=variant-variant2-variant6-variant7-variant8-variant10-variant22-variant28-variant32-variant34-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:74,67:141:99:2591,0,3486:42,32,38,29 chr1 43200526 . T C 995.33 PASS AC=1;AF=0.731;AN=2;DP=2773;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,41:83:99:999,0,907:23,19,18,23 chr1 43201216 . A C 1324.27 PASS AC=1;AF=0.718;AN=2;DP=3684;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:72,61:133:99:1618,0,1841:44,28,31,30 chr1 43212111 . C T 517.94 PASS AC=1;AF=0.756;AN=2;DP=2577;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,27:69:99:643,0,1116:28,14,19,8 chr1 43212431 . A G 2547.93 PASS AC=2;AF=1;AN=2;DP=5967;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,149:149:99:4817,445,0:0,0,69,80 chr1 43213499 . C T 856.87 PASS AC=1;AF=0.724;AN=2;DP=3156;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,41:90:99:1067,0,1325:16,33,13,28 chr1 43221042 . C T 893.57 PASS AC=1;AF=0.5;AN=2;DP=420;MQ=60;set=variant2-variant7-variant8-variant22-variant35 GT:AD:DP:GQ:PL:SB 0/1:37,42:79:99:1090,0,1064:14,23,23,19 chr1 43223412 . G A 506.14 PASS AC=1;AF=0.5;AN=2;DP=153;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant8-variant22-variant35 GT:AD:DP:GQ:PL:SB 0/1:15,12:27:99:281,0,443:11,4,8,4 chr1 43228189 . T A 2151.23 PASS AC=1;AF=0.989;AN=2;DP=3235;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:55,31:86:99:746,0,1352:22,33,11,20 chr1 43232807 . C G 393.51 PASS AC=1;AF=0.73;AN=2;DP=1870;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,22:42:99:635,0,591:10,10,10,12 chr1 43232877 . A T 1008.75 PASS AC=1;AF=0.614;AN=2;DP=1801;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant20-variant21-variant23-variant24-variant26-variant28-variant32-variant34-variant35-variant36-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,54:104:99:1340,0,1321:30,20,29,25 chr1 43239395 . G A 752.35 PASS AC=1;AF=0.744;AN=2;DP=1964;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,26:51:99:768,0,694:7,18,5,21 chr1 43282455 . C T 537.67 PASS AC=1;AF=0.607;AN=2;DP=1433;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant30-variant32-variant33-variant34-variant35-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,38:66:99:866,0,678:15,13,19,19 chr1 43296118 . G A 598.37 PASS AC=1;AF=0.579;AN=2;DP=2137;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant10-variant20-variant21-variant23-variant24-variant26-variant28-variant32-variant34-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:70,45:115:99:1222,0,1757:37,33,28,17 chr1 43296354 . G T 1702.23 PASS AC=1;AF=0.6;AN=2;DP=2899;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant7-variant8-variant9-variant12-variant14-variant15-variant16-variant18-variant22-variant24-variant27-variant29-variant31-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:87,67:154:99:1540,0,2176:39,48,31,36 chr1 43300663 . T C 848.65 PASS AC=1;AF=0.711;AN=2;DP=1660;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:16,15:31:99:525,0,572:13,3,12,3 chr1 43300921 . C G 639.91 PASS AC=1;AF=0.817;AN=2;DP=2865;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:58,42:100:99:1080,0,1458:20,38,14,28 chr1 43302574 . T TA 300.99 PASS AC=1;AF=0.55;AN=2;DP=411;set=variant-variant4-variant8-variant9-variant10-variant11-variant19-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant32-variant34-variant35-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,20:29:99:352,0,133:7,2,11,9 chr1 43302971 . C G 121.44 PASS AC=1;AF=0.619;AN=2;DP=192;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant8-variant9-variant10-variant11-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant32-variant34-variant35-variant37-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,6:10:96:240,0,96:1,3,0,6 chr1 43309548 . G A 7414.55 PASS AC=2;AF=0.989;AN=2;DP=9516;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,224:224:99:6873,671,0:0,0,104,120 chr1 43309842 . G C 1344.08 PASS AC=2;AF=1;AN=2;DP=1462;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:1106,96,0:0,0,13,19 chr1 43310639 . A G 1509.2 PASS AC=1;AF=0.5;AN=2;DP=2658;MQ=60;set=variant2-variant6-variant7-variant11-variant12-variant15-variant17-variant19-variant20-variant25-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:80,53:133:99:1232,0,1929:34,46,21,32 chr1 43312157 . T C 879.73 PASS AC=2;AF=1;AN=2;DP=1397;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:846,81,0:0,0,18,9 chr1 43312493 . C CG 2486.36 PASS AC=2;AF=1;AN=2;DP=4920;FS=0;MQ=60;MQRankSum=1.338;ReadPosRankSum=1.627;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,130:130:99:5224,396,0:0,0,43,87 chr1 43312499 . G A 893.65 PASS AC=1;AF=0.5;AN=2;DP=194;MQ=60;set=variant7-variant35 GT:AD:DP:GQ:PL:SB 0/1:49,65:114:99:1844,0,1797:14,35,17,48 chr1 43312506 . G C 870.93 PASS AC=1;AF=0.545;AN=2;DP=952;MQ=60;set=variant-variant4-variant10-variant11-variant19-variant25-variant34-variant35-variant37-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:62,47:109:99:1218,0,2406:17,45,14,33 chr1 43317793 . G A 675.23 PASS AC=1;AF=0.5;AN=2;DP=1215;MQ=60;set=variant2-variant7-variant11-variant12-variant15-variant17-variant19-variant20-variant25-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:28,48:76:99:1277,0,683:17,11,26,22 chr1 43392250 . C G 858.46 PASS AC=1;AF=0.5;AN=2;DP=947;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant9-variant10-variant11-variant17-variant22-variant24-variant29-variant34-variant35-variant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:46,29:75:99:685,0,1451:31,15,20,9 chr1 43393245 . G GGGTGAGAAAT 187.73 PASS AC=1;AF=0.621;AN=2;DP=345;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant9-variant11-variant14-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant29-variant30-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,1:6:99:110,0,588:4,1,1,0 chr1 43395635 . C T 1644.1 PASS AC=1;AF=0.5;AN=2;DP=1352;MQ=60;set=variant-variant2-variant9-variant11-variant17-variant22-variant27-variant29-variant35 GT:AD:DP:GQ:PL:SB 0/1:102,78:180:99:1864,0,2669:45,57,31,47 chr1 43396414 . G A 1585.73 PASS AC=1;AF=0.5;AN=2;DP=2063;MQ=60;set=variant-variant2-variant9-variant10-variant11-variant17-variant22-variant29-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:115,125:240:99:3206,0,2932:67,48,70,55 chr1 43408966 . G A 1008.15 PASS AC=1;AF=0.5;AN=2;DP=1617;MQ=60;set=variant-variant2-variant9-variant10-variant17-variant22-variant26-variant29-variant35-variant37-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:82,57:139:99:1358,0,2258:41,41,28,29 chr1 43409179 . G T 2626.18 PASS AC=1;AF=0.533;AN=2;DP=1089;MQ=60;set=variant3-variant5-variant6-variant7-variant11-variant13-variant16-variant17-variant20-variant21-variant23-variant24-variant35-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:23,39:62:99:1064,0,515:10,13,14,25 chr1 43409364 . T C 675.33 PASS AC=1;AF=0.538;AN=2;DP=222;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant6-variant7-variant11-variant16-variant17-variant20-variant21-variant23-variant24-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:12,8:20:99:184,0,293:5,7,3,5 chr1 43418026 . C T 656.13 PASS AC=1;AF=0.852;AN=2;DP=2866;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:31,43:74:99:1170,0,823:13,18,17,26 chr1 43418056 . AT A 2906.52 PASS AC=1;AF=0.533;AN=2;DP=887;MQ=60;set=variant3-variant5-variant6-variant7-variant11-variant13-variant16-variant17-variant20-variant21-variant23-variant24-variant35-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:28,35:63:99:1117,0,855:12,16,13,22 chr1 43424519 . T G 2179 PASS AC=1;AF=0.5;AN=2;DP=2639;MQ=60;set=variant-variant2-variant9-variant10-variant17-variant22-variant26-variant29-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:107,106:213:99:2778,0,2471:46,61,42,64 chr1 43424711 . CT C 305.74 PASS AC=1;AF=0.5;AN=2;DP=207;MQ=60;set=variant-variant2-variant9-variant10-variant17-variant22-variant26-variant29-variant35-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,9:19:99:307,0,347:1,9,0,9 chr1 43610910 . T G 775.64 PASS AC=2;AF=0.667;AN=2;DP=3497;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant16-variant17-variant19-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,116:116:99:3574,348,0:0,0,55,61 chr1 43611005 . G A 1119.07 PASS AC=2;AF=0.605;AN=2;DP=1842;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36 GT:AD:DP:GQ:PL:SB 1/1:0,69:69:99:2191,206,0:0,0,27,42 chr1 43613786 . G T 834.37 PASS AC=2;AF=0.614;AN=2;DP=2019;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,115:115:99:3745,346,0:0,0,32,83 chr1 43613850 . C CA 351.33 PASS AC=2;AF=0.614;AN=2;DP=611;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-filterInvariant32-variant34-variant35-variant36-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,29:29:86:892,86,0:0,0,1,28 chr1 43618596 . G A 2502.69 PASS AC=2;AF=0.605;AN=2;DP=4309;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36 GT:AD:DP:GQ:PL:SB 1/1:1,216:217:99:6255,639,0:1,0,116,100 chr1 43632536 . C T 2320.56 PASS AC=2;AF=0.625;AN=2;DP=3990;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,215:215:99:6119,643,0:0,0,98,117 chr1 43632815 . T G 2156.29 PASS AC=2;AF=0.625;AN=2;DP=2432;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,111:111:99:4963,334,0:0,0,51,60 chr1 43632816 . T C 2156.29 PASS AC=2;AF=0.625;AN=2;DP=2425;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,111:111:99:4963,334,0:0,0,51,60 chr1 43632997 . A G 544.48 PASS AC=2;AF=0.625;AN=2;DP=674;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:1034,84,0:0,0,6,22 chr1 43634867 . C T 302.59 PASS AC=2;AF=0.625;AN=2;DP=545;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:880,78,0:0,0,7,19 chr1 43636484 . C G 981.43 PASS AC=2;AF=0.625;AN=2;DP=2125;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant41 GT:AD:DP:GQ:PL:SB 1/1:1,109:110:99:3182,285,0:1,0,50,59 chr1 43636974 . C T 550.3 PASS AC=2;AF=0.625;AN=2;DP=806;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:1059,96,0:0,0,21,11 chr1 43637549 . A G 464.44 PASS AC=2;AF=0.625;AN=2;DP=796;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1548,117,0:0,0,28,11 chr1 43637932 . T C 4674.31 PASS AC=2;AF=0.625;AN=2;DP=6893;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant41 GT:AD:DP:GQ:PL:SB 1/1:2,358:360:99:10880,1030,0:1,1,166,192 chr1 43638185 . A G 220.22 PASS AC=2;AF=0.625;AN=2;DP=412;set=variant2-variant3-variant4-variant5-variant6-variant7-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:740,66,0:0,0,9,13 chr1 43638334 . A T 609.33 PASS AC=2;AF=0.625;AN=2;DP=627;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:791,57,0:0,0,19,0 chr1 43638410 . G C 1283.92 PASS AC=2;AF=0.625;AN=2;DP=2194;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,99:99:99:3125,297,0:0,0,65,34 chr1 43638457 . T A 1736.15 PASS AC=2;AF=0.625;AN=2;DP=2864;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,144:144:99:4421,430,0:0,0,92,52 chr1 43642988 . G T 676.14 PASS AC=2;AF=0.625;AN=2;DP=896;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1555,138,0:0,0,12,34 chr1 43649508 . A G 927.61 PASS AC=1;AF=0.661;AN=2;DP=2472;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant16-variant17-variant19-variant21-variant22-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:50,60:110:99:1614,0,1380:29,21,27,33 chr1 43650741 . T C 778.13 PASS AC=1;AF=0.646;AN=2;DP=1347;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant17-variant21-variant22-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:42,25:67:99:643,0,996:25,17,18,7 chr1 43651024 . C G 1026.66 PASS AC=1;AF=0.5;AN=2;DP=203;FractionInformativeReads=1;MQ=60;set=variant7-variant35 GT:AD:DP:GQ:PL:SB 0/1:55,54:109:99:1242,0,1453:27,28,22,32 chr1 43652369 . T C 2902.15 PASS AC=2;AF=1;AN=2;DP=5358;FS=0;MQ=60;MQRankSum=-0.485;ReadPosRankSum=0.596;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,126:126:99:4244,378,0:0,0,75,51 chr1 43663376 . A G 1740.15 PASS AC=2;AF=0.955;AN=2;DP=2934;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,82:82:99:2520,246,0:0,0,30,52 chr1 43664119 . A G 566.31 PASS AC=1;AF=0.614;AN=2;DP=781;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant21-variant22-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:18,19:37:99:641,0,458:13,5,17,2 chr1 43664218 . C T 1256.01 PASS AC=1;AF=0.614;AN=2;DP=1887;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant21-variant22-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:45,49:94:99:1180,0,1086:23,22,24,25 chr1 43664319 . TA T,TAA 417.06 PASS AC=1,0;AF=0.587,0.022;AN=2;DP=932;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant40-variant41 GT:DP:GQ:SB 0/1:38:99:7,13,5,13 chr1 43665255 . AAG A 100.79 PASS AC=1;AF=0.605;AN=2;DP=383;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant21-variant22-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant41 GT:AD:DP:GQ:PL:SB 0/1:10,14:24:99:526,0,353:2,8,3,11 chr1 43672636 . T G 631.42 PASS AC=1;AF=0.714;AN=2;DP=1362;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant28-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,25:46:99:885,0,583:5,16,3,22 chr1 43675467 . G A 2377.63 PASS AC=2;AF=0.909;AN=2;DP=9610;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,235:235:99:7126,702,0:0,0,125,110 chr1 43676287 . G A 264.37 PASS AC=2;AF=1;AN=2;DP=801;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:275,30,0:0,0,5,5 chr1 43676608 . C CA 63.08 PASS AC=2;AF=0.57;AN=2;DP=954;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-filterInvariant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,13:14:15:293,15,0:0,1,5,8 chr1 43680839 . T TG 459.68 PASS AC=1;AF=0.583;AN=2;DP=763;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant21-variant22-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:22,23:45:99:607,0,547:17,5,18,5 chr1 43680855 . G A 1849.01 PASS AC=2;AF=1;AN=2;DP=2533;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:2353,180,0:0,0,44,16 chr1 43681184 . C T 1066.72 PASS AC=2;AF=0.909;AN=2;DP=2827;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,85:85:99:2755,254,0:0,0,25,60 chr1 43687798 . G A 780.95 PASS AC=1;AF=0.5;AN=2;DP=63;FS=0;FractionInformativeReads=0.984;MQ=60;MQRankSum=1.044;QD=12.4;ReadPosRankSum=-0.48;SOR=0.671;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:29,33:62:99:809,0,792:16,13,18,15 chr1 43688743 . G A 151.35 PASS AC=1;AF=0.611;AN=2;DP=535;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant21-variant22-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:11,17:28:99:469,0,290:3,8,4,13 chr1 43698054 . A C 403.74 PASS AC=1;AF=0.5;AN=2;DP=36;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.353;QD=11.21;ReadPosRankSum=3.369;SOR=0.559;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:21,15:36:99:432,0,652:12,9,8,7 chr1 43699813 . A G 268.79 PASS AC=1;AF=0.872;AN=2;DP=788;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,16:25:99:506,0,232:5,4,13,3 chr1 43699935 . C T 2121.63 PASS AC=2;AF=1;AN=2;DP=4775;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,131:132:99:4267,382,0:1,0,81,50 chr1 43700140 . A G 6913.96 PASS AC=1;AF=0.872;AN=2;DP=10437;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:152,144:296:99:3608,0,3665:78,74,65,79 chr1 43735694 . C CAAGCCAG 1267.54 PASS AC=1;AF=0.58;AN=2;DP=844;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant17-variant19-variant20-variant21-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:18,20:38:99:827,0,2086:10,8,10,10 chr1 43735695 . T G 1276.57 PASS AC=1;AF=0.58;AN=2;DP=820;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant17-variant19-variant20-variant21-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:18,21:39:99:827,0,2086:10,8,11,10 chr1 43738340 . A C 4930.89 PASS AC=1;AF=0.645;AN=2;DP=4719;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:95,67:162:99:1603,0,2383:43,52,34,33 chr1 43747937 . G GA 121.49 PASS AC=1;AF=0.829;AN=2;DP=615;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,14:19:42:308,0,42:3,2,10,4 chr1 43748051 . A G 1601.68 PASS AC=1;AF=0.58;AN=2;DP=1091;FractionInformativeReads=1;set=variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant16-variant17-variant19-variant21-variant24-variant25-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:34,25:59:99:502,0,776:18,16,12,13 chr1 43748132 . A G 1336.78 PASS AC=2;AF=1;AN=2;DP=2124;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:1922,171,0:0,0,34,23 chr1 43766593 . T C 112.42 PASS AC=1;AF=0.5;AN=2;DP=384;set=variant7-variant17-variant22-filterInvariant26-variant28-filterInvariant32-variant34-filterInvariant35-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,6:41:97:97,0,1157:13,22,6,0 chr1 43771016 . TA T 1065.18 PASS AC=1;AF=0.718;AN=2;DP=4892;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:80,80:160:99:2362,0,2358:31,49,29,51 chr1 43771090 . G A 415.91 PASS AC=1;AF=0.718;AN=2;DP=2077;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,33:71:99:831,0,888:14,24,10,23 chr1 43773033 . A G 1235.57 PASS AC=1;AF=0.731;AN=2;DP=3759;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,77:136:99:2152,0,1571:22,37,27,50 chr1 43774292 . C T 119.26 PASS AC=1;AF=0.737;AN=2;DP=345;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,3:9:99:108,0,198:5,1,2,1 chr1 43774437 . G A 673.66 PASS AC=1;AF=0.731;AN=2;DP=1423;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,21:43:99:491,0,540:12,10,12,9 chr1 43774495 . G C 637.16 PASS AC=1;AF=0.697;AN=2;DP=1617;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:24,22:46:99:595,0,600:14,10,12,10 chr1 43774878 . C T 119.23 PASS AC=1;AF=0.596;AN=2;DP=568;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant25-variant28-variant29-variant31-variant32-variant33-variant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,15:28:99:558,0,386:4,9,7,8 chr1 43777852 . C T 5504.3 PASS AC=2;AF=0.875;AN=2;DP=6018;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,140:140:99:5143,420,0:0,0,66,74 chr1 43779564 . T C 902.74 PASS AC=1;AF=0.731;AN=2;DP=5616;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:79,70:149:99:1728,0,1875:42,37,36,34 chr1 43779869 . T G 1351.44 PASS AC=1;AF=0.731;AN=2;DP=2916;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,35:73:99:907,0,984:19,19,17,18 chr1 43782846 . G A 102.87 PASS AC=1;AF=0.731;AN=2;DP=921;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,23:31:99:562,0,211:7,1,16,7 chr1 43784956 . A G 913.72 PASS AC=1;AF=0.596;AN=2;DP=2621;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant25-variant28-variant29-variant31-variant32-variant33-variant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,49:100:99:1262,0,1132:27,24,29,20 chr1 43812075 . G A 496.96 PASS AC=1;AF=0.589;AN=2;DP=1459;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant25-variant28-variant29-variant31-variant32-variant33-variant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,22:40:99:598,0,535:15,3,14,8 chr1 43814864 . T C 633.54 PASS AC=1;AF=0.596;AN=2;DP=1890;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant25-variant28-variant29-variant31-variant32-variant33-variant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,31:72:99:891,0,1055:26,15,22,9 chr1 43824489 . GC G 37.71 PASS AC=1;AF=0.658;AN=2;DP=140;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant6-variant8-variant10-variant15-variant18-variant20-variant21-variant25-variant29-variant31-variant32-variant33-variant35-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:94:94,0,94:2,1,2,1 chr1 43825644 . T C 1509.01 PASS AC=1;AF=0.589;AN=2;DP=3224;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant25-variant28-variant29-variant31-variant32-variant33-variant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:73,65:138:99:1668,0,1835:40,33,40,25 chr1 43826312 . C A 4485.83 PASS AC=1;AF=0.738;AN=2;DP=17435;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:251,220:471:99:5128,0,6265:128,123,110,110 chr1 43829424 . G A 935.79 PASS AC=1;AF=0.5;AN=2;DP=72;FS=1.998;FractionInformativeReads=1;MQ=60;MQRankSum=-2.742;QD=13;ReadPosRankSum=0.298;SOR=1.074;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:36,36:72:99:964,0,942:20,16,23,13 chr1 43850473 . A G 2907.89 PASS AC=1;AF=0.596;AN=2;DP=4595;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant25-variant28-variant29-variant31-variant32-variant33-variant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:95,82:177:99:2179,0,2483:51,44,36,46 chr1 43855546 . A G 623.1 PASS AC=1;AF=0.589;AN=2;DP=3464;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant25-variant28-variant29-variant31-variant32-variant33-variant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,58:116:99:1332,0,1319:25,33,24,34 chr1 43855578 . G C 760.42 PASS AC=1;AF=0.75;AN=2;DP=4693;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,48:103:99:1185,0,1433:22,33,19,29 chr1 43869235 . G C 1270.33 PASS AC=1;AF=0.583;AN=2;DP=3308;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant25-variant28-variant29-variant31-variant32-variant33-variant35-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,52:119:99:1200,0,1685:37,30,28,24 chr1 43872067 . C T 1162.82 PASS AC=1;AF=0.574;AN=2;DP=3053;set=variant-variant3-variant4-variant5-variant6-variant7-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant28-variant29-variant31-variant32-variant33-variant35-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:72,43:115:99:964,0,1710:40,32,25,18 chr1 43886494 . C T 1559 PASS AC=1;AF=0.577;AN=2;DP=6040;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant28-variant29-variant31-variant32-variant33-variant35-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:89,115:204:99:3191,0,2353:54,35,72,43 chr1 43887146 . G A 328.21 PASS AC=1;AF=0.577;AN=2;DP=691;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant28-variant29-variant31-variant32-variant33-variant35-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,13:31:99:402,0,586:3,15,1,12 chr1 43888602 . G A 34.48 PASS AC=1;AF=0.569;AN=2;DP=756;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant28-variant29-variant31-variant32-variant33-variant35-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,14:25:99:417,0,351:2,9,6,8 chr1 43890538 . G T 1834.51 PASS AC=1;AF=0.5;AN=2;DP=149;FS=0;FractionInformativeReads=0.993;MQ=60;MQRankSum=-0.038;QD=12.31;ReadPosRankSum=2.815;SOR=0.643;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:75,73:148:99:1863,0,1874:36,39,36,37 chr1 43892189 . G A 4568.38 PASS AC=1;AF=0.574;AN=2;DP=12376;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant28-variant29-variant31-variant32-variant33-variant35-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:258,264:522:99:5919,0,5997:121,137,123,141 chr1 43897496 . G A 1152.69 PASS AC=1;AF=0.5;AN=2;DP=106;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.679;QD=10.87;ReadPosRankSum=-1.412;SOR=0.718;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:59,47:106:99:1181,0,1510:28,31,22,25 chr1 43901011 . A C 560.16 PASS AC=1;AF=0.577;AN=2;DP=1532;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant28-variant29-variant31-variant32-variant33-variant35-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,36:74:99:936,0,905:11,27,13,23 chr1 43903589 . G T 402.15 PASS AC=1;AF=0.574;AN=2;DP=1165;set=variant-variant3-variant4-variant5-variant6-variant7-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant28-variant29-variant31-variant32-variant33-variant35-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,28:57:99:771,0,805:7,22,8,20 chr1 43905819 . T C 1046.38 PASS AC=1;AF=0.577;AN=2;DP=1683;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant28-variant29-variant31-variant32-variant33-variant35-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,41:68:99:1053,0,584:11,16,20,21 chr1 43906896 . A G 1205.52 PASS AC=1;AF=0.574;AN=2;DP=3455;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant28-variant29-variant31-variant32-variant33-variant35-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:76,77:153:99:1834,0,1856:40,36,47,30 chr1 43909265 . T C 857.76 PASS AC=1;AF=0.574;AN=2;DP=4460;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant28-variant29-variant31-variant32-variant33-variant35-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:100,85:185:99:2279,0,2547:41,59,29,56 chr1 43912590 . A G 342.46 PASS AC=1;AF=0.577;AN=2;DP=1715;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant28-variant29-variant31-variant32-variant33-variant35-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,34:62:99:875,0,699:18,10,20,14 chr1 43916642 . T C 1210.98 PASS AC=1;AF=0.725;AN=2;DP=7452;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:90,122:212:99:3166,0,2457:48,42,62,60 chr1 43917409 . T C 1701.96 PASS AC=1;AF=0.556;AN=2;DP=4061;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant28-variant29-variant31-variant32-variant33-variant35-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:84,81:165:99:2024,0,2100:40,44,39,42 chr1 43917637 . G A 1531.6 PASS AC=1;AF=0.574;AN=2;DP=5170;set=variant-variant3-variant4-variant5-variant6-variant7-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant28-variant29-variant31-variant32-variant33-variant35-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:99,101:200:99:2544,0,2493:59,40,56,45 chr1 43919413 . A G 386.7 PASS AC=1;AF=0.726;AN=2;DP=2405;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,34:69:99:720,0,863:13,22,14,20 chr1 43996613 . GGGCTCC G,GGGCTCCGGCTCC 534.34 PASS AC=0,1;AF=0.333,0.167;AN=2;DP=177;MQ=60;set=variant19-variant22-variant35 GT:DP:GQ:SB 0/2:56:99:15,18,10,13 chr1 43998397 . GT G 1531.62 PASS AC=2;AF=1;AN=2;DP=2351;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1371,132,0:0,0,17,27 chr1 44035472 . G A 111.51 PASS AC=1;AF=0.56;AN=2;DP=795;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant10-variant12-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant26-variant28-variant29-variant32-variant33-variant35-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,10:22:99:303,0,273:5,7,3,7 chr1 44063250 . T C 156.22 PASS AC=2;AF=0.943;AN=2;DP=653;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:453,42,0:0,0,10,4 chr1 44063404 . A C 99.61 PASS AC=1;AF=0.5;AN=2;DP=1139;set=filterInvariant3-filterInvariant5-filterInvariant6-filterInvariant8-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant16-variant18-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant27-filterInvariant31-filterInvariant33-filterInvariant35-filterInvariant39-variant40-filterInvariant41-filterInvariant42-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:52,18:70:85:85,0,1981:18,34,18,0 chr1 44070691 . A G 865.13 PASS AC=1;AF=0.565;AN=2;DP=1555;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant7-variant12-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant26-variant28-variant29-variant32-variant33-variant35-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,39:77:99:1101,0,1117:15,23,16,23 chr1 44071221 . G A 4526.21 PASS AC=1;AF=0.756;AN=2;DP=6626;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:123,88:211:99:2052,0,3076:55,68,40,48 chr1 44072420 . A G 1600.28 PASS AC=1;AF=0.744;AN=2;DP=2729;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,44:99:99:1084,0,1374:33,22,27,17 chr1 44075227 . T C 275.08 PASS AC=2;AF=0.977;AN=2;DP=1224;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:1096,87,0:0,0,9,20 chr1 44078384 . T C 3000.08 PASS AC=1;AF=0.694;AN=2;DP=2539;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,57:111:99:1382,0,1340:29,25,33,24 chr1 44078602 . C A 699.42 PASS AC=1;AF=0.568;AN=2;DP=1104;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant12-variant14-variant15-variant18-variant20-variant21-variant22-variant26-variant28-variant29-variant32-variant33-variant35-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,26:43:99:652,0,519:5,12,9,17 chr1 44079411 . T C 1844.66 PASS AC=1;AF=0.694;AN=2;DP=3905;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,70:128:99:1959,0,1408:21,37,23,47 chr1 44083110 . C T 2081.98 PASS AC=1;AF=0.732;AN=2;DP=4174;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,65:117:99:1654,0,1372:37,15,44,21 chr1 44083507 . T C 1283.04 PASS AC=1;AF=0.732;AN=2;DP=4243;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,65:129:99:1576,0,1472:26,38,26,39 chr1 44083519 . G A 1109.6 PASS AC=1;AF=0.732;AN=2;DP=3848;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,57:115:99:1283,0,1316:24,34,23,34 chr1 44084739 . C T 3105.79 PASS AC=1;AF=0.732;AN=2;DP=6934;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:95,109:204:99:2766,0,2204:47,48,55,54 chr1 44086080 . T C 1701.12 PASS AC=1;AF=0.732;AN=2;DP=4162;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:76,51:127:99:1115,0,1844:41,35,30,21 chr1 44086831 . C T 4647.15 PASS AC=1;AF=0.689;AN=2;DP=8362;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:119,126:245:99:2954,0,2875:50,69,59,67 chr1 44087496 . C T 3521.7 PASS AC=1;AF=0.756;AN=2;DP=6138;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:108,94:202:99:2161,0,2968:74,34,61,33 chr1 44121557 . C G 404.76 PASS AC=1;AF=0.571;AN=2;DP=266;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant12-variant14-variant15-variant18-variant20-variant21-variant22-variant26-variant28-variant29-variant32-variant33-variant35-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,4:9:99:150,0,198:0,5,0,4 chr1 44137257 . C A 2100.26 PASS AC=1;AF=0.713;AN=2;DP=4403;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:70,48:118:99:1107,0,1793:33,37,23,25 chr1 44154479 . G C 665.89 PASS AC=1;AF=0.525;AN=2;DP=1394;FractionInformativeReads=1;MQ=60;set=variant5-variant6-variant7-variant12-variant14-variant15-variant18-variant20-variant21-variant22-variant26-variant28-variant29-variant32-variant33-variant35-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,50:105:99:1234,0,1367:28,27,25,25 chr1 44160186 . CAAA CAA,CA,CAAAA,C 35.48 PASS AC=2,0,0,0;AF=0.441,0.118,0.029,0.029;AN=2;DP=221;set=variant-variant5-variant7-variant11-variant12-variant18-variant19-variant20-variant22-variant27-variant29-variant33-variant35-variant36-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:8:12:1,0,7,0 chr1 44170440 . ATG ATGTG,A 374.7 PASS AC=0,1;AF=0.083,0.417;AN=2;DP=284;MQ=60;set=variant6-filterInvariant10-variant14-variant19-variant25-filterInvariant35 GT:DP:GQ:SB 0/2:40:68:16,19,2,3 chr1 44171211 . C T 256.08 PASS AC=1;AF=0.525;AN=2;DP=333;MQ=60;set=variant5-variant6-variant7-variant12-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant28-variant29-variant32-variant33-variant35-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,7:12:99:170,0,150:2,3,2,5 chr1 44173423 . G A 144.76 PASS AC=1;AF=0.525;AN=2;DP=594;MQ=60;set=variant5-variant6-variant7-variant12-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant26-variant28-variant29-variant32-variant33-variant35-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:16,13:29:99:291,0,388:7,9,5,8 chr1 44280381 . A T 1368.68 PASS AC=2;AF=0.898;AN=2;DP=1415;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1576,135,0:0,0,31,14 chr1 44290530 . A G 1099.17 PASS AC=1;AF=0.589;AN=2;DP=3303;MQ=60;set=variant5-variant6-variant7-variant8-variant10-variant11-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:71,59:130:99:1446,0,1607:37,34,30,29 chr1 44303786 . CA CAAAAAAAAAA,CAAAAAAAAAAAA,CAAAAAAAAA,CAAAAAAAAAAAAA,CAAAAAAAA,CAAAAAAAAAAA,C,CAAAAA,CAAAAAAA 1323.96 PASS AC=2,0,0,0,0,0,0,0,0;AF=0.226,0.016,0.194,0.065,0.194,0.161,0.016,0.032,0.016;AN=2;DP=535;set=variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant41-variant42-variant43 GT:DP:GQ:SB 1/1:4:41:0,0,4,0 chr1 44323736 . T C 1480.17 PASS AC=2;AF=0.92;AN=2;DP=2748;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1891,168,0:0,0,36,20 chr1 44344796 . T C 1309.12 PASS AC=1;AF=0.563;AN=2;DP=1923;MQ=60;set=variant2-variant3-variant5-variant6-variant8-variant10-variant11-variant13-variant25-variant27-variant30-variant34-variant35-variant37-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:55,64:119:99:1542,0,1230:24,31,29,35 chr1 44365529 . G A 906.96 PASS AC=1;AF=0.845;AN=2;DP=1767;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,30:64:99:779,0,911:12,22,10,20 chr1 44386305 . C T 377.45 PASS AC=1;AF=0.881;AN=2;DP=885;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,16:25:99:585,0,243:5,4,5,11 chr1 44386615 . A G 1628.99 PASS AC=1;AF=0.881;AN=2;DP=3669;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:73,58:131:99:1350,0,1648:31,42,31,27 chr1 44395786 . C T 3372.24 PASS AC=1;AF=0.768;AN=2;DP=5202;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:84,54:138:99:1365,0,2410:32,52,23,31 chr1 44396646 . C G 1969.18 PASS AC=1;AF=0.768;AN=2;DP=3066;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,38:88:99:859,0,1248:27,23,21,17 chr1 44399176 . A T 1801.2 PASS AC=2;AF=0.989;AN=2;DP=4072;MQ=60;MQRankSum=-0.852;ReadPosRankSum=1.245;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,113:113:99:3471,338,0:0,0,62,51 chr1 44399942 . G A 381.35 PASS AC=1;AF=0.763;AN=2;DP=727;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,8:22:99:169,0,355:6,8,4,4 chr1 44401384 . A G 3186.67 PASS AC=1;AF=0.881;AN=2;DP=5552;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:83,59:142:99:1528,0,2060:41,42,25,34 chr1 44402565 . G A 1031.66 PASS AC=1;AF=0.75;AN=2;DP=1967;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,26:59:99:715,0,914:17,16,11,15 chr1 44415415 . C T 4281.95 PASS AC=1;AF=0.768;AN=2;DP=9541;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:163,141:304:99:3326,0,4327:69,94,71,70 chr1 44426025 . G A 3003.28 PASS AC=1;AF=0.78;AN=2;DP=5207;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:77,48:125:99:1031,0,1809:38,39,26,22 chr1 44426948 . G A 1849.08 PASS AC=1;AF=0.929;AN=2;DP=4944;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,67:116:99:1661,0,1351:12,37,26,41 chr1 44431715 . T C 1171.93 PASS AC=1;AF=0.768;AN=2;DP=2208;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,32:71:99:803,0,1045:19,20,17,15 chr1 44432500 . C G 1124.74 PASS AC=1;AF=0.768;AN=2;DP=2837;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,31:65:99:893,0,944:18,16,14,17 chr1 44438974 . C T 12015.3 PASS AC=1;AF=0.756;AN=2;DP=13298;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:192,172:364:99:3869,0,4435:99,93,85,87 chr1 44442521 . A C 3212.21 PASS AC=1;AF=0.798;AN=2;DP=3709;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,52:113:99:1344,0,1714:26,35,24,28 chr1 44446634 . A G 578.52 PASS AC=1;AF=0.919;AN=2;DP=874;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,9:19:99:262,0,265:7,3,8,1 chr1 44451115 . A AGG 41.3 PASS AC=1;AF=0.75;AN=2;DP=10;FS=0;MQ=60;MQRankSum=0.406;ReadPosRankSum=0.406;set=variant19-variant35 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:55:221,0,55:2,1,3,0 chr1 44455871 . T C 2038.43 PASS AC=1;AF=0.588;AN=2;DP=624;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant6-variant7-variant10-variant11-variant13-variant18-variant25-variant26-variant30-variant31-variant35-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,28:49:99:934,0,550:15,6,23,5 chr1 44456742 . C T 2672.42 PASS AC=1;AF=0.563;AN=2;DP=474;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant10-variant11-variant13-variant30-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:40,26:66:99:612,0,1005:15,25,11,15 chr1 44457215 . G A 3216.74 PASS AC=1;AF=0.764;AN=2;DP=2960;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,51:102:99:1447,0,1432:29,22,31,20 chr1 44457305 . G A 5186.13 PASS AC=1;AF=0.764;AN=2;DP=6203;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:110,100:210:99:2274,0,2669:67,43,57,43 chr1 44457739 . T TC 1271.11 PASS AC=2;AF=1;AN=2;DP=1891;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:1791,144,0:0,0,16,32 chr1 44459318 . CAA CA,C 161.86 PASS AC=1,0;AF=0.476,0.024;AN=2;DP=1769;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-filterInvariant17-variant18-variant19-variant20-filterInvariant21-variant22-variant23-variant24-filterInvariant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-filterInvariant38-variant39-variant41-variant42-variant43 GT:DP:GQ:SB 0/1:38:99:16,6,14,2 chr1 44460857 . C T 2013.82 PASS AC=1;AF=0.583;AN=2;DP=309;FractionInformativeReads=1;MQ=60;set=variant3-variant10-variant11-variant30-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:24,27:51:99:674,0,618:13,11,14,13 chr1 44462273 . C T 580.9 PASS AC=1;AF=0.5;AN=2;DP=128;MQ=60;set=variant7-variant35 GT:AD:DP:GQ:PL:SB 0/1:33,35:68:99:692,0,907:18,15,20,15 chr1 44463170 . G A 5186.75 PASS AC=1;AF=0.563;AN=2;DP=926;MQ=60;set=variant3-variant6-variant10-variant11-variant13-variant30-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:59,82:141:99:2752,0,1926:42,17,60,22 chr1 44466606 . G A 12065.8 PASS AC=1;AF=0.563;AN=2;DP=2425;MQ=60;set=variant3-variant6-variant10-variant11-variant13-variant30-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:157,112:269:99:2736,0,3833:86,71,67,45 chr1 44468235 . G A 5811.52 PASS AC=1;AF=0.563;AN=2;DP=1368;MQ=60;set=variant3-variant6-variant10-variant11-variant13-variant30-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:119,76:195:99:1796,0,3099:52,67,31,45 chr1 44475586 . G A 1173.33 PASS AC=1;AF=0.625;AN=2;DP=247;MQ=60;set=variant3-variant6-variant10-variant11-variant13-variant30-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:13,18:31:99:557,0,437:11,2,15,3 chr1 44482312 . C T 241.4 PASS AC=1;AF=0.6;AN=2;DP=164;FS=0;MQ=60;set=variant2-variant3-variant5-variant6-variant10-variant11-variant27-variant30-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:10,9:19:99:302,0,332:1,9,1,8 chr1 44483040 . AACACACACAC AACACACAC,AACAC,AAC,AACACAC,A 260.83 PASS AC=0,2,0,0,0;AF=0.43,0.163,0.105,0.186,0.012;AN=2;DP=1523;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 2/2:19:57:0,0,4,15 chr1 44596379 . CCAA C 1855.65 PASS AC=1;AF=0.5;AN=2;DP=2358;MQ=60;set=variant2-variant7-variant9-variant11-variant18-variant20-variant22-variant25-variant27-variant28-variant29-variant31-variant32-variant35-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:91,52:143:99:1910,0,3820:39,52,20,32 chr1 44598832 . C T 100.31 PASS AC=2;AF=0.839;AN=2;DP=165;MQ=60;set=variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant17-variant18-variant20-variant22-variant25-variant26-variant27-variant28-variant32-variant34-variant35-variant36-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:126,12,0:0,0,3,1 chr1 44600329 . C T 380.23 PASS AC=2;AF=0.604;AN=2;DP=658;MQ=60;set=variant2-variant7-variant8-variant9-variant11-variant16-variant18-variant19-variant20-variant21-variant22-variant25-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:785,78,0:0,0,17,9 chr1 44679556 . A G 3320.31 PASS AC=2;AF=0.776;AN=2;DP=4542;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,128:128:99:3827,383,0:0,0,63,65 chr1 44680719 . G C 1617.69 PASS AC=1;AF=0.5;AN=2;DP=3269;MQ=60;set=variant2-variant7-variant9-variant11-variant18-variant20-variant22-variant25-variant27-variant28-variant29-variant31-variant32-variant35-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:92,99:191:99:2579,0,2594:42,50,51,48 chr1 44686322 . T C 1556.66 PASS AC=2;AF=0.545;AN=2;DP=2573;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant8-variant9-variant11-variant18-variant19-variant20-variant21-variant22-variant25-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,139:139:99:4462,417,0:0,0,64,75 chr1 44788398 . A T 1784.41 PASS AC=2;AF=0.966;AN=2;DP=3252;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,89:89:99:2583,266,0:0,0,47,42 chr1 44818337 . G T 221.11 PASS AC=2;AF=0.708;AN=2;DP=336;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:294,21,0:0,0,7,0 chr1 44878509 . C G 405.9 PASS AC=2;AF=0.672;AN=2;DP=545;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:855,69,0:0,0,3,20 chr1 45011263 . G A 523.4 PASS AC=1;AF=0.5;AN=2;DP=358;FractionInformativeReads=1;MQ=60;set=variant5-variant7-variant12-variant22-variant28-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:23,28:51:99:736,0,679:6,17,7,21 chr1 45088629 . G A 1224.31 PASS AC=1;AF=0.589;AN=2;DP=997;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant18-variant20-variant22-variant23-variant24-variant25-variant28-variant31-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,33:52:99:955,0,613:2,17,9,24 chr1 45097639 . T C 467.65 PASS AC=1;AF=0.583;AN=2;DP=1173;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant18-variant20-variant22-variant23-variant24-variant25-variant28-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,38:52:99:885,0,279:6,8,20,18 chr1 45100903 . C G 205.86 PASS AC=1;AF=0.591;AN=2;DP=475;set=variant-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant18-variant20-variant22-variant23-variant24-variant25-variant28-variant35-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,13:26:99:328,0,303:8,5,9,4 chr1 45100927 . T C 211.38 PASS AC=1;AF=0.587;AN=2;DP=618;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant10-variant11-filterInvariant12-variant18-variant20-variant22-variant23-variant24-variant25-variant28-variant35-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,17:30:99:453,0,275:7,6,12,5 chr1 45101478 . T C 1664 PASS AC=1;AF=0.589;AN=2;DP=1763;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant18-variant20-variant22-variant23-variant24-variant25-variant28-variant31-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,42:91:99:1030,0,1256:21,28,22,20 chr1 45102355 . T C 157.66 PASS AC=1;AF=0.587;AN=2;DP=464;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant18-variant20-variant22-variant23-variant24-variant25-variant28-variant35-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,12:30:99:407,0,488:8,10,5,7 chr1 45111294 . G A 356.63 PASS AC=1;AF=0.583;AN=2;DP=421;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant22-variant23-variant24-variant28-variant35-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,16:27:99:542,0,372:2,9,3,13 chr1 45116935 . C T 779.22 PASS AC=1;AF=0.595;AN=2;DP=1361;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant18-variant22-variant23-variant24-variant28-variant35-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,38:65:99:1158,0,683:13,14,18,20 chr1 45116985 . C T 2301.59 PASS AC=1;AF=0.596;AN=2;DP=1993;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant18-variant22-variant23-variant24-variant28-variant31-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,38:74:99:1062,0,950:21,15,20,18 chr1 45117300 . G A 550.43 PASS AC=1;AF=0.595;AN=2;DP=908;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant18-variant22-variant23-variant24-variant28-variant35-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,21:47:99:569,0,679:11,15,11,10 chr1 45118901 . C T 165.67 PASS AC=1;AF=0.618;AN=2;DP=139;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant10-variant11-variant22-variant23-variant24-variant28-variant35-variant37-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:2,4:6:69:146,0,69:2,0,4,0 chr1 45119390 . A G 1543.18 PASS AC=1;AF=0.595;AN=2;DP=2021;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant18-variant22-variant23-variant24-variant28-variant35-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:62,45:107:99:1339,0,1748:38,24,33,12 chr1 45119965 . C T 492.49 PASS AC=1;AF=0.595;AN=2;DP=1313;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant18-variant22-variant23-variant24-variant28-variant35-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,34:64:99:859,0,709:15,15,18,16 chr1 45120068 . A G 544.23 PASS AC=1;AF=0.595;AN=2;DP=1170;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant18-variant22-variant23-variant24-variant28-variant35-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,29:52:99:748,0,542:12,11,13,16 chr1 45140619 . CTGGA C,CTGGATGGA 300.01 PASS AC=1,0;AF=0.607,0.036;AN=2;DP=753;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:20:99:1,8,4,7 chr1 45219630 . CTT C,CT 59.1 PASS AC=0,1;AF=0.5,0.167;AN=2;DP=48;MQ=60;set=variant8-variant17-variant35 GT:DP:GQ:SB 0/2:7:9:0,2,0,5 chr1 45241587 . G A 3184.49 PASS AC=1;AF=0.5;AN=2;DP=1191;MQ=60;set=variant4-variant18-variant25-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:118,125:243:99:2933,0,2748:70,48,70,55 chr1 45266875 . CTTT CTT,CTTTT,CTTTTT,C 108.02 PASS AC=0,0,1,0;AF=0.211,0.211,0.079,0.026;AN=2;DP=744;set=variant2-filterInvariant3-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant19-filterInvariant20-variant22-variant24-filterInvariant30-variant31-variant35-filterInvariant39-variant40-filterInvariant41-variant42-filterInvariant43-filterInvariant44 GT:DP:GQ:SB 0/3:8:16:0,2,1,5 chr1 45285720 . C G 951.79 PASS AC=1;AF=0.5;AN=2;DP=183;FractionInformativeReads=1;MQ=60;set=variant7-variant12-variant35 GT:AD:DP:GQ:PL:SB 0/1:33,33:66:99:862,0,880:19,14,21,12 chr1 45468606 . A G 1501.08 PASS AC=2;AF=0.833;AN=2;DP=2145;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1477,153,0:0,0,26,25 chr1 45468631 . A T 1496.1 PASS AC=2;AF=1;AN=2;DP=2081;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:1402,143,0:0,0,25,23 chr1 45470130 . T C 365.24 PASS AC=2;AF=0.942;AN=2;DP=1331;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1190,104,0:0,0,11,24 chr1 45472798 . TTGTGTGTGTGTGTG TTGTGTGTG,TTGTGTGTGTG,TTGTGTG,TTGTG,T,TTG 1780.35 PASS AC=1,0,1,0,0,0;AF=0.352,0.216,0.398,0.011,0.011,0.011;AN=2;DP=2719;set=Intersection GT:DP:GQ:SB 3/1:57:99:1,0,32,24 chr1 45473767 . C A 296.94 PASS AC=1;AF=0.5;AN=2;DP=191;FractionInformativeReads=1;MQ=60;set=variant7-variant12-variant25-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:21,16:37:99:395,0,559:13,8,10,6 chr1 45474157 . G A 3229 PASS AC=2;AF=0.788;AN=2;DP=4609;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,133:133:99:4248,397,0:0,0,73,60 chr1 45475566 . A G 1116.24 PASS AC=2;AF=1;AN=2;DP=2102;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:2033,177,0:0,0,38,21 chr1 45475881 . T C 1386.55 PASS AC=1;AF=0.5;AN=2;DP=352;FractionInformativeReads=1;MQ=60;set=variant7-variant12-variant35 GT:AD:DP:GQ:PL:SB 0/1:41,74:115:99:2073,0,1162:10,31,26,48 chr1 45476069 . C A 645.43 PASS AC=2;AF=1;AN=2;DP=1665;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1387,122,0:0,0,28,13 chr1 45478585 . G C 952.14 PASS AC=1;AF=0.5;AN=2;DP=145;MQ=60;set=variant7-variant35 GT:AD:DP:GQ:PL:SB 0/1:43,32:75:99:922,0,1475:16,27,12,20 chr1 45479874 . G T 1387 PASS AC=2;AF=1;AN=2;DP=2468;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,67:67:99:2101,200,0:0,0,26,41 chr1 45480733 . C T 1328.68 PASS AC=2;AF=1;AN=2;DP=1917;FS=0;MQ=60;MQRankSum=1.209;ReadPosRankSum=0.49;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1335,128,0:0,0,20,23 chr1 45500294 . A G 851.22 PASS AC=2;AF=0.795;AN=2;DP=976;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:501,39,0:0,0,2,11 chr1 45504720 . G C 677.06 PASS AC=1;AF=0.703;AN=2;DP=2593;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,34:79:99:763,0,1038:25,20,18,16 chr1 45504858 . G T 296.14 PASS AC=1;AF=0.556;AN=2;DP=285;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant11-variant15-variant18-variant25-variant30-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:17,17:34:99:333,0,458:6,11,6,11 chr1 45524213 . C T 998.6 PASS AC=1;AF=0.869;AN=2;DP=4821;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,57:114:99:1443,0,1381:30,27,31,26 chr1 45671599 . G A 889.44 PASS AC=1;AF=0.556;AN=2;DP=461;MQ=60;set=variant-variant4-variant11-variant15-variant18-variant25-variant30-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:35,23:58:99:694,0,1150:20,15,11,12 chr1 45671966 . A G 2034.29 PASS AC=1;AF=0.565;AN=2;DP=4185;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant11-variant15-variant18-variant19-variant21-variant25-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:93,116:209:99:2966,0,2195:40,53,46,70 chr1 45795900 . CAAAA CAA,CA,C,CAAA 84.98 PASS AC=2,0,0,0;AF=0.348,0.261,0.043,0.043;AN=2;DP=264;set=variant-variant2-variant3-variant4-variant5-variant7-variant10-variant11-variant13-variant14-variant15-variant17-variant20-variant22-variant23-variant27-variant32-variant35-variant36-variant37-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:10:12:1,0,8,1 chr1 45796269 . G C 2426.22 PASS AC=2;AF=0.909;AN=2;DP=4104;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,103:103:99:3269,308,0:0,0,41,62 chr1 45797505 . C G 802.16 PASS AC=1;AF=0.583;AN=2;DP=1640;MQ=60;set=variant-variant2-variant8-variant11-variant13-variant17-variant18-variant19-variant20-variant25-variant27-variant30-variant32-variant34-variant35-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:66,61:127:99:1634,0,1873:20,46,18,43 chr1 45798555 . T C 2265.91 PASS AC=2;AF=0.909;AN=2;DP=6469;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,151:151:99:5022,453,0:0,0,70,81 chr1 45804050 . C T 1339.73 PASS AC=1;AF=0.583;AN=2;DP=2021;MQ=60;set=variant-variant2-variant8-variant11-variant13-variant17-variant18-variant19-variant20-variant25-variant27-variant30-variant32-variant34-variant35-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:89,63:152:99:1698,0,2474:44,45,31,32 chr1 45804419 . T TG 242.94 PASS AC=1;AF=0.5;AN=2;DP=37;FractionInformativeReads=1;MQ=60;set=variant25-variant35 GT:AD:DP:GQ:PL:SB 0/1:6,10:16:99:384,0,222:1,5,2,8 chr1 45804422 . T TTG 321.45 PASS AC=1;AF=0.721;AN=2;DP=537;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant20-variant21-variant22-variant23-variant25-variant26-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,6:15:99:222,0,392:2,7,1,5 chr1 45804427 . G T 151.69 PASS AC=1;AF=0.636;AN=2;DP=124;set=variant-variant2-variant8-variant17-variant19-variant25-variant27-variant30-variant34-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:6,8:14:99:318,0,228:1,5,2,6 chr1 45804428 . TTTG T 289.62 PASS AC=1;AF=0.727;AN=2;DP=428;FractionInformativeReads=1;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant20-variant21-variant22-variant23-variant25-variant26-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,6:14:99:228,0,318:2,6,1,5 chr1 45805566 . G C 3549.32 PASS AC=2;AF=1;AN=2;DP=7256;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,176:177:99:5262,520,0:1,0,91,85 chr1 45810091 . A G 592.71 PASS AC=1;AF=0.583;AN=2;DP=1041;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant8-variant11-variant13-variant17-variant18-variant19-variant20-variant25-variant27-variant30-variant32-variant34-variant35-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:33,36:69:99:926,0,888:17,16,19,17 chr1 45810230 . T A 999.71 PASS AC=1;AF=0.5;AN=2;DP=173;FractionInformativeReads=1;MQ=60;set=variant7-variant35 GT:AD:DP:GQ:PL:SB 0/1:46,46:92:99:1222,0,1091:20,26,25,21 chr1 45810923 . G A 1604.67 PASS AC=1;AF=0.5;AN=2;DP=982;FractionInformativeReads=1;MQ=60;set=variant-variant11-variant18-variant25-variant30-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:76,92:168:99:2557,0,2139:38,38,51,41 chr1 45813441 . T C 819.97 PASS AC=1;AF=0.583;AN=2;DP=677;MQ=60;set=variant-variant2-variant8-variant11-variant13-variant17-variant18-variant19-variant20-variant25-variant27-variant30-variant32-variant34-variant35-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:27,15:42:99:435,0,891:11,16,8,7 chr1 45813820 . G A 676.76 PASS AC=1;AF=0.583;AN=2;DP=970;MQ=60;set=variant-variant2-variant8-variant11-variant13-variant17-variant18-variant19-variant20-variant25-variant27-variant30-variant32-variant34-variant35-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:47,28:75:99:763,0,1361:12,35,5,23 chr1 45864695 . C A 164.12 PASS AC=1;AF=0.656;AN=2;DP=109;FractionInformativeReads=1;set=variant-variant2-variant8-variant11-variant17-variant18-variant19-variant20-variant25-variant27-variant32-variant34-variant35-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:1,3:4:30:79,0,30:0,1,1,2 chr1 45887288 . T C 202.44 PASS AC=1;AF=0.6;AN=2;DP=271;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant8-variant11-variant17-variant18-variant19-variant20-variant27-variant30-variant32-variant34-variant35-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:16,10:26:99:320,0,562:14,2,9,1 chr1 45956700 . C A 1928.41 PASS AC=2;AF=0.756;AN=2;DP=7260;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,203:204:99:6013,584,0:1,0,110,93 chr1 45960135 . CAA C,CA,CAAA 141.92 PASS AC=0,1,0;AF=0.071,0.5,0.018;AN=2;DP=451;set=variant-variant2-variant3-variant6-variant8-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant27-variant29-variant30-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant42 GT:DP:GQ:SB 0/2:12:77:5,1,5,1 chr1 45961327 . CTTTTTTTTTTTTTT CTT,C,CT 200.49 PASS AC=0,0,2;AF=0.204,0.056,0.537;AN=2;DP=267;FS=0;set=variant2-variant4-variant5-variant7-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant21-variant22-variant23-variant25-variant26-variant29-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant43-variant44 GT:DP:GQ:SB 3/3:6:19:0,0,1,5 chr1 45961955 . A G 1044.75 PASS AC=2;AF=0.756;AN=2;DP=4260;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,107:107:99:3338,321,0:0,0,66,41 chr1 45965307 . G A 2090.19 PASS AC=2;AF=0.667;AN=2;DP=6125;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,201:201:99:6455,601,0:0,0,75,126 chr1 45965340 . T C 1055.79 PASS AC=2;AF=0.756;AN=2;DP=5229;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,133:133:99:4524,398,0:0,0,41,92 chr1 45965703 . G T 466.43 PASS AC=2;AF=0.756;AN=2;DP=3039;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:2453,227,0:0,0,45,31 chr1 45973435 . A AT 197.25 PASS AC=2;AF=0.768;AN=2;DP=684;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:486,39,0:0,0,5,8 chr1 45973928 . G A 1429.46 PASS AC=2;AF=0.667;AN=2;DP=5446;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,147:147:99:4433,441,0:0,0,70,77 chr1 45975145 . GCA G 622.4 PASS AC=1;AF=0.5;AN=2;DP=53;FS=0;MQ=60;set=variant7-variant35 GT:AD:DP:GQ:PL:SB 0/1:11,6:17:99:219,0,444:0,11,0,6 chr1 45975739 . ACT A 208.69 PASS AC=2;AF=0.833;AN=2;DP=227;set=variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:450,30,0:0,0,8,2 chr1 45975748 . CAA C,CA,CAAA 72.8 PASS AC=0,1,0;AF=0.083,0.333,0.083;AN=2;DP=57;FS=0;set=variant16-variant17-variant19-variant27-variant35-variant37 GT:DP:GQ:SB 0/2:13:92:5,2,4,2 chr1 45975856 . C G 190.38 PASS AC=2;AF=0.667;AN=2;DP=1120;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:982,105,0:0,0,20,15 chr1 45976147 . G A 76.26 PASS AC=2;AF=0.75;AN=2;DP=742;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:488,36,0:0,0,8,4 chr1 45976263 . C CT 334.67 PASS AC=2;AF=0.744;AN=2;DP=1630;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1816,135,0:0,0,25,20 chr1 45976472 . G C 431.96 PASS AC=2;AF=0.667;AN=2;DP=1677;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1424,123,0:0,0,22,19 chr1 45976587 . A G 1266.88 PASS AC=2;AF=0.756;AN=2;DP=3002;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:1864,174,0:0,0,30,28 chr1 45981512 . T C 1022.57 PASS AC=2;AF=0.756;AN=2;DP=4559;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,111:111:99:3370,332,0:0,0,51,60 chr1 45984353 . G A 149.16 PASS AC=2;AF=0.756;AN=2;DP=481;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:451,39,0:0,0,10,3 chr1 46016687 . T C 1732.98 PASS AC=2;AF=0.671;AN=2;DP=4591;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,147:147:99:5066,441,0:0,0,62,85 chr1 46027355 . T C 1728.02 PASS AC=2;AF=0.643;AN=2;DP=4747;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,158:158:99:4792,474,0:0,0,97,61 chr1 46035760 . A T 546.26 PASS AC=2;AF=0.629;AN=2;DP=2558;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:2786,231,0:0,0,17,60 chr1 46050004 . TTCGG T 2295.87 PASS AC=2;AF=0.795;AN=2;DP=4956;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,138:138:99:6139,415,0:0,0,43,95 chr1 46057144 . A G 128.26 PASS AC=2;AF=0.923;AN=2;DP=140;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant6-variant9-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant35-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:139,12,0:0,0,1,3 chr1 46065998 . T C 3160.01 PASS AC=2;AF=0.966;AN=2;DP=4088;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,83:83:99:2597,248,0:0,0,50,33 chr1 46073489 . G A 1164.11 PASS AC=2;AF=0.643;AN=2;DP=3490;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,133:133:99:4276,399,0:0,0,66,67 chr1 46078630 . A G 84.37 PASS AC=2;AF=0.803;AN=2;DP=567;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:614,48,0:0,0,14,2 chr1 46078854 . A G 759.56 PASS AC=2;AF=0.795;AN=2;DP=2945;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:2137,204,0:0,0,30,38 chr1 46078884 . C T 613.07 PASS AC=2;AF=0.795;AN=2;DP=2840;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:2016,195,0:0,0,27,38 chr1 46080220 . GT G 478.74 PASS AC=2;AF=0.795;AN=2;DP=1597;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1490,147,0:0,0,14,35 chr1 46080530 . T C 509.1 PASS AC=2;AF=0.629;AN=2;DP=1611;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:1882,180,0:0,0,39,21 chr1 46080947 . A C 1022.9 PASS AC=2;AF=0.795;AN=2;DP=4512;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,95:95:99:2948,284,0:0,0,56,39 chr1 46081940 . T A 3073.33 PASS AC=2;AF=0.966;AN=2;DP=3685;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,82:82:99:2566,245,0:0,0,46,36 chr1 46081960 . C T 552.55 PASS AC=2;AF=0.795;AN=2;DP=3408;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,89:90:99:2697,258,0:0,1,48,41 chr1 46082431 . C A 1489.5 PASS AC=2;AF=0.795;AN=2;DP=5530;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,135:135:99:4232,403,0:0,0,57,78 chr1 46084614 . C CTTT,CTTTT 2374.94 PASS AC=2,0;AF=0.577,0.218;AN=2;DP=5531;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:154:99:1,0,58,95 chr1 46085852 . C T 606.34 PASS AC=2;AF=0.795;AN=2;DP=2488;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:1787,171,0:0,0,35,22 chr1 46085879 . C G 652.05 PASS AC=2;AF=0.795;AN=2;DP=3031;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:2445,231,0:0,0,47,30 chr1 46086077 . C T 803.36 PASS AC=2;AF=0.795;AN=2;DP=3949;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,111:111:99:3497,332,0:0,0,57,54 chr1 46086913 . C T 501.96 PASS AC=2;AF=0.795;AN=2;DP=1973;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1924,168,0:0,0,31,25 chr1 46087577 . G A 3681.26 PASS AC=2;AF=0.795;AN=2;DP=10006;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,273:273:99:8420,810,0:0,0,99,174 chr1 46087879 . A G 431.1 PASS AC=2;AF=0.795;AN=2;DP=2996;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,78:80:99:2285,190,0:1,1,44,34 chr1 46089225 . C G 1696.73 PASS AC=2;AF=0.795;AN=2;DP=7074;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,185:185:99:5590,554,0:0,0,95,90 chr1 46089801 . G A 222.13 PASS AC=2;AF=0.811;AN=2;DP=638;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:552,54,0:0,0,5,13 chr1 46095126 . T TCCCCCCCC,TCCCCCCC,TTC,TCCCCCC,TCCCCC,TCCC,TCCCCCCCCC 79.26 PASS AC=0,0,0,0,0,0,1;AF=0.038,0.038,0.115,0.115,0.154,0.077,0.038;AN=2;DP=86;set=variant3-variant7-variant8-variant10-variant12-variant15-variant16-variant20-variant23-variant28-variant30-variant35-variant38 GT:DP:GQ:SB 0/7:8:99:0,3,5,0 chr1 46095140 . A C 56.77 PASS AC=1;AF=0.5;AN=2;DP=161;set=variant-variant3-variant7-variant10-variant11-variant15-variant16-variant19-variant20-variant23-variant24-variant28-variant30-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:8,4:12:99:185,0,504:4,4,4,0 chr1 46096442 . CA C 1303.92 PASS AC=2;AF=0.989;AN=2;DP=1774;FS=0;MQ=60;MQRankSum=1.195;ReadPosRankSum=-0.46;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:896,78,0:0,0,9,17 chr1 46269352 . T G 1410.59 PASS AC=2;AF=1;AN=2;DP=2440;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1546,147,0:0,0,21,28 chr1 46347875 . A T 535.35 PASS AC=2;AF=0.75;AN=2;DP=92;set=variant4-variant7-variant9-variant22-variant25-variant31-variant32-variant33-variant35-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:90,6,0:0,0,2,0 chr1 46347878 . AT A 526.41 PASS AC=2;AF=0.75;AN=2;DP=102;set=variant4-variant7-variant9-variant22-variant25-variant31-variant32-variant33-variant35-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:90,6,0:0,0,2,0 chr1 46347910 . G A 639.53 PASS AC=2;AF=0.81;AN=2;DP=680;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:303,24,0:0,0,7,1 chr1 46379518 . A G 3379.99 PASS AC=2;AF=0.795;AN=2;DP=5965;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,155:155:99:4514,463,0:0,0,83,72 chr1 46424864 . G T 585.82 PASS AC=2;AF=0.625;AN=2;DP=1166;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant16-variant17-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,31:31:93:980,93,0:0,0,21,10 chr1 46424964 . G A 2447.99 PASS AC=2;AF=1;AN=2;DP=3191;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:2200,195,0:0,0,48,17 chr1 46466721 . T C 1060.32 PASS AC=2;AF=0.625;AN=2;DP=3959;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant16-variant17-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,130:130:99:3813,389,0:0,0,61,69 chr1 46476587 . T G 2687.02 PASS AC=2;AF=0.795;AN=2;DP=5290;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,119:119:99:3789,357,0:0,0,57,62 chr1 46485548 . G T 186.17 PASS AC=2;AF=0.625;AN=2;DP=504;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant16-variant17-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:550,42,0:0,0,1,13 chr1 46485562 . C T 106.21 PASS AC=2;AF=0.788;AN=2;DP=406;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant26-variant28-variant29-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:385,30,0:0,0,1,9 chr1 46487552 . G A 2622.17 PASS AC=2;AF=0.625;AN=2;DP=3684;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant16-variant17-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,138:138:99:6218,421,0:0,0,76,62 chr1 46487560 . A G 2695.1 PASS AC=2;AF=0.763;AN=2;DP=4822;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,145:145:99:6503,448,0:0,0,79,66 chr1 46491635 . C T 716.6 PASS AC=2;AF=0.763;AN=2;DP=1712;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1769,146,0:0,0,9,40 chr1 46493460 . T G 989.01 PASS AC=2;AF=0.625;AN=2;DP=2792;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant16-variant17-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,94:94:99:2900,280,0:0,0,53,41 chr1 46495434 . G A 565.39 PASS AC=2;AF=0.645;AN=2;DP=1951;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant16-variant17-variant18-variant20-variant21-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,61:61:99:2139,183,0:0,0,40,21 chr1 46496709 . A G 666.3 PASS AC=2;AF=0.776;AN=2;DP=2416;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,83:83:99:2569,249,0:0,0,45,38 chr1 46497500 . T A 504.91 PASS AC=2;AF=0.641;AN=2;DP=1323;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant16-variant17-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,49:50:99:1539,139,0:0,1,16,33 chr1 46498375 . A G 807.79 PASS AC=2;AF=0.789;AN=2;DP=3831;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,105:105:99:3347,315,0:0,0,44,61 chr1 46505785 . A AC 496.61 PASS AC=2;AF=0.9;AN=2;DP=124;FS=0;MQ=60;set=variant3-variant4-variant8-variant9-variant12-variant15-variant16-variant18-variant20-variant31-variant32-variant35-variant36-variant38-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:400,36,0:0,0,5,7 chr1 46508769 . A G 1100.34 PASS AC=2;AF=0.776;AN=2;DP=3889;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,108:110:99:3748,281,0:1,1,34,74 chr1 46511487 . G C 197.35 PASS AC=2;AF=0.8;AN=2;DP=472;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant13-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:316,24,0:0,0,7,1 chr1 46521517 . G A 928.46 PASS AC=2;AF=0.776;AN=2;DP=3439;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,87:87:99:2582,260,0:0,0,35,52 chr1 46521559 . A T 880.67 PASS AC=2;AF=0.789;AN=2;DP=2766;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,61:61:99:2011,183,0:0,0,20,41 chr1 46546208 . T C 195.8 PASS AC=2;AF=0.645;AN=2;DP=567;FractionInformativeReads=1;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant16-variant17-variant20-variant21-variant22-variant23-variant25-variant26-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:1092,87,0:0,0,21,8 chr1 46598269 . C A 6550.05 PASS AC=2;AF=0.641;AN=2;DP=9753;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant16-variant17-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,311:311:99:13794,948,0:0,0,176,135 chr1 46598273 . A C 6571.55 PASS AC=2;AF=0.776;AN=2;DP=11664;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,313:313:99:13786,950,0:0,0,176,137 chr1 46641741 . A G 64.74 PASS AC=2;AF=0.65;AN=2;DP=428;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant25-variant26-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:568,39,0:0,0,13,0 chr1 46655158 . T C 1956.67 PASS AC=2;AF=1;AN=2;DP=3580;FS=0;MQ=60;MQRankSum=1.504;ReadPosRankSum=0.524;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,101:101:99:3032,303,0:0,0,51,50 chr1 46655645 . C T 1423.53 PASS AC=1;AF=0.5;AN=2;DP=230;FractionInformativeReads=1;MQ=60;set=variant7-variant35 GT:AD:DP:GQ:PL:SB 0/1:78,57:135:99:1267,0,1960:30,48,24,33 chr1 46747301 . T C 595.43 PASS AC=1;AF=0.577;AN=2;DP=543;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant15-variant16-variant20-variant21-variant23-variant24-variant28-variant29-variant30-variant33-variant34-variant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,11:24:99:288,0,421:4,9,3,8 chr1 46806242 . G T 1323.47 PASS AC=1;AF=0.565;AN=2;DP=2280;MQ=60;set=variant-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant15-variant16-variant21-variant23-variant24-variant29-variant30-variant33-variant34-variant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,61:129:99:1510,0,1618:34,34,27,34 chr1 46806274 . CAG C 1776.48 PASS AC=1;AF=0.565;AN=2;DP=2013;MQ=60;set=variant-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant15-variant16-variant21-variant23-variant24-variant29-variant30-variant33-variant34-variant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,45:98:99:1699,0,2101:22,31,16,29 chr1 46806393 . T C 664.8 PASS AC=1;AF=0.565;AN=2;DP=2104;MQ=60;set=variant-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant15-variant16-variant21-variant23-variant24-variant29-variant30-variant33-variant34-variant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,48:93:99:1133,0,1047:23,22,23,25 chr1 46806429 . A T 666.37 PASS AC=1;AF=0.565;AN=2;DP=2108;MQ=60;set=variant-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant15-variant16-variant21-variant23-variant24-variant29-variant30-variant33-variant34-variant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,40:87:99:963,0,1137:25,22,19,21 chr1 46806480 . C T 631.01 PASS AC=1;AF=0.565;AN=2;DP=1996;MQ=60;set=variant-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant15-variant16-variant21-variant23-variant24-variant29-variant30-variant33-variant34-variant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,38:93:99:862,0,1433:27,28,16,22 chr1 46806550 . C T 922.84 PASS AC=1;AF=0.565;AN=2;DP=2097;MQ=60;set=variant-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant15-variant16-variant21-variant23-variant24-variant29-variant30-variant33-variant34-variant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,44:104:99:1053,0,1590:28,32,22,22 chr1 46806703 . A G 320.4 PASS AC=1;AF=0.565;AN=2;DP=1597;MQ=60;set=variant-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant15-variant16-variant21-variant23-variant24-variant29-variant30-variant33-variant34-variant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,26:59:99:739,0,803:14,19,13,13 chr1 46806959 . C T 283.44 PASS AC=1;AF=0.6;AN=2;DP=307;MQ=60;set=variant2-variant4-variant9-variant10-variant14-variant17-variant19-variant20-variant22-variant23-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,7:18:99:209,0,374:1,10,1,6 chr1 46810405 . TG T 963.96 PASS AC=1;AF=0.568;AN=2;DP=1575;MQ=60;set=variant-variant5-variant6-variant7-variant9-variant12-variant13-variant15-variant16-variant21-variant23-variant24-variant29-variant30-variant33-variant34-variant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,50:96:99:1336,0,1205:31,15,35,15 chr1 46810530 . A G 1911.71 PASS AC=1;AF=0.596;AN=2;DP=4184;MQ=60;set=variant2-variant4-variant9-variant10-variant14-variant17-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:94,82:176:99:2043,0,2285:50,44,45,37 chr1 46810670 . T C 1487.94 PASS AC=1;AF=0.568;AN=2;DP=3298;MQ=60;set=variant-variant5-variant6-variant7-variant9-variant12-variant13-variant15-variant16-variant21-variant23-variant24-variant29-variant30-variant33-variant34-variant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:72,84:156:99:2309,0,1767:28,44,33,51 chr1 46810842 . C T 159.12 PASS AC=1;AF=0.568;AN=2;DP=558;MQ=60;set=variant-variant5-variant6-variant7-variant9-variant12-variant13-variant15-variant16-variant21-variant23-variant24-variant29-variant30-variant33-variant34-variant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,21:35:99:569,0,359:5,9,6,15 chr1 46812339 . C T 250.65 PASS AC=1;AF=0.575;AN=2;DP=269;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant7-variant9-variant12-variant13-variant15-variant16-variant21-variant23-variant24-variant29-variant30-variant33-variant34-variant35-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,9:15:99:357,0,267:5,1,7,2 chr1 46812360 . C T 562.79 PASS AC=1;AF=0.571;AN=2;DP=437;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant6-variant7-variant9-variant12-variant13-variant15-variant16-variant21-variant23-variant24-variant29-variant30-variant33-variant34-variant35-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,13:25:99:510,0,465:10,2,10,3 chr1 46812374 . T C 644.8 PASS AC=1;AF=0.571;AN=2;DP=546;FractionInformativeReads=1;set=variant-variant5-variant6-variant7-variant9-variant12-variant13-variant15-variant16-variant21-variant23-variant24-variant29-variant30-variant33-variant34-variant35-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,16:29:99:584,0,458:10,3,12,4 chr1 46812444 . A G 1283.88 PASS AC=1;AF=0.568;AN=2;DP=1652;MQ=60;set=variant-variant5-variant6-variant7-variant9-variant12-variant13-variant15-variant16-variant21-variant23-variant24-variant29-variant30-variant33-variant34-variant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,41:83:99:1132,0,1107:30,12,29,12 chr1 46812519 . A G 1595.9 PASS AC=1;AF=0.568;AN=2;DP=2810;MQ=60;set=variant-variant5-variant6-variant7-variant9-variant12-variant13-variant15-variant16-variant21-variant23-variant24-variant29-variant30-variant33-variant34-variant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:71,67:138:99:1659,0,1845:39,32,36,31 chr1 46812888 . C T 133.04 PASS AC=1;AF=0.676;AN=2;DP=114;FractionInformativeReads=1;MQ=60;set=variant5-variant7-variant9-variant13-variant16-variant21-variant23-variant29-variant30-variant33-variant34-variant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,2:6:72:72,0,160:1,3,0,2 chr1 46818442 . G A 317.85 PASS AC=1;AF=0.568;AN=2;DP=349;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant6-variant7-variant9-variant12-variant13-variant15-variant16-variant21-variant23-variant24-variant29-variant30-variant33-variant34-variant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,4:7:99:156,0,206:3,0,3,1 chr1 46818452 . A G 311.84 PASS AC=1;AF=0.568;AN=2;DP=393;MQ=60;set=variant-variant5-variant6-variant7-variant9-variant12-variant13-variant15-variant16-variant21-variant23-variant24-variant29-variant30-variant33-variant34-variant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,3:9:99:150,0,292:6,0,3,0 chr1 46818479 . C T 281.07 PASS AC=1;AF=0.568;AN=2;DP=563;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant6-variant7-variant9-variant12-variant13-variant15-variant16-variant21-variant23-variant24-variant29-variant30-variant33-variant34-variant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,5:20:99:157,0,443:11,4,5,0 chr1 46818508 . T C 491.67 PASS AC=1;AF=0.568;AN=2;DP=859;MQ=60;set=variant-variant5-variant6-variant7-variant9-variant12-variant13-variant15-variant16-variant21-variant23-variant24-variant29-variant30-variant33-variant34-variant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,11:32:99:275,0,581:15,6,8,3 chr1 46818836 . T C 345.58 PASS AC=1;AF=0.568;AN=2;DP=732;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant6-variant7-variant9-variant12-variant13-variant15-variant16-variant21-variant23-variant24-variant29-variant30-variant33-variant34-variant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,12:31:99:264,0,573:6,13,4,8 chr1 46818898 . T C 153.14 PASS AC=1;AF=0.568;AN=2;DP=361;MQ=60;set=variant-variant5-variant6-variant7-variant9-variant12-variant13-variant15-variant16-variant21-variant23-variant24-variant29-variant30-variant33-variant34-variant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,3:13:72:72,0,275:3,7,1,2 chr1 46826587 . C A 644.74 PASS AC=1;AF=0.568;AN=2;DP=1076;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant6-variant7-variant9-variant12-variant13-variant15-variant16-variant21-variant23-variant24-variant29-variant30-variant33-variant34-variant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,29:68:99:803,0,1117:13,26,12,17 chr1 46827214 . A C 1126.24 PASS AC=2;AF=1;AN=2;DP=1449;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,25:25:74:952,74,0:0,0,24,1 chr1 46827485 . C T 1789.16 PASS AC=1;AF=0.568;AN=2;DP=2692;MQ=60;set=variant-variant5-variant6-variant7-variant9-variant12-variant13-variant15-variant16-variant21-variant23-variant24-variant29-variant30-variant33-variant34-variant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:72,71:143:99:1651,0,1694:35,37,26,45 chr1 46827728 . A C 597.01 PASS AC=1;AF=0.568;AN=2;DP=1114;MQ=60;set=variant-variant5-variant6-variant7-variant9-variant12-variant13-variant15-variant16-variant21-variant23-variant24-variant29-variant30-variant33-variant34-variant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,13:48:99:279,0,902:19,16,5,8 chr1 46827769 . C T 501.22 PASS AC=1;AF=0.568;AN=2;DP=942;MQ=60;set=variant-variant5-variant6-variant7-variant9-variant12-variant13-variant15-variant16-variant21-variant23-variant24-variant29-variant30-variant33-variant34-filterInvariant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,8:46:99:100,0,901:21,17,3,5 chr1 46827871 . G A 129.03 PASS AC=1;AF=0.568;AN=2;DP=270;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant6-variant7-variant9-variant12-variant13-variant15-variant16-variant21-variant23-variant24-variant29-variant30-variant33-variant34-variant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,4:14:88:88,0,285:3,7,1,3 chr1 46860237 . G A 1813.54 PASS AC=1;AF=0.568;AN=2;DP=2611;set=variant-variant5-variant6-variant7-variant9-variant12-variant13-variant15-variant16-variant21-variant23-variant24-variant29-variant30-variant33-variant34-variant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:69,57:126:99:1381,0,1834:32,37,25,32 chr1 46871986 . T C 2373.43 PASS AC=2;AF=0.875;AN=2;DP=10955;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,255:255:99:7927,765,0:0,0,143,112 chr1 46877180 . G A 520.48 PASS AC=1;AF=0.565;AN=2;DP=2005;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant6-variant7-variant9-variant11-variant12-variant13-variant15-variant16-variant21-variant23-variant24-variant29-variant30-variant33-variant34-variant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,53:96:99:1340,0,1014:24,19,29,24 chr1 46879562 . T G 959.27 PASS AC=2;AF=0.779;AN=2;DP=2379;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:2227,228,0:0,0,29,47 chr1 46976837 . C T 1778.25 PASS AC=2;AF=0.586;AN=2;DP=5885;MQ=60;set=variant-variant4-variant6-variant7-variant9-variant10-variant12-variant14-variant15-variant16-variant19-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,214:214:99:6421,640,0:0,0,95,119 chr1 46979222 . C T 1016.71 PASS AC=2;AF=0.757;AN=2;DP=1726;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,61:61:99:1901,182,0:0,0,33,28 chr1 47013180 . A G 4737.81 PASS AC=2;AF=0.814;AN=2;DP=8793;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,234:234:99:6874,700,0:0,0,124,110 chr1 47013364 . T C 2855.38 PASS AC=2;AF=0.989;AN=2;DP=4195;MQ=60;MQRankSum=-0.926;ReadPosRankSum=2.695;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,87:87:99:2649,259,0:0,0,35,52 chr1 47014821 . A AAAAAG,AAAAAAG 3093.52 PASS AC=2,0;AF=0.821,0.012;AN=2;DP=4131;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:95:99:0,0,58,37 chr1 47023055 . TA T,TAA 136.33 PASS AC=1,0;AF=0.45,0.05;AN=2;DP=1428;MQ=60;set=filterInvariant6-filterInvariant12-filterInvariant15-filterInvariant16-variant18-filterInvariant22-filterInvariant24-variant33-filterInvariant35-filterInvariant43 GT:DP:GQ:SB 0/1:148:99:65,57,16,10 chr1 47059934 . T C 3858.4 PASS AC=2;AF=1;AN=2;DP=4778;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,127:127:99:3853,381,0:0,0,57,70 chr1 47074621 . G C 1470.79 PASS AC=2;AF=1;AN=2;DP=2021;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:1859,165,0:0,0,26,29 chr1 47074774 . TCATGGTCTGATGGTCC T,ACATGGTCTGATGGTCC 1618.02 PASS AC=2,0;AF=0.656,0.344;AN=2;DP=1662;FS=0;MQ=60;set=variant3-variant4-variant6-variant7-variant-variant10-variant9-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant37-variant38-variant40-variant42-variant43 GT:DP:GQ:SB 1/1:42:99:0,0,27,15 chr1 47080983 . G A 1610.42 PASS AC=2;AF=0.677;AN=2;DP=2893;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant37-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,120:121:99:3416,348,0:0,1,58,62 chr1 47082212 . G T 44.51 PASS AC=1;AF=0.5;AN=2;DP=17;FS=0;MQ=60;set=variant-variant35-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:3,4:7:99:115,0,113:1,2,1,3 chr1 47099090 . G GA 3348.56 PASS AC=2;AF=0.667;AN=2;DP=10531;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,220:222:99:6221,591,0:1,1,124,96 chr1 47099235 . A C 5454.23 PASS AC=2;AF=0.609;AN=2;DP=13193;MQ=60;set=variant-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant35-variant36-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,415:416:99:12632,1211,0:1,0,197,218 chr1 47099346 . C A 5441.01 PASS AC=2;AF=0.989;AN=2;DP=6364;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,175:175:99:6123,525,0:0,0,59,116 chr1 47099721 . T C 189.81 PASS AC=2;AF=0.667;AN=2;DP=856;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-filterInvariant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:585,45,0:0,0,5,10 chr1 47100049 . C T 287.99 PASS AC=2;AF=0.989;AN=2;DP=590;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:492,42,0:0,0,3,11 chr1 47101015 . C A 1026.69 PASS AC=2;AF=0.989;AN=2;DP=1657;FS=0;MQ=60;MQRankSum=1.588;ReadPosRankSum=-1.241;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1329,132,0:0,0,21,23 chr1 47108828 . T C 1396.8 PASS AC=2;AF=0.989;AN=2;DP=1541;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1273,111,0:0,0,29,8 chr1 47109089 . A G 1076.33 PASS AC=2;AF=0.667;AN=2;DP=2522;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,61:62:99:1945,175,0:1,0,16,45 chr1 47110668 . G C 321.04 PASS AC=2;AF=0.671;AN=2;DP=1074;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:862,78,0:0,0,18,8 chr1 47110712 . C T 472.38 PASS AC=2;AF=0.667;AN=2;DP=1710;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1284,111,0:0,0,23,14 chr1 47110766 . G GC 1757.53 PASS AC=2;AF=0.989;AN=2;DP=2726;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1930,156,0:0,0,35,15 chr1 47133811 . T C 1228.86 PASS AC=2;AF=0.852;AN=2;DP=2236;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1499,158,0:0,0,30,23 chr1 47138444 . C T 1021.64 PASS AC=2;AF=1;AN=2;DP=1265;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:833,72,0:0,0,19,5 chr1 47140775 . AT A 463.97 PASS AC=2;AF=0.609;AN=2;DP=794;set=variant-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant35-variant36-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:698,75,0:0,0,24,1 chr1 47141718 . T C 5377.31 PASS AC=2;AF=0.852;AN=2;DP=6318;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,150:150:99:4626,449,0:0,0,86,64 chr1 47181920 . CAAAAA CAAAA,CAA,CAAA,CAAAAAAAA,C 188.17 PASS AC=0,0,1,0,0;AF=0.232,0.125,0.179,0.018,0.018;AN=2;DP=589;set=variant3-variant4-variant5-variant6-variant8-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant27-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/3:23:99:9,7,7,0 chr1 47351034 . T A 48.53 PASS AC=2;AF=0.969;AN=2;DP=62;FS=0;FractionInformativeReads=1;MQRankSum=-1.733;ReadPosRankSum=-0.898;set=variant2-filterInvariant4-filterInvariant5-variant7-variant8-variant13-variant16-variant20-variant21-variant29-variant31-variant35-variant36-variant37-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:84,9,0:0,0,3,0 chr1 47351052 . A T 209.47 PASS AC=2;AF=0.852;AN=2;DP=268;set=variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant13-variant16-variant18-variant19-variant20-variant21-variant22-filterInvariant26-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:155,12,0:0,0,4,0 chr1 47395973 . G A 2211.59 PASS AC=2;AF=0.798;AN=2;DP=3073;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:2391,213,0:0,0,17,54 chr1 47398743 . G C 4057.04 PASS AC=2;AF=0.798;AN=2;DP=5698;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,137:137:99:4437,411,0:0,0,67,70 chr1 47400059 . A G 1652.67 PASS AC=2;AF=1;AN=2;DP=3182;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,64:64:99:2203,192,0:0,0,46,18 chr1 47401424 . A T 2219.21 PASS AC=2;AF=0.798;AN=2;DP=4350;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,121:121:99:3423,362,0:0,0,52,69 chr1 47401466 . T C 1742.99 PASS AC=2;AF=0.798;AN=2;DP=2931;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,82:83:99:2721,241,0:1,0,21,61 chr1 47402453 . C G 1955.06 PASS AC=1;AF=0.5;AN=2;DP=176;FS=2.619;FractionInformativeReads=0.989;MQ=59.84;MQRankSum=-0.904;QD=11.11;ReadPosRankSum=-2.04;SOR=0.854;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:91,83:174:99:1983,0,2207:45,46,45,38 chr1 47402487 . TTGTGTG TTGTG,TTG,T 3457.34 PASS AC=0,2,0;AF=0.128,0.663,0.116;AN=2;DP=6990;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 2/2:109:99:2,2,52,53 chr1 47571943 . CTTT C,CTT,CTTTT,CTTTTT 1895.97 PASS AC=0,0,1,0;AF=0.369,0.155,0.06,0.012;AN=2;DP=2950;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-filterInvariant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/3:76:99:20,22,15,19 chr1 47652870 . CCTTG C 1054.24 PASS AC=1;AF=0.733;AN=2;DP=2110;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,38:80:99:1508,0,1688:34,8,30,8 chr1 47652872 . T C 691.03 PASS AC=1;AF=0.5;AN=2;DP=169;MQ=60;set=variant2-variant7-variant35 GT:AD:DP:GQ:PL:SB 0/1:38,41:79:99:1265,0,1473:30,8,34,7 chr1 47652875 . AGC A 1091.89 PASS AC=1;AF=0.733;AN=2;DP=2183;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,39:83:99:1502,0,1764:35,9,31,8 chr1 47652879 . T A 1101.09 PASS AC=1;AF=0.733;AN=2;DP=2281;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,39:84:99:1502,0,1763:36,9,31,8 chr1 47655816 . A G 901.09 PASS AC=2;AF=0.826;AN=2;DP=1751;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1391,111,0:0,0,6,31 chr1 47656575 . G A 514.46 PASS AC=1;AF=0.695;AN=2;DP=2439;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,36:72:99:1000,0,1010:15,21,17,19 chr1 47682017 . T G 245.55 PASS AC=1;AF=0.724;AN=2;DP=960;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,21:39:99:586,0,469:12,6,14,7 chr1 47682046 . G A 669.91 PASS AC=1;AF=0.5;AN=2;DP=44;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.208;QD=15.23;ReadPosRankSum=-0.521;SOR=0.784;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:19,25:44:99:698,0,481:11,8,15,10 chr1 47683464 . G A 766.25 PASS AC=1;AF=0.5;AN=2;DP=189;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant35 GT:AD:DP:GQ:PL:SB 0/1:39,27:66:99:761,0,947:18,21,12,15 chr1 47683607 . G C 456.74 PASS AC=1;AF=0.55;AN=2;DP=733;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant11-variant12-variant17-variant22-variant23-variant24-variant27-variant28-variant29-variant32-variant35-variant36-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:15,20:35:99:537,0,442:8,7,9,11 chr1 47684677 . T G 570.42 PASS AC=1;AF=0.711;AN=2;DP=2705;MQ=60;set=variant-variant2-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,39:76:99:1057,0,926:18,19,20,19 chr1 47685455 . T C 3917.62 PASS AC=2;AF=1;AN=2;DP=6400;FS=0;MQ=60;MQRankSum=1.31;ReadPosRankSum=1.711;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,177:177:99:4859,531,0:0,0,79,98 chr1 47689842 . C G 110.91 PASS AC=1;AF=0.716;AN=2;DP=889;MQ=60;set=variant-variant2-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,14:30:99:372,0,441:5,11,4,10 chr1 47691568 . GCAGA G 1709.59 PASS AC=1;AF=0.667;AN=2;DP=5134;MQ=60;set=variant-variant2-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:102,70:172:99:2599,0,5225:48,54,29,41 chr1 47695225 . A C 196.24 PASS AC=1;AF=0.5;AN=2;DP=1342;set=filterInvariant3-variant4-variant5-filterInvariant7-filterInvariant9-filterInvariant16-variant17-filterInvariant21-variant23-filterInvariant24-filterInvariant25-filterInvariant27-variant31-variant32-variant34-filterInvariant35-variant36-filterInvariant37-filterInvariant39-filterInvariant41-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:54,11:65:88:88,0,1289:18,36,11,0 chr1 47697319 . C G 740.61 PASS AC=1;AF=0.5;AN=2;DP=197;FractionInformativeReads=1;MQ=60;set=variant7-variant35 GT:AD:DP:GQ:PL:SB 0/1:54,38:92:99:881,0,1258:27,27,18,20 chr1 47716040 . TAA T 2129.64 PASS AC=1;AF=0.667;AN=2;DP=4500;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:54,43:97:99:1611,0,2098:35,19,31,12 chr1 47717189 . A G 2056.13 PASS AC=1;AF=0.667;AN=2;DP=4726;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:75,69:144:99:1691,0,1880:39,36,34,35 chr1 47735280 . T C 482.78 PASS AC=1;AF=0.667;AN=2;DP=1179;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:16,9:25:99:211,0,437:11,5,7,2 chr1 47746678 . G C 1317.1 PASS AC=1;AF=0.5;AN=2;DP=771;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant10-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:65,58:123:99:1436,0,1610:29,36,26,32 chr1 47753405 . G A 606.04 PASS AC=1;AF=0.625;AN=2;DP=1467;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:35,14:49:99:361,0,950:12,23,5,9 chr1 47765490 . T C 79.49 PASS AC=1;AF=0.621;AN=2;DP=397;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant14-variant16-variant17-variant18-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,5:11:99:192,0,238:6,0,5,0 chr1 47767141 . C A 345.54 PASS AC=1;AF=0.621;AN=2;DP=520;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant14-variant16-variant17-variant18-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,7:21:99:200,0,485:12,2,5,2 chr1 47767914 . G A 1294.02 PASS AC=1;AF=0.625;AN=2;DP=3589;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant14-variant16-variant17-variant18-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,65:116:99:1649,0,1225:30,21,38,27 chr1 47770441 . A C 43.71 PASS AC=1;AF=0.629;AN=2;DP=313;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant14-variant17-variant18-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,4:7:99:141,0,116:3,0,3,1 chr1 47770466 . T C 357.57 PASS AC=1;AF=0.5;AN=2;DP=208;MQ=60;set=variant-variant2-variant4-variant7-variant9-variant10-variant14-variant17-variant35-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,7:16:99:259,0,329:9,0,6,1 chr1 47770786 . T A 851.96 PASS AC=1;AF=0.625;AN=2;DP=2132;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:19,27:46:99:805,0,523:4,15,7,20 chr1 47778520 . T C 2625.86 PASS AC=1;AF=0.625;AN=2;DP=4198;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant14-variant16-variant17-variant18-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,65:124:99:1889,0,1630:44,15,49,16 chr1 47799639 . G C 271.11 PASS AC=1;AF=0.606;AN=2;DP=1168;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant14-variant16-variant17-variant18-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,19:41:99:431,0,504:11,11,12,7 chr1 47824248 . C T 4295.11 PASS AC=2;AF=1;AN=2;DP=5431;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,103:103:99:3435,308,0:0,0,55,48 chr1 47824400 . C T 9343.73 PASS AC=2;AF=1;AN=2;DP=10479;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,242:242:99:7334,725,0:0,0,128,114 chr1 47841038 . G GA 461.07 PASS AC=1;AF=0.625;AN=2;DP=1452;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:13,16:29:99:400,0,310:3,10,4,12 chr1 47841104 . C T 30.47 PASS AC=1;AF=0.5;AN=2;DP=133;MQ=60;set=variant-variant2-variant4-variant7-variant9-variant10-variant14-variant17-variant35-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,5:11:99:185,0,237:0,6,0,5 chr1 47841109 . T C 241.77 PASS AC=2;AF=0.989;AN=2;DP=465;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:476,33,0:0,0,0,11 chr1 47842431 . G A 7070.87 PASS AC=2;AF=1;AN=2;DP=10429;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,276:276:99:8131,825,0:0,0,160,116 chr1 47842666 . A T 10404 PASS AC=2;AF=1;AN=2;DP=13088;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,296:296:99:9079,888,0:0,0,139,157 chr1 47842777 . C T 3144.95 PASS AC=1;AF=0.622;AN=2;DP=5854;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:71,83:154:99:2354,0,2050:34,37,39,44 chr1 47844017 . A G 3329.34 PASS AC=1;AF=0.5;AN=2;DP=2688;MQ=60;set=variant-variant2-variant4-variant7-variant9-variant10-variant14-variant17-variant35-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:140,123:263:99:2936,0,3533:76,64,64,59 chr1 47844464 . G A 2356.35 PASS AC=1;AF=0.622;AN=2;DP=5968;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:87,77:164:99:1814,0,2163:33,54,30,47 chr1 47882497 . C T 916.28 PASS AC=1;AF=0.635;AN=2;DP=2328;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant16-variant18-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,52:111:99:1494,0,1743:21,38,17,35 chr1 47883019 . T C 215.84 PASS AC=2;AF=0.909;AN=2;DP=2112;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,63:63:99:2775,190,0:0,0,34,29 chr1 47883024 . A G 899.13 PASS AC=2;AF=1;AN=2;DP=2158;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:2817,193,0:0,0,34,28 chr1 47902286 . G A 1715.81 PASS AC=1;AF=0.657;AN=2;DP=5907;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:82,73:155:99:1734,0,2244:40,42,29,44 chr1 47902817 . G A 1376.31 PASS AC=1;AF=0.5;AN=2;DP=537;MQ=60;set=variant7-variant10-variant12-variant34-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:67,57:124:99:1555,0,1839:31,36,27,30 chr1 47903063 . G C 2634.41 PASS AC=1;AF=0.643;AN=2;DP=7941;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:131,151:282:99:3439,0,2990:59,72,68,83 chr1 47904000 . G A 794.05 PASS AC=1;AF=0.5;AN=2;DP=454;FractionInformativeReads=1;MQ=60;set=variant7-variant10-variant12-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:68,57:125:99:1162,0,1617:27,41,24,33 chr1 47904668 . T TCCGCAC 2466.02 PASS AC=2;AF=1;AN=2;DP=2901;FS=0;MQ=60;MQRankSum=0.137;ReadPosRankSum=1.745;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:3203,215,0:0,0,36,35 chr1 47904909 . G C 3349.55 PASS AC=2;AF=1;AN=2;DP=3030;FS=0;MQ=60;MQRankSum=0.628;ReadPosRankSum=-0.075;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,80:80:99:2839,240,0:0,0,56,24 chr1 47905555 . AG A 296.26 PASS AC=2;AF=0.743;AN=2;DP=1498;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,52:52:99:1619,156,0:0,0,21,31 chr1 47906338 . G A 484.8 PASS AC=2;AF=1;AN=2;DP=1193;FS=0;MQ=60;MQRankSum=0.528;ReadPosRankSum=1.281;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:661,63,0:0,0,8,13 chr1 47906425 . G A 61.77 PASS AC=2;AF=0.989;AN=2;DP=355;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.751;ReadPosRankSum=0.751;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:352,27,0:0,0,2,7 chr1 48459907 . C T 2955.26 PASS AC=1;AF=0.529;AN=2;DP=6098;MQ=60;set=variant-variant3-variant6-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant20-variant27-variant32-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:212,179:391:99:4047,0,5074:115,97,89,90 chr1 48695081 . G A 2236.42 PASS AC=2;AF=0.6;AN=2;DP=1720;MQ=60;set=variant7-variant13-variant14-variant16-variant18-variant22-variant23-variant24-variant35-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,191:191:99:5869,572,0:0,0,101,90 chr1 48697733 . T G 1912.91 PASS AC=2;AF=1;AN=2;DP=5274;FS=0;MQ=60;MQRankSum=0.822;ReadPosRankSum=0.164;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,97:97:99:3006,290,0:0,0,37,60 chr1 48701567 . C T 1171.65 PASS AC=2;AF=0.625;AN=2;DP=633;FractionInformativeReads=1;MQ=60;set=variant7-variant14-variant16-variant18-variant22-variant23-variant24-variant35 GT:AD:DP:GQ:PL:SB 1/1:0,78:78:99:2340,234,0:0,0,32,46 chr1 48707838 . A G 2326.55 PASS AC=2;AF=0.955;AN=2;DP=2413;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,58:59:99:1925,166,0:1,0,20,38 chr1 48708228 . G T 1212.68 PASS AC=2;AF=0.6;AN=2;DP=1007;MQ=60;set=variant7-variant13-variant14-variant16-variant18-variant22-variant23-variant24-variant35-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,114:114:99:3396,338,0:0,0,44,70 chr1 48761154 . T A 550.49 PASS AC=2;AF=0.569;AN=2;DP=1547;MQ=60;set=variant2-variant4-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1258,132,0:0,0,20,24 chr1 48762797 . GGTGTGTGT GGTGTGT,GGTGT,GGTGTGTGTGT,GGT,GGTGTGTGTGTGTGTGT,GGTGTGTGTGTGTGT,GGTGTGTGTGTGTGTGTGT,G,GGTGTGTGTGTGTGTGTGTGT,GGTGTGTGTGTGT 343.1 PASS AC=0,0,0,0,1,1,0,0,0,0;AF=0.398,0.102,0.023,0.08,0.068,0.023,0.023,0.011,0.011,0.011;AN=2;DP=5936;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-filterInvariant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 6/5:83:99:1,0,53,29 chr1 48902977 . G C 835.33 PASS AC=2;AF=0.977;AN=2;DP=697;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:535,42,0:0,0,5,9 chr1 48998708 . T C,A 182.97 PASS AC=2,0;AF=0.744,0.218;AN=2;DP=240;FS=0;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:8:24:0,0,4,4 chr1 48999555 . T C 2775.64 PASS AC=1;AF=0.587;AN=2;DP=5420;MQ=60;set=variant2-variant5-variant7-variant9-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant24-variant27-variant29-variant30-variant31-variant33-variant35-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:129,108:237:99:2680,0,3273:53,76,40,68 chr1 49049525 . G GT,GTT,GTTT 86.96 PASS AC=1,0,0;AF=0.544,0.059,0.044;AN=2;DP=410;set=variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-filterInvariant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:12:13:1,1,8,2 chr1 49051568 . T C 1775.06 PASS AC=2;AF=0.731;AN=2;DP=2375;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,61:61:99:1897,183,0:0,0,29,32 chr1 49056762 . A AC,ACC 52.42 PASS AC=2,0;AF=0.6,0.1;AN=2;DP=38;FS=0;MQ=60;set=variant11-variant15-variant17-variant6-variant35 GT:DP:GQ:SB 1/1:6:18:0,0,0,6 chr1 49193394 . G T 2981.62 PASS AC=1;AF=0.893;AN=2;DP=4911;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:69,68:137:99:1568,0,1715:40,29,34,34 chr1 49224584 . G T 1218.4 PASS AC=2;AF=0.898;AN=2;DP=3088;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2229,209,0:0,0,36,34 chr1 49242456 . C T 2343.64 PASS AC=1;AF=0.5;AN=2;DP=483;MQ=60;set=variant7-variant35 GT:AD:DP:GQ:PL:SB 0/1:120,113:233:99:2473,0,2722:56,64,56,57 chr1 49283412 . C T 1120.6 PASS AC=2;AF=0.989;AN=2;DP=1807;MQ=60;MQRankSum=-1.397;ReadPosRankSum=1.678;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1605,135,0:0,0,25,20 chr1 49332724 . A C 1594.45 PASS AC=1;AF=0.756;AN=2;DP=3165;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,38:80:99:1029,0,1067:26,16,24,14 chr1 49332969 . A G 990 PASS AC=1;AF=0.756;AN=2;DP=1504;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,20:43:99:591,0,575:7,16,3,17 chr1 49511424 . A G 1748.76 PASS AC=1;AF=0.538;AN=2;DP=2103;MQ=60;set=variant4-variant7-variant9-variant15-variant20-variant21-variant22-variant26-variant27-variant29-variant34-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:88,63:151:99:1711,0,2375:30,58,19,44 chr1 50163361 . A G 196.77 PASS AC=2;AF=0.879;AN=2;DP=154;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant11-variant12-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:82,6,0:0,0,0,2 chr1 50331725 . T C 414.3 PASS AC=2;AF=0.953;AN=2;DP=942;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:59:581,59,0:0,0,8,12 chr1 50489302 . G A 3321.78 PASS AC=1;AF=0.5;AN=2;DP=600;FractionInformativeReads=1;MQ=60;set=variant7-variant35 GT:AD:DP:GQ:PL:SB 0/1:158,170:328:99:4242,0,3885:94,64,107,63 chr1 50661411 . C T 2159.04 PASS AC=2;AF=0.943;AN=2;DP=5411;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,138:138:99:4074,411,0:0,0,68,70 chr1 50661688 . T C 456.07 PASS AC=2;AF=0.964;AN=2;DP=643;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:584,45,0:0,0,2,13 chr1 50666515 . C T 2549.56 PASS AC=2;AF=0.93;AN=2;DP=4866;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,160:160:99:5199,477,0:0,0,112,48 chr1 50884230 . G C 1153.19 PASS AC=1;AF=0.907;AN=2;DP=1920;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,28:69:99:767,0,1109:16,25,14,14 chr1 50884778 . G A 2754.64 PASS AC=2;AF=0.825;AN=2;DP=3524;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,91:91:99:2772,268,0:0,0,43,48 chr1 50956163 . AAAGG A 337.34 PASS AC=1;AF=0.661;AN=2;DP=819;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-filterInvariant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,8:19:99:303,0,426:9,2,5,3 chr1 50956212 . C CAAATACAGTGG 2796.52 PASS AC=2;AF=1;AN=2;DP=2438;FS=0;MQ=60;MQRankSum=1.13;ReadPosRankSum=1.506;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1926,129,0:0,0,24,13 chr1 50957509 . A T 1005.29 PASS AC=1;AF=0.884;AN=2;DP=1225;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,13:29:99:324,0,505:3,13,4,9 chr1 51121198 . T C 655.01 PASS AC=1;AF=0.563;AN=2;DP=1151;MQ=60;set=variant2-variant7-variant8-variant9-variant11-variant12-variant21-variant24-variant25-variant30-variant35-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:33,41:74:99:889,0,883:13,20,19,22 chr1 51180660 . A G 789.71 PASS AC=1;AF=0.5;AN=2;DP=757;MQ=60;set=variant2-variant5-variant8-variant10-variant14-variant26-variant27-variant29-variant34-variant35-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,28:65:99:642,0,922:19,18,15,13 chr1 51433821 . G GC 4003.05 PASS AC=2;AF=1;AN=2;DP=5111;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,133:133:99:4694,400,0:0,0,54,79 chr1 51433863 . G GC 2555.53 PASS AC=2;AF=1;AN=2;DP=3260;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,87:87:99:3122,265,0:0,0,33,54 chr1 51433888 . A AG 2310.98 PASS AC=2;AF=1;AN=2;DP=2875;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:2168,174,0:0,0,23,35 chr1 51611227 . T C 348.03 PASS AC=1;AF=0.5;AN=2;DP=231;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant8-variant10-variant26-variant29-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:24,13:37:99:312,0,590:10,14,5,8 chr1 51764057 . C T 998.17 PASS AC=1;AF=0.5;AN=2;DP=205;FS=0;FractionInformativeReads=1;MQ=60;set=variant7-variant35 GT:AD:DP:GQ:PL:SB 0/1:66,47:113:99:1128,0,1584:37,29,26,21 chr1 51787215 . C T 543.1 PASS AC=1;AF=0.5;AN=2;DP=28;FS=3.332;FractionInformativeReads=1;MQ=60;MQRankSum=0.921;QD=19.4;ReadPosRankSum=0.276;SOR=1.954;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:13,15:28:99:571,0,487:12,1,15,0 chr1 51808567 . C T 659.74 PASS AC=1;AF=0.595;AN=2;DP=1313;MQ=60;set=variant-variant6-variant7-variant8-variant11-variant14-variant15-variant16-variant17-variant20-variant26-variant27-variant29-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,17:46:99:403,0,716:18,11,8,9 chr1 51810525 . G A 1073.17 PASS AC=1;AF=0.5;AN=2;DP=411;FractionInformativeReads=1;MQ=60;set=variant7-variant35-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:64,50:114:99:1161,0,1549:38,26,29,21 chr1 51820990 . T G 2137.79 PASS AC=1;AF=0.595;AN=2;DP=2627;set=variant-variant6-variant7-variant8-variant11-variant14-variant15-variant16-variant17-variant20-variant26-variant27-variant29-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,54:115:99:1691,0,1745:33,28,35,19 chr1 51826742 . G C 724.12 PASS AC=1;AF=0.5;AN=2;DP=223;FractionInformativeReads=1;MQ=60;set=variant7-variant35-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:32,41:73:99:1111,0,920:24,8,29,12 chr1 51826921 . T C 1764.49 PASS AC=1;AF=0.595;AN=2;DP=2805;MQ=60;set=variant-variant6-variant7-variant8-variant11-variant14-variant15-variant16-variant17-variant20-variant26-variant27-variant29-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,56:117:99:1545,0,1506:28,33,21,35 chr1 51829745 . T C 855.9 PASS AC=1;AF=0.5;AN=2;DP=93;FractionInformativeReads=1;MQ=60;set=variant7-variant35 GT:AD:DP:GQ:PL:SB 0/1:28,20:48:99:556,0,808:7,21,4,16 chr1 51866384 . CAAAAAAA CAAAAA,CA,CAAAAAA,C 38.45 PASS AC=0,0,0,2;AF=0.125,0.125,0.125,0.25;AN=2;DP=26;MQ=60;set=variant3-variant7-variant10-variant35 GT:DP:GQ:SB 4/4:3:9:0,0,3,0 chr1 51868063 . C CT 73.19 PASS AC=1;AF=0.5;AN=2;DP=81;MQ=60;set=variant7-variant35-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:13,6:19:99:117,0,333:8,5,4,2 chr1 51871438 . G GACTC 365.22 PASS AC=1;AF=0.595;AN=2;DP=408;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant7-variant8-variant11-variant14-variant15-variant16-variant17-variant20-variant26-variant27-variant29-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,12:22:99:474,0,570:9,1,11,1 chr1 51873951 . G A 2727.23 PASS AC=2;AF=0.789;AN=2;DP=3063;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:2411,236,0:0,0,33,46 chr1 51905949 . CTGTGTGTGTG CTGTGTG,CTGTGTGTGTGTG,CTGTGTGTG,CTGTGTGTGTGTGTG,CTGTG,C 2181.46 PASS AC=1,1,0,0,0,0;AF=0.225,0.263,0.075,0.025,0.063,0.013;AN=2;DP=2747;set=variant-variant2-variant4-filterInvariant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-filterInvariant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 1/2:40:99:4,2,23,11 chr1 51912760 . T G 742.41 PASS AC=1;AF=0.5;AN=2;DP=211;FractionInformativeReads=1;MQ=60;set=variant7-variant35-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:24,36:60:99:913,0,654:6,18,18,18 chr1 51923614 . C A 1875.42 PASS AC=1;AF=0.595;AN=2;DP=2688;MQ=60;set=variant-variant6-variant7-variant8-variant11-variant14-variant15-variant16-variant17-variant20-variant26-variant27-variant29-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:73,73:146:99:1906,0,1773:40,33,43,30 chr1 51929504 . TA T 411.85 PASS AC=1;AF=0.595;AN=2;DP=778;MQ=60;set=variant-variant6-variant7-variant8-variant11-variant14-variant15-variant16-variant17-variant20-variant26-variant27-variant29-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,11:33:99:313,0,719:8,14,3,8 chr1 52082594 . G C 838 PASS AC=1;AF=0.536;AN=2;DP=894;MQ=60;set=variant3-variant5-variant6-variant10-variant13-variant19-variant22-variant23-variant32-variant33-variant35-variant36-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:30,25:55:99:572,0,705:15,15,10,15 chr1 52213864 . A C 330.39 PASS AC=1;AF=0.542;AN=2;DP=198;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant6-variant10-variant13-variant19-variant23-variant32-variant33-variant35-variant36-variant40 GT:AD:DP:GQ:PL:SB 0/1:10,9:19:99:274,0,272:8,2,7,2 chr1 52215419 . G T 455.47 PASS AC=1;AF=0.5;AN=2;DP=401;FractionInformativeReads=1;MQ=60;set=variant6-variant7-variant9-variant11-variant12-variant14-variant35-variant36-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:24,21:45:99:527,0,629:7,17,8,13 chr1 52248017 . A G 49.51 PASS AC=1;AF=0.536;AN=2;DP=105;MQ=60;set=variant5-variant10-variant13-variant14-variant17-variant19-variant23-variant32-variant33-variant35-variant36-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:4,3:7:99:102,0,143:3,1,3,0 chr1 52253793 . C T 3160.79 PASS AC=1;AF=0.531;AN=2;DP=3122;MQ=60;set=variant3-variant5-variant6-variant10-variant13-variant14-variant17-variant19-variant23-variant32-variant33-variant35-variant36-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:103,91:194:99:2162,0,2551:42,61,38,53 chr1 52253864 . G A 1595.63 PASS AC=1;AF=0.531;AN=2;DP=1076;set=variant3-variant5-variant6-variant10-variant13-variant14-variant17-variant19-variant23-variant32-variant33-variant35-variant36-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:29,35:64:99:1127,0,717:8,21,10,25 chr1 52264064 . A G 1084.39 PASS AC=2;AF=0.632;AN=2;DP=1536;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant23-variant30-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,66:66:99:2035,198,0:0,0,26,40 chr1 52266120 . C T 1207.33 PASS AC=1;AF=0.5;AN=2;DP=849;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant13-variant23-variant32-variant33-variant35-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:42,47:89:99:1173,0,1069:26,16,33,14 chr1 52279650 . T G 1391.65 PASS AC=2;AF=0.75;AN=2;DP=3859;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,112:112:99:3296,335,0:0,0,61,51 chr1 52293570 . G A 643.62 PASS AC=1;AF=0.691;AN=2;DP=1578;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,32:53:99:811,0,539:7,14,13,19 chr1 52293638 . G A 324.76 PASS AC=2;AF=1;AN=2;DP=540;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:619,48,0:0,0,2,14 chr1 52374952 . A C 2628.45 PASS AC=1;AF=0.735;AN=2;DP=6404;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:85,105:190:99:2598,0,2006:45,40,64,41 chr1 52375424 . T C 1481.3 PASS AC=1;AF=0.763;AN=2;DP=4926;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,62:129:99:1549,0,1620:29,38,30,32 chr1 52375564 . T C 1107.37 PASS AC=1;AF=0.5;AN=2;DP=581;MQ=60;set=variant7-variant15-variant17-variant24-variant28-variant31-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:26,41:67:99:1153,0,696:14,12,16,25 chr1 52375612 . T G 745.46 PASS AC=1;AF=0.798;AN=2;DP=2266;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,28:57:99:770,0,789:17,12,11,17 chr1 52375872 . T C 445.5 PASS AC=1;AF=0.763;AN=2;DP=1572;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,14:40:99:335,0,717:14,12,6,8 chr1 52378274 . A T 46.69 PASS AC=2;AF=1;AN=2;DP=94;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant10-variant12-variant13-variant15-variant16-variant17-variant21-variant22-variant26-variant28-variant29-variant30-variant31-variant34-variant35-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:165,15,0:0,0,4,1 chr1 52379149 . C T 452.7 PASS AC=1;AF=0.726;AN=2;DP=1404;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-filterInvariant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,19:37:99:513,0,360:6,12,4,15 chr1 52381363 . GTTT G 1997.31 PASS AC=1;AF=0.729;AN=2;DP=3876;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:63,52:115:99:1969,0,2563:21,42,21,31 chr1 52381552 . G A 373.85 PASS AC=1;AF=0.75;AN=2;DP=443;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,16:20:99:531,0,114:2,2,11,5 chr1 52383083 . G A 72.22 PASS AC=1;AF=0.798;AN=2;DP=812;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,9:16:99:195,0,132:4,3,5,4 chr1 52383255 . T C 96.2 PASS AC=1;AF=0.848;AN=2;DP=212;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant24-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,5:9:72:114,0,72:2,2,2,3 chr1 52384643 . CTTTTTTTTTTTTT C,CTTTTTTTTTTTT,CTTTTTTTTTT,CTTTTTTTTTTT,CTTTTTTTTT 937.68 PASS AC=1,0,0,0,0;AF=0.571,0.095,0.012,0.036,0.012;AN=2;DP=2150;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-filterInvariant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-filterInvariant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:44:99:3,19,1,21 chr1 52402856 . T G 1465.15 PASS AC=2;AF=0.932;AN=2;DP=1997;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1209,108,0:0,0,24,12 chr1 52402956 . G A 2926.21 PASS AC=2;AF=0.932;AN=2;DP=4858;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,132:133:99:3771,388,0:0,1,73,59 chr1 52489322 . G A 3191.24 PASS AC=2;AF=1;AN=2;DP=3943;FS=0;MQ=60;MQRankSum=-1.102;ReadPosRankSum=0.824;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,83:83:99:2802,248,0:0,0,22,61 chr1 52490418 . C T 1241.39 PASS AC=2;AF=0.886;AN=2;DP=1233;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:1007,84,0:0,0,6,22 chr1 52517412 . A G 3673.1 PASS AC=2;AF=0.886;AN=2;DP=6232;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,179:179:99:5122,535,0:0,0,104,75 chr1 52520879 . A AT 1127.87 PASS AC=1;AF=0.5;AN=2;DP=271;MQ=60;set=variant7-variant35 GT:AD:DP:GQ:PL:SB 0/1:74,55:129:99:1091,0,1665:47,27,31,24 chr1 52521062 . A T 2350.32 PASS AC=2;AF=1;AN=2;DP=4471;FS=0;MQ=60;MQRankSum=-0.485;ReadPosRankSum=1.704;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,120:120:99:3970,360,0:0,0,47,73 chr1 52521776 . C T 1164 PASS AC=2;AF=1;AN=2;DP=3057;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,64:64:99:2041,191,0:0,0,32,32 chr1 52521798 . G T 1275.48 PASS AC=2;AF=1;AN=2;DP=3045;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,60:61:99:1910,172,0:0,1,28,32 chr1 52530736 . CTG C 1089.26 PASS AC=1;AF=0.575;AN=2;DP=1194;MQ=60;set=variant3-variant4-variant7-variant8-variant12-variant13-variant15-variant17-variant18-variant21-variant22-variant24-variant26-variant28-variant31-variant32-variant34-variant35-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,24:55:99:915,0,1230:9,22,6,18 chr1 52555388 . C T 8798.47 PASS AC=2;AF=0.943;AN=2;DP=9418;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,236:236:99:7211,701,0:0,0,130,106 chr1 52555593 . C G 11249.3 PASS AC=2;AF=0.943;AN=2;DP=11056;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,259:259:99:8260,774,0:0,0,125,134 chr1 52608109 . G C 2279.93 PASS AC=2;AF=0.966;AN=2;DP=2912;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,83:83:99:2407,248,0:0,0,37,46 chr1 52818188 . G A 452.56 PASS AC=2;AF=0.724;AN=2;DP=767;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant9-variant11-variant13-variant14-variant15-variant17-variant19-variant20-variant23-variant24-variant25-variant28-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1271,123,0:0,0,22,19 chr1 52819888 . A G 617.18 PASS AC=2;AF=1;AN=2;DP=707;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:585,45,0:0,0,14,1 chr1 52820226 . G A 3563.65 PASS AC=2;AF=1;AN=2;DP=5972;FS=0;MQ=60;MQRankSum=0.554;ReadPosRankSum=-0.091;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,149:149:99:4655,446,0:0,0,64,85 chr1 52851729 . G A 363.32 PASS AC=2;AF=0.69;AN=2;DP=769;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant7-variant9-variant11-variant14-variant15-variant17-variant19-variant20-variant23-variant24-variant25-variant28-variant30-variant31-variant33-variant35-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1483,150,0:0,0,18,32 chr1 52859250 . A T 2953.82 PASS AC=1;AF=0.5;AN=2;DP=234;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.628;QD=12.62;ReadPosRankSum=0.091;SOR=0.72;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:113,121:234:99:2982,0,2831:54,59,57,64 chr1 52888937 . T A 747.69 PASS AC=2;AF=1;AN=2;DP=1142;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:741,72,0:0,0,15,9 chr1 52992160 . TA T 54.39 PASS AC=1;AF=0.6;AN=2;DP=63;MQ=60;set=variant3-variant9-variant20-variant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:8,4:12:67:67,0,162:0,8,1,3 chr1 53067914 . T G 36.65 PASS AC=2;AF=0.694;AN=2;DP=502;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:591,51,0:0,0,11,6 chr1 53072454 . T C 884.59 PASS AC=2;AF=0.884;AN=2;DP=5198;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,159:160:99:5049,475,0:1,0,73,86 chr1 53074532 . C A 3801.54 PASS AC=2;AF=0.667;AN=2;DP=12420;set=variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,344:344:99:10482,1030,0:0,0,196,148 chr1 53153044 . T C 2116.39 PASS AC=1;AF=0.672;AN=2;DP=6581;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant14-variant17-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:137,123:260:99:3079,0,3615:78,59,70,53 chr1 53153432 . T C 2716.49 PASS AC=1;AF=0.625;AN=2;DP=6391;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant14-variant17-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:138,126:264:99:3069,0,3379:82,56,72,54 chr1 53153916 . AT A,ATT 48.8 PASS AC=1,0;AF=0.48,0.02;AN=2;DP=965;MQ=60;set=variant-filterInvariant2-variant3-variant4-filterInvariant6-variant7-filterInvariant12-variant13-filterInvariant15-variant16-variant19-variant20-filterInvariant21-filterInvariant24-variant27-variant29-variant30-filterInvariant32-variant33-variant34-filterInvariant35-variant37-variant39-variant41-filterInvariant43 GT:DP:GQ:SB 0/1:31:99:5,15,2,9 chr1 53164220 . C T 106.77 PASS AC=1;AF=0.703;AN=2;DP=274;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant14-variant17-variant18-variant19-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,5:9:99:117,0,114:1,3,2,3 chr1 53192082 . T G 597.65 PASS AC=1;AF=0.633;AN=2;DP=987;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:8,24:32:99:684,0,107:5,3,15,9 chr1 53192112 . T C 861.24 PASS AC=1;AF=0.633;AN=2;DP=1499;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:14,34:48:99:854,0,227:8,6,21,13 chr1 53192187 . C T 2618.59 PASS AC=2;AF=0.989;AN=2;DP=3504;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,72:73:99:2048,208,0:1,0,38,34 chr1 53237526 . G A 496.5 PASS AC=1;AF=0.603;AN=2;DP=544;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant18-variant21-variant22-variant24-variant27-variant28-variant29-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:14,6:20:99:210,0,447:3,11,1,5 chr1 53245472 . A T 627.14 PASS AC=1;AF=0.603;AN=2;DP=2663;FractionInformativeReads=1;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant18-variant21-variant22-variant24-variant27-variant28-variant29-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:48,55:103:99:1312,0,1107:29,19,34,21 chr1 53250650 . G A 1392.28 PASS AC=1;AF=0.603;AN=2;DP=3435;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant18-variant21-variant22-variant24-variant27-variant28-variant29-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:64,71:135:99:1801,0,1604:28,36,32,39 chr1 53271225 . T C 573.28 PASS AC=1;AF=0.611;AN=2;DP=1058;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant18-variant21-variant22-variant24-variant27-variant28-variant29-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:24,15:39:99:335,0,590:9,15,5,10 chr1 53289190 . GTT GTTT,GT,G 211.93 PASS AC=0,1,0;AF=0.304,0.174,0.022;AN=2;DP=2693;set=filterInvariant2-filterInvariant3-filterInvariant5-filterInvariant6-filterInvariant8-filterInvariant9-filterInvariant12-filterInvariant14-filterInvariant19-filterInvariant20-filterInvariant22-filterInvariant24-filterInvariant25-variant28-filterInvariant33-filterInvariant35-filterInvariant36-variant39-variant40-variant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:DP:GQ:SB 0/2:99:99:46,32,10,11 chr1 53291325 . TAAAA TA,TAA,TAAA,T 2024.96 PASS AC=0,1,0,0;AF=0.298,0.357,0.119,0.06;AN=2;DP=4946;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:60:0:2,4,22,32 chr1 53291550 . A G 2541.41 PASS AC=1;AF=0.7;AN=2;DP=7920;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:113,115:228:99:2857,0,2860:66,47,69,46 chr1 53292285 . C T 4130.95 PASS AC=1;AF=0.5;AN=2;DP=1992;MQ=60;set=variant4-variant7-variant11-variant25-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:199,161:360:99:3932,0,5199:95,104,77,84 chr1 53292607 . T A 6546.51 PASS AC=1;AF=0.737;AN=2;DP=14592;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:150,192:342:99:4916,0,3477:78,72,95,97 chr1 53308256 . TCTGGGGAGG T 830.12 PASS AC=1;AF=0.667;AN=2;DP=877;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,7:15:99:270,0,727:7,1,7,0 chr1 53308665 . C G 2012.19 PASS AC=1;AF=0.697;AN=2;DP=7467;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:126,114:240:99:2808,0,3051:50,76,46,68 chr1 53320274 . G T 1956.35 PASS AC=1;AF=0.724;AN=2;DP=5908;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:82,67:149:99:1500,0,2050:33,49,33,34 chr1 53323492 . C A 1400.66 PASS AC=2;AF=0.915;AN=2;DP=1055;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1385,114,0:0,0,7,31 chr1 53333116 . A G 188.41 PASS AC=1;AF=0.703;AN=2;DP=644;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,12:22:99:462,0,294:7,3,11,1 chr1 53359973 . G A 580.02 PASS AC=1;AF=0.5;AN=2;DP=46;FS=4.288;FractionInformativeReads=1;MQ=60;MQRankSum=-2.271;QD=12.61;ReadPosRankSum=-1.407;SOR=0.814;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:20,26:46:99:608,0,566:12,8,11,15 chr1 53364976 . A G 943.52 PASS AC=1;AF=0.724;AN=2;DP=3211;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,42:87:99:1006,0,1076:22,23,19,23 chr1 53365235 . G C 115.2 PASS AC=1;AF=0.724;AN=2;DP=797;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,11:16:99:325,0,181:0,5,3,8 chr1 53387379 . G C 983.98 PASS AC=1;AF=0.703;AN=2;DP=3130;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,50:100:99:1243,0,1415:18,32,20,30 chr1 53392908 . A G 302.38 PASS AC=1;AF=0.743;AN=2;DP=721;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,12:22:99:400,0,156:5,5,8,4 chr1 53513437 . T C 941.41 PASS AC=1;AF=0.672;AN=2;DP=568;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant12-variant13-variant15-variant16-variant18-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:9,8:17:99:306,0,315:8,1,7,1 chr1 53535478 . G A 1236.26 PASS AC=1;AF=0.638;AN=2;DP=2641;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant18-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:39,44:83:99:1005,0,884:19,20,23,21 chr1 53537266 . G A 4011.22 PASS AC=1;AF=0.617;AN=2;DP=9718;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant18-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:174,154:328:99:3653,0,4301:82,92,73,81 chr1 53543112 . C G 1788.6 PASS AC=2;AF=0.977;AN=2;DP=2399;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2882,211,0:0,0,5,65 chr1 53544439 . G A 10011 PASS AC=2;AF=0.718;AN=2;DP=16669;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,428:429:99:13025,1270,0:0,1,195,233 chr1 53544597 . T C 1118.32 PASS AC=2;AF=0.94;AN=2;DP=6001;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,179:180:99:5658,528,0:1,0,63,116 chr1 53550187 . C T 790.42 PASS AC=2;AF=0.965;AN=2;DP=1887;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:1605,144,0:0,0,37,11 chr1 53553485 . A G 1247.09 PASS AC=2;AF=0.726;AN=2;DP=4466;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,118:118:99:3839,354,0:0,0,62,56 chr1 53553702 . A G 2324.32 PASS AC=2;AF=1;AN=2;DP=4683;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,134:134:99:4113,401,0:0,0,70,64 chr1 53553754 . T C 3027.88 PASS AC=2;AF=0.718;AN=2;DP=4433;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,139:139:99:4504,417,0:0,0,71,68 chr1 53555783 . A C 781.59 PASS AC=2;AF=0.929;AN=2;DP=3981;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,96:96:99:2876,288,0:0,0,39,57 chr1 53556483 . G A 2786.07 PASS AC=1;AF=0.5;AN=2;DP=560;FractionInformativeReads=1;MQ=60;set=variant7-variant35 GT:AD:DP:GQ:PL:SB 0/1:156,161:317:99:3615,0,3745:68,88,70,91 chr1 53558270 . A G 1270.01 PASS AC=2;AF=0.767;AN=2;DP=5153;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,122:122:99:4162,366,0:0,0,79,43 chr1 53559310 . T C 315.02 PASS AC=2;AF=0.756;AN=2;DP=1659;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:1742,144,0:0,0,11,37 chr1 53569399 . A G 90.18 PASS AC=2;AF=0.786;AN=2;DP=497;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:504,39,0:0,0,3,10 chr1 53571288 . C G 1066.5 PASS AC=2;AF=1;AN=2;DP=1280;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.315;ReadPosRankSum=-0.788;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1358,114,0:0,0,28,10 chr1 53573622 . C T 183.33 PASS AC=1;AF=0.5;AN=2;DP=40;FS=0;FractionInformativeReads=1;MQ=60;set=variant7-variant35 GT:AD:DP:GQ:PL:SB 0/1:10,7:17:99:223,0,285:8,2,6,1 chr1 53574076 . G A 554.68 PASS AC=2;AF=0.756;AN=2;DP=2621;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:2147,195,0:0,0,39,26 chr1 53574123 . C T 3255.45 PASS AC=2;AF=1;AN=2;DP=3899;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,87:87:99:2946,260,0:0,0,59,28 chr1 53608133 . C A 1909.24 PASS AC=1;AF=0.5;AN=2;DP=2023;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant6-variant8-variant10-variant13-variant15-variant20-variant21-variant22-variant32-variant34-variant35-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:60,81:141:99:2149,0,1533:28,32,33,48 chr1 53608375 . A G 191.53 PASS AC=2;AF=1;AN=2;DP=560;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:619,60,0:0,0,7,13 chr1 53608425 . C A 189.77 PASS AC=2;AF=0.75;AN=2;DP=146;FS=0;FractionInformativeReads=1;MQ=60;set=variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant18-variant20-variant21-variant22-variant24-variant33-variant35-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:430,30,0:0,0,1,9 chr1 53676448 . G A 2675.13 PASS AC=1;AF=0.7;AN=2;DP=3545;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,62:105:99:1674,0,1148:27,16,35,27 chr1 53679878 . T C 3099.38 PASS AC=1;AF=0.58;AN=2;DP=2824;MQ=60;set=variant2-variant3-variant7-variant8-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant22-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,58:114:99:1713,0,1591:19,37,20,38 chr1 53680090 . G A 2111.27 PASS AC=1;AF=0.58;AN=2;DP=1567;MQ=60;set=variant2-variant3-variant7-variant8-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant22-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,25:61:99:683,0,980:18,18,14,11 chr1 53683921 . C G 2421.2 PASS AC=1;AF=0.58;AN=2;DP=1608;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant7-variant8-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant22-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,33:60:99:943,0,792:11,16,13,20 chr1 53684324 . A G 972.16 PASS AC=1;AF=0.58;AN=2;DP=764;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant7-variant8-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant22-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,19:34:99:558,0,319:5,10,5,14 chr1 53684525 . C G 3093.41 PASS AC=1;AF=0.805;AN=2;DP=3603;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,45:97:99:1183,0,1430:35,17,30,15 chr1 53686383 . C G 400.06 PASS AC=1;AF=0.805;AN=2;DP=853;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,5:16:99:123,0,300:4,7,2,3 chr1 53692437 . T A 169.58 PASS AC=1;AF=0.587;AN=2;DP=203;MQ=60;set=variant2-variant3-variant7-variant8-variant11-variant13-variant15-variant16-variant18-variant19-variant22-variant25-variant26-variant27-variant29-variant31-variant32-variant34-variant35-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,4:6:52:136,0,52:1,1,4,0 chr1 53692488 . A G 430.8 PASS AC=1;AF=0.587;AN=2;DP=457;MQ=60;set=variant2-variant3-variant7-variant8-variant11-variant12-variant13-variant15-variant16-variant19-variant22-variant25-variant26-variant27-variant29-variant31-variant32-variant34-variant35-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,8:12:99:202,0,104:3,1,4,4 chr1 53694388 . T C 649.22 PASS AC=1;AF=0.583;AN=2;DP=422;MQ=60;set=variant2-variant3-variant7-variant8-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant22-variant25-variant26-variant27-variant29-variant31-variant32-variant34-variant35-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,7:18:99:206,0,346:9,2,6,1 chr1 53699129 . G C 1447.96 PASS AC=1;AF=0.643;AN=2;DP=786;MQ=60;set=variant2-variant3-variant22-variant25-variant26-variant27-variant29-variant30-variant31-variant34-variant35-variant37-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,30:69:99:736,0,909:22,17,21,9 chr1 53711735 . G C 1261.34 PASS AC=1;AF=0.643;AN=2;DP=1657;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant22-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,34:69:99:900,0,1079:23,12,20,14 chr1 53712223 . GT G,GTT 352.82 PASS AC=1,0;AF=0.459,0.041;AN=2;DP=2959;MQ=60;set=variant-variant2-variant3-variant4-variant5-filterInvariant6-variant7-filterInvariant8-variant9-variant10-filterInvariant11-filterInvariant12-variant13-filterInvariant14-variant15-variant16-filterInvariant17-variant18-filterInvariant19-filterInvariant21-filterInvariant22-variant24-filterInvariant25-filterInvariant27-variant28-filterInvariant30-variant31-filterInvariant33-variant34-filterInvariant35-variant36-variant38-filterInvariant39-variant40-filterInvariant42-variant43-variant44 GT:DP:GQ:SB 0/1:72:76:31,27,8,6 chr1 53712727 . C T 1202.39 PASS AC=1;AF=0.643;AN=2;DP=2788;set=variant-variant2-variant3-variant7-variant8-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant22-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,75:140:99:1902,0,1737:20,45,30,45 chr1 53716416 . G A 1413.98 PASS AC=1;AF=0.643;AN=2;DP=3787;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant22-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:69,73:142:99:1803,0,1726:33,36,33,40 chr1 53722752 . A C 227.43 PASS AC=1;AF=0.643;AN=2;DP=435;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant22-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,6:16:99:214,0,353:7,3,6,0 chr1 53723190 . G T 841.73 PASS AC=1;AF=0.643;AN=2;DP=3904;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant22-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,73:141:99:1760,0,1723:28,40,27,46 chr1 53723349 . T C 169.22 PASS AC=1;AF=0.643;AN=2;DP=311;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant22-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,5:13:99:145,0,281:1,7,1,4 chr1 53732315 . G T 1289.66 PASS AC=1;AF=0.643;AN=2;DP=3469;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant22-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,89:148:99:2227,0,1444:19,40,33,56 chr1 53736613 . A G 209.12 PASS AC=1;AF=0.643;AN=2;DP=758;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant22-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,15:39:99:493,0,824:20,4,14,1 chr1 53738183 . A G 194.32 PASS AC=1;AF=0.643;AN=2;DP=1404;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant22-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,31:59:99:838,0,756:19,9,23,8 chr1 53742506 . A G 497.86 PASS AC=1;AF=0.625;AN=2;DP=1917;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant22-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,36:103:99:954,0,1672:28,39,17,19 chr1 53746134 . G A 446.86 PASS AC=1;AF=0.621;AN=2;DP=1523;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant22-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,20:52:99:476,0,917:22,10,10,10 chr1 53746595 . A T 494.24 PASS AC=1;AF=0.621;AN=2;DP=1210;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant22-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,18:43:99:423,0,625:11,14,7,11 chr1 53755151 . T C 304.39 PASS AC=1;AF=0.683;AN=2;DP=2360;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:70,61:131:99:1470,0,1583:40,30,39,22 chr1 53792651 . A C 1511.81 PASS AC=2;AF=0.609;AN=2;DP=5091;MQ=60;set=variant-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:1,149:150:99:4661,411,0:1,0,51,98 chr1 53793170 . C T 82.67 PASS AC=2;AF=0.607;AN=2;DP=353;FractionInformativeReads=1;MQ=60;set=variant7-variant9-variant10-variant11-variant12-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:65:695,65,0:0,0,12,10 chr1 53793248 . T G 40.7 PASS AC=2;AF=0.625;AN=2;DP=362;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant7-variant9-variant10-variant11-variant12-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:65:762,65,0:0,0,16,6 chr1 53793510 . CTG C 146.83 PASS AC=1;AF=0.5;AN=2;DP=190;MQ=60;set=variant31-variant33-filterInvariant35 GT:AD:DP:GQ:PL:SB 0/1:38,5:43:83:83,0,1536:17,21,3,2 chr1 53793511 . T C 682.58 PASS AC=1;AF=0.532;AN=2;DP=1505;MQ=60;set=variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:5,38:43:89:974,0,89:3,2,17,21 chr1 53793513 . CA C 146.74 PASS AC=1;AF=0.5;AN=2;DP=194;MQ=60;set=variant31-variant33-filterInvariant35 GT:AD:DP:GQ:PL:SB 0/1:40,5:45:83:83,0,1536:18,22,3,2 chr1 53930360 . G A 584.13 PASS AC=1;AF=0.5;AN=2;DP=510;MQ=60;set=variant4-variant7-variant14-variant20-variant23-variant26-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:44,36:80:99:978,0,1173:28,16,25,11 chr1 53933225 . T C 48.22 PASS AC=1;AF=0.625;AN=2;DP=81;FS=0;FractionInformativeReads=1;MQ=60;set=variant11-variant14-variant18-variant20-variant23-variant26-variant32-variant34-variant35-variant37-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:2,4:6:74:121,0,74:1,1,1,3 chr1 53972205 . T C 1189.48 PASS AC=1;AF=0.611;AN=2;DP=1883;MQ=60;set=variant-variant5-variant6-variant7-variant11-variant18-variant20-variant21-variant23-variant28-variant32-variant34-variant35-variant36-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:63,75:138:99:1964,0,1550:34,29,41,34 chr1 53974987 . G T 805.06 PASS AC=2;AF=0.829;AN=2;DP=3093;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,81:81:99:2543,241,0:0,0,27,54 chr1 53986118 . C T 454.85 PASS AC=1;AF=0.5;AN=2;DP=121;FractionInformativeReads=1;MQ=60;set=variant7-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:23,24:47:99:655,0,617:15,8,16,8 chr1 53990321 . C T 2116.62 PASS AC=2;AF=0.837;AN=2;DP=2565;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:2217,176,0:0,0,51,8 chr1 54065648 . G A 53.54 PASS AC=2;AF=0.93;AN=2;DP=353;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:409,36,0:0,0,9,3 chr1 54065778 . C T 659.41 PASS AC=2;AF=0.932;AN=2;DP=1635;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1370,136,0:0,0,25,21 chr1 54065831 . G T 1052.99 PASS AC=2;AF=0.932;AN=2;DP=2295;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:1654,173,0:0,0,32,26 chr1 54065924 . G A 1481.64 PASS AC=2;AF=0.932;AN=2;DP=2916;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:2338,230,0:0,0,41,36 chr1 54065997 . A T 1146.95 PASS AC=2;AF=0.932;AN=2;DP=1846;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:2013,141,0:0,0,19,27 chr1 54066012 . A G 1003.04 PASS AC=2;AF=0.932;AN=2;DP=1521;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1773,123,0:0,0,18,23 chr1 54066038 . C T 582.66 PASS AC=2;AF=0.932;AN=2;DP=1004;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1062,111,0:0,0,15,22 chr1 54252939 . GA G 71.89 PASS AC=1;AF=0.5;AN=2;DP=295;MQ=60;set=filterInvariant4-filterInvariant6-variant29-variant33-filterInvariant35-filterInvariant38-variant39-filterInvariant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,6:20:67:67,0,316:3,11,2,4 chr1 54317697 . T C 1266.61 PASS AC=2;AF=1;AN=2;DP=2397;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1359,135,0:0,0,26,19 chr1 54318058 . G A 242.99 PASS AC=2;AF=1;AN=2;DP=76;FS=0;FractionInformativeReads=1;MQ=60;set=variant6-variant7-variant9-variant10-variant13-variant16-variant19-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:90,6,0:0,0,0,2 chr1 54331715 . C G 208.21 PASS AC=1;AF=0.593;AN=2;DP=610;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant34-variant35-variant36-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,20:30:99:779,0,310:9,1,20,0 chr1 54331763 . A G 545.25 PASS AC=1;AF=0.63;AN=2;DP=1554;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant34-variant35-variant36-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,43:73:99:1385,0,746:20,10,35,8 chr1 54344282 . C A 1103.92 PASS AC=2;AF=0.689;AN=2;DP=3037;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,88:88:99:2711,264,0:0,0,53,35 chr1 54354658 . T G 302.21 PASS AC=1;AF=0.5;AN=2;DP=899;MQ=60;set=variant2-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant18-variant24-variant28-variant35-variant37-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:25,25:50:99:592,0,735:6,19,8,17 chr1 54354935 . G C 142.67 PASS AC=1;AF=0.5;AN=2;DP=342;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant18-variant24-variant28-variant35-variant37-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:8,8:16:99:183,0,211:6,2,5,3 chr1 54355041 . A G 229.33 PASS AC=1;AF=0.5;AN=2;DP=475;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant6-variant7-filterInvariant8-variant9-variant13-variant14-variant15-variant16-variant18-variant24-variant28-variant35-variant37-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:14,16:30:99:421,0,317:6,8,8,8 chr1 54355105 . A G 85.48 PASS AC=2;AF=0.667;AN=2;DP=587;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant22-variant24-variant26-variant27-variant28-variant29-variant31-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:687,60,0:0,0,10,10 chr1 54355554 . A T,C 718.3 PASS AC=1,1;AF=0.382,0.279;AN=2;DP=2256;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant22-variant24-variant26-variant27-variant28-variant29-variant31-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:DP:GQ:SB 2/1:67:99:0,0,26,41 chr1 54355646 . T C 203.33 PASS AC=1;AF=0.591;AN=2;DP=377;MQ=60;set=variant-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant16-variant17-variant18-variant22-variant26-variant27-variant28-variant29-variant31-variant34-variant35-variant36-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,10:23:99:238,0,354:3,10,3,7 chr1 54356002 . G T 151.84 PASS AC=1;AF=0.5;AN=2;DP=332;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant18-variant24-variant28-variant35-variant37-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:9,7:16:99:264,0,309:6,3,6,1 chr1 54356106 . G A 704.06 PASS AC=1;AF=0.5;AN=2;DP=1667;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant18-variant24-variant28-variant35-variant37-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:33,42:75:99:1202,0,878:24,9,28,14 chr1 54356341 . C G 400.99 PASS AC=1;AF=0.5;AN=2;DP=625;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant18-variant24-variant28-variant35-variant37-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:27,18:45:99:668,0,1333:7,20,1,17 chr1 54356347 . A T 385.27 PASS AC=1;AF=0.5;AN=2;DP=533;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant18-variant24-variant28-variant35-variant37-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:23,16:39:99:632,0,1303:6,17,1,15 chr1 54356361 . C A 246.86 PASS AC=1;AF=0.5;AN=2;DP=375;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant6-variant7-variant9-variant12-variant13-variant14-variant15-variant16-variant18-variant24-variant35-variant37-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:16,11:27:99:394,0,451:4,12,0,11 chr1 54360467 . C G 594.96 PASS AC=1;AF=0.591;AN=2;DP=714;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant16-variant17-variant18-variant22-variant26-variant27-variant28-variant29-variant31-variant34-variant35-variant36-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,13:25:99:313,0,347:2,10,5,8 chr1 54370264 . A T 1048.42 PASS AC=1;AF=0.596;AN=2;DP=2504;set=variant-variant2-variant3-variant6-variant7-variant13-variant14-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:65,55:120:99:1255,0,1654:40,25,31,24 chr1 54375570 . C A 4527.08 PASS AC=2;AF=0.672;AN=2;DP=4928;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant11-variant14-variant16-variant17-variant19-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,171:171:99:5123,510,0:0,0,74,97 chr1 54375701 . C T 1180.88 PASS AC=2;AF=0.6;AN=2;DP=2360;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant14-variant16-variant17-variant19-variant22-variant23-variant24-variant25-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,97:97:99:2811,290,0:0,0,42,55 chr1 54389774 . TAG T 266.18 PASS AC=2;AF=0.69;AN=2;DP=250;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant14-variant16-variant17-variant19-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:225,15,0:0,0,0,5 chr1 54395673 . CA C 395.49 PASS AC=1;AF=0.5;AN=2;DP=4259;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-filterInvariant15-variant16-variant17-variant18-filterInvariant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-filterInvariant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-filterInvariant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,34:87:99:423,0,706:24,29,17,17 chr1 54474472 . T C 341.99 PASS AC=1;AF=0.652;AN=2;DP=888;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant9-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant24-variant27-variant29-variant30-variant34-variant35-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,18:41:99:411,0,631:13,10,12,6 chr1 54483694 . C T 263.31 PASS AC=1;AF=0.609;AN=2;DP=1184;set=variant2-variant3-variant4-variant5-variant9-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant24-variant27-variant29-variant30-variant34-variant35-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,23:56:99:521,0,937:22,11,16,7 chr1 54507506 . C A 603.56 PASS AC=1;AF=0.5;AN=2;DP=371;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant10-variant20-variant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:34,35:69:99:820,0,726:14,20,15,20 chr1 54509644 . T C 9275.9 PASS AC=2;AF=1;AN=2;DP=12229;FS=0;MQ=60;MQRankSum=0.014;ReadPosRankSum=0.839;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,307:307:99:9213,919,0:0,0,145,162 chr1 54510014 . CA CAAAAAAAA,CAAAAAA,CAAAAAAAAA,CAAAAAAA,CAAAAA,C 1310.65 PASS AC=1,0,0,1,0,0;AF=0.475,0.05,0.3,0.075,0.05,0.025;AN=2;DP=589;set=variant-variant6-variant7-variant8-variant10-variant11-variant20-variant22-variant25-variant26-variant28-variant31-variant32-variant3-variant35-variant36-variant37-variant40-variant43-variant44 GT:DP:GQ:SB 4/1:24:78:1,0,18,5 chr1 54510181 . GT G,GTT 213.14 PASS AC=1,0;AF=0.453,0.047;AN=2;DP=2622;set=filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-variant7-variant8-filterInvariant9-filterInvariant10-variant11-filterInvariant12-filterInvariant13-filterInvariant14-variant15-variant16-variant17-filterInvariant18-filterInvariant19-filterInvariant21-filterInvariant22-variant23-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant31-filterInvariant32-variant33-variant34-filterInvariant35-filterInvariant37-filterInvariant38-variant40-filterInvariant41 GT:DP:GQ:SB 0/1:71:99:19,29,4,19 chr1 54563039 . G A 6923.58 PASS AC=2;AF=0.977;AN=2;DP=11128;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,256:256:99:7402,766,0:0,0,133,123 chr1 54604576 . G A 156.22 PASS AC=2;AF=1;AN=2;DP=206;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:181,18,0:0,0,4,2 chr1 54605318 . T TG,TGG 403.76 PASS AC=1,0;AF=0.34,0.26;AN=2;DP=1407;MQ=60;set=variant-variant3-variant4-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant25-variant27-variant29-variant30-variant33-variant34-variant35-filterInvariant36-variant37-variant40-variant41-variant43-variant44 GT:DP:GQ:SB 0/1:70:99:21,16,22,11 chr1 54605319 . G GC 315.63 PASS AC=1;AF=0.716;AN=2;DP=2227;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:37,38:75:99:919,0,846:22,15,22,16 chr1 54606804 . C T 3171.84 PASS AC=2;AF=0.872;AN=2;DP=4859;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,129:129:99:4331,385,0:0,0,93,36 chr1 54607051 . A G 4671.27 PASS AC=2;AF=1;AN=2;DP=8469;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,192:192:99:6125,574,0:0,0,67,125 chr1 54607157 . G A 1506.45 PASS AC=2;AF=0.872;AN=2;DP=2137;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1610,150,0:0,0,16,34 chr1 54618435 . A T 1472.1 PASS AC=1;AF=0.756;AN=2;DP=7763;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:98,133:231:99:3273,0,2150:52,46,76,57 chr1 54619337 . C T 813.08 PASS AC=2;AF=0.932;AN=2;DP=1418;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:807,72,0:0,0,11,13 chr1 54619404 . C T 515.44 PASS AC=1;AF=0.577;AN=2;DP=369;MQ=60;set=variant7-variant11-variant12-variant17-variant19-variant20-variant21-variant24-variant25-variant31-variant32-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:12,17:29:99:453,0,486:5,7,8,9 chr1 54619416 . GC G 132.73 PASS AC=1;AF=0.559;AN=2;DP=475;MQ=60;set=variant-variant3-variant6-variant10-variant13-variant14-variant15-variant17-variant21-variant22-variant23-variant30-variant33-variant34-variant35-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,12:28:99:326,0,604:7,9,5,7 chr1 54636977 . T C 441.25 PASS AC=1;AF=0.526;AN=2;DP=1300;MQ=60;set=variant-variant3-variant6-variant10-variant13-variant14-variant15-variant17-variant19-variant21-variant22-variant23-variant30-variant31-variant33-variant34-variant35-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,29:59:99:642,0,834:12,18,13,16 chr1 54637167 . T C 86.95 PASS AC=1;AF=0.775;AN=2;DP=605;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,6:14:99:144,0,215:2,6,2,4 chr1 54661150 . C T 460.86 PASS AC=1;AF=0.54;AN=2;DP=2207;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant10-variant11-variant12-variant17-variant18-variant19-variant20-variant24-variant25-variant26-variant28-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:52,48:100:99:1179,0,1245:29,23,29,19 chr1 54681920 . G C 4098.39 PASS AC=2;AF=0.826;AN=2;DP=6892;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,185:185:99:5437,554,0:0,0,89,96 chr1 54686374 . T C 738.23 PASS AC=1;AF=0.671;AN=2;DP=3997;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,60:117:99:1531,0,1544:33,24,34,26 chr1 54686464 . C T 1941.25 PASS AC=1;AF=0.523;AN=2;DP=3603;MQ=60;set=variant2-variant3-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant17-variant18-variant19-variant23-variant24-variant25-variant27-variant28-variant31-variant35-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:84,103:187:99:2531,0,2170:45,39,58,45 chr1 54690954 . T C 1836.94 PASS AC=1;AF=0.645;AN=2;DP=4732;MQ=60;set=variant-variant3-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant34-variant35-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:94,100:194:99:2688,0,2387:52,42,54,46 chr1 54694214 . G A 100.87 PASS AC=1;AF=0.558;AN=2;DP=425;MQ=60;set=variant-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant32-variant34-variant35-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,11:20:99:380,0,297:2,7,4,7 chr1 54704462 . C CCAG 519.76 PASS AC=1;AF=0.727;AN=2;DP=2013;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant37-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,31:63:99:1205,0,1250:16,16,16,15 chr1 54704510 . A C 684.15 PASS AC=1;AF=0.758;AN=2;DP=1791;MQ=60;set=variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,34:76:99:758,0,1069:19,23,16,18 chr1 54704567 . A G 1203.72 PASS AC=1;AF=0.942;AN=2;DP=1881;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,26:52:99:554,0,618:12,14,10,16 chr1 54704629 . C T 211.72 PASS AC=1;AF=0.741;AN=2;DP=810;MQ=60;set=variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant34-variant35-variant37-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,17:34:99:508,0,625:4,13,5,12 chr1 54706733 . A G 629.55 PASS AC=1;AF=0.712;AN=2;DP=2679;MQ=60;set=variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,47:96:99:1066,0,1278:19,30,19,28 chr1 54709186 . T G 203.15 PASS AC=1;AF=0.5;AN=2;DP=12;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.289;QD=16.93;ReadPosRankSum=-0.289;SOR=0.446;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:4,8:12:99:231,0,143:1,3,3,5 chr1 54870481 . TG TGGG,TGG,T,TGGGG 292.94 PASS AC=0,1,0,0;AF=0.161,0.25,0.089,0.018;AN=2;DP=1208;MQ=60;set=variant-variant3-variant4-variant6-filterInvariant8-filterInvariant9-variant11-variant14-variant15-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-filterInvariant27-filterInvariant28-filterInvariant29-variant30-filterInvariant31-variant32-variant33-variant35-variant36-filterInvariant37-variant43 GT:DP:GQ:SB 0/2:25:99:12,3,10,0 chr1 54870494 . T G 132.05 PASS AC=1;AF=0.5;AN=2;DP=765;MQ=60;set=filterInvariant3-filterInvariant6-variant10-variant15-filterInvariant16-filterInvariant17-variant19-filterInvariant23-filterInvariant24-filterInvariant25-variant26-variant29-variant32-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:22,22:44:99:423,0,373:11,11,19,3 chr1 54871024 . G T 1319.97 PASS AC=1;AF=0.632;AN=2;DP=2957;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,55:98:99:1299,0,1053:29,14,34,21 chr1 54871709 . TCGCCGCCGC TCGCCGCCGCCGCCGC,TCGCCGCCGCCGC,TCGCCGCCGCCGCCGCCGCCGC,T 637.2 PASS AC=1,0,0,0;AF=0.543,0.014,0.071,0.014;AN=2;DP=1795;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:52:99:12,11,16,13 chr1 54872035 . TGCCGCCGCC TGCCGCC,T 4449.98 PASS AC=2,0;AF=0.932,0.011;AN=2;DP=3387;set=Intersection GT:DP:GQ:SB 1/1:92:99:0,0,52,40 chr1 55014099 . C T 1466.01 PASS AC=2;AF=0.786;AN=2;DP=5274;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,130:130:99:4207,388,0:0,0,42,88 chr1 55014160 . C T 888.54 PASS AC=2;AF=0.786;AN=2;DP=3068;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,61:61:99:2020,183,0:0,0,20,41 chr1 55059505 . C T 662.24 PASS AC=1;AF=0.5;AN=2;DP=157;FractionInformativeReads=1;MQ=60;set=variant10-variant14-variant29-variant35 GT:AD:DP:GQ:PL:SB 0/1:18,22:40:99:623,0,517:14,4,16,6 chr1 55066759 . T C 169.68 PASS AC=1;AF=0.679;AN=2;DP=369;set=variant-variant2-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,3:8:99:147,0,713:5,0,3,0 chr1 55066789 . CAT C 271.56 PASS AC=1;AF=0.679;AN=2;DP=766;set=variant-variant2-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:10,12:22:99:516,0,1023:9,1,9,3 chr1 55066813 . C CAT 505.46 PASS AC=1;AF=0.679;AN=2;DP=1086;set=variant-variant2-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:18,21:39:99:814,0,1364:13,5,13,8 chr1 55069986 . T C 932.14 PASS AC=1;AF=0.788;AN=2;DP=3319;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,32:79:99:795,0,1048:28,19,19,13 chr1 55072726 . T C 398.4 PASS AC=1;AF=0.75;AN=2;DP=1792;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,40:65:99:1109,0,585:18,7,29,11 chr1 55074647 . G A 651.1 PASS AC=1;AF=0.5;AN=2;DP=356;FractionInformativeReads=1;set=variant-variant3-variant7-variant35 GT:AD:DP:GQ:PL:SB 0/1:60,48:108:99:1110,0,1502:38,22,32,16 chr1 55074840 . T A 811.78 PASS AC=1;AF=0.643;AN=2;DP=4197;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:71,74:145:99:2026,0,1916:33,38,29,45 chr1 55074922 . G A 1130.34 PASS AC=1;AF=0.583;AN=2;DP=2637;MQ=60;set=variant-variant3-variant7-variant8-variant9-variant15-variant17-variant20-variant23-variant25-variant28-variant31-variant33-variant35-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:80,78:158:99:2025,0,2212:46,34,45,33 chr1 55075452 . G A 1546.33 PASS AC=1;AF=0.643;AN=2;DP=4168;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:72,71:143:99:1723,0,1878:37,35,36,35 chr1 55076137 . CCACTCCACATTCAGACCGTCATCCCCAGG C 391.44 PASS AC=1;AF=0.5;AN=2;DP=384;MQ=60;set=variant10-variant13-variant14-variant29-variant35 GT:AD:DP:GQ:PL:SB 0/1:45,14:59:99:434,0,12646:22,23,5,9 chr1 55078046 . T C 772.11 PASS AC=2;AF=0.907;AN=2;DP=1094;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1283,99,0:0,0,30,3 chr1 55080612 . GGTGT G,GGTGTGTGTGT,GGTGTGTGT 2367.76 PASS AC=1,1,0;AF=0.273,0.477,0.011;AN=2;DP=4698;set=Intersection GT:DP:GQ:SB 1/2:89:99:4,5,26,54 chr1 55080629 . A G 2467.89 PASS AC=2;AF=0.739;AN=2;DP=3722;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:5,80:85:88:3180,88,0:2,3,27,53 chr1 55080635 . G A,GTGTGCA 3016.52 PASS AC=1,0;AF=0.554,0.162;AN=2;DP=2741;set=variant4-variant2-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant3-variant14-variant-variant16-variant19-variant20-variant5-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:81:99:17,28,10,26 chr1 55080745 . TAG T 118.68 PASS AC=1;AF=0.611;AN=2;DP=304;MQ=60;set=variant-variant3-variant7-variant8-variant9-variant15-variant17-variant20-variant23-variant24-variant25-variant28-variant31-variant33-variant35-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,6:11:99:237,0,195:1,4,2,4 chr1 55085499 . T C 345.83 PASS AC=1;AF=0.742;AN=2;DP=1377;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,37:59:99:935,0,611:16,6,23,14 chr1 55089316 . A C 253.56 PASS AC=1;AF=0.661;AN=2;DP=425;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant30-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,9:16:99:357,0,358:1,6,1,8 chr1 55089317 . T C 253.56 PASS AC=1;AF=0.661;AN=2;DP=422;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant30-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,9:16:99:357,0,358:1,6,1,8 chr1 55096518 . C T 150.18 PASS AC=1;AF=0.5;AN=2;DP=35;FS=1.478;FractionInformativeReads=1;MQ=60;MQRankSum=0.623;QD=4.29;ReadPosRankSum=-2.057;SOR=1.002;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:26,9:35:99:178,0,613:11,15,3,6 chr1 55100328 . T C 272.29 PASS AC=1;AF=0.667;AN=2;DP=540;FractionInformativeReads=1;set=variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant24-variant27-variant29-variant30-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,15:27:99:382,0,347:8,4,11,4 chr1 55103945 . A G 30.22 PASS AC=1;AF=0.685;AN=2;DP=352;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant24-variant27-variant29-variant30-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:2,8:10:19:229,0,19:1,1,3,5 chr1 55104317 . G C 403.29 PASS AC=1;AF=0.661;AN=2;DP=844;FractionInformativeReads=1;set=variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant29-variant30-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,12:28:99:361,0,461:10,6,9,3 chr1 55104355 . T C 615.92 PASS AC=1;AF=0.604;AN=2;DP=1075;set=variant3-variant4-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant18-variant19-variant20-variant22-variant24-variant25-variant27-variant30-variant32-variant34-variant35-variant36-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,25:44:99:724,0,587:14,5,18,7 chr1 55104647 . T C 1228.94 PASS AC=1;AF=0.604;AN=2;DP=2176;set=variant3-variant4-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant18-variant19-variant20-variant22-variant24-variant25-variant27-variant30-variant32-variant34-variant35-variant36-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,56:115:99:1574,0,1718:14,45,12,44 chr1 55107607 . G A 315.93 PASS AC=2;AF=1;AN=2;DP=1091;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:910,87,0:0,0,12,17 chr1 55117497 . T G 138.89 PASS AC=2;AF=0.906;AN=2;DP=290;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant28-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:215,18,0:0,0,4,2 chr1 55118566 . C G 2343.41 PASS AC=2;AF=1;AN=2;DP=5145;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,121:121:99:3602,363,0:0,0,62,59 chr1 55119144 . A G 1695.21 PASS AC=2;AF=0.645;AN=2;DP=4552;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant30-variant32-variant34-variant35-variant36-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,174:174:99:5507,521,0:0,0,95,79 chr1 55119289 . G C 5352.67 PASS AC=2;AF=0.705;AN=2;DP=6215;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,179:179:99:5886,537,0:0,0,86,93 chr1 55119546 . A G 3176.3 PASS AC=2;AF=1;AN=2;DP=8282;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,214:214:99:6549,639,0:0,0,95,119 chr1 55129372 . A C 295.54 PASS AC=1;AF=0.615;AN=2;DP=668;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant16-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant30-variant32-variant35-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,13:20:99:498,0,263:3,4,10,3 chr1 55129374 . AC A 286.54 PASS AC=1;AF=0.64;AN=2;DP=691;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant16-variant19-variant20-variant22-variant24-variant25-variant27-variant30-variant32-variant35-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,13:21:99:498,0,263:4,4,10,3 chr1 55130931 . C T 731.34 PASS AC=2;AF=0.689;AN=2;DP=2695;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:2518,227,0:0,0,21,55 chr1 55130946 . G C 644.13 PASS AC=2;AF=0.703;AN=2;DP=2158;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,61:61:99:2026,183,0:0,0,17,44 chr1 55130972 . C T 259.9 PASS AC=2;AF=0.884;AN=2;DP=1694;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1536,135,0:0,0,10,35 chr1 55134379 . C T 490.9 PASS AC=2;AF=0.884;AN=2;DP=1085;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:899,81,0:0,0,20,7 chr1 55136067 . T G 285.14 PASS AC=2;AF=0.895;AN=2;DP=1261;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1459,114,0:0,0,29,9 chr1 55139105 . T C 79.96 PASS AC=1;AF=0.673;AN=2;DP=337;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant10-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant27-variant29-variant30-variant32-variant34-variant35-variant36-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,3:9:67:67,0,178:3,3,1,2 chr1 55139618 . G A 688.84 PASS AC=1;AF=0.655;AN=2;DP=1914;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant27-variant29-variant30-variant32-variant34-variant35-variant36-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,41:91:99:1029,0,1373:24,26,21,20 chr1 55139741 . A G 1115.68 PASS AC=2;AF=0.86;AN=2;DP=3946;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,121:121:99:3609,362,0:0,0,58,63 chr1 55139912 . T G 542.42 PASS AC=1;AF=0.542;AN=2;DP=538;MQ=60;set=variant2-variant10-variant12-variant15-variant26-variant30-variant35-variant36-variant37-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:15,22:37:99:650,0,393:5,10,5,17 chr1 55163655 . G A 1713.19 PASS AC=1;AF=0.619;AN=2;DP=1655;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant10-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant26-variant34-variant35-variant36-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,43:89:99:1022,0,1072:20,26,21,22 chr1 55163751 . T C 1509.64 PASS AC=1;AF=0.619;AN=2;DP=1848;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant10-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant26-variant34-variant35-variant36-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,42:95:99:1051,0,1322:28,25,19,23 chr1 55163836 . A C 1810.76 PASS AC=1;AF=0.619;AN=2;DP=1662;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant10-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant26-variant34-variant35-variant36-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,34:84:99:810,0,1282:26,24,14,20 chr1 55164116 . T G 3392.5 PASS AC=1;AF=0.619;AN=2;DP=2449;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant10-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant26-variant34-variant35-variant36-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,66:131:99:1600,0,1786:37,28,33,33 chr1 55164470 . CT C 432.37 PASS AC=1;AF=0.658;AN=2;DP=430;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant10-variant12-variant14-variant15-variant16-variant20-variant21-variant22-variant26-variant35-variant36-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,18:25:99:360,0,107:0,7,3,15 chr1 55165268 . G A 583.49 PASS AC=2;AF=0.643;AN=2;DP=735;set=variant-variant2-variant3-variant7-variant8-variant10-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant26-variant34-variant35-variant36-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1178,123,0:0,0,24,17 chr1 55165573 . G A 1236.87 PASS AC=2;AF=0.643;AN=2;DP=1000;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant10-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant26-variant34-variant35-variant36-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1366,134,0:0,0,24,21 chr1 55165942 . G A 3337.05 PASS AC=2;AF=0.643;AN=2;DP=3052;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant10-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant26-variant34-variant35-variant36-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:3,155:158:99:4762,378,0:1,2,78,77 chr1 55166842 . C T 832.68 PASS AC=2;AF=0.704;AN=2;DP=1029;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant10-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant26-variant27-variant28-variant32-variant34-variant35-variant36-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1511,147,0:0,0,31,18 chr1 55167064 . C T 329.1 PASS AC=1;AF=0.5;AN=2;DP=33;FS=3.133;FractionInformativeReads=1;MQ=60;MQRankSum=1.876;QD=9.97;ReadPosRankSum=0.273;SOR=1.314;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:19,14:33:99:357,0,478:8,11,4,10 chr1 55167773 . T A 2209.81 PASS AC=2;AF=0.837;AN=2;DP=3909;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,94:94:99:2902,281,0:0,0,48,46 chr1 55175322 . A G 529 PASS AC=2;AF=0.677;AN=2;DP=483;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant30-variant32-variant33-variant35-variant36-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:551,51,0:0,0,11,6 chr1 55182300 . T A 2579.29 PASS AC=2;AF=0.697;AN=2;DP=2675;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant30-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,91:91:99:2795,273,0:0,0,48,43 chr1 55199104 . T A 614.39 PASS AC=2;AF=0.717;AN=2;DP=292;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant15-variant17-variant21-variant22-variant27-variant28-variant30-variant33-variant35-variant36-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:48:626,48,0:0,0,11,3 chr1 55199105 . A T 614.39 PASS AC=2;AF=0.675;AN=2;DP=269;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant10-variant11-variant17-variant21-variant22-variant27-variant28-variant30-variant33-variant35-variant36-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:626,48,0:0,0,13,3 chr1 55199420 . ATTTTTTTTTT AT,ATT,A,ATTTTTTT,ATTTTTT,ATTTTTTTTT,ATTTTTTTT 1694.42 PASS AC=2,0,0,0,0,0,0;AF=0.129,0.403,0.081,0.016,0.016,0.032,0.032;AN=2;DP=2204;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-filterInvariant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant24-variant28-filterInvariant29-variant30-variant31-variant32-variant35-variant37-variant38-variant40-variant43-variant44 GT:DP:GQ:SB 1/1:40:64:3,0,8,29 chr1 55207754 . C G 1311.08 PASS AC=2;AF=0.712;AN=2;DP=1553;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant30-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,48:50:99:1459,101,0:1,1,29,19 chr1 55208299 . G C 330.43 PASS AC=2;AF=0.712;AN=2;DP=776;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant30-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:883,90,0:0,0,11,19 chr1 55222466 . A G 46.5 PASS AC=2;AF=0.78;AN=2;DP=136;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant15-variant16-variant20-variant21-variant22-variant24-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:177,12,0:0,0,4,0 chr1 55224131 . T C 1587.98 PASS AC=2;AF=0.647;AN=2;DP=1671;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant9-variant10-variant15-variant16-variant18-variant20-variant21-variant24-variant28-variant35-variant38-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,107:107:99:3317,320,0:0,0,58,49 chr1 55224751 . C A 3185.03 PASS AC=2;AF=0.647;AN=2;DP=2877;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant9-variant10-variant15-variant16-variant18-variant20-variant21-variant24-variant28-variant35-variant38-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,172:172:99:5096,514,0:0,0,75,97 chr1 55230233 . T C 1938.96 PASS AC=2;AF=0.689;AN=2;DP=2841;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,111:113:99:3198,288,0:1,1,46,65 chr1 55245639 . A G 540.6 PASS AC=1;AF=0.5;AN=2;DP=279;MQ=60;set=variant11-variant18-variant29-variant35-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:18,23:41:99:622,0,580:9,9,9,14 chr1 55247518 . C A 362.3 PASS AC=1;AF=0.5;AN=2;DP=280;MQ=60;set=variant11-variant13-variant18-variant29-variant32-variant34-variant35-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:9,15:24:99:391,0,305:2,7,4,11 chr1 55250684 . A G 1612.8 PASS AC=1;AF=0.5;AN=2;DP=1142;MQ=60;set=variant5-variant11-variant13-variant18-variant29-variant32-variant34-variant35-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:52,52:104:99:1367,0,1226:23,29,27,25 chr1 55250823 . G A 982.79 PASS AC=1;AF=0.5;AN=2;DP=607;FractionInformativeReads=1;MQ=60;set=variant11-variant13-variant18-variant29-variant32-variant34-variant35-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:35,29:64:99:732,0,835:19,16,12,17 chr1 55251314 . G A 121.43 PASS AC=1;AF=0.5;AN=2;DP=104;FractionInformativeReads=1;MQ=60;set=variant5-variant11-variant18-variant29-variant35-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:9,7:16:99:226,0,261:2,7,1,6 chr1 55251689 . T C 2837.61 PASS AC=2;AF=1;AN=2;DP=4165;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,125:125:99:3736,374,0:0,0,76,49 chr1 55253346 . G A 1767.77 PASS AC=1;AF=0.545;AN=2;DP=2403;MQ=60;set=variant3-variant8-variant10-variant11-variant12-variant13-variant18-variant19-variant20-variant23-variant25-variant27-variant29-variant31-variant32-variant34-variant35-variant36-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:45,64:109:99:1610,0,1200:28,17,36,28 chr1 55253575 . T C 2504.49 PASS AC=2;AF=1;AN=2;DP=4136;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,124:124:99:3935,371,0:0,0,50,74 chr1 55253594 . G A 630.56 PASS AC=1;AF=0.5;AN=2;DP=830;MQ=60;set=variant5-variant11-variant13-variant18-variant29-variant32-variant34-variant35-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:60,50:110:99:1419,0,1581:29,31,21,29 chr1 55266845 . C T 2205.25 PASS AC=2;AF=0.654;AN=2;DP=8213;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,214:214:99:6573,638,0:0,0,91,123 chr1 55271774 . A G 1938.32 PASS AC=2;AF=0.654;AN=2;DP=6845;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,193:193:99:5993,582,0:0,0,95,98 chr1 55273580 . G T 663.66 PASS AC=2;AF=0.667;AN=2;DP=3293;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,88:88:99:2731,263,0:0,0,45,43 chr1 55277430 . T A 355.84 PASS AC=2;AF=0.684;AN=2;DP=1266;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:630,66,0:0,0,12,10 chr1 55277599 . T C 3047.53 PASS AC=2;AF=1;AN=2;DP=6748;FS=0;MQ=60;MQRankSum=1.687;ReadPosRankSum=0.849;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,167:167:99:4763,499,0:0,0,100,67 chr1 55279345 . CCCGGCCT C 367.95 PASS AC=2;AF=1;AN=2;DP=420;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:450,30,0:0,0,7,3 chr1 55282556 . A G 148.16 PASS AC=2;AF=0.711;AN=2;DP=1414;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant18-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:961,84,0:0,0,20,8 chr1 55308039 . T G 52.74 PASS AC=2;AF=0.864;AN=2;DP=113;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant6-variant7-variant8-variant9-variant12-variant15-variant22-variant24-variant25-variant26-variant28-variant31-variant34-variant35-variant36-variant37-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:205,15,0:0,0,0,5 chr1 55315351 . T C 788.67 PASS AC=2;AF=1;AN=2;DP=1277;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:1122,96,0:0,0,24,8 chr1 55316082 . A C 1014.64 PASS AC=2;AF=1;AN=2;DP=2012;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:1605,144,0:0,0,24,24 chr1 55319902 . A G 739.66 PASS AC=2;AF=0.718;AN=2;DP=3432;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,91:91:99:2835,273,0:0,0,42,49 chr1 55330966 . T C 1271.51 PASS AC=2;AF=1;AN=2;DP=1947;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.675;ReadPosRankSum=1.321;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1478,126,0:0,0,32,10 chr1 55336950 . C G 121.67 PASS AC=1;AF=0.675;AN=2;DP=989;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,13:29:99:402,0,477:12,4,10,3 chr1 55341106 . C T 100.16 PASS AC=1;AF=0.647;AN=2;DP=347;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant15-variant16-variant20-variant21-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,6:10:99:186,0,111:1,3,2,4 chr1 55341915 . T G 296.06 PASS AC=1;AF=0.647;AN=2;DP=604;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant15-variant16-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,10:21:99:251,0,316:4,7,3,7 chr1 55446373 . C A 143.17 PASS AC=2;AF=0.857;AN=2;DP=370;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:215,21,0:0,0,4,3 chr1 55446664 . G C 3707.51 PASS AC=2;AF=0.821;AN=2;DP=4442;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,129:129:99:5769,397,0:0,0,80,49 chr1 55446671 . C T 3850.44 PASS AC=2;AF=0.821;AN=2;DP=4762;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,134:134:99:5838,406,0:0,0,83,51 chr1 55446697 . G A 4037.04 PASS AC=2;AF=0.821;AN=2;DP=6210;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,164:164:99:5208,488,0:0,0,101,63 chr1 55457710 . G A 4007.12 PASS AC=2;AF=0.854;AN=2;DP=5467;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,175:175:99:5432,524,0:0,0,84,91 chr1 55457815 . C T 1776.9 PASS AC=2;AF=0.854;AN=2;DP=3964;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,118:118:99:3666,354,0:0,0,50,68 chr1 55464743 . T C 2312.39 PASS AC=2;AF=0.78;AN=2;DP=3940;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,104:104:99:3608,312,0:0,0,72,32 chr1 55464790 . C G 3781.15 PASS AC=2;AF=0.78;AN=2;DP=5876;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,177:177:99:5458,529,0:0,0,101,76 chr1 55473043 . G A 609.69 PASS AC=1;AF=0.667;AN=2;DP=874;MQ=60;set=variant2-variant4-variant5-variant7-variant10-variant11-variant12-variant13-variant14-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,24:40:99:594,0,398:10,6,14,10 chr1 55474325 . A C 1098.89 PASS AC=1;AF=0.609;AN=2;DP=2747;MQ=60;set=variant2-variant4-variant7-variant10-variant12-variant13-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant31-variant32-variant33-variant35-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,58:119:99:1478,0,1583:36,25,31,27 chr1 55474476 . C G 1204.74 PASS AC=1;AF=0.625;AN=2;DP=2785;MQ=60;set=variant2-variant4-variant7-variant9-variant10-variant12-variant13-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant31-variant32-variant33-variant35-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:78,52:130:99:1291,0,2038:35,43,26,26 chr1 55474679 . A G 881.2 PASS AC=1;AF=0.609;AN=2;DP=2123;MQ=60;set=variant2-variant4-variant7-variant10-variant12-variant13-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant31-variant32-variant33-variant35-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,43:93:99:1220,0,1350:25,25,18,25 chr1 55474772 . T C 821.13 PASS AC=1;AF=0.591;AN=2;DP=882;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant19-variant20-variant23-variant24-variant27-variant29-variant32-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:45,47:92:99:1122,0,1257:22,23,22,25 chr1 55474938 . G A 887.18 PASS AC=1;AF=0.609;AN=2;DP=2046;MQ=60;set=variant2-variant4-variant7-variant10-variant12-variant13-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant31-variant32-variant33-variant35-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,57:121:99:1242,0,1631:35,29,31,26 chr1 55475104 . A C 851.78 PASS AC=1;AF=0.609;AN=2;DP=1683;MQ=60;set=variant2-variant4-variant7-variant10-variant12-variant13-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant31-variant32-variant33-variant35-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,47:98:99:1227,0,1320:22,29,21,26 chr1 55475483 . A G 198.86 PASS AC=1;AF=0.656;AN=2;DP=137;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant10-variant12-variant13-variant19-variant21-variant23-variant24-variant26-variant27-variant29-variant33-variant35-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,6:13:99:184,0,197:2,5,3,3 chr1 55475888 . G A 361.44 PASS AC=1;AF=0.609;AN=2;DP=1240;MQ=60;set=variant2-variant4-variant7-variant10-variant12-variant13-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant31-variant32-variant33-variant35-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,36:62:99:956,0,681:14,12,20,16 chr1 55475966 . T C 633.12 PASS AC=1;AF=0.577;AN=2;DP=688;MQ=60;set=variant2-variant7-variant10-variant13-variant19-variant20-variant23-variant24-variant27-variant29-variant32-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:33,26:59:99:735,0,781:16,17,13,13 chr1 55476178 . A G 858.34 PASS AC=1;AF=0.63;AN=2;DP=1831;MQ=60;set=variant2-variant4-variant7-variant10-variant12-variant13-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant31-variant32-variant33-variant35-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,62:101:99:1531,0,995:19,20,31,31 chr1 55505224 . G A 1561.12 PASS AC=1;AF=0.5;AN=2;DP=267;FractionInformativeReads=1;MQ=60;set=variant29-variant35 GT:AD:DP:GQ:PL:SB 0/1:58,71:129:99:1701,0,1459:33,25,39,32 chr1 55505732 . A G 4357.89 PASS AC=2;AF=0.955;AN=2;DP=5856;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,144:144:99:4517,432,0:0,0,54,90 chr1 55516781 . G T 2367.12 PASS AC=2;AF=1;AN=2;DP=4447;FS=0;MQ=60;MQRankSum=-0.17;ReadPosRankSum=0.374;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,104:104:99:3043,311,0:0,0,59,45 chr1 55517861 . C G 729.13 PASS AC=2;AF=0.647;AN=2;DP=1983;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:1797,171,0:0,0,37,20 chr1 55517883 . C G 774.29 PASS AC=1;AF=0.586;AN=2;DP=2225;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant15-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,37:74:99:880,0,959:23,14,23,14 chr1 55517940 . G A 1521.29 PASS AC=1;AF=0.6;AN=2;DP=591;MQ=60;set=variant16-variant20-variant26-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:55,67:122:99:1493,0,1343:30,25,33,34 chr1 55518093 . G A 721.52 PASS AC=1;AF=0.6;AN=2;DP=304;FractionInformativeReads=1;MQ=60;set=variant16-variant20-variant26-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:55,27:82:99:612,0,1543:27,28,11,16 chr1 55518160 . C A 697.74 PASS AC=1;AF=0.583;AN=2;DP=328;FractionInformativeReads=1;MQ=60;set=variant10-variant16-variant20-variant26-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:36,23:59:99:714,0,1356:18,18,19,4 chr1 55518166 . G A 280.12 PASS AC=1;AF=0.659;AN=2;DP=2342;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,37:66:99:1110,0,1011:22,7,19,18 chr1 55518190 . AC A,ACC 1031.66 PASS AC=1,0;AF=0.722,0.042;AN=2;DP=2375;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant41-variant43-variant44 GT:DP:GQ:SB 0/1:75:99:27,12,22,14 chr1 55518287 . G A 1078.22 PASS AC=1;AF=0.6;AN=2;DP=595;MQ=60;set=variant16-variant20-variant26-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:71,72:143:99:1724,0,1823:41,30,39,33 chr1 55518467 . A G 842.49 PASS AC=1;AF=0.567;AN=2;DP=3167;set=variant-variant4-variant5-variant6-variant10-variant11-variant12-variant13-variant14-variant16-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:71,65:136:99:1577,0,1637:31,40,26,39 chr1 55518528 . C A 322.46 PASS AC=2;AF=0.738;AN=2;DP=2619;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,78:78:99:2170,231,0:0,0,32,46 chr1 55523033 . A G 1968.13 PASS AC=2;AF=1;AN=2;DP=4295;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,128:128:99:3935,382,0:0,0,59,69 chr1 55523984 . C T 88.67 PASS AC=2;AF=0.92;AN=2;DP=513;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:523,42,0:0,0,6,8 chr1 55524116 . C T 254.14 PASS AC=2;AF=0.92;AN=2;DP=1316;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:956,102,0:0,0,17,17 chr1 55524197 . A G 258.28 PASS AC=2;AF=0.92;AN=2;DP=1434;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:877,84,0:0,0,10,18 chr1 55524237 . G A 319.44 PASS AC=2;AF=0.92;AN=2;DP=1228;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:544,57,0:0,0,8,11 chr1 55525399 . C T 464.53 PASS AC=1;AF=0.583;AN=2;DP=208;FractionInformativeReads=1;MQ=60;set=variant10-variant13-variant16-variant20-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:17,16:33:99:406,0,654:6,11,7,9 chr1 55525400 . G A 707.07 PASS AC=1;AF=0.805;AN=2;DP=1456;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,16:32:99:396,0,624:7,9,6,10 chr1 55527323 . G A 1814.01 PASS AC=1;AF=0.805;AN=2;DP=2334;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,32:65:99:779,0,842:11,22,12,20 chr1 55527479 . A G 251.71 PASS AC=2;AF=0.92;AN=2;DP=393;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:177,12,0:0,0,2,2 chr1 55529187 . G A 1395.39 PASS AC=2;AF=0.932;AN=2;DP=5564;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,152:152:99:4627,454,0:0,0,68,84 chr1 55529828 . C T 1961.29 PASS AC=2;AF=0.845;AN=2;DP=3177;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,66:66:99:1969,197,0:0,0,34,32 chr1 55530627 . T G 4850.47 PASS AC=2;AF=1;AN=2;DP=4441;FS=0;MQ=60;MQRankSum=0.369;ReadPosRankSum=0.54;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,111:111:99:3770,332,0:0,0,31,80 chr1 55532742 . G C 1096.79 PASS AC=2;AF=0.886;AN=2;DP=3270;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:2407,211,0:0,0,34,37 chr1 55538385 . T C 644.36 PASS AC=2;AF=0.932;AN=2;DP=1719;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:939,87,0:0,0,21,8 chr1 55541174 . A G 2345.44 PASS AC=2;AF=0.857;AN=2;DP=3409;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,96:96:99:2900,288,0:0,0,43,53 chr1 55541338 . ACACCACCAC AACCACCAC,A 536.79 PASS AC=1,0;AF=0.775,0.088;AN=2;DP=553;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:24:18:0,2,5,17 chr1 55541340 . ACCACCACC A,AACCACC 121.03 PASS AC=1,0;AF=0.721,0.081;AN=2;DP=600;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:24:18:0,2,5,17 chr1 55545515 . C G 452.25 PASS AC=2;AF=0.886;AN=2;DP=1008;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:388,39,0:0,0,5,8 chr1 55546895 . T C 427.21 PASS AC=2;AF=0.869;AN=2;DP=525;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:567,39,0:0,0,13,0 chr1 55555285 . G A 328.53 PASS AC=2;AF=0.857;AN=2;DP=811;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:982,96,0:0,0,21,11 chr1 55557859 . A ATT 505.4 PASS AC=2;AF=0.932;AN=2;DP=1239;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:1059,72,0:0,0,4,20 chr1 55557864 . C T 1096.77 PASS AC=2;AF=0.857;AN=2;DP=1002;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:63:945,63,0:0,0,2,18 chr1 55558661 . A G 370.74 PASS AC=2;AF=0.875;AN=2;DP=390;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:266,18,0:0,0,0,6 chr1 55560796 . T C 227.17 PASS AC=2;AF=0.886;AN=2;DP=665;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:603,42,0:0,0,14,0 chr1 55562125 . G T 108.93 PASS AC=2;AF=0.951;AN=2;DP=330;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:325,36,0:0,0,7,5 chr1 55566411 . TTAGTC T 523.58 PASS AC=2;AF=0.875;AN=2;DP=765;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,27:27:82:1190,82,0:0,0,22,5 chr1 55567143 . T C 197.59 PASS AC=2;AF=0.932;AN=2;DP=718;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:544,51,0:0,0,12,5 chr1 55567410 . A G 1208.71 PASS AC=2;AF=0.932;AN=2;DP=4480;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,129:129:99:3962,387,0:0,0,52,77 chr1 55572867 . G A 2615.81 PASS AC=2;AF=0.857;AN=2;DP=3373;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,74:74:99:2457,222,0:0,0,51,23 chr1 55575670 . A C 362.08 PASS AC=2;AF=0.882;AN=2;DP=304;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:267,18,0:0,0,6,0 chr1 55614036 . CAT C 727.87 PASS AC=2;AF=0.893;AN=2;DP=538;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:630,42,0:0,0,13,1 chr1 55619422 . G A 148.54 PASS AC=2;AF=0.895;AN=2;DP=196;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:90,6,0:0,0,2,0 chr1 55638075 . G A 923.77 PASS AC=2;AF=0.932;AN=2;DP=3176;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,61:61:99:1945,183,0:0,0,39,22 chr1 55643837 . TA T 202.72 PASS AC=2;AF=0.932;AN=2;DP=1701;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1410,123,0:0,0,4,37 chr1 56961051 . G A 1175.47 PASS AC=2;AF=1;AN=2;DP=2790;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,67:67:99:2098,201,0:0,0,36,31 chr1 56961354 . T C 1382.1 PASS AC=2;AF=0.966;AN=2;DP=2715;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:2499,224,0:0,0,33,42 chr1 56961756 . A G 485.75 PASS AC=2;AF=0.743;AN=2;DP=1111;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1193,111,0:0,0,19,18 chr1 57111169 . C G 1756.07 PASS AC=1;AF=0.617;AN=2;DP=5049;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant26-variant27-variant29-variant34-variant35-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:135,80:215:99:1749,0,3475:58,77,37,43 chr1 57158293 . G A 241.76 PASS AC=1;AF=0.63;AN=2;DP=348;MQ=60;set=variant-variant4-variant5-variant6-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant22-variant23-variant26-variant27-variant29-variant34-variant35-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,5:11:99:185,0,185:1,5,0,5 chr1 57170229 . T C 197.93 PASS AC=1;AF=0.621;AN=2;DP=448;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant26-variant27-variant29-variant34-variant35-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,3:12:58:58,0,335:2,7,1,2 chr1 57175158 . A C 4232.46 PASS AC=1;AF=0.667;AN=2;DP=10443;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:157,125:282:99:3368,0,4121:78,79,64,61 chr1 57177789 . G A 4262.62 PASS AC=1;AF=0.652;AN=2;DP=10917;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:158,171:329:99:4493,0,4245:74,84,88,83 chr1 57178492 . G T 259.55 PASS AC=1;AF=0.5;AN=2;DP=27;FS=0;FractionInformativeReads=1;MQ=60;set=variant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:1,8:9:19:203,0,19:1,0,4,4 chr1 57179397 . AT A 1791.94 PASS AC=1;AF=0.567;AN=2;DP=2495;MQ=60;set=variant-variant7-variant9-variant11-variant13-variant17-variant21-variant25-variant26-variant29-variant32-variant34-variant35-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,50:118:99:1140,0,1611:31,37,24,26 chr1 57179521 . TAA TA,TAAA,T,TAAAA 254.71 PASS AC=1,0,0,0;AF=0.235,0.235,0.044,0.029;AN=2;DP=2341;set=variant-variant2-filterInvariant3-variant6-variant8-variant10-filterInvariant11-variant13-variant14-variant16-variant18-variant20-variant22-variant23-variant24-variant25-variant26-filterInvariant27-variant28-variant29-variant30-filterInvariant31-filterInvariant32-variant34-variant35-variant36-filterInvariant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:37:99:10,8,10,9 chr1 57180699 . GA G 1841.58 PASS AC=1;AF=0.519;AN=2;DP=3193;MQ=60;set=variant-variant5-variant7-variant8-variant9-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant24-variant25-variant26-variant30-variant31-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:63,48:111:99:1102,0,1481:38,25,30,18 chr1 57180867 . A G 6439.51 PASS AC=1;AF=0.721;AN=2;DP=7202;MQ=60;set=variant-variant5-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:100,90:190:99:2331,0,2478:47,53,48,42 chr1 57184465 . T G 1424.56 PASS AC=1;AF=0.833;AN=2;DP=1989;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,22:33:99:540,0,270:6,5,10,12 chr1 57185818 . A G 3411.71 PASS AC=1;AF=0.857;AN=2;DP=3747;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,46:75:99:1147,0,636:15,14,28,18 chr1 57257668 . C A 192.91 PASS AC=1;AF=0.591;AN=2;DP=122;FractionInformativeReads=1;MQ=60;set=variant6-variant10-variant19-variant22-variant25-variant26-variant27-variant28-variant31-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:5,8:13:99:256,0,182:5,0,7,1 chr1 57395251 . T C 3207.21 PASS AC=2;AF=0.875;AN=2;DP=4262;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,88:88:99:2703,264,0:0,0,42,46 chr1 57395434 . C G 109.85 PASS AC=2;AF=0.6;AN=2;DP=134;FractionInformativeReads=1;MQ=60;set=variant4-variant8-variant9-variant13-variant16-variant21-variant25-variant35-variant36-variant39 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:556,42,0:0,0,2,12 chr1 57406392 . T C 467.92 PASS AC=2;AF=0.671;AN=2;DP=1137;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:816,72,0:0,0,18,6 chr1 57422484 . C T 6742.71 PASS AC=2;AF=0.932;AN=2;DP=9498;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,246:246:99:7247,737,0:0,0,126,120 chr1 57431629 . A G 876.46 PASS AC=1;AF=0.5;AN=2;DP=246;FractionInformativeReads=1;MQ=60;set=variant13-variant19-variant25-variant35 GT:AD:DP:GQ:PL:SB 0/1:42,33:75:99:1003,0,1041:15,27,13,20 chr1 57476377 . G A 1459.42 PASS AC=1;AF=0.5;AN=2;DP=108;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.819;QD=13.51;ReadPosRankSum=0.139;SOR=0.632;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:48,60:108:99:1488,0,1202:20,28,26,34 chr1 57498844 . T TAC,TACAC,TACACAC 539.35 PASS AC=0,1,0;AF=0.029,0.618,0.029;AN=2;DP=460;set=variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant38-variant39-variant40-variant41-variant42-variant44 GT:DP:GQ:SB 0/2:18:99:6,1,9,2 chr1 57528772 . A G 309.11 PASS AC=2;AF=0.898;AN=2;DP=1352;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1448,120,0:0,0,10,30 chr1 57537062 . G A 339.13 PASS AC=1;AF=0.625;AN=2;DP=583;MQ=60;set=variant-variant2-variant6-variant7-variant9-variant12-variant13-variant15-variant16-variant17-variant18-variant22-variant25-variant27-variant29-variant30-variant31-variant35-variant36-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,11:22:99:382,0,327:9,2,9,2 chr1 57602334 . G A 2662.86 PASS AC=1;AF=0.538;AN=2;DP=1623;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant8-variant16-variant19-variant24-variant25-variant27-variant28-variant35-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:58,47:105:99:1114,0,1480:31,27,23,24 chr1 57602383 . T C 2013.42 PASS AC=1;AF=0.531;AN=2;DP=1463;MQ=60;set=variant-variant2-variant4-variant8-variant13-variant16-variant19-variant24-variant25-variant27-variant28-variant33-variant35-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:48,33:81:99:849,0,1300:20,28,12,21 chr1 57889822 . C T 137.97 PASS AC=2;AF=0.917;AN=2;DP=45;FS=0;MQ=60;MQRankSum=0.731;ReadPosRankSum=0.731;set=variant-variant3-variant5-variant11-variant35-variant38 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:175,21,0:0,0,3,4 chr1 57889896 . C T 52.74 PASS AC=1;AF=0.583;AN=2;DP=263;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant11-variant13-variant19-variant28-variant35-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,12:28:99:327,0,379:10,6,8,4 chr1 58939335 . C T 354.65 PASS AC=2;AF=1;AN=2;DP=424;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:273,21,0:0,0,7,0 chr1 58996203 . T C 366.03 PASS AC=1;AF=0.536;AN=2;DP=472;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant9-variant20-variant24-variant27-variant28-variant29-variant30-variant35-variant36-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:18,11:29:99:277,0,474:12,6,8,3 chr1 59004979 . C T 3756.04 PASS AC=2;AF=1;AN=2;DP=5386;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,128:128:99:3935,383,0:0,0,53,75 chr1 59012404 . A C 3266.3 PASS AC=2;AF=0.829;AN=2;DP=5296;MQ=60;set=variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,136:136:99:4153,407,0:0,0,75,61 chr1 59012431 . C T 2823.41 PASS AC=2;AF=0.829;AN=2;DP=5172;MQ=60;set=variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,138:138:99:4022,412,0:0,0,73,65 chr1 59042001 . G A 4349.43 PASS AC=1;AF=0.5;AN=2;DP=2959;MQ=60;set=variant9-variant20-variant24-variant27-variant28-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:221,271:492:99:6802,0,5333:129,92,147,124 chr1 59120399 . T G 259.35 PASS AC=1;AF=0.721;AN=2;DP=703;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,6:15:99:168,0,269:7,2,5,1 chr1 59120563 . A G 942.52 PASS AC=1;AF=0.577;AN=2;DP=834;FractionInformativeReads=1;MQ=60;set=variant2-variant10-variant16-variant18-variant19-variant22-variant23-variant33-variant34-variant35-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,25:46:99:803,0,585:11,10,15,10 chr1 59120579 . G A 828.29 PASS AC=2;AF=0.905;AN=2;DP=3178;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1765,129,0:0,0,26,17 chr1 59120589 . C T 946.76 PASS AC=1;AF=0.577;AN=2;DP=852;MQ=60;set=variant2-variant10-variant16-variant18-variant19-variant22-variant23-variant33-variant34-variant35-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,20:45:99:661,0,743:15,10,13,7 chr1 59120650 . C T 729.44 PASS AC=2;AF=0.905;AN=2;DP=3805;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:2370,225,0:0,0,41,34 chr1 59120961 . G A 2837.18 PASS AC=1;AF=0.577;AN=2;DP=2925;MQ=60;set=variant2-variant10-variant16-variant18-variant19-variant22-variant23-variant33-variant34-variant35-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:120,115:235:99:2914,0,2911:70,50,72,43 chr1 59120990 . AT A 2841.68 PASS AC=2;AF=0.905;AN=2;DP=11717;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,278:278:99:8562,835,0:0,0,153,125 chr1 59121144 . A AT 3652.26 PASS AC=1;AF=0.577;AN=2;DP=2228;MQ=60;set=variant2-variant10-variant16-variant18-variant19-variant22-variant23-variant33-variant34-variant35-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:72,71:143:99:1773,0,1777:28,44,29,42 chr1 59121166 . G A 3402.31 PASS AC=1;AF=0.577;AN=2;DP=1823;MQ=60;set=variant2-variant10-variant16-variant18-variant19-variant22-variant23-variant33-variant34-variant35-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,65:126:99:1717,0,1655:22,39,27,38 chr1 59121343 . T A 911.11 PASS AC=1;AF=0.577;AN=2;DP=1328;FractionInformativeReads=1;MQ=60;set=variant2-variant10-variant16-variant18-variant19-variant22-variant23-variant33-variant34-variant35-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,45:87:99:1094,0,932:20,22,27,18 chr1 59121768 . G C 815.07 PASS AC=1;AF=0.577;AN=2;DP=793;MQ=60;set=variant2-variant10-variant16-variant18-variant19-variant22-variant23-variant33-variant34-variant35-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,40:85:99:1049,0,1155:16,29,14,26 chr1 59122289 . T G 3457.18 PASS AC=1;AF=0.577;AN=2;DP=3464;MQ=60;set=variant2-variant10-variant16-variant18-variant19-variant22-variant23-variant33-variant34-variant35-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:114,125:239:99:3122,0,2807:52,62,56,69 chr1 59122871 . C T 2293.81 PASS AC=1;AF=0.714;AN=2;DP=5103;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:75,75:150:99:1944,0,1863:34,41,35,40 chr1 59122910 . G GA,GAA 1446.39 PASS AC=2,0;AF=0.881,0.012;AN=2;DP=5407;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:111:99:1,2,48,60 chr1 59123655 . C T 4631.81 PASS AC=1;AF=0.619;AN=2;DP=7421;MQ=60;set=variant2-variant3-variant4-variant5-variant8-variant9-variant11-variant12-variant13-variant18-variant21-variant27-variant28-variant30-variant32-variant33-variant35-variant36-variant37-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:175,153:328:99:3829,0,4628:72,103,66,87 chr1 59124546 . A G 1741.88 PASS AC=1;AF=0.714;AN=2;DP=3854;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,64:116:99:1655,0,1231:26,26,29,35 chr1 59124630 . AACAC A,AACACACACACACAC,AACACACACACACACAC,AACACACACACAC,AACACACACAC,AACACACACACACACACAC,AACACACACACACACACACAC,AAC 3716.07 PASS AC=0,0,2,0,0,0,0,0;AF=0.125,0.295,0.352,0.114,0.023,0.057,0.011,0.011;AN=2;DP=3883;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-filterInvariant41-variant42-variant43-variant44 GT:DP:GQ:SB 3/3:46:99:0,0,26,20 chr1 59124803 . C T 5764.57 PASS AC=1;AF=0.714;AN=2;DP=9638;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:122,137:259:99:3376,0,2897:61,61,67,70 chr1 59125683 . C T 1049.05 PASS AC=1;AF=0.577;AN=2;DP=1010;FractionInformativeReads=1;MQ=60;set=variant2-variant10-variant16-variant18-variant19-variant22-variant23-variant33-variant34-variant35-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,45:89:99:1187,0,1065:21,23,23,22 chr1 59126676 . A C 37.49 PASS AC=2;AF=0.915;AN=2;DP=542;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:398,30,0:0,0,8,2 chr1 59127086 . G A 1121.15 PASS AC=1;AF=0.619;AN=2;DP=2150;set=variant2-variant3-variant4-variant5-variant8-variant9-variant11-variant12-variant13-variant18-variant21-variant27-variant28-variant30-variant32-variant33-variant35-variant36-variant37-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,38:88:99:838,0,1312:23,27,18,20 chr1 59127193 . C T 234.1 PASS AC=1;AF=0.619;AN=2;DP=786;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant8-variant9-variant11-variant12-variant13-variant18-variant21-variant27-variant28-variant30-variant32-variant33-variant35-variant36-variant37-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,19:37:99:538,0,512:6,12,5,14 chr1 59127207 . T C 578.94 PASS AC=1;AF=0.577;AN=2;DP=374;MQ=60;set=variant2-variant10-variant16-variant18-variant19-variant22-variant23-variant33-variant34-variant35-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,15:31:99:452,0,461:4,12,3,12 chr1 59131088 . A G 518.61 PASS AC=1;AF=0.577;AN=2;DP=455;FractionInformativeReads=1;MQ=60;set=variant2-variant10-variant16-variant18-variant19-variant22-variant23-variant33-variant34-variant35-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,22:39:99:873,0,929:13,4,18,4 chr1 59131089 . A C 518.61 PASS AC=1;AF=0.577;AN=2;DP=464;FractionInformativeReads=1;MQ=60;set=variant2-variant10-variant16-variant18-variant19-variant22-variant23-variant33-variant34-variant35-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,22:39:99:873,0,929:13,4,18,4 chr1 59131311 . G T 975.44 PASS AC=2;AF=0.905;AN=2;DP=2881;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:2391,226,0:0,0,22,54 chr1 59133024 . T G 64.09 PASS AC=1;AF=0.636;AN=2;DP=96;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant10-variant16-variant18-variant19-variant23-variant33-variant34-variant35-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:99:141,0,155:0,4,0,4 chr1 59134607 . C CAG,CA 5443.28 PASS AC=2,0;AF=0.989,0.011;AN=2;DP=4688;FS=0;MQ=60;MQRankSum=-0.485;ReadPosRankSum=1.538;set=Intersection GT:DP:GQ:SB 1/1:92:99:0,0,45,47 chr1 59134615 . C T 668.85 PASS AC=1;AF=0.5;AN=2;DP=92;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.836;QD=7.27;ReadPosRankSum=-0.169;SOR=0.647;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:57,35:92:99:697,0,1434:27,30,17,18 chr1 59137783 . A G 502.75 PASS AC=1;AF=0.721;AN=2;DP=752;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,19:30:99:605,0,316:2,9,3,16 chr1 59139223 . C G 1060.92 PASS AC=1;AF=0.714;AN=2;DP=3019;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,36:97:99:904,0,1584:36,25,24,12 chr1 59142713 . T C 1606.56 PASS AC=1;AF=0.714;AN=2;DP=4006;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,52:95:99:1316,0,1010:17,26,20,32 chr1 59147420 . G A 365.29 PASS AC=1;AF=0.721;AN=2;DP=844;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,10:23:99:293,0,345:8,5,8,2 chr1 59147926 . T C 1272.13 PASS AC=1;AF=0.714;AN=2;DP=2705;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,41:77:99:1124,0,1120:22,14,24,17 chr1 59148118 . A T 2128.57 PASS AC=1;AF=0.591;AN=2;DP=2180;FractionInformativeReads=1;MQ=60;set=variant10-variant16-variant18-variant22-variant23-variant33-variant34-variant35-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:116,121:237:99:2849,0,2712:52,64,57,64 chr1 59150941 . G A 442.12 PASS AC=2;AF=0.905;AN=2;DP=1534;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1387,147,0:0,0,22,27 chr1 59150997 . TA T 48.61 PASS AC=1;AF=0.786;AN=2;DP=437;MQ=60;set=variant-variant3-variant5-variant6-variant10-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant34-variant35-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,8:18:99:159,0,194:2,8,1,7 chr1 59156155 . C T 397.55 PASS AC=1;AF=0.714;AN=2;DP=1115;FractionInformativeReads=1;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,12:34:99:282,0,546:9,13,5,7 chr1 59158632 . T C 904.75 PASS AC=1;AF=0.714;AN=2;DP=1697;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,19:40:99:481,0,524:7,14,6,13 chr1 59160724 . TA T 74.38 PASS AC=1;AF=0.712;AN=2;DP=580;MQ=60;set=variant-variant2-variant3-filterInvariant5-variant6-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,4:11:74:74,0,246:6,1,4,0 chr1 59160735 . A G 845.15 PASS AC=1;AF=0.655;AN=2;DP=640;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant18-variant21-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,7:12:99:213,0,138:4,1,6,1 chr1 59160885 . A G 1024.45 PASS AC=1;AF=0.655;AN=2;DP=1733;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant18-variant21-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,37:66:99:845,0,568:13,16,18,19 chr1 59160982 . ATACT A 400.6 PASS AC=1;AF=0.655;AN=2;DP=640;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant18-variant21-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,12:21:99:477,0,525:4,5,4,8 chr1 59247313 . T C 31.99 PASS AC=1;AF=0.5;AN=2;DP=535;MQ=60;set=filterInvariant5-filterInvariant7-filterInvariant10-filterInvariant15-variant18-filterInvariant20-filterInvariant22-filterInvariant24-filterInvariant29-filterInvariant35-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,18:48:99:450,0,4349:1,29,18,0 chr1 59247318 . A C 41.05 PASS AC=1;AF=0.5;AN=2;DP=263;MQ=60;set=filterInvariant18-variant20-filterInvariant24-filterInvariant29-filterInvariant35-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,14:44:99:437,0,4589:1,29,14,0 chr1 59247323 . T C 79.92 PASS AC=1;AF=0.5;AN=2;DP=133;MQ=60;set=variant20-filterInvariant24-filterInvariant35 GT:AD:DP:GQ:PL:SB 0/1:34,12:46:99:368,0,4878:5,29,12,0 chr1 59247330 . G C 157.71 PASS AC=1;AF=0.5;AN=2;DP=96;MQ=60;set=variant24-variant35 GT:AD:DP:GQ:PL:SB 0/1:38,11:49:99:337,0,5085:9,29,11,0 chr1 59247332 . T C 280.43 PASS AC=1;AF=0.5;AN=2;DP=47;FS=38.565;FractionInformativeReads=1;MQ=60;MQRankSum=-2.59;QD=5.97;ReadPosRankSum=-3.411;SOR=4.396;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:39,8:47:99:309,0,5006:10,29,8,0 chr1 59247333 . T C 254.83 PASS AC=1;AF=0.5;AN=2;DP=47;FS=31.274;FractionInformativeReads=1;MQ=60;MQRankSum=-0.239;QD=5.42;ReadPosRankSum=-2.885;SOR=3.894;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:41,6:47:99:283,0,5009:10,31,6,0 chr1 59248813 . G C 4705.36 PASS AC=2;AF=1;AN=2;DP=6786;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,135:136:99:4568,397,0:0,1,36,99 chr1 59249031 . T G 2145.5 PASS AC=2;AF=1;AN=2;DP=3077;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,68:69:99:1984,196,0:1,0,29,39 chr1 59249347 . G C 2252.33 PASS AC=2;AF=1;AN=2;DP=4282;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,119:119:99:3621,357,0:0,0,61,58 chr1 59762955 . C T 280.12 PASS AC=1;AF=0.594;AN=2;DP=222;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant7-variant11-variant12-variant19-variant27-variant30-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,7:13:99:273,0,235:1,5,0,7 chr1 59787350 . T G 359.33 PASS AC=1;AF=0.591;AN=2;DP=1121;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant9-variant11-variant12-variant19-variant27-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:36,25:61:99:563,0,878:13,23,11,14 chr1 59844471 . G A 1291.4 PASS AC=1;AF=0.577;AN=2;DP=2625;MQ=60;set=variant2-variant4-variant6-variant7-variant9-variant11-variant12-variant19-variant23-variant24-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,40:69:99:960,0,770:19,10,21,19 chr1 60199133 . G GTTTT 291.73 PASS AC=1;AF=0.62;AN=2;DP=393;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant11-variant13-variant14-variant15-variant16-variant19-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant32-variant34-variant35-variant36-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:10,10:20:99:285,0,320:3,7,4,6 chr1 60199134 . T TTTTG 183.66 PASS AC=1;AF=0.5;AN=2;DP=51;FS=0;MQ=60;set=variant33-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:10,9:19:99:263,0,338:4,6,3,6 chr1 60199154 . T C 175.05 PASS AC=1;AF=0.5;AN=2;DP=12;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.259;QD=14.59;ReadPosRankSum=1.191;SOR=1.329;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:6,6:12:99:203,0,234:3,3,2,4 chr1 60228310 . T TTC 1947.29 PASS AC=2;AF=0.795;AN=2;DP=6509;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,153:153:99:6938,466,0:0,0,87,66 chr1 60228548 . CT CTT,C,CTTT,CTTTT 61.5 PASS AC=0,1,0,0;AF=0.08,0.18,0.26,0.02;AN=2;DP=1559;set=filterInvariant-variant5-variant6-filterInvariant7-variant9-filterInvariant10-filterInvariant14-filterInvariant16-filterInvariant18-variant19-variant20-filterInvariant21-variant25-variant26-variant28-filterInvariant33-variant34-filterInvariant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:DP:GQ:SB 0/2:39:99:5,19,2,13 chr1 60280749 . GT G 12087.5 PASS AC=2;AF=1;AN=2;DP=15049;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,362:362:99:14632,1090,0:0,0,194,168 chr1 60299820 . C G,A 2042.14 PASS AC=2,0;AF=0.898,0.023;AN=2;DP=3655;MQ=60;set=Intersection GT:DP:GQ:SB 1/1:98:99:0,0,51,47 chr1 60373775 . T C 511.77 PASS AC=1;AF=0.657;AN=2;DP=355;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:2,6:8:52:195,0,52:0,2,1,5 chr1 60466814 . T C 791.79 PASS AC=2;AF=0.707;AN=2;DP=1753;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant30-variant33-variant34-variant35-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:2262,212,0:0,0,42,29 chr1 60466911 . ACAG A 925.35 PASS AC=1;AF=0.726;AN=2;DP=3845;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,44:91:99:1704,0,1940:20,27,21,23 chr1 60475930 . C G 363.78 PASS AC=2;AF=0.779;AN=2;DP=2666;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:1673,162,0:0,0,36,18 chr1 60505578 . A G 480.75 PASS AC=2;AF=0.909;AN=2;DP=992;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:763,72,0:0,0,15,9 chr1 61331160 . CTT CTTT,CT,C,CTTTT,CTTTTT 51.45 PASS AC=0,0,0,0,1;AF=0.125,0.125,0.042,0.125,0.104;AN=2;DP=1123;MQ=60;set=filterInvariant-filterInvariant2-variant3-filterInvariant7-filterInvariant8-filterInvariant10-variant11-filterInvariant12-variant17-filterInvariant20-variant21-variant22-filterInvariant23-variant24-variant25-filterInvariant29-filterInvariant31-filterInvariant32-variant34-variant35-variant38-variant42-variant43-variant44 GT:DP:GQ:SB 0/5:23:99:3,9,2,9 chr1 61542892 . A G 254.14 PASS AC=2;AF=1;AN=2;DP=1193;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:861,78,0:0,0,16,10 chr1 61548344 . TTCTC TTCTCTC,TTC,T 684.58 PASS AC=0,1,0;AF=0.167,0.25,0.083;AN=2;DP=356;MQ=60;set=variant20-filterInvariant35-filterInvariant36-variant41-filterInvariant43-variant44 GT:DP:GQ:SB 0/2:53:99:20,25,3,5 chr1 61743160 . G A 3298.98 PASS AC=1;AF=0.576;AN=2;DP=4028;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:56,52:108:99:1399,0,1263:29,27,27,25 chr1 61818422 . A G 384.2 PASS AC=1;AF=0.878;AN=2;DP=510;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,11:12:8:446,0,8:1,0,0,11 chr1 61818428 . TACACACAC T,TACACACACACAC,TACACAC,TACACACACAC,TACACACACACACAC,TACAC 375.77 PASS AC=0,0,2,0,0,0;AF=0.056,0.236,0.306,0.292,0.014,0.014;AN=2;DP=398;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant19-variant20-variant21-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 3/3:10:28:0,0,0,10 chr1 61869783 . G A 2951.53 PASS AC=2;AF=0.583;AN=2;DP=5134;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant16-variant21-variant23-variant26-variant27-variant34-variant35-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,213:213:99:6687,638,0:0,0,129,84 chr1 61892301 . T TG 3478.93 PASS AC=2;AF=1;AN=2;DP=4530;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,100:100:99:3689,301,0:0,0,40,60 chr1 61921185 . AT ATT,A 3119.62 PASS AC=1,0;AF=0.5,0.012;AN=2;DP=7615;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-filterInvariant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:183:99:17,19,75,72 chr1 61922046 . T TA,TAA 1569.72 PASS AC=1,1;AF=0.7,0.038;AN=2;DP=2977;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/2:53:99:2,2,29,20 chr1 61924359 . CTTT CTT,CTTTT,CT,C 509.74 PASS AC=0,1,0,0;AF=0.273,0.152,0.03,0.076;AN=2;DP=4041;set=variant-filterInvariant2-variant3-filterInvariant4-filterInvariant5-filterInvariant6-variant7-filterInvariant8-variant11-variant13-variant14-variant18-variant19-variant20-variant21-variant22-filterInvariant23-filterInvariant24-variant25-filterInvariant28-filterInvariant29-filterInvariant32-filterInvariant33-filterInvariant34-variant35-variant36-variant37-filterInvariant38-variant39-filterInvariant40-variant41-variant43-filterInvariant44 GT:DP:GQ:SB 0/2:70:99:9,36,12,13 chr1 61927876 . G A 545.49 PASS AC=2;AF=0.821;AN=2;DP=2011;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1459,152,0:0,0,30,21 chr1 62160542 . A G 406.49 PASS AC=2;AF=0.929;AN=2;DP=453;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:473,36,0:0,0,1,11 chr1 62189541 . T C 803.91 PASS AC=1;AF=0.559;AN=2;DP=659;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant12-variant16-variant17-variant18-variant20-variant21-variant24-variant29-variant32-variant35-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,13:22:99:429,0,311:0,9,5,8 chr1 62208273 . T G 790.96 PASS AC=2;AF=1;AN=2;DP=2126;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1491,147,0:0,0,21,28 chr1 62208337 . G A 312.4 PASS AC=1;AF=0.756;AN=2;DP=900;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,12:22:99:239,0,288:2,8,4,8 chr1 62231924 . T TTGA 403.5 PASS AC=1;AF=0.671;AN=2;DP=632;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,5:6:33:228,0,33:1,0,3,2 chr1 62232031 . C T 2978.92 PASS AC=2;AF=0.943;AN=2;DP=3967;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,74:74:99:2034,221,0:0,0,41,33 chr1 62232173 . T C 828.33 PASS AC=1;AF=0.5;AN=2;DP=373;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant7-variant21-variant32-variant35-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,17:43:99:385,0,653:9,17,7,10 chr1 62257036 . A C 884.03 PASS AC=1;AF=0.545;AN=2;DP=1026;MQ=60;set=variant-variant4-variant7-variant10-variant11-variant13-variant15-variant20-variant21-variant23-variant35 GT:AD:DP:GQ:PL:SB 0/1:41,58:99:99:1341,0,995:19,22,25,33 chr1 62261168 . A G 1975.37 PASS AC=1;AF=0.606;AN=2;DP=6071;set=variant-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:124,76:200:99:1638,0,3071:58,66,35,41 chr1 62263307 . G A 58.2 PASS AC=1;AF=0.597;AN=2;DP=325;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,3:8:99:104,0,201:1,4,1,2 chr1 62267321 . C T 211.71 PASS AC=1;AF=0.5;AN=2;DP=28;FS=1.631;FractionInformativeReads=1;MQ=60;MQRankSum=-1.033;QD=7.56;ReadPosRankSum=-1.23;SOR=1.262;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:19,9:28:99:240,0,407:10,9,6,3 chr1 62330080 . T G 2878.81 PASS AC=2;AF=1;AN=2;DP=4416;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,96:96:99:2963,288,0:0,0,52,44 chr1 62340855 . G C 569.01 PASS AC=1;AF=0.596;AN=2;DP=819;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant10-variant14-variant15-variant17-variant18-variant19-variant24-variant25-variant26-variant27-variant29-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,14:34:99:393,0,591:15,5,11,3 chr1 62341157 . T C 570.04 PASS AC=2;AF=0.805;AN=2;DP=483;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:344,24,0:0,0,0,8 chr1 62350123 . GTTTTTT G,GT,GTTT,GTT,GTTTT 1230.72 PASS AC=0,1,0,0,0;AF=0.256,0.436,0.077,0.051,0.051;AN=2;DP=2005;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:38:90:3,4,5,26 chr1 62365217 . C T 1300.29 PASS AC=1;AF=0.711;AN=2;DP=1904;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,27:50:99:641,0,520:15,8,18,9 chr1 62365428 . G GA 532.82 PASS AC=1;AF=0.632;AN=2;DP=924;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,13:22:99:385,0,255:1,8,2,11 chr1 62374267 . T C 361.25 PASS AC=1;AF=0.769;AN=2;DP=411;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,7:10:53:269,0,53:0,3,0,7 chr1 62380124 . A G 631.18 PASS AC=2;AF=0.692;AN=2;DP=1169;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1369,117,0:0,0,30,9 chr1 62380270 . C T 3038.52 PASS AC=1;AF=0.78;AN=2;DP=5107;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,72:127:99:1794,0,1234:23,32,30,42 chr1 62380298 . G A 2452.33 PASS AC=1;AF=0.667;AN=2;DP=4112;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,64:112:99:1701,0,1159:17,31,25,39 chr1 62393394 . A G 4608.49 PASS AC=1;AF=0.869;AN=2;DP=6478;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:117,81:198:99:1754,0,2584:59,58,42,39 chr1 62417951 . A AG 508.43 PASS AC=1;AF=0.857;AN=2;DP=1862;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,9:31:99:224,0,1492:16,6,6,3 chr1 62417952 . A AGAGAGAG,AG,AGAGAGAGAG,AGAGAGAGAGAGAG,AGAGAGAGAGAGAGAGAGAG,AGAGAG,AGAGAGAGAGAGAGAGAG,AGAGAGAGAGAG 476.85 PASS AC=0,0,0,1,0,0,0,0;AF=0.155,0.226,0.333,0.071,0.012,0.012,0.036,0.024;AN=2;DP=1865;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/4:31:99:16,6,6,3 chr1 62545085 . C T 524.71 PASS AC=1;AF=0.646;AN=2;DP=810;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant17-variant20-variant22-variant25-variant26-variant27-variant28-variant29-variant31-variant35-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,19:34:99:567,0,444:12,3,14,5 chr1 62579523 . C T 250.68 PASS AC=2;AF=0.811;AN=2;DP=371;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:463,39,0:0,0,10,3 chr1 62579672 . A C 1003.74 PASS AC=2;AF=0.829;AN=2;DP=1746;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1405,135,0:0,0,23,22 chr1 62579823 . G A 930.69 PASS AC=2;AF=0.795;AN=2;DP=3625;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,87:87:99:2525,261,0:0,0,44,43 chr1 62587014 . T TA,TAAA,TAAAA,TAA 1025.01 PASS AC=2,0,0,0;AF=0.659,0.098,0.049,0.024;AN=2;DP=2811;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:45:99:1,0,11,33 chr1 62593893 . T C 118.67 PASS AC=2;AF=0.73;AN=2;DP=547;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:353,30,0:0,0,2,8 chr1 62594593 . C T 1330.63 PASS AC=2;AF=0.703;AN=2;DP=4126;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,89:89:99:2795,267,0:0,0,43,46 chr1 62594677 . T C 1040.71 PASS AC=1;AF=0.673;AN=2;DP=2038;MQ=60;set=variant-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant17-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant35-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,39:71:99:836,0,812:10,22,16,23 chr1 62614164 . G A 783.07 PASS AC=1;AF=0.5;AN=2;DP=618;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant10-variant15-variant19-variant20-variant24-variant27-variant28-variant33-variant34-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,9:31:99:187,0,633:7,15,3,6 chr1 62627675 . G A 4985.31 PASS AC=2;AF=0.718;AN=2;DP=14032;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,373:373:99:12112,1117,0:0,0,185,188 chr1 62644118 . A G 604.98 PASS AC=1;AF=0.744;AN=2;DP=1602;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,22:36:99:723,0,322:5,9,3,19 chr1 62660523 . T A 1326.99 PASS AC=1;AF=0.553;AN=2;DP=1860;MQ=60;set=variant3-variant4-variant8-variant10-variant11-variant12-variant16-variant18-variant22-variant23-variant25-variant26-variant28-variant30-variant31-variant32-variant35-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,50:85:99:1353,0,692:19,16,28,22 chr1 62660669 . G C 352.26 PASS AC=2;AF=0.757;AN=2;DP=1051;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1128,110,0:0,0,12,25 chr1 62662156 . G C 1385.52 PASS AC=1;AF=0.567;AN=2;DP=754;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant7-variant9-variant13-variant17-variant24-variant25-variant33-variant35-variant36-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:23,37:60:99:918,0,587:11,12,17,20 chr1 62672041 . A ATTT 67.58 PASS AC=2;AF=0.726;AN=2;DP=340;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant31-variant32-variant33-variant35-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:48:694,48,0:0,0,12,3 chr1 62672546 . G A 2617.26 PASS AC=2;AF=0.886;AN=2;DP=2267;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:1660,144,0:0,0,20,28 chr1 62673037 . T C 810.32 PASS AC=2;AF=0.722;AN=2;DP=2497;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,86:86:99:2757,258,0:0,0,45,41 chr1 62673225 . G A 806.13 PASS AC=2;AF=0.722;AN=2;DP=2339;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-filterInvariant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:1920,186,0:0,0,28,34 chr1 62673287 . A C 1089.31 PASS AC=1;AF=0.591;AN=2;DP=444;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant7-variant9-variant13-variant25-variant33-variant35-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:18,14:32:99:328,0,387:8,10,4,10 chr1 62675261 . G A 933.49 PASS AC=2;AF=0.66;AN=2;DP=697;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant16-variant18-variant22-variant23-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant35-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:688,69,0:0,0,14,9 chr1 62675619 . C T 1758.46 PASS AC=2;AF=0.643;AN=2;DP=1299;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant16-variant17-variant18-variant22-variant23-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1614,146,0:0,0,25,24 chr1 62675892 . A G 420.98 PASS AC=2;AF=0.729;AN=2;DP=2797;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,91:91:99:2655,273,0:0,0,40,51 chr1 62676284 . C T 1180.34 PASS AC=1;AF=0.556;AN=2;DP=1491;MQ=60;set=variant3-variant4-variant8-variant11-variant12-variant16-variant18-variant22-variant23-variant25-variant26-variant28-variant30-variant31-variant32-variant35-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,59:93:99:1494,0,762:18,16,31,28 chr1 62676612 . A G 1392.78 PASS AC=1;AF=0.594;AN=2;DP=1613;FractionInformativeReads=1;set=variant-variant2-variant3-variant5-variant7-variant9-variant13-variant17-variant25-variant33-variant35-variant36-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:54,51:105:99:1378,0,1318:25,29,28,23 chr1 62677048 . G T 2298.47 PASS AC=2;AF=0.65;AN=2;DP=2878;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant16-variant17-variant18-variant22-variant23-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,96:96:99:3815,296,0:0,0,51,45 chr1 62677050 . C T 2298.47 PASS AC=1;AF=0.571;AN=2;DP=1358;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant9-variant13-variant25-variant33-variant35-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:45,57:102:99:1513,0,1157:24,21,31,26 chr1 62677118 . A G 1732.47 PASS AC=1;AF=0.594;AN=2;DP=1994;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant9-variant13-variant17-variant25-variant33-variant35-variant36-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:54,77:131:99:2079,0,1215:26,28,41,36 chr1 62677366 . G A 130.7 PASS AC=1;AF=0.594;AN=2;DP=201;FractionInformativeReads=1;set=variant-variant2-variant3-variant5-variant7-variant9-variant13-variant17-variant25-variant33-variant35-variant36-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,7:15:99:226,0,195:4,4,2,5 chr1 62677568 . C T 157.45 PASS AC=1;AF=0.722;AN=2;DP=78;FractionInformativeReads=1;set=variant2-variant9-variant13-variant20-variant21-variant25-variant30-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:3,8:11:86:187,0,86:3,0,4,4 chr1 62677845 . C A 447.54 PASS AC=1;AF=0.556;AN=2;DP=398;MQ=60;set=variant3-variant4-variant8-variant11-variant12-variant16-variant18-variant22-variant23-variant25-variant26-variant28-variant30-variant31-variant32-variant35-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,5:20:99:153,0,533:12,3,4,1 chr1 62702637 . C T 111.22 PASS AC=2;AF=0.988;AN=2;DP=368;FractionInformativeReads=1;MQ=60;MQRankSum=-1.733;ReadPosRankSum=-0.533;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:427,42,0:0,0,8,6 chr1 62702720 . T C 51.2 PASS AC=1;AF=0.571;AN=2;DP=278;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant13-variant20-variant21-variant22-variant30-variant31-variant33-variant35-variant37-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,10:15:99:240,0,118:2,3,5,5 chr1 62702803 . CTTTT CTTT,CTTTTT,C,CTTTTTT 120.91 PASS AC=1,0,0,0;AF=0.357,0.107,0.071,0.036;AN=2;DP=268;set=variant3-variant6-variant10-variant12-variant15-variant16-variant17-variant21-variant26-variant31-variant33-variant35-variant36-variant40 GT:DP:GQ:SB 0/1:12:44:3,1,7,1 chr1 62703236 . A C 729.29 PASS AC=1;AF=0.571;AN=2;DP=1484;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant13-variant20-variant21-variant22-variant25-variant30-variant31-variant33-variant35-variant37-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:33,43:76:99:1074,0,839:16,17,19,24 chr1 62704134 . A G 827.83 PASS AC=1;AF=0.563;AN=2;DP=1718;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant13-variant17-variant20-variant21-variant22-variant25-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:27,31:58:99:722,0,639:9,18,10,21 chr1 62713224 . C G 1518.47 PASS AC=2;AF=0.989;AN=2;DP=3844;MQ=60;MQRankSum=0.136;ReadPosRankSum=0.716;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,117:117:99:3352,350,0:0,0,62,55 chr1 62713246 . G A 314.23 PASS AC=1;AF=0.643;AN=2;DP=2632;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant12-variant13-variant17-variant20-variant21-variant22-variant25-variant26-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:59,58:117:99:1303,0,1438:30,29,32,26 chr1 62728596 . T C 106.77 PASS AC=1;AF=0.8;AN=2;DP=236;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant24-variant27-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,5:11:99:174,0,199:5,1,5,0 chr1 62728628 . C T 454.7 PASS AC=1;AF=0.583;AN=2;DP=274;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant20-variant21-variant22-variant24-variant25-variant26-variant30-variant31-variant33-variant35-variant37-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:14,10:24:99:252,0,350:9,5,8,2 chr1 62728784 . A G 1536.89 PASS AC=1;AF=0.756;AN=2;DP=3133;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,52:101:99:1233,0,1355:30,19,27,25 chr1 62728838 . T C 2129.46 PASS AC=1;AF=0.756;AN=2;DP=3674;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:62,54:116:99:1933,0,2405:36,26,31,23 chr1 62728861 . T C 2214.23 PASS AC=1;AF=0.756;AN=2;DP=3938;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,59:117:99:2095,0,2249:27,31,31,28 chr1 62728918 . G A 1859.59 PASS AC=1;AF=0.756;AN=2;DP=4721;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,67:132:99:1611,0,1560:30,35,32,35 chr1 62729015 . G A 1826.1 PASS AC=1;AF=0.756;AN=2;DP=4455;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,62:127:99:1656,0,1611:31,34,32,30 chr1 62733939 . G A 905.48 PASS AC=1;AF=0.607;AN=2;DP=1232;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant17-variant20-variant21-variant22-variant24-variant25-variant27-variant30-variant31-variant33-variant35-variant37-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:21,25:46:99:668,0,644:15,6,16,9 chr1 62737372 . A C 1836.27 PASS AC=1;AF=0.65;AN=2;DP=2090;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant17-variant20-variant21-variant22-variant24-variant25-variant27-variant30-variant31-variant33-variant34-variant35-variant37-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:38,40:78:99:1130,0,935:20,18,20,20 chr1 62738077 . C T 1845.35 PASS AC=1;AF=0.694;AN=2;DP=1504;FractionInformativeReads=1;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant17-variant20-variant21-variant22-variant24-variant25-variant27-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:20,19:39:99:492,0,555:13,7,9,10 chr1 62738904 . T C 1044.28 PASS AC=1;AF=0.75;AN=2;DP=3347;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:37,50:87:99:1157,0,882:19,18,27,23 chr1 62739198 . G A 3031 PASS AC=1;AF=0.64;AN=2;DP=2592;MQ=60;set=variant2-variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant13-variant20-variant21-variant22-variant24-variant25-variant27-variant30-variant31-variant33-variant34-variant35-variant37-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:65,47:112:99:1149,0,1786:35,30,25,22 chr1 62740065 . A G 4746.64 PASS AC=1;AF=0.694;AN=2;DP=5129;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant17-variant20-variant21-variant22-variant24-variant25-variant27-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:94,94:188:99:2306,0,2102:51,43,48,46 chr1 62740446 . T C 1797.73 PASS AC=1;AF=0.75;AN=2;DP=5429;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:76,71:147:99:2697,0,3769:44,32,42,29 chr1 62740449 . T C 1796.75 PASS AC=1;AF=0.75;AN=2;DP=5496;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:75,69:144:99:2705,0,3800:43,32,41,28 chr1 62939634 . C T 1211.19 PASS AC=2;AF=1;AN=2;DP=2085;FS=0;MQ=60;MQRankSum=1.256;ReadPosRankSum=0.173;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,52:52:99:1585,155,0:0,0,27,25 chr1 62943264 . C T 2673.67 PASS AC=2;AF=1;AN=2;DP=2721;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2164,210,0:0,0,45,25 chr1 62945418 . A G 62.98 PASS AC=2;AF=0.824;AN=2;DP=327;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:353,33,0:0,0,7,4 chr1 62953183 . C T 568.13 PASS AC=2;AF=1;AN=2;DP=885;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:586,54,0:0,0,7,11 chr1 62960250 . T C 131.36 PASS AC=2;AF=0.814;AN=2;DP=461;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:627,48,0:0,0,3,13 chr1 62961928 . T C 409.95 PASS AC=2;AF=1;AN=2;DP=457;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:414,33,0:0,0,9,2 chr1 62970184 . T C 102.99 PASS AC=2;AF=0.838;AN=2;DP=196;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:270,18,0:0,0,6,0 chr1 62973795 . A G 424.06 PASS AC=2;AF=0.797;AN=2;DP=719;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:846,66,0:0,0,2,20 chr1 62976472 . T G 490.19 PASS AC=2;AF=1;AN=2;DP=730;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:852,66,0:0,0,2,20 chr1 63001120 . A C 778.38 PASS AC=2;AF=0.789;AN=2;DP=2836;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,69:71:99:2169,163,0:1,1,48,21 chr1 63027411 . AG A 2179.42 PASS AC=2;AF=1;AN=2;DP=1829;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,52:52:99:2102,157,0:0,0,21,31 chr1 63070017 . G A 220.06 PASS AC=1;AF=0.5;AN=2;DP=14;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.936;QD=15.72;ReadPosRankSum=-0.78;SOR=0.693;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:7,7:14:99:248,0,269:0,7,0,7 chr1 63113511 . C A 318.52 PASS AC=2;AF=0.789;AN=2;DP=2138;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1769,153,0:0,0,12,39 chr1 63113689 . T C 233.09 PASS AC=2;AF=1;AN=2;DP=368;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:211,15,0:0,0,5,0 chr1 63113719 . T C 246.42 PASS AC=2;AF=0.797;AN=2;DP=541;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:309,27,0:0,0,7,2 chr1 63249975 . A G 314.9 PASS AC=1;AF=0.756;AN=2;DP=1062;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,22:40:99:602,0,473:4,14,9,13 chr1 63306960 . C T 52.74 PASS AC=2;AF=0.944;AN=2;DP=28;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.736;ReadPosRankSum=0.736;set=variant3-variant9-variant17-variant21-variant22-variant26-variant35-variant38-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:90,6,0:0,0,2,0 chr1 63330217 . G A 2491.98 PASS AC=1;AF=0.662;AN=2;DP=7429;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:109,114:223:99:2811,0,2508:60,49,58,56 chr1 63790503 . T C 1090.23 PASS AC=1;AF=0.6;AN=2;DP=383;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant7-variant9-variant17-variant20-variant21-variant24-variant26-variant27-variant31-variant32-variant33-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:17,13:30:99:370,0,588:10,7,5,8 chr1 63836513 . C G 5087.35 PASS AC=1;AF=0.525;AN=2;DP=7352;MQ=60;set=variant-variant2-variant7-variant9-variant16-variant17-variant18-variant19-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:195,202:397:99:5058,0,4549:101,94,105,97 chr1 63872600 . T C 706.58 PASS AC=1;AF=0.533;AN=2;DP=415;FractionInformativeReads=1;MQ=60;set=variant-variant7-variant9-variant16-variant17-variant18-variant19-variant23-variant24-variant28-variant29-variant31-variant33-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:4,17:21:99:559,0,120:4,0,14,3 chr1 63872871 . A G 1082.48 PASS AC=1;AF=0.7;AN=2;DP=2108;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,32:65:99:834,0,877:10,23,12,20 chr1 63881552 . C T 531.09 PASS AC=1;AF=0.768;AN=2;DP=2300;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,24:57:99:524,0,734:20,13,15,9 chr1 63885222 . T G 37.42 PASS AC=1;AF=0.591;AN=2;DP=62;FractionInformativeReads=1;MQ=60;set=variant-variant9-variant16-variant17-variant19-variant24-variant29-variant31-variant35-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:3,2:5:67:67,0,110:0,3,0,2 chr1 63903452 . T C 617.54 PASS AC=1;AF=0.7;AN=2;DP=1654;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,22:41:99:637,0,487:7,12,12,10 chr1 63903478 . CATTAT C 1273.87 PASS AC=1;AF=0.531;AN=2;DP=787;set=variant-variant2-variant7-variant9-variant16-variant17-variant18-variant19-variant23-variant24-variant28-variant29-variant31-variant33-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:19,29:48:99:1132,0,922:9,10,18,11 chr1 63903846 . A AT 5045.9 PASS AC=1;AF=0.529;AN=2;DP=5330;MQ=60;set=variant-variant2-variant7-variant9-variant16-variant17-variant18-variant19-variant23-variant24-variant28-variant29-variant31-variant33-variant35-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:160,151:311:99:4714,0,5031:85,75,78,73 chr1 63904294 . T C 756.89 PASS AC=1;AF=0.775;AN=2;DP=880;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,12:21:99:274,0,219:5,4,5,7 chr1 63906371 . A G 947.84 PASS AC=1;AF=0.559;AN=2;DP=819;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant7-variant9-variant16-variant17-variant18-variant19-variant23-variant24-variant28-variant29-variant31-variant33-variant35-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:16,15:31:99:419,0,442:12,4,11,4 chr1 63912546 . G T 673.61 PASS AC=1;AF=0.563;AN=2;DP=1413;set=variant-variant2-variant7-variant9-variant16-variant17-variant18-variant19-variant23-variant24-variant28-variant29-variant31-variant33-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:43,36:79:99:692,0,1068:20,23,16,20 chr1 63920515 . C G 378.18 PASS AC=1;AF=0.529;AN=2;DP=556;MQ=60;set=variant-variant3-variant4-variant8-variant15-variant20-variant25-variant26-variant29-variant30-variant32-variant33-variant35-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,25:29:50:658,0,50:3,1,15,10 chr1 63975830 . T C 112.45 PASS AC=2;AF=1;AN=2;DP=196;FS=0;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:90,6,0:0,0,1,1 chr1 63988904 . G A 708.41 PASS AC=1;AF=0.568;AN=2;DP=1347;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant12-variant13-variant14-variant15-variant20-variant22-variant25-variant26-variant29-variant30-variant32-variant33-variant35-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:32,37:69:99:852,0,906:13,19,18,19 chr1 63991140 . T C 282.97 PASS AC=2;AF=1;AN=2;DP=687;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:764,57,0:0,0,18,1 chr1 63997633 . A T 782.86 PASS AC=1;AF=0.563;AN=2;DP=1017;MQ=60;set=variant-variant2-variant7-variant9-variant16-variant17-variant18-variant19-variant23-variant24-variant28-variant29-variant31-variant33-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:42,41:83:99:964,0,1152:18,24,17,24 chr1 63999826 . C T 979.26 PASS AC=1;AF=0.563;AN=2;DP=1085;MQ=60;set=variant-variant2-variant7-variant9-variant16-variant17-variant18-variant19-variant23-variant24-variant28-variant29-variant31-variant33-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:40,40:80:99:928,0,935:17,23,18,22 chr1 63999868 . T C 699.18 PASS AC=1;AF=0.563;AN=2;DP=726;MQ=60;set=variant-variant2-variant7-variant9-variant16-variant17-variant18-variant19-variant23-variant24-variant28-variant29-variant31-variant33-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:26,29:55:99:731,0,623:10,16,10,19 chr1 63999891 . T C 502.2 PASS AC=1;AF=0.563;AN=2;DP=478;MQ=60;set=variant-variant2-variant7-variant9-variant16-variant17-variant18-variant19-variant23-variant24-variant28-variant29-variant31-variant33-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:20,16:36:99:447,0,539:6,14,4,12 chr1 64015217 . G A 263.57 PASS AC=1;AF=0.714;AN=2;DP=1114;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,10:30:99:302,0,542:5,15,2,8 chr1 64021096 . G A 1167.22 PASS AC=1;AF=0.563;AN=2;DP=1712;MQ=60;set=variant-variant2-variant7-variant9-variant16-variant17-variant18-variant19-variant23-variant24-variant28-variant29-variant31-variant33-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:52,55:107:99:1324,0,1124:25,27,23,32 chr1 64022708 . C CAA,CA 61.6 PASS AC=1,0;AF=0.333,0.167;AN=2;DP=29;set=variant2-variant7-variant35 GT:DP:GQ:SB 0/1:8:77:4,0,4,0 chr1 64036838 . G A 765.89 PASS AC=1;AF=0.563;AN=2;DP=774;MQ=60;set=variant-variant2-variant7-variant9-variant16-variant17-variant18-variant19-variant23-variant24-variant28-variant29-variant31-variant33-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:33,19:52:99:417,0,884:13,20,7,12 chr1 64038107 . G T 299.84 PASS AC=1;AF=0.563;AN=2;DP=864;MQ=60;set=variant-variant2-variant7-variant9-variant16-variant17-variant18-variant19-variant23-variant24-variant28-variant29-variant31-variant33-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:36,24:60:99:561,0,899:20,16,13,11 chr1 64100478 . A T 845.11 PASS AC=1;AF=0.625;AN=2;DP=2012;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant10-variant13-variant14-variant15-variant18-variant21-variant22-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:33,34:67:99:904,0,838:20,13,24,10 chr1 64102114 . A G 720.07 PASS AC=1;AF=0.62;AN=2;DP=928;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant18-variant21-variant22-variant25-variant26-variant28-variant29-variant30-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:30,32:62:99:895,0,758:10,20,9,23 chr1 64125544 . C T 726.74 PASS AC=1;AF=0.55;AN=2;DP=706;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant16-variant28-variant35-variant37-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:35,42:77:99:1102,0,959:14,21,15,27 chr1 64240240 . C T 39.43 PASS AC=1;AF=0.611;AN=2;DP=58;FractionInformativeReads=1;MQ=60;set=variant-variant7-variant10-variant25-variant35-variant36-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,3:11:91:91,0,192:3,5,0,3 chr1 64474804 . C T 223.35 PASS AC=2;AF=0.795;AN=2;DP=1087;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,31:31:93:905,93,0:0,0,16,15 chr1 64515379 . C T 1054.04 PASS AC=2;AF=0.852;AN=2;DP=5028;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,123:123:99:3726,369,0:0,0,74,49 chr1 64608329 . G T 4896.52 PASS AC=2;AF=1;AN=2;DP=6544;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,167:167:99:5178,501,0:0,0,77,90 chr1 64624612 . G A 1684.06 PASS AC=2;AF=1;AN=2;DP=1797;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1247,99,0:0,0,28,5 chr1 64644707 . GAAA GA,GAA,G 556.75 PASS AC=1,0,0;AF=0.195,0.402,0.024;AN=2;DP=3491;set=variant-filterInvariant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-filterInvariant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-filterInvariant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant43-variant44 GT:DP:GQ:SB 0/1:52:99:12,14,10,16 chr1 64672478 . A G 427.73 PASS AC=1;AF=0.5;AN=2;DP=291;MQ=60;set=variant11-variant12-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:51,28:79:99:664,0,1176:28,23,16,12 chr1 64680654 . G A 758.45 PASS AC=1;AF=0.5;AN=2;DP=260;MQ=60;set=variant-variant8-variant10-variant20-variant23-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,21:46:99:588,0,630:11,14,8,13 chr1 64680682 . C G 1343.56 PASS AC=2;AF=0.713;AN=2;DP=1142;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:723,72,0:0,0,8,16 chr1 64698411 . T C 873.2 PASS AC=1;AF=0.596;AN=2;DP=1022;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant25-variant27-variant28-variant31-variant32-variant33-variant35-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:20,20:40:99:502,0,598:4,16,6,14 chr1 64707243 . G C 61.77 PASS AC=2;AF=0.817;AN=2;DP=170;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant17-variant19-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant40-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:231,18,0:0,0,6,0 chr1 64709891 . A G 2375.31 PASS AC=1;AF=0.56;AN=2;DP=8453;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant25-variant27-variant28-variant32-variant33-variant35-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:151,173:324:99:3863,0,3211:68,83,75,98 chr1 64726149 . C CTCAG 242.08 PASS AC=1;AF=0.568;AN=2;DP=207;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant21-variant25-variant27-variant28-variant32-variant33-variant35-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:6,4:10:99:150,0,338:6,0,4,0 chr1 64726414 . A C 1725.72 PASS AC=2;AF=0.713;AN=2;DP=2078;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,52:52:99:1628,156,0:0,0,19,33 chr1 65016349 . A T 4099.04 PASS AC=2;AF=0.909;AN=2;DP=6412;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,136:136:99:4314,407,0:0,0,72,64 chr1 65016399 . G A 2554.2 PASS AC=1;AF=0.583;AN=2;DP=905;MQ=60;set=variant3-variant6-variant11-variant21-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:62,79:141:99:1927,0,1473:31,31,39,40 chr1 65045602 . TA T 607.22 PASS AC=2;AF=0.909;AN=2;DP=2978;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,71:72:99:1935,190,0:0,1,39,32 chr1 65068638 . T C 2624.45 PASS AC=2;AF=0.989;AN=2;DP=3311;MQ=60;MQRankSum=0.347;ReadPosRankSum=0.962;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1662,167,0:0,0,20,36 chr1 65099978 . G A 1577.56 PASS AC=2;AF=0.977;AN=2;DP=2195;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1446,135,0:0,0,14,31 chr1 65100057 . G GTATT 142.73 PASS AC=2;AF=0.963;AN=2;DP=277;FS=0;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant25-variant26-variant27-variant29-variant32-variant33-variant35-variant36-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:249,18,0:0,0,0,6 chr1 65100061 . G T 152.28 PASS AC=2;AF=0.973;AN=2;DP=340;FS=0;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:249,18,0:0,0,0,6 chr1 65107372 . C T 722.84 PASS AC=2;AF=1;AN=2;DP=1222;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1126,99,0:0,0,25,8 chr1 65107850 . T C 743.47 PASS AC=2;AF=1;AN=2;DP=892;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.085;ReadPosRankSum=-0.217;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:454,48,0:0,0,6,10 chr1 65113351 . T C 498.48 PASS AC=2;AF=1;AN=2;DP=767;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:789,69,0:0,0,19,4 chr1 65113568 . T C 3538.45 PASS AC=2;AF=1;AN=2;DP=6428;FS=0;MQ=60;MQRankSum=1.35;ReadPosRankSum=1.183;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,177:177:99:5057,530,0:0,0,93,84 chr1 65158724 . C T 10864.3 PASS AC=2;AF=0.905;AN=2;DP=13252;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,290:290:99:8628,867,0:0,0,131,159 chr1 65247394 . T C 54.27 PASS AC=1;AF=0.6;AN=2;DP=72;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant7-variant10-variant14-variant26-variant33-variant35-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:2,3:5:68:113,0,68:0,2,0,3 chr1 65255018 . G A 1743.72 PASS AC=1;AF=0.605;AN=2;DP=1037;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant26-variant28-variant29-variant33-variant35-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:28,33:61:99:1000,0,932:25,3,27,6 chr1 65297240 . A G 2540.25 PASS AC=1;AF=0.58;AN=2;DP=2021;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant9-variant10-variant11-variant13-variant14-variant19-variant24-variant26-variant27-variant28-variant32-variant33-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,46:86:99:1292,0,1035:17,23,20,26 chr1 65297855 . CTAT C 20179.8 PASS AC=1;AF=0.654;AN=2;DP=10868;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant19-variant24-variant26-variant28-variant32-variant33-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:218,231:449:99:8948,0,9375:95,123,103,128 chr1 65297983 . A T 12601.7 PASS AC=1;AF=0.587;AN=2;DP=7662;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant9-variant10-variant13-variant14-variant19-variant24-variant26-variant28-variant32-variant33-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:145,181:326:99:4593,0,3375:65,80,81,100 chr1 65298623 . AAGTC A 2823.35 PASS AC=1;AF=0.654;AN=2;DP=1756;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant19-variant24-variant26-variant28-variant32-variant33-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,36:75:99:1395,0,2091:12,27,18,18 chr1 65298791 . A T 6021.96 PASS AC=1;AF=0.587;AN=2;DP=4771;set=variant-variant2-variant5-variant6-variant7-variant9-variant10-variant13-variant14-variant19-variant24-variant26-variant28-variant32-variant33-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:103,106:209:99:2623,0,2362:55,48,51,55 chr1 65299551 . G GAATT 813.01 PASS AC=1;AF=0.58;AN=2;DP=1040;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant9-variant10-variant11-variant13-variant14-variant19-variant24-variant26-variant27-variant28-variant32-variant33-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,19:43:99:725,0,1324:15,9,11,8 chr1 65301669 . C A 419.74 PASS AC=1;AF=0.587;AN=2;DP=510;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant9-variant10-variant13-variant14-variant19-variant24-variant26-variant28-variant32-variant33-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,7:18:99:180,0,431:11,0,5,2 chr1 65303510 . G A 1087.53 PASS AC=1;AF=0.625;AN=2;DP=77;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant14-variant28-variant35 GT:AD:DP:GQ:PL:SB 0/1:13,4:17:80:80,0,429:11,2,3,1 chr1 65311262 . G A 3741.08 PASS AC=1;AF=0.563;AN=2;DP=1007;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant6-variant14-variant28-variant33-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:92,86:178:99:1983,0,2024:42,50,48,38 chr1 65326095 . TTGCA T 386.57 PASS AC=1;AF=0.639;AN=2;DP=258;MQ=60;set=variant5-variant6-variant7-variant9-variant12-variant13-variant14-variant19-variant24-variant26-variant28-variant32-variant33-variant35-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,4:12:99:144,0,386:2,6,0,4 chr1 65431920 . G C 138.21 PASS AC=1;AF=0.5;AN=2;DP=199;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant14-variant28-variant29-variant33-variant34-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:13,19:32:99:472,0,360:8,5,11,8 chr1 65690461 . G A 343.43 PASS AC=1;AF=0.611;AN=2;DP=412;FractionInformativeReads=1;set=variant-variant3-variant6-variant7-variant8-variant9-variant11-variant12-variant18-variant19-variant22-variant24-variant26-variant33-variant34-variant35-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:14,10:24:99:334,0,452:10,4,8,2 chr1 65694404 . GTT GT,G 5488.65 PASS AC=2,0;AF=0.643,0.054;AN=2;DP=12038;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant19-variant21-variant23-variant24-variant26-variant27-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant43-variant44 GT:DP:GQ:SB 1/1:437:99:20,3,202,212 chr1 65694612 . C T 1681.83 PASS AC=1;AF=0.556;AN=2;DP=1107;MQ=60;set=variant4-variant12-variant14-variant15-variant21-variant27-variant35-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,72:107:99:2060,0,899:20,15,28,44 chr1 65694697 . T G 1767.51 PASS AC=1;AF=0.556;AN=2;DP=1493;FractionInformativeReads=1;MQ=60;set=variant4-variant12-variant14-variant15-variant21-variant27-variant35-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:86,80:166:99:1916,0,2043:45,41,41,39 chr1 65694819 . G A 904.5 PASS AC=1;AF=0.65;AN=2;DP=1706;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant17-variant19-variant24-variant26-variant33-variant34-variant35-variant37-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:48,55:103:99:1359,0,1187:20,28,24,31 chr1 65695054 . G A 473.56 PASS AC=1;AF=0.556;AN=2;DP=207;FractionInformativeReads=1;MQ=60;set=variant4-variant12-variant14-variant15-variant21-variant27-variant35-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,10:22:99:209,0,376:5,7,4,6 chr1 65695853 . A G 824.63 PASS AC=2;AF=0.696;AN=2;DP=2427;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant19-variant21-variant23-variant24-variant26-variant27-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,83:83:99:2733,249,0:0,0,37,46 chr1 65695930 . G A 1229.97 PASS AC=2;AF=0.696;AN=2;DP=2474;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant19-variant21-variant23-variant24-variant26-variant27-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:2054,186,0:0,0,37,25 chr1 65696034 . G C 4104.74 PASS AC=1;AF=0.643;AN=2;DP=5322;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant17-variant19-variant24-variant25-variant26-variant33-variant34-variant35-variant37-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:128,98:226:99:2632,0,3417:80,48,65,33 chr1 65696189 . T G 5168.42 PASS AC=1;AF=0.556;AN=2;DP=3985;MQ=60;set=variant4-variant12-variant14-variant15-variant21-variant27-variant35-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:210,207:417:99:5229,0,5378:107,103,100,107 chr1 65775187 . G C 117.67 PASS AC=2;AF=1;AN=2;DP=630;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,12:12:35:340,35,0:0,0,8,4 chr1 65775330 . AT ATT,A 44.67 DRAGENHardINDEL AC=0,1;AF=0.071,0.429;AN=2;DP=507;MQ=60;set=FilteredInAll GT:DP:GQ:SB 0/2:72:99:33,24,10,5 chr1 65830297 . G T 509.9 PASS AC=2;AF=0.671;AN=2;DP=903;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:6,27:33:22:536,22,0:5,1,20,7 chr1 65830299 . T G 509.9 PASS AC=2;AF=0.6;AN=2;DP=963;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-filterInvariant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:6,31:37:22:536,22,0:5,1,23,8 chr1 65830608 . T C 1135.18 PASS AC=2;AF=0.738;AN=2;DP=1177;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1214,99,0:0,0,7,26 chr1 65844963 . A G 3118.07 PASS AC=2;AF=0.695;AN=2;DP=3706;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,106:106:99:3300,317,0:0,0,67,39 chr1 65852310 . A G 117.98 PASS AC=2;AF=0.629;AN=2;DP=447;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:71:783,71,0:0,0,18,6 chr1 65852870 . A G 342.51 PASS AC=2;AF=0.7;AN=2;DP=689;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:406,30,0:0,0,2,8 chr1 65858088 . T C 1238.8 PASS AC=2;AF=0.683;AN=2;DP=2092;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:1419,141,0:0,0,29,18 chr1 65858145 . G A 1536.71 PASS AC=2;AF=0.659;AN=2;DP=2934;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:1812,185,0:0,0,37,25 chr1 65860687 . A C 3426.11 PASS AC=2;AF=0.72;AN=2;DP=5235;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,122:122:99:3355,364,0:0,0,59,63 chr1 65867391 . C G 1839.87 PASS AC=2;AF=0.707;AN=2;DP=2812;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1632,147,0:0,0,30,19 chr1 65881132 . AAC AACACAC,AACACACAC,A,AACAC 1833.54 PASS AC=0,0,1,0;AF=0.274,0.119,0.071,0.226;AN=2;DP=3478;set=variant-variant2-variant3-variant4-variant5-variant6-filterInvariant7-variant8-variant9-variant10-variant11-variant14-variant15-filterInvariant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/3:61:99:24,17,9,11 chr1 65897981 . G A 1049.13 PASS AC=2;AF=0.604;AN=2;DP=1826;MQ=60;set=variant3-variant5-variant7-variant9-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant25-variant27-variant28-variant31-variant33-variant35-variant36-variant37-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,93:94:99:3419,248,0:0,1,27,66 chr1 65898249 . TAA TAAA,T,TA 106.44 PASS AC=0,2,0;AF=0.167,0.372,0.09;AN=2;DP=1901;set=variant2-variant3-variant4-variant5-variant6-variant7-filterInvariant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant35-variant36-variant37-filterInvariant38-variant39-variant40-variant41-variant42-filterInvariant43-variant44 GT:DP:GQ:SB 2/2:39:99:0,0,25,14 chr1 65898873 . G C 899.83 PASS AC=2;AF=0.604;AN=2;DP=1023;MQ=60;set=variant3-variant5-variant7-variant9-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant25-variant27-variant28-variant31-variant33-variant35-variant36-variant37-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1622,132,0:0,0,13,31 chr1 65898972 . G A 2487.06 PASS AC=2;AF=1;AN=2;DP=2593;FS=0;MQ=60;MQRankSum=-0.247;ReadPosRankSum=0.46;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:2707,228,0:0,0,47,29 chr1 65900357 . G T 942.38 PASS AC=2;AF=0.604;AN=2;DP=1806;MQ=60;set=variant3-variant5-variant7-variant9-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant25-variant27-variant28-variant31-variant33-variant35-variant36-variant37-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,73:73:99:2355,218,0:0,0,31,42 chr1 65901053 . T TC 225.13 PASS AC=1;AF=0.5;AN=2;DP=2609;set=filterInvariant3-filterInvariant5-variant7-variant9-variant11-filterInvariant14-variant15-variant16-variant17-variant18-filterInvariant19-variant21-variant23-variant24-filterInvariant25-filterInvariant27-variant28-variant31-variant33-variant35-filterInvariant36-filterInvariant37-filterInvariant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,47:70:99:912,0,374:5,18,13,34 chr1 65901119 . T C 620.05 PASS AC=2;AF=0.805;AN=2;DP=761;FractionInformativeReads=1;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:683,48,0:0,0,1,15 chr1 66036501 . G T 1489.78 PASS AC=2;AF=1;AN=2;DP=1607;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1453,132,0:0,0,12,32 chr1 66037973 . GTT G,GT,GTTT,GTTTT 168.52 PASS AC=0,1,0,0;AF=0.111,0.315,0.093,0.019;AN=2;DP=1295;set=variant-variant2-variant3-filterInvariant4-variant5-filterInvariant6-variant10-variant11-filterInvariant12-variant13-variant16-filterInvariant20-filterInvariant21-variant22-filterInvariant23-variant26-filterInvariant29-variant30-variant31-filterInvariant32-variant33-variant35-variant38-filterInvariant39-variant40-variant42-filterInvariant43 GT:DP:GQ:SB 0/2:20:78:5,4,8,3 chr1 66096093 . T TA,TAA 147.06 PASS AC=1,0;AF=0.333,0.2;AN=2;DP=311;set=variant2-variant4-variant9-filterInvariant11-variant12-variant17-variant20-variant22-filterInvariant24-variant25-variant28-variant31-variant32-variant35-variant41 GT:DP:GQ:SB 0/1:17:73:8,3,4,2 chr1 66096106 . G A 83.07 PASS AC=2;AF=0.773;AN=2;DP=1505;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:954,81,0:0,0,20,7 chr1 66100979 . TA T 1227.04 PASS AC=2;AF=0.583;AN=2;DP=1275;set=variant5-variant7-variant14-variant16-variant22-variant28-variant29-variant31-variant33-variant35-variant40-variant42 GT:AD:DP:GQ:PL:SB 1/1:7,78:85:60:1953,60,0:4,3,39,39 chr1 66103042 . AAC A,AACAC 5397.55 PASS AC=1,0;AF=0.438,0.175;AN=2;DP=15102;MQ=60;set=variant-filterInvariant2-variant3-variant4-filterInvariant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-filterInvariant13-filterInvariant14-variant15-filterInvariant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-filterInvariant29-variant30-variant31-variant32-variant33-filterInvariant35-variant36-variant37-filterInvariant38-variant39-filterInvariant40-variant41-variant43-variant44 GT:DP:GQ:SB 0/1:392:97:179,177,15,21 chr1 66106447 . CT C,CTT,CTTT 526.92 PASS AC=1,0,0;AF=0.326,0.151,0.035;AN=2;DP=6329;set=variant-variant2-variant3-filterInvariant4-variant5-filterInvariant6-variant7-filterInvariant8-variant9-variant10-variant11-variant12-variant13-filterInvariant14-variant15-filterInvariant16-variant17-variant18-filterInvariant19-variant20-filterInvariant21-filterInvariant22-variant23-variant24-filterInvariant25-filterInvariant26-filterInvariant27-filterInvariant29-variant30-variant31-variant32-filterInvariant33-filterInvariant34-variant35-variant36-filterInvariant37-filterInvariant38-filterInvariant39-filterInvariant40-variant41-variant42-variant43-filterInvariant44 GT:DP:GQ:SB 0/1:103:99:13,51,7,32 chr1 66618316 . TACACACACAC TACACAC,T,TACAC 224.54 PASS AC=2,0,0;AF=0.545,0.227,0.136;AN=2;DP=75;FS=0;MQ=60;set=variant10-variant11-variant15-variant16-variant21-variant29-variant32-variant33-variant35-variant37-variant40 GT:DP:GQ:SB 1/1:3:9:0,0,1,2 chr1 66731886 . G C 6855.68 PASS AC=1;AF=0.724;AN=2;DP=8910;MQ=60;set=variant2-variant5-variant6-variant8-variant9-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:150,164:314:99:3940,0,3468:68,82,75,89 chr1 66732386 . G A 4047.73 PASS AC=1;AF=0.724;AN=2;DP=3966;MQ=60;set=variant2-variant5-variant6-variant8-variant9-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,73:122:99:1820,0,1203:28,21,43,30 chr1 66732529 . A T 1264.81 PASS AC=1;AF=0.721;AN=2;DP=1389;MQ=60;set=variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,31:59:99:847,0,712:7,21,7,24 chr1 66829262 . A G 2454.52 PASS AC=2;AF=0.802;AN=2;DP=3324;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,98:98:99:2881,293,0:0,0,40,58 chr1 66831370 . G A 1066.02 PASS AC=1;AF=0.682;AN=2;DP=3117;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,58:111:99:1368,0,1181:28,25,29,29 chr1 67094288 . A G 296.62 PASS AC=1;AF=0.559;AN=2;DP=347;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant7-variant8-variant11-variant12-variant13-variant16-variant18-variant19-variant20-variant26-variant31-variant34-variant35-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,9:22:99:240,0,403:3,10,2,7 chr1 67154730 . CAA CA,C 199.59 PASS AC=1,0;AF=0.385,0.308;AN=2;DP=1382;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:28:99:10,5,10,3 chr1 67160548 . T C 2466.1 PASS AC=1;AF=0.559;AN=2;DP=3266;MQ=60;set=variant-variant2-variant7-variant8-variant9-variant11-variant12-variant13-variant18-variant19-variant20-variant26-variant31-variant34-variant35-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:97,99:196:99:2419,0,2595:53,44,47,52 chr1 67160938 . TA TAAAA,TAAA,TAAAAAAAAAAAA,TAAAAAAAAAA,TAA,TAAAAAAAAA,T,TAAAAAAAAAAA,TAAAAAAAAAAAAAAAAA,TAAAAA,TAAAAAAAAAAAAA 502.94 PASS AC=0,0,0,0,0,0,1,0,0,0,0;AF=0.135,0.162,0.014,0.041,0.054,0.014,0.068,0.081,0.014,0.041,0.014;AN=2;DP=2334;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-filterInvariant11-variant15-variant16-variant17-filterInvariant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-filterInvariant35-variant36-filterInvariant37-variant38-variant39-filterInvariant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/7:70:99:30,26,8,6 chr1 67195184 . C G 1874.2 PASS AC=2;AF=0.638;AN=2;DP=2526;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant26-variant27-variant29-variant30-variant31-variant34-variant35-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,83:83:99:3477,253,0:0,0,22,61 chr1 67195192 . C G 1772.24 PASS AC=2;AF=0.638;AN=2;DP=2174;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant26-variant27-variant29-variant30-variant31-variant34-variant35-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:3145,217,0:0,0,14,54 chr1 67209088 . G A 1963.57 PASS AC=1;AF=0.559;AN=2;DP=3544;MQ=60;set=variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant27-variant29-variant30-variant31-variant35-variant37-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:126,117:243:99:2715,0,3153:53,73,50,67 chr1 67209562 . T C 1954.14 PASS AC=2;AF=0.643;AN=2;DP=5232;MQ=60;set=variant-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant26-variant27-variant29-variant30-variant31-variant34-variant35-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,199:201:99:6009,553,0:1,1,113,86 chr1 67209818 . A G 1550.48 PASS AC=2;AF=0.78;AN=2;DP=2141;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:1946,165,0:0,0,33,22 chr1 67209860 . C A 1425.72 PASS AC=1;AF=0.5;AN=2;DP=205;FractionInformativeReads=1;MQ=60;set=variant12-variant35 GT:AD:DP:GQ:PL:SB 0/1:48,52:100:99:1522,0,1383:32,16,40,12 chr1 67242200 . G A 552.61 PASS AC=1;AF=0.575;AN=2;DP=611;MQ=60;set=variant-variant6-variant8-variant10-variant12-variant16-variant19-variant20-variant21-variant24-variant25-variant27-variant29-variant32-variant33-variant35-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,23:35:99:563,0,257:3,9,9,14 chr1 67242243 . GGT GGTGT,G 54.83 PASS AC=1,0;AF=0.531,0.031;AN=2;DP=218;MQ=60;set=variant-variant8-variant12-variant16-variant19-variant20-variant21-variant24-variant25-filterInvariant26-variant27-variant29-variant32-variant35-variant40-variant43 GT:DP:GQ:SB 0/1:4:24:0,1,0,3 chr1 67243024 . C A 2232.74 PASS AC=1;AF=0.575;AN=2;DP=3500;MQ=60;set=variant-variant6-variant8-variant10-variant12-variant16-variant19-variant20-variant21-variant24-variant25-variant27-variant29-variant32-variant33-variant35-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:98,74:172:99:1791,0,2492:56,42,41,33 chr1 67244243 . A T 4444.81 PASS AC=1;AF=0.571;AN=2;DP=7304;MQ=60;set=variant-variant5-variant6-variant8-variant10-variant12-variant16-variant19-variant20-variant21-variant24-variant25-variant27-variant29-variant32-variant33-variant35-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:159,165:324:99:4253,0,3914:70,89,65,100 chr1 67244488 . T TA 595.21 PASS AC=1;AF=0.633;AN=2;DP=1595;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant27-variant29-variant32-variant33-variant35-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:30,26:56:99:826,0,948:8,22,9,17 chr1 67266756 . T A 1175.39 PASS AC=2;AF=0.919;AN=2;DP=3781;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,83:83:99:2696,249,0:0,0,50,33 chr1 67267080 . C T 325.59 PASS AC=2;AF=0.605;AN=2;DP=443;MQ=60;set=variant5-variant9-variant10-variant11-variant12-variant13-variant18-variant19-variant20-variant21-variant24-variant28-variant29-variant34-variant35-variant37-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:1038,84,0:0,0,6,22 chr1 67292473 . A AT 2212.73 PASS AC=2;AF=0.735;AN=2;DP=1996;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,65:67:77:2842,77,0:1,1,46,19 chr1 67292478 . T A 2246.46 PASS AC=2;AF=0.735;AN=2;DP=2184;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,70:72:89:2964,89,0:1,1,48,22 chr1 67303303 . A G 1207.32 PASS AC=1;AF=0.613;AN=2;DP=2133;MQ=60;set=variant-variant2-variant5-variant6-variant9-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,37:69:99:822,0,783:22,10,23,14 chr1 67306054 . C A 607.85 PASS AC=1;AF=0.6;AN=2;DP=360;FractionInformativeReads=1;MQ=60;set=variant5-variant12-variant13-variant16-variant17-variant23-variant25-variant28-variant32-variant33-variant34-variant35-variant37-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,16:25:99:578,0,278:8,1,15,1 chr1 67337285 . C A 165.13 PASS AC=1;AF=0.542;AN=2;DP=102;FS=0;FractionInformativeReads=1;MQ=60;set=variant5-variant12-variant13-variant16-variant17-variant24-variant28-variant32-variant33-variant34-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:3,6:9:87:236,0,87:0,3,0,6 chr1 67359195 . T A 233.51 PASS AC=1;AF=0.625;AN=2;DP=123;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant6-variant9-variant11-variant13-variant14-variant16-variant17-variant20-variant22-variant26-variant27-variant28-variant34-variant35-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:2,7:9:64:247,0,64:0,2,1,6 chr1 67372726 . T C 82.71 PASS AC=1;AF=0.5;AN=2;DP=142;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant10-variant22-variant26-variant35-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:8,5:13:99:135,0,201:4,4,2,3 chr1 67390416 . G C 5783.18 PASS AC=2;AF=0.833;AN=2;DP=10222;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,234:234:99:6769,700,0:0,0,121,113 chr1 67390468 . C G 5604.71 PASS AC=2;AF=0.845;AN=2;DP=8734;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,214:214:99:6835,641,0:0,0,87,127 chr1 67390999 . G C 466.77 PASS AC=2;AF=0.854;AN=2;DP=618;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:1033,75,0:0,0,5,20 chr1 67391003 . G C 466.77 PASS AC=2;AF=0.854;AN=2;DP=569;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,19:19:60:869,60,0:0,0,3,16 chr1 67394707 . AG A 1477.05 PASS AC=1;AF=0.5;AN=2;DP=198;FS=0;MQ=60;set=variant-variant35 GT:AD:DP:GQ:PL:SB 0/1:45,48:93:99:1648,0,1498:20,25,21,27 chr1 67396222 . T G 901.52 PASS AC=2;AF=0.898;AN=2;DP=1047;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:961,69,0:0,0,4,19 chr1 67412261 . G T 7499.66 PASS AC=1;AF=0.5;AN=2;DP=995;FractionInformativeReads=1;MQ=60;set=variant-variant35 GT:AD:DP:GQ:PL:SB 0/1:234,221:455:99:5442,0,5524:123,111,121,100 chr1 67412822 . T G 7497.27 PASS AC=2;AF=0.845;AN=2;DP=8560;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,209:210:99:6488,618,0:1,0,123,86 chr1 67412918 . G C 13448 PASS AC=2;AF=0.845;AN=2;DP=14622;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,354:354:99:11286,1062,0:0,0,203,151 chr1 67413051 . A G 5853.81 PASS AC=1;AF=0.5;AN=2;DP=2875;MQ=60;set=variant19-variant24-variant35-variant36-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:273,236:509:99:5684,0,6792:133,140,109,127 chr1 67413478 . A G 1628.54 PASS AC=2;AF=0.845;AN=2;DP=2778;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,86:86:99:2729,258,0:0,0,40,46 chr1 67423997 . T TTTCTC 52.73 PASS AC=2;AF=0.894;AN=2;DP=213;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant16-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:78,6,0:0,0,0,2 chr1 67424488 . A G 591.3 PASS AC=1;AF=0.5;AN=2;DP=81;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant35 GT:AD:DP:GQ:PL:SB 0/1:25,16:41:99:486,0,801:20,5,13,3 chr1 67425311 . T G 768.38 PASS AC=2;AF=0.845;AN=2;DP=1253;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1026,107,0:0,0,22,14 chr1 67425494 . A AT 279.83 PASS AC=2;AF=0.878;AN=2;DP=495;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:187,21,0:0,0,2,5 chr1 67436446 . A G 118.94 PASS AC=1;AF=0.5;AN=2;DP=159;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant15-variant21-variant24-variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,7:17:99:240,0,231:7,3,7,0 chr1 67438492 . C T 635.55 PASS AC=1;AF=0.5;AN=2;DP=43;FS=3.278;FractionInformativeReads=1;MQ=60;MQRankSum=0.135;QD=14.78;ReadPosRankSum=-1.186;SOR=0.247;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:19,24:43:99:664,0,647:16,3,17,7 chr1 67451487 . G A 218.14 PASS AC=1;AF=0.5;AN=2;DP=69;FractionInformativeReads=1;MQ=60;set=variant-variant35 GT:AD:DP:GQ:PL:SB 0/1:19,17:36:99:493,0,619:3,16,3,14 chr1 67452414 . G T 3588.16 PASS AC=1;AF=0.5;AN=2;DP=1321;FractionInformativeReads=1;MQ=60;set=variant-variant35 GT:AD:DP:GQ:PL:SB 0/1:377,151:528:99:2787,0,9938:197,180,79,72 chr1 67452482 . G A 3612.13 PASS AC=1;AF=0.5;AN=2;DP=1210;FractionInformativeReads=1;MQ=60;set=variant-variant35 GT:AD:DP:GQ:PL:SB 0/1:345,151:496:99:3155,0,8865:160,185,79,72 chr1 67452723 . C A 6569.81 PASS AC=1;AF=0.5;AN=2;DP=2417;FractionInformativeReads=1;set=variant-variant14-variant21-variant35-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:257,107:364:99:2278,0,6851:129,128,50,57 chr1 67453035 . A G 32552.5 PASS AC=2;AF=0.966;AN=2;DP=22026;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,654:655:99:19953,1949,0:0,1,362,292 chr1 67453445 . A AAT 3524.68 PASS AC=1;AF=0.5;AN=2;DP=1944;MQ=60;set=variant-variant3-variant4-variant6-variant22-variant30-variant35-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:88,92:180:99:2919,0,2827:46,42,52,40 chr1 67467173 . C G 1020.55 PASS AC=1;AF=0.5;AN=2;DP=366;FractionInformativeReads=1;MQ=60;set=variant19-variant24-variant35-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:32,36:68:99:837,0,897:13,19,15,21 chr1 67468190 . T C 5279.62 PASS AC=1;AF=0.5;AN=2;DP=700;MQ=60;set=variant-variant35 GT:AD:DP:GQ:PL:SB 0/1:133,190:323:99:4649,0,3038:66,67,90,100 chr1 67474880 . T C 330.5 PASS AC=1;AF=0.5;AN=2;DP=167;MQ=60;set=variant-variant3-variant4-variant6-variant22-variant35-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:6,15:21:92:378,0,92:2,4,5,10 chr1 67487109 . T C 570.26 PASS AC=1;AF=0.5;AN=2;DP=133;FractionInformativeReads=1;MQ=60;set=variant-variant35 GT:AD:DP:GQ:PL:SB 0/1:45,36:81:99:938,0,1857:27,18,22,14 chr1 67487119 . C A 730.94 PASS AC=1;AF=0.756;AN=2;DP=3589;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,53:96:99:1390,0,1493:24,19,32,21 chr1 67487374 . TCCAACACAGACACAGACACAGACA TCAGACACAGACACAGACA,T 421.76 PASS AC=1,0;AF=0.63,0.019;AN=2;DP=1401;set=variant2-filterInvariant3-variant5-variant6-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant26-variant27-variant28-filterInvariant31-variant33-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:55:99:10,27,11,7 chr1 67487377 . AACACAG A,GACACAG 351.29 PASS AC=1,0;AF=0.5,0.25;AN=2;DP=106;MQRankSum=-0.401;ReadPosRankSum=1.127;set=variant29-variant35 GT:DP:GQ:SB 0/1:33:99:12,10,1,10 chr1 67487395 . G C 120.98 PASS AC=1;AF=0.521;AN=2;DP=1147;set=variant-variant3-variant7-variant9-filterInvariant10-filterInvariant11-variant12-variant14-variant17-variant19-filterInvariant20-filterInvariant25-variant26-filterInvariant28-variant29-variant30-variant31-variant33-variant35-variant38-variant39-variant40-variant42-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:26,8:34:99:252,0,1027:6,20,3,5 chr1 67487401 . G C 127.41 PASS AC=1;AF=0.703;AN=2;DP=1427;set=variant-variant2-variant5-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-filterInvariant36-variant37-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:21,8:29:99:262,0,841:4,17,3,5 chr1 67487407 . G C 531.73 PASS AC=1;AF=0.8;AN=2;DP=1419;set=variant-variant3-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,10:25:99:371,0,546:2,13,3,7 chr1 67508067 . A G 1275.4 PASS AC=1;AF=0.5;AN=2;DP=187;MQ=60;set=variant-variant35 GT:AD:DP:GQ:PL:SB 0/1:47,45:92:99:1128,0,1091:18,29,16,29 chr1 67519422 . G A 133.71 PASS AC=1;AF=0.5;AN=2;DP=101;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant12-variant15-variant35 GT:AD:DP:GQ:PL:SB 0/1:17,17:34:99:519,0,447:12,5,12,5 chr1 67558169 . T C 3586.91 PASS AC=1;AF=0.86;AN=2;DP=4407;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,53:108:99:1320,0,1609:32,23,33,20 chr1 67558360 . C T 3143.35 PASS AC=1;AF=0.5;AN=2;DP=2303;MQ=60;set=variant-variant3-variant4-variant6-variant8-variant12-variant15-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:114,118:232:99:2979,0,3015:59,55,64,54 chr1 67558739 . C T 2802.81 PASS AC=1;AF=0.86;AN=2;DP=3473;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,31:77:99:837,0,1137:18,28,17,14 chr1 67560897 . A G 7471.05 PASS AC=1;AF=0.86;AN=2;DP=7873;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:109,89:198:99:2237,0,2764:57,52,40,49 chr1 67560956 . C T 7237.36 PASS AC=1;AF=0.86;AN=2;DP=7745;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:99,80:179:99:2003,0,2685:51,48,40,40 chr1 67561251 . C T 2219.97 PASS AC=1;AF=0.571;AN=2;DP=1064;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant8-variant12-variant15-variant25-variant26-variant30-variant32-variant35-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:41,34:75:99:995,0,1121:18,23,13,21 chr1 67561311 . T A 529.28 PASS AC=1;AF=0.5;AN=2;DP=522;MQ=60;set=variant-variant3-variant4-variant6-variant8-variant12-variant15-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:38,27:65:99:643,0,961:15,23,11,16 chr1 67577367 . A T 647.1 PASS AC=1;AF=0.798;AN=2;DP=3064;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,45:76:99:1056,0,770:16,15,20,25 chr1 67579386 . A G 1248.24 PASS AC=1;AF=0.86;AN=2;DP=2114;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,30:52:99:707,0,510:11,11,17,13 chr1 67591660 . G A 201.16 PASS AC=1;AF=0.81;AN=2;DP=529;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,7:9:52:207,0,52:0,2,3,4 chr1 67600665 . A C 355.42 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=5947;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:122,49:171:99:574,0,2730:4,118,48,1 chr1 67633812 . G T 788.36 PASS AC=1;AF=0.641;AN=2;DP=2131;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant26-variant27-variant28-variant29-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,33:65:99:836,0,757:19,13,18,15 chr1 67633963 . C T 373.03 PASS AC=1;AF=0.5;AN=2;DP=243;FractionInformativeReads=1;MQ=60;set=variant6-variant9-variant19-variant21-variant33-variant35-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,12:23:99:390,0,313:2,9,2,10 chr1 67648460 . T C 896.25 PASS AC=1;AF=0.884;AN=2;DP=1113;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,19:28:99:528,0,272:8,1,13,6 chr1 67685387 . T C 2488.87 PASS AC=2;AF=0.875;AN=2;DP=2966;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:1953,194,0:0,0,27,38 chr1 67685443 . G A 582.04 PASS AC=1;AF=0.608;AN=2;DP=1402;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,10:41:99:189,0,810:11,20,4,6 chr1 67705574 . C T 225.91 PASS AC=1;AF=0.686;AN=2;DP=691;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,8:22:99:173,0,346:9,5,5,3 chr1 67705726 . A G 2301.66 PASS AC=2;AF=0.875;AN=2;DP=3236;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1732,153,0:0,0,31,20 chr1 67795319 . T C 4593.16 PASS AC=2;AF=0.977;AN=2;DP=5714;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,135:136:99:4002,398,0:1,0,64,71 chr1 67852141 . A G 1471.34 PASS AC=2;AF=0.692;AN=2;DP=1216;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1139,99,0:0,0,24,9 chr1 67852335 . G A 5417.79 PASS AC=2;AF=0.657;AN=2;DP=5316;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,152:154:99:4587,410,0:1,1,75,77 chr1 67852555 . T A 99.54 PASS AC=2;AF=0.9;AN=2;DP=18;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.736;ReadPosRankSum=0.736;set=variant8-variant25-variant29-variant32-variant35 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:160,12,0:0,0,0,4 chr1 67861520 . C A 2778 PASS AC=2;AF=0.689;AN=2;DP=5949;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,191:191:99:6273,572,0:0,0,102,89 chr1 67862466 . G T 156.22 PASS AC=2;AF=0.988;AN=2;DP=459;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.529;ReadPosRankSum=0.529;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:226,18,0:0,0,1,5 chr1 67874252 . CA CAA,C 692.39 PASS AC=1,0;AF=0.346,0.154;AN=2;DP=6373;set=variant-filterInvariant2-variant3-variant4-variant5-filterInvariant8-filterInvariant9-variant10-variant11-variant12-variant13-variant14-filterInvariant15-variant16-variant17-filterInvariant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-filterInvariant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:100:99:25,18,35,22 chr1 67875011 . GT GTT,GTTT,G 184 PASS AC=1,0,0;AF=0.5,0.036,0.036;AN=2;DP=559;set=variant-variant2-variant4-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant16-variant21-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:25:68:3,3,8,11 chr1 67875102 . ACCCC ACC,A 37.95 PASS AC=1,0;AF=0.517,0.017;AN=2;DP=1041;set=filterInvariant-filterInvariant2-variant3-variant4-filterInvariant5-variant6-variant8-variant9-variant10-variant11-filterInvariant12-variant13-filterInvariant15-variant17-variant18-variant19-variant20-variant24-variant26-variant28-variant29-variant30-variant31-filterInvariant35-variant38-variant39-variant41-variant43-variant44 GT:DP:GQ:SB 0/1:22:96:13,3,5,1 chr1 67875104 . C A,CACACACA,CA 287.13 PASS AC=1,0,0;AF=0.447,0.053,0.053;AN=2;DP=677;set=variant16-variant21-variant2-variant23-variant25-variant27-filterInvariant28-variant29-filterInvariant30-filterInvariant31-variant32-variant33-variant34-variant35-variant36-filterInvariant39-variant41-variant42-variant44 GT:DP:GQ:SB 0/1:20:99:5,1,11,3 chr1 67875106 . C A 600.1 PASS AC=2;AF=0.567;AN=2;DP=1074;set=variant-variant2-filterInvariant4-variant5-filterInvariant6-variant8-variant10-variant11-variant12-filterInvariant16-filterInvariant17-variant19-variant22-filterInvariant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:74:1031,74,0:0,0,19,6 chr1 67875414 . T C 1240.29 PASS AC=2;AF=0.657;AN=2;DP=1015;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:1108,81,0:0,0,7,20 chr1 67875533 . T A 2153.02 PASS AC=2;AF=0.643;AN=2;DP=1990;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1794,168,0:0,0,36,20 chr1 67876484 . C T 6584.15 PASS AC=2;AF=0.689;AN=2;DP=7151;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,197:197:99:6425,590,0:0,0,88,109 chr1 67890526 . A G 145.31 PASS AC=2;AF=0.694;AN=2;DP=242;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant16-variant18-variant19-variant21-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:288,30,0:0,0,6,4 chr1 68151980 . T G 1608.69 PASS AC=2;AF=0.878;AN=2;DP=3000;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,86:86:99:3427,259,0:0,0,74,12 chr1 68152363 . G A 349.91 PASS AC=2;AF=0.767;AN=2;DP=621;MQ=60;set=variant-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant18-variant19-variant21-variant22-variant23-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,21:21:62:731,62,0:0,0,3,18 chr1 68152388 . T C 385.6 PASS AC=2;AF=0.814;AN=2;DP=483;MQ=60;set=variant-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:443,33,0:0,0,2,9 chr1 68154086 . G C 731.07 PASS AC=2;AF=0.819;AN=2;DP=1115;MQ=60;set=variant-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:596,51,0:0,0,4,13 chr1 68167491 . C T 1702.85 PASS AC=1;AF=0.734;AN=2;DP=3013;set=variant-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,58:98:99:1587,0,1103:13,27,21,37 chr1 68169257 . C A 1048.66 PASS AC=1;AF=0.5;AN=2;DP=123;FS=1.491;FractionInformativeReads=1;MQ=60;MQRankSum=-1.07;QD=8.53;ReadPosRankSum=-3.074;SOR=0.873;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:76,47:123:99:1077,0,1955:42,34,28,19 chr1 68170255 . C A 290.66 PASS AC=1;AF=0.734;AN=2;DP=1178;set=variant-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,27:46:99:1002,0,593:14,5,20,7 chr1 68173264 . C T 2770.85 PASS AC=1;AF=0.734;AN=2;DP=5722;set=variant-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:72,78:150:99:1962,0,1820:33,39,38,40 chr1 68516583 . C T 120.83 PASS AC=1;AF=0.5;AN=2;DP=17;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.01;QD=7.11;ReadPosRankSum=-2.55;SOR=0.941;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:9,8:17:99:149,0,273:4,5,3,5 chr1 68517066 . C T 411.42 PASS AC=2;AF=0.886;AN=2;DP=849;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:634,57,0:0,0,14,5 chr1 68591104 . A G 3804.97 PASS AC=2;AF=0.779;AN=2;DP=10173;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,239:239:99:7355,714,0:0,0,143,96 chr1 68591173 . A G 5592.93 PASS AC=2;AF=0.767;AN=2;DP=14556;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,356:356:99:10869,1067,0:0,0,194,162 chr1 68591405 . G A 4623.36 PASS AC=2;AF=0.791;AN=2;DP=12565;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,330:330:99:9878,988,0:0,0,135,195 chr1 68593131 . C G 280.3 PASS AC=2;AF=0.652;AN=2;DP=375;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant15-variant16-variant18-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:366,30,0:0,0,2,8 chr1 68603432 . C T 175.43 PASS AC=2;AF=0.667;AN=2;DP=344;FractionInformativeReads=1;MQ=60;set=variant-variant7-variant8-variant18-variant20-variant22-variant24-variant28-variant29-variant33-variant35-variant39 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:996,84,0:0,0,21,7 chr1 68603586 . C T 1022.83 PASS AC=2;AF=0.604;AN=2;DP=2135;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant15-variant16-variant18-variant20-variant22-variant24-variant26-variant27-variant28-variant29-variant33-variant35-variant36-variant37-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,103:103:99:3241,309,0:0,0,53,50 chr1 68603731 . A G 341.22 PASS AC=2;AF=0.798;AN=2;DP=1292;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1323,123,0:0,0,13,28 chr1 68614013 . A G 1757.67 PASS AC=2;AF=1;AN=2;DP=2127;FS=0;MQ=60;MQRankSum=1.354;ReadPosRankSum=1.669;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1540,134,0:0,0,13,32 chr1 68620762 . G A 1024.13 PASS AC=2;AF=0.63;AN=2;DP=2391;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant35-variant36-variant37-variant39-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:2251,227,0:0,0,45,31 chr1 68660205 . A C 40.73 PASS AC=1;AF=0.729;AN=2;DP=169;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant13-variant14-variant15-variant17-variant19-variant22-variant23-variant25-variant26-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:3,4:7:62:108,0,62:0,3,1,3 chr1 68693796 . A G 175.7 PASS AC=1;AF=0.5;AN=2;DP=27;FS=0;FractionInformativeReads=1;MQ=60;set=variant23-variant30-variant32-variant35 GT:AD:DP:GQ:PL:SB 0/1:3,4:7:99:152,0,116:3,0,4,0 chr1 68939744 . A G 759.61 PASS AC=2;AF=0.609;AN=2;DP=1415;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant7-variant8-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1837,147,0:0,0,39,10 chr1 68939908 . A G 11214 PASS AC=2;AF=0.977;AN=2;DP=13453;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,297:297:99:9052,890,0:0,0,157,140 chr1 68940883 . T TTA 3497.65 PASS AC=2;AF=0.763;AN=2;DP=8525;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,221:221:99:9814,664,0:0,0,103,118 chr1 68943436 . G A 498.72 PASS AC=2;AF=0.75;AN=2;DP=989;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:1215,81,0:0,0,14,13 chr1 68943442 . A G 501.72 PASS AC=2;AF=0.743;AN=2;DP=1024;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:1240,84,0:0,0,14,14 chr1 68943665 . T G 335.59 PASS AC=2;AF=0.606;AN=2;DP=1974;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant7-variant8-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,69:69:99:1903,206,0:0,0,34,35 chr1 68947318 . C CA 354.35 PASS AC=2;AF=0.852;AN=2;DP=3103;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,61:61:99:1972,186,0:0,0,27,34 chr1 68952564 . AACACACACAC AACACAC,AACACACAC,AACAC,A 93.24 PASS AC=0,1,0,0;AF=0.125,0.528,0.125,0.014;AN=2;DP=478;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:16:95:7,3,3,3 chr1 68960476 . T G 622.24 PASS AC=2;AF=0.765;AN=2;DP=519;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:453,39,0:0,0,3,10 chr1 70034052 . C T 1092.29 PASS AC=1;AF=0.542;AN=2;DP=1152;MQ=60;set=variant8-variant14-variant16-variant23-variant25-variant27-variant31-variant32-variant35-variant36-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,51:106:99:1355,0,1480:38,17,34,17 chr1 70034370 . C CCAGCCGCGTG 2219.88 PASS AC=2;AF=0.943;AN=2;DP=8469;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,208:208:99:9067,626,0:0,0,69,139 chr1 70226125 . T C 862.67 PASS AC=1;AF=0.542;AN=2;DP=470;MQ=60;set=variant4-variant8-variant9-variant11-variant14-variant15-variant31-variant33-variant34-variant35-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:28,23:51:99:582,0,907:4,24,8,15 chr1 70304758 . A G 952.03 PASS AC=1;AF=0.688;AN=2;DP=2386;MQ=60;set=variant-variant3-variant5-variant6-variant8-variant10-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,29:79:99:641,0,1225:25,25,18,11 chr1 70340629 . G A 2594.96 PASS AC=1;AF=0.722;AN=2;DP=7785;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:93,114:207:99:2799,0,2193:35,58,46,68 chr1 70397087 . T C 3168.89 PASS AC=1;AF=0.722;AN=2;DP=6777;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:103,121:224:99:2978,0,2438:58,45,68,53 chr1 70481939 . A AT 66.04 PASS AC=1;AF=0.5;AN=2;DP=7;FS=3.68;FractionInformativeReads=1;MQ=60;MQRankSum=-0.937;QD=9.43;ReadPosRankSum=-0.55;SOR=2.494;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:3,4:7:72:103,0,72:2,1,4,0 chr1 70587360 . C T 1755.48 PASS AC=1;AF=0.774;AN=2;DP=2499;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,17:52:99:400,0,917:20,15,10,7 chr1 70611347 . A G 5810.49 PASS AC=2;AF=0.966;AN=2;DP=7695;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,180:180:99:5668,540,0:0,0,97,83 chr1 70639201 . G A 497.99 PASS AC=1;AF=0.5;AN=2;DP=171;MQ=60;set=variant23-variant35 GT:AD:DP:GQ:PL:SB 0/1:53,36:89:99:745,0,1330:29,24,19,17 chr1 70644681 . A G 558.54 PASS AC=1;AF=0.5;AN=2;DP=45;FS=1.154;FractionInformativeReads=1;MQ=60;MQRankSum=-0.811;QD=12.41;ReadPosRankSum=-0.354;SOR=0.525;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:20,25:45:99:587,0,552:7,13,10,15 chr1 70654981 . GAAA GAA,GA,G,GAAAA 142.08 PASS AC=1,0,0,0;AF=0.265,0.176,0.118,0.015;AN=2;DP=3233;set=variant-variant2-variant3-filterInvariant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant29-variant31-variant34-variant35-variant36-filterInvariant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:DP:GQ:SB 0/1:64:99:10,23,14,17 chr1 70718273 . A ATT 8320.52 PASS AC=2;AF=1;AN=2;DP=7006;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,171:171:99:7579,518,0:0,0,93,78 chr1 70728221 . C A 1786.76 PASS AC=1;AF=0.5;AN=2;DP=278;MQ=60;set=variant23-variant35 GT:AD:DP:GQ:PL:SB 0/1:80,69:149:99:1890,0,2147:56,24,51,18 chr1 70819816 . C G 3366.44 PASS AC=1;AF=0.5;AN=2;DP=260;FS=0.949;FractionInformativeReads=1;MQ=60;MQRankSum=3.095;QD=12.95;ReadPosRankSum=-2.639;SOR=0.773;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:124,136:260:99:3395,0,2902:66,58,75,61 chr1 70896152 . A G 393.24 PASS AC=1;AF=0.5;AN=2;DP=56;FractionInformativeReads=1;MQ=60;set=variant26-variant35 GT:AD:DP:GQ:PL:SB 0/1:14,17:31:99:455,0,451:3,11,5,12 chr1 70904523 . T TTGTG,TTGTGTG,TTGTGTGTG,TTG 645.31 PASS AC=1,1,0,0;AF=0.488,0.321,0.024,0.012;AN=2;DP=2516;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:DP:GQ:SB 1/2:19:99:0,0,6,13 chr1 70904800 . G T 1456.49 PASS AC=1;AF=0.609;AN=2;DP=2732;MQ=60;set=variant-variant4-variant6-variant8-variant9-variant12-variant16-variant18-variant19-variant21-variant22-variant24-variant25-variant27-variant28-variant34-variant35-variant36-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,57:114:99:1439,0,1437:33,24,35,22 chr1 70905333 . A T 88.15 PASS AC=1;AF=0.625;AN=2;DP=156;MQ=60;set=variant2-variant3-variant8-variant15-variant17-variant23-variant26-variant27-variant29-variant30-variant33-variant35-variant36-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,4:10:95:95,0,158:1,5,0,4 chr1 71318261 . T C 1924.25 PASS AC=1;AF=0.55;AN=2;DP=1474;MQ=60;set=variant-variant11-variant13-variant22-variant25-variant26-variant34-variant35-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:83,68:151:99:1772,0,2284:40,43,28,40 chr1 71327936 . T TA 418.23 PASS AC=1;AF=0.684;AN=2;DP=896;MQ=60;set=variant-variant4-variant6-variant11-variant12-variant13-variant15-variant18-variant21-variant22-variant23-variant25-variant26-variant34-variant35-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,20:49:99:474,0,680:19,10,17,3 chr1 71328234 . A G 160.65 PASS AC=1;AF=0.711;AN=2;DP=289;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant6-variant11-variant12-variant13-variant15-variant18-variant21-variant22-variant23-variant25-variant26-variant34-variant35-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,8:19:99:295,0,375:1,10,1,7 chr1 71331430 . G A 1389.85 PASS AC=1;AF=0.583;AN=2;DP=1733;MQ=60;set=variant-variant11-variant12-variant13-variant18-variant25-variant26-variant34-variant35-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:66,92:158:99:2139,0,1719:30,36,46,46 chr1 71331498 . A G 3027.21 PASS AC=2;AF=0.955;AN=2;DP=5342;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,123:123:99:3723,369,0:0,0,56,67 chr1 71334870 . C T 1172.73 PASS AC=1;AF=0.672;AN=2;DP=3747;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:62,69:131:99:1645,0,1537:35,27,42,27 chr1 71419499 . C T 1045.7 PASS AC=2;AF=0.86;AN=2;DP=1554;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:973,84,0:0,0,8,20 chr1 71436747 . C A 3689.55 PASS AC=1;AF=0.529;AN=2;DP=4183;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant13-variant18-variant21-variant22-variant24-variant29-variant31-variant32-variant35-variant36-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:129,97:226:99:2548,0,3451:68,61,45,52 chr1 71440217 . C T 121.69 PASS AC=1;AF=0.71;AN=2;DP=243;FractionInformativeReads=1;MQ=60;set=variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant23-variant26-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,5:10:99:195,0,195:1,4,0,5 chr1 71474782 . A G 2877.86 PASS AC=1;AF=0.6;AN=2;DP=4180;MQ=60;set=variant-variant2-variant5-variant13-variant18-variant21-variant22-variant24-variant29-variant31-variant32-variant35-variant36-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:116,106:222:99:2767,0,3220:65,51,67,39 chr1 71475710 . C T 5253.68 PASS AC=1;AF=0.6;AN=2;DP=6165;MQ=60;set=variant-variant2-variant5-variant13-variant18-variant21-variant22-variant24-variant29-variant31-variant32-variant35-variant36-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:203,186:389:99:4663,0,5154:108,95,92,94 chr1 71476872 . G A 1641.41 PASS AC=1;AF=0.633;AN=2;DP=3930;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant23-variant26-variant28-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:80,57:137:99:1637,0,2354:32,48,19,38 chr1 71477315 . A T 5382.82 PASS AC=1;AF=0.63;AN=2;DP=4112;MQ=60;set=variant-variant2-variant5-variant9-variant11-variant13-variant16-variant18-variant19-variant21-variant22-variant24-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:74,75:149:99:1999,0,2227:30,44,33,42 chr1 71536574 . G C 1265.12 PASS AC=1;AF=0.536;AN=2;DP=1293;MQ=60;set=variant2-variant4-variant11-variant17-variant20-variant23-variant26-variant28-variant30-variant35-variant37-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:49,40:89:99:944,0,1109:24,25,23,17 chr1 71869849 . T A 462.97 PASS AC=1;AF=0.5;AN=2;DP=121;FractionInformativeReads=1;MQ=60;set=variant5-variant35 GT:AD:DP:GQ:PL:SB 0/1:32,35:67:99:867,0,797:17,15,21,14 chr1 71870127 . G A 7671.11 PASS AC=2;AF=1;AN=2;DP=10283;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,227:227:99:6993,680,0:0,0,92,135 chr1 71870272 . C CT 1494.3 PASS AC=2;AF=1;AN=2;DP=2492;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1697,168,0:0,0,26,30 chr1 72058367 . C T 823.56 PASS AC=2;AF=0.989;AN=2;DP=918;MQ=60;MQRankSum=1.256;ReadPosRankSum=-2.927;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:788,69,0:0,0,18,5 chr1 72058405 . T C 1230.37 PASS AC=2;AF=0.989;AN=2;DP=1599;MQ=60;MQRankSum=0.456;ReadPosRankSum=-0.76;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1517,135,0:0,0,32,13 chr1 72058552 . G A 2583.01 PASS AC=2;AF=0.989;AN=2;DP=4517;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,104:104:99:3257,312,0:0,0,47,57 chr1 72058775 . G A 145.31 PASS AC=2;AF=0.988;AN=2;DP=345;FS=0;MQ=60;MQRankSum=0.198;ReadPosRankSum=1.495;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:501,39,0:0,0,2,11 chr1 72242039 . G A 356.44 PASS AC=2;AF=0.951;AN=2;DP=574;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:492,42,0:0,0,3,11 chr1 72748277 . ATTTTTTTT ATTTTTTTTT,ATTTTTTTTTT,A,ATTTTTTTTTTTT,ATTTTTTTTTTT,ATTTTTTTTTTTTT,AT 36.03 PASS AC=0,1,0,0,0,0,0;AF=0.25,0.115,0.038,0.058,0.077,0.038,0.019;AN=2;DP=2234;set=filterInvariant2-variant3-filterInvariant5-variant8-filterInvariant10-filterInvariant11-filterInvariant13-variant15-filterInvariant16-filterInvariant17-filterInvariant18-variant21-variant22-filterInvariant24-variant25-filterInvariant26-variant27-filterInvariant28-filterInvariant29-filterInvariant31-filterInvariant32-variant33-variant34-filterInvariant35-variant36-filterInvariant37 GT:DP:GQ:SB 0/2:15:39:0,4,2,9 chr1 74491800 . T A 4303.35 PASS AC=2;AF=0.953;AN=2;DP=5238;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,130:130:99:3887,388,0:0,0,80,50 chr1 74507711 . T G 535.76 PASS AC=2;AF=0.964;AN=2;DP=464;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:215,15,0:0,0,0,5 chr1 74575182 . C T 1488.2 PASS AC=2;AF=0.953;AN=2;DP=2300;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:1996,204,0:0,0,40,28 chr1 74610233 . TAA TA,TAAA,T 196.97 PASS AC=1,0,0;AF=0.283,0.133,0.1;AN=2;DP=887;set=variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant22-variant23-variant24-filterInvariant25-variant27-variant28-variant31-variant33-variant34-variant35-variant36-filterInvariant37-filterInvariant39-variant40-variant41-variant44 GT:DP:GQ:SB 0/1:21:99:4,7,4,6 chr1 74645641 . A G 3363.68 PASS AC=2;AF=0.953;AN=2;DP=3463;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,89:89:99:3046,267,0:0,0,67,22 chr1 74646514 . C T 1605.52 PASS AC=2;AF=1;AN=2;DP=2047;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1407,108,0:0,0,5,31 chr1 74663709 . G A 374.6 PASS AC=1;AF=0.712;AN=2;DP=1665;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,31:61:99:858,0,681:18,12,20,11 chr1 74663814 . C G 1136.42 PASS AC=1;AF=0.712;AN=2;DP=3691;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:63,53:116:99:1242,0,1440:33,30,26,27 chr1 74664149 . T C 919.85 PASS AC=1;AF=0.712;AN=2;DP=3458;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,50:107:99:1348,0,1389:22,35,19,31 chr1 74665493 . G A 1513.15 PASS AC=1;AF=0.712;AN=2;DP=5057;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:79,71:150:99:1631,0,2006:34,45,29,42 chr1 74666507 . T C 891.92 PASS AC=1;AF=0.625;AN=2;DP=1208;MQ=60;set=variant-variant2-variant5-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant20-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant35-variant36-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:40,27:67:99:571,0,913:21,19,14,13 chr1 74669973 . T G 399.7 PASS AC=2;AF=0.964;AN=2;DP=377;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:135,9,0:0,0,3,0 chr1 74670172 . A G 1719.88 PASS AC=1;AF=0.625;AN=2;DP=2840;MQ=60;set=variant-variant2-variant5-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant20-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant35-variant36-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:69,71:140:99:1697,0,1592:38,31,41,30 chr1 74671519 . A G 4618.95 PASS AC=1;AF=0.712;AN=2;DP=8828;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:120,150:270:99:3671,0,2930:56,64,82,68 chr1 74672323 . C A 4620.89 PASS AC=1;AF=0.712;AN=2;DP=12005;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:192,181:373:99:4660,0,5166:101,91,100,81 chr1 74672474 . G A 3804.42 PASS AC=1;AF=0.712;AN=2;DP=13061;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:240,220:460:99:5241,0,5883:109,131,101,119 chr1 74672640 . T A 4971.62 PASS AC=1;AF=0.712;AN=2;DP=13530;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:207,204:411:99:4996,0,5121:111,96,113,91 chr1 74699331 . C G 1073.11 PASS AC=1;AF=0.71;AN=2;DP=3197;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:63,34:97:99:836,0,1624:32,31,15,19 chr1 74701295 . T A 236.09 PASS AC=2;AF=1;AN=2;DP=231;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:312,21,0:0,0,1,6 chr1 74701950 . T A 354.72 PASS AC=1;AF=0.655;AN=2;DP=1113;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant15-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,32:47:99:847,0,314:5,10,12,20 chr1 74716515 . CT CTT,C 472.78 PASS AC=1,0;AF=0.329,0.195;AN=2;DP=4467;set=variant-variant2-filterInvariant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-filterInvariant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-filterInvariant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:65:99:8,22,11,24 chr1 74819077 . T G 2467.88 PASS AC=2;AF=0.932;AN=2;DP=4018;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,84:84:99:2580,252,0:0,0,35,49 chr1 74836916 . A G 2895.57 PASS AC=2;AF=0.756;AN=2;DP=8992;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,217:217:99:6394,650,0:0,0,127,90 chr1 74836977 . A T 3743.5 PASS AC=2;AF=0.756;AN=2;DP=12687;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,281:281:99:8387,838,0:0,0,133,148 chr1 74837216 . T TAG 7050.36 PASS AC=2;AF=1;AN=2;DP=7081;FS=0;MQ=60;MQRankSum=2.045;ReadPosRankSum=0.574;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,149:149:99:6644,448,0:0,0,79,70 chr1 74837776 . GAAAAAAAAA GA,G,GAAAAAAA,GAAAAAAAA 3323.8 PASS AC=2,0,0,0;AF=0.795,0.057,0.011,0.057;AN=2;DP=5576;set=Intersection GT:DP:GQ:SB 1/1:91:99:0,1,44,46 chr1 74838026 . A G 4433.92 PASS AC=1;AF=0.69;AN=2;DP=3069;MQ=60;set=variant2-variant3-variant6-variant8-variant11-variant12-variant17-variant19-variant20-variant21-variant22-variant23-variant27-variant29-variant32-variant33-variant34-variant35-variant37-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:80,62:142:99:1637,0,2046:29,51,20,42 chr1 74841173 . A C 1553.67 PASS AC=2;AF=1;AN=2;DP=2525;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,63:63:99:2144,189,0:0,0,39,24 chr1 74936374 . A G 3468.76 PASS AC=2;AF=0.743;AN=2;DP=3977;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,94:94:99:3124,282,0:0,0,44,50 chr1 74936454 . G C 3039.5 PASS AC=2;AF=0.716;AN=2;DP=4099;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,85:85:99:2639,254,0:0,0,46,39 chr1 74937749 . A G 4541.5 PASS AC=2;AF=0.716;AN=2;DP=6028;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,180:180:99:5542,539,0:0,0,90,90 chr1 74941210 . C T 5433.34 PASS AC=2;AF=0.716;AN=2;DP=6287;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,158:158:99:4795,473,0:0,0,90,68 chr1 74941293 . G A 7972.53 PASS AC=2;AF=0.743;AN=2;DP=9160;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,261:261:99:8074,781,0:0,0,134,127 chr1 75005776 . A G 118.69 PASS AC=2;AF=0.639;AN=2;DP=120;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant6-variant7-variant13-variant16-variant17-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant32-variant35-variant36-variant37 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:357,24,0:0,0,7,1 chr1 75006076 . G A 1109.78 PASS AC=2;AF=0.966;AN=2;DP=1278;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:851,72,0:0,0,5,19 chr1 75010117 . T C 4196.43 PASS AC=2;AF=0.966;AN=2;DP=5150;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,113:113:99:3873,338,0:0,0,26,87 chr1 75010153 . A G 2191.27 PASS AC=2;AF=0.966;AN=2;DP=2302;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:2033,147,0:0,0,4,45 chr1 75035240 . C T 2146.72 PASS AC=1;AF=0.591;AN=2;DP=4935;MQ=60;set=variant2-variant3-variant6-variant8-variant11-variant12-variant13-variant17-variant19-variant21-variant22-variant23-variant24-variant33-variant34-variant35-variant36-variant37-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:95,104:199:99:2500,0,2377:47,48,48,56 chr1 75036783 . T C 3240.83 PASS AC=2;AF=1;AN=2;DP=5005;FS=0;MQ=60;MQRankSum=0.214;ReadPosRankSum=-1.538;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,105:105:99:3591,315,0:0,0,67,38 chr1 75036812 . C T 4009.56 PASS AC=2;AF=1;AN=2;DP=6400;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,137:137:99:4576,410,0:0,0,87,50 chr1 75037845 . A G 1282.58 PASS AC=1;AF=0.614;AN=2;DP=2900;MQ=60;set=variant2-variant3-variant6-variant8-variant11-variant12-variant13-variant17-variant19-variant21-variant22-variant23-variant24-variant33-variant34-variant35-variant36-variant37-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:92,69:161:99:1629,0,2199:45,47,35,34 chr1 75038228 . A C 2164.17 PASS AC=1;AF=0.609;AN=2;DP=3764;MQ=60;set=variant2-variant3-variant6-variant8-variant11-variant12-variant13-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant33-variant34-variant35-variant36-variant37-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:93,107:200:99:2500,0,2127:47,46,57,50 chr1 75072264 . G T 190.65 PASS AC=1;AF=0.639;AN=2;DP=881;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,21:34:99:497,0,331:10,3,14,7 chr1 75097426 . G C 866.23 PASS AC=1;AF=0.667;AN=2;DP=3500;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,42:87:99:1084,0,1060:27,18,27,15 chr1 75100640 . A G 94.66 PASS AC=1;AF=0.662;AN=2;DP=706;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,7:20:99:129,0,367:6,7,3,4 chr1 75108863 . A C 1486.22 PASS AC=1;AF=0.791;AN=2;DP=2175;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,29:60:99:693,0,891:9,22,10,19 chr1 75112573 . GACAC GACACACACAC,GACACACAC,G 156.8 PASS AC=1,0,0;AF=0.618,0.029,0.059;AN=2;DP=77;FS=0;set=variant2-variant6-variant7-variant9-variant10-variant12-variant17-variant24-variant27-variant28-variant31-variant32-variant35-variant38-variant41-variant42-variant44 GT:DP:GQ:SB 0/1:5:58:1,0,3,1 chr1 75171109 . A T 201.09 PASS AC=1;AF=0.63;AN=2;DP=391;MQ=60;set=variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant17-variant19-variant20-variant21-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:7,3:10:99:105,0,234:6,1,3,0 chr1 75171211 . G A 1179.01 PASS AC=1;AF=0.63;AN=2;DP=2885;MQ=60;set=variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant17-variant19-variant20-variant21-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:63,55:118:99:1331,0,1610:42,21,36,19 chr1 75171751 . T C 3588.85 PASS AC=2;AF=0.703;AN=2;DP=12748;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,326:326:99:10142,976,0:0,0,158,168 chr1 75172001 . T A 2157.25 PASS AC=1;AF=0.63;AN=2;DP=4085;MQ=60;set=variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant17-variant19-variant20-variant21-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:105,90:195:99:2163,0,2740:50,55,48,42 chr1 75172756 . TAA TA,TAAA,T 509.32 PASS AC=2,0,0;AF=0.392,0.054,0.311;AN=2;DP=2336;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:68:99:1,1,32,34 chr1 75190452 . C T 2572.53 PASS AC=2;AF=0.775;AN=2;DP=3741;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,97:97:99:2898,291,0:0,0,47,50 chr1 75198740 . A C 1169.71 PASS AC=1;AF=0.692;AN=2;DP=1333;FractionInformativeReads=1;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,19:36:99:492,0,527:11,6,9,10 chr1 75198763 . A C 698.8 PASS AC=2;AF=1;AN=2;DP=1735;FS=0;MQ=60;MQRankSum=-0.433;ReadPosRankSum=1.589;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1861,126,0:0,0,23,17 chr1 75198787 . G A 639.53 PASS AC=1;AF=0.5;AN=2;DP=268;MQ=60;set=variant3-variant28-variant31-variant35-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,32:56:99:786,0,590:14,10,18,14 chr1 75199152 . C T 3618.33 PASS AC=2;AF=1;AN=2;DP=5827;FS=0;MQ=60;MQRankSum=1.641;ReadPosRankSum=0.524;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,140:140:99:4727,420,0:0,0,52,88 chr1 75199299 . C G 1253.73 PASS AC=1;AF=0.692;AN=2;DP=1365;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,22:43:99:585,0,597:5,16,6,16 chr1 75214375 . CCAAA C 1036.23 PASS AC=1;AF=0.5;AN=2;DP=322;MQ=60;set=variant3-variant28-variant31-variant35-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,27:60:99:1035,0,1304:20,13,16,11 chr1 75214390 . G C 552.22 PASS AC=1;AF=0.645;AN=2;DP=1619;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,38:67:99:938,0,626:18,11,23,15 chr1 75232213 . G A 167.85 PASS AC=1;AF=0.673;AN=2;DP=305;set=variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant20-variant23-variant25-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,8:14:99:182,0,191:5,1,5,3 chr1 75600506 . ATT A,AT,ATTTT 392.99 PASS AC=0,0,1;AF=0.263,0.171,0.368;AN=2;DP=882;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant42-variant43-variant44 GT:DP:GQ:SB 0/3:18:89:3,1,9,5 chr1 75602384 . G T 2626.13 PASS AC=1;AF=0.609;AN=2;DP=2834;MQ=60;set=variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant19-variant20-variant22-variant25-variant28-variant29-variant30-variant34-variant35-variant36-variant37-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:45,72:117:99:1911,0,1257:10,35,22,50 chr1 75603055 . A G 2827.66 PASS AC=2;AF=1;AN=2;DP=3764;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,97:97:99:3099,291,0:0,0,39,58 chr1 75603101 . A G 1217.7 PASS AC=1;AF=0.609;AN=2;DP=1487;MQ=60;set=variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant19-variant20-variant22-variant25-variant28-variant29-variant30-variant34-variant35-variant36-variant37-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:36,37:73:99:955,0,940:14,22,16,21 chr1 75603207 . G T 363.4 PASS AC=1;AF=0.63;AN=2;DP=456;MQ=60;set=variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant19-variant20-variant22-variant25-variant28-variant29-variant30-variant34-variant35-variant36-variant37-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:7,8:15:99:256,0,227:0,7,1,7 chr1 75614380 . CT C 750.98 PASS AC=1;AF=0.763;AN=2;DP=2933;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,35:62:99:677,0,515:10,17,11,24 chr1 75622616 . C T 3215.79 PASS AC=1;AF=0.625;AN=2;DP=3840;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant12-variant13-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,81:141:99:2009,0,1512:34,26,37,44 chr1 75626420 . A T 2176.96 PASS AC=2;AF=0.943;AN=2;DP=1979;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1576,120,0:0,0,36,4 chr1 75627328 . C T 1962.09 PASS AC=2;AF=0.943;AN=2;DP=1910;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,61:61:99:2348,183,0:0,0,6,55 chr1 75627354 . C CA,CAA 61.24 PASS AC=1,0;AF=0.161,0.532;AN=2;DP=619;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant35-variant36-variant37-variant38-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:20:99:0,8,0,12 chr1 75670670 . C A 2618.44 PASS AC=1;AF=0.567;AN=2;DP=3512;MQ=60;set=variant2-variant4-variant5-variant9-variant10-variant11-variant13-variant14-variant15-variant22-variant27-variant35-variant37-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:143,97:240:99:2747,0,3735:69,74,44,53 chr1 75670957 . G A 2385.39 PASS AC=1;AF=0.556;AN=2;DP=1552;set=variant4-variant9-variant10-variant11-variant15-variant22-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:104,74:178:99:1729,0,2476:48,56,28,46 chr1 75671215 . C T 873.1 PASS AC=1;AF=0.563;AN=2;DP=759;MQ=60;set=variant4-variant9-variant10-variant11-variant15-variant22-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:38,55:93:99:1597,0,1030:22,16,36,19 chr1 75671687 . T C 5138.71 PASS AC=1;AF=0.567;AN=2;DP=5882;MQ=60;set=variant2-variant4-variant5-variant9-variant10-variant11-variant13-variant14-variant15-variant22-variant27-variant35-variant37-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:157,199:356:99:5086,0,3995:71,86,92,107 chr1 75672134 . T C 1254.96 PASS AC=1;AF=0.567;AN=2;DP=2128;MQ=60;set=variant2-variant4-variant5-variant9-variant10-variant11-variant13-variant14-variant15-variant22-variant27-variant35-variant37-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:55,69:124:99:1878,0,1590:29,26,34,35 chr1 75679569 . C CT,CTT 108.32 PASS AC=0,1;AF=0.25,0.313;AN=2;DP=682;MQ=60;set=variant2-variant4-variant5-variant9-variant10-variant11-variant13-variant14-variant15-variant21-variant22-variant27-variant35-variant37-variant41-variant42 GT:DP:GQ:SB 0/2:27:99:6,7,4,10 chr1 75680433 . G A 1839.74 PASS AC=1;AF=0.661;AN=2;DP=1787;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant6-variant8-variant12-variant13-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,21:66:99:390,0,1272:16,29,9,12 chr1 75680545 . T G 1085.63 PASS AC=1;AF=0.857;AN=2;DP=1204;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,15:38:99:427,0,587:8,15,5,10 chr1 75680565 . G A 1019.52 PASS AC=1;AF=0.857;AN=2;DP=1006;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,12:31:99:319,0,507:7,12,4,8 chr1 75681351 . A T 981.97 PASS AC=1;AF=0.857;AN=2;DP=811;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,13:21:99:401,0,277:8,0,11,2 chr1 75681511 . T C 4173.6 PASS AC=1;AF=0.907;AN=2;DP=6078;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:74,51:125:99:1126,0,1696:34,40,24,27 chr1 75685403 . T C 2428.61 PASS AC=1;AF=0.685;AN=2;DP=2412;MQ=60;set=variant-variant2-variant3-variant6-variant8-variant12-variant13-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,44:99:99:1006,0,1211:31,24,28,16 chr1 75699646 . T C 479.53 PASS AC=1;AF=0.583;AN=2;DP=1409;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant11-variant13-variant14-variant19-variant20-variant24-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,43:59:99:1127,0,388:13,3,28,15 chr1 75699771 . A G 837.83 PASS AC=1;AF=0.583;AN=2;DP=2783;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant11-variant13-variant14-variant19-variant20-variant24-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,59:117:99:1406,0,1309:29,29,26,33 chr1 75699831 . G A 527.6 PASS AC=1;AF=0.583;AN=2;DP=1691;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant11-variant13-variant14-variant19-variant20-variant24-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,33:70:99:812,0,923:15,22,12,21 chr1 75699932 . G A 196.77 PASS AC=1;AF=0.632;AN=2;DP=166;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant8-variant11-variant13-variant14-variant19-variant20-variant24-variant26-variant27-variant28-variant32-variant35-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,5:13:99:137,0,294:0,8,1,4 chr1 75702674 . G A 876.38 PASS AC=1;AF=0.55;AN=2;DP=1044;MQ=60;set=variant-variant3-variant6-variant8-variant11-variant13-variant19-variant20-variant24-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,20:41:99:560,0,504:14,7,14,6 chr1 75704070 . CATATATATATATAT CAT,C 143.09 PASS AC=2,0;AF=0.714,0.214;AN=2;DP=137;FS=0;MQ=60;set=variant-variant2-variant3-variant5-variant8-variant11-variant13-variant14-variant19-variant20-variant24-variant27-variant28-variant32-variant33-variant34-variant35-variant39-variant41-variant42-variant44 GT:DP:GQ:SB 1/1:6:19:0,0,4,2 chr1 75707410 . C T 43.71 PASS AC=1;AF=0.579;AN=2;DP=203;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant6-variant8-variant13-variant19-variant20-variant24-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,5:7:70:204,0,70:2,0,5,0 chr1 75707652 . C T 946.26 PASS AC=1;AF=0.583;AN=2;DP=2768;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant11-variant13-variant14-variant19-variant20-variant24-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:70,62:132:99:1511,0,1829:33,37,29,33 chr1 75708529 . A T 1261.13 PASS AC=1;AF=0.583;AN=2;DP=2034;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant11-variant13-variant14-variant19-variant20-variant24-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,58:107:99:1452,0,1161:31,18,39,19 chr1 75716925 . C T 754.59 PASS AC=1;AF=0.75;AN=2;DP=3949;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,50:108:99:1127,0,1600:21,37,22,28 chr1 75766186 . G A 205.42 PASS AC=1;AF=0.697;AN=2;DP=331;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,6:8:67:205,0,67:2,0,5,1 chr1 75823084 . C T 365.08 PASS AC=2;AF=0.988;AN=2;DP=762;FractionInformativeReads=1;MQ=60;MQRankSum=-1.264;ReadPosRankSum=-1.92;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:882,75,0:0,0,5,20 chr1 75868236 . G T 170.81 PASS AC=1;AF=0.575;AN=2;DP=284;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant6-variant8-variant11-variant13-variant16-variant19-variant20-variant24-variant26-variant27-variant28-variant33-variant34-variant35-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,7:18:99:239,0,323:3,8,0,7 chr1 76143505 . T C 345.13 PASS AC=2;AF=0.955;AN=2;DP=502;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:276,24,0:0,0,2,6 chr1 76190216 . G A 2131.28 PASS AC=1;AF=0.595;AN=2;DP=5021;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant8-variant10-variant11-variant12-variant13-variant16-variant25-variant26-variant30-variant32-variant34-variant35-variant36-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:115,123:238:99:2724,0,2798:60,55,61,62 chr1 76190568 . C T 1156.03 PASS AC=1;AF=0.533;AN=2;DP=1583;MQ=60;set=variant-variant2-variant3-variant4-variant8-variant11-variant12-variant16-variant25-variant30-variant34-variant35-variant36-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:68,44:112:99:1003,0,1817:24,44,13,31 chr1 76194229 . GT G 3235.25 PASS AC=2;AF=1;AN=2;DP=3651;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,66:66:99:2272,199,0:0,0,25,41 chr1 76194306 . A G 1137.78 PASS AC=2;AF=0.943;AN=2;DP=781;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:684,48,0:0,0,0,16 chr1 76229326 . T C 400 PASS AC=1;AF=0.744;AN=2;DP=717;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,13:23:99:376,0,250:3,7,4,9 chr1 76234886 . A G 1056.39 PASS AC=2;AF=0.955;AN=2;DP=1855;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:1300,143,0:0,0,23,25 chr1 76235001 . A G 167.47 PASS AC=1;AF=0.565;AN=2;DP=219;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant11-variant15-variant16-variant18-variant22-variant24-variant27-variant28-variant29-variant35-variant36-variant37-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,6:10:99:196,0,145:0,4,1,5 chr1 76251746 . T C 597.25 PASS AC=1;AF=0.724;AN=2;DP=1067;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:21,17:38:99:472,0,692:17,4,12,5 chr1 76252011 . G A 2043.55 PASS AC=1;AF=0.718;AN=2;DP=8543;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:105,97:202:99:2467,0,2729:46,59,36,61 chr1 76252687 . T C 778.03 PASS AC=1;AF=0.718;AN=2;DP=1537;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:21,36:57:99:938,0,476:14,7,22,14 chr1 76253045 . T TA 79.12 PASS AC=1;AF=0.605;AN=2;DP=343;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant8-variant12-variant13-variant16-variant25-variant26-variant30-variant32-variant34-variant35-variant36-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:14,14:28:99:437,0,440:9,5,8,6 chr1 76255613 . A G 828.93 PASS AC=1;AF=0.605;AN=2;DP=893;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant8-variant12-variant13-variant16-variant25-variant26-variant30-variant32-variant34-variant35-variant36-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:22,24:46:99:607,0,678:18,4,16,8 chr1 76257074 . AT ATT,A 762.4 PASS AC=1,0;AF=0.548,0.024;AN=2;DP=2048;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant11-variant15-variant18-variant24-variant27-variant28-variant29-filterInvariant31-variant35-variant36-variant37-variant38-variant39-variant44 GT:DP:GQ:SB 0/1:92:99:20,32,16,24 chr1 76257892 . A T 2559.55 PASS AC=2;AF=0.943;AN=2;DP=3603;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2232,210,0:0,0,44,26 chr1 76260866 . CTTTTT CTT,CTTT,CT,CTTTT,CTTTTTT,C 222.11 PASS AC=0,2,0,0,0,0;AF=0.214,0.143,0.143,0.071,0.018,0.036;AN=2;DP=1323;set=variant-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant16-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-filterInvariant42 GT:DP:GQ:SB 2/2:12:4:2,1,1,8 chr1 76269460 . G A 1117.07 PASS AC=1;AF=0.605;AN=2;DP=1307;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant8-variant12-variant13-variant16-variant25-variant26-variant30-variant32-variant34-variant35-variant36-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:38,32:70:99:687,0,993:25,13,18,14 chr1 76272837 . A G 750.9 PASS AC=1;AF=0.55;AN=2;DP=1205;FractionInformativeReads=1;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant11-variant15-variant18-variant24-variant27-variant28-variant29-variant35-variant36-variant37-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,31:63:99:720,0,729:14,18,13,18 chr1 76280543 . A G 161.28 PASS AC=2;AF=0.905;AN=2;DP=264;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:271,21,0:0,0,6,1 chr1 76333352 . G A 237.06 PASS AC=1;AF=0.571;AN=2;DP=155;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant9-variant28-variant35-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,9:17:99:270,0,273:1,7,2,7 chr1 76344011 . C A 2054.29 PASS AC=2;AF=0.756;AN=2;DP=2784;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,81:81:99:2464,242,0:0,0,30,51 chr1 76344705 . T C 985.85 PASS AC=1;AF=0.575;AN=2;DP=2054;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant11-variant15-variant18-variant24-variant27-variant28-variant29-variant35-variant36-variant37-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,55:107:99:1340,0,1205:30,22,33,22 chr1 76344711 . A T 3982.71 PASS AC=2;AF=0.756;AN=2;DP=4172;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,110:112:99:4010,287,0:1,1,65,45 chr1 76344920 . G A 670.76 PASS AC=2;AF=1;AN=2;DP=602;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:781,54,0:0,0,0,18 chr1 76345640 . G T 625.87 PASS AC=2;AF=0.697;AN=2;DP=853;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:875,87,0:0,0,19,10 chr1 76345884 . T A 212.07 PASS AC=1;AF=0.575;AN=2;DP=330;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant11-variant15-variant18-variant24-variant27-variant28-variant29-variant35-variant36-variant37-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,7:15:99:186,0,195:3,5,2,5 chr1 76346920 . C CAT 4262.9 PASS AC=2;AF=1;AN=2;DP=3567;FS=0;MQ=60;MQRankSum=0.137;ReadPosRankSum=-2.254;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,80:80:99:3574,241,0:0,0,53,27 chr1 76349534 . C G 752.44 PASS AC=1;AF=0.605;AN=2;DP=902;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant8-variant12-variant13-variant16-variant25-variant26-variant30-variant32-variant34-variant35-variant36-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:20,26:46:99:690,0,551:4,16,6,20 chr1 76363505 . A C 253.59 PASS AC=1;AF=0.605;AN=2;DP=246;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant8-variant12-variant13-variant16-variant25-variant26-variant30-variant32-variant34-variant35-variant36-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:10,4:14:97:97,0,327:8,2,3,1 chr1 76378275 . G C 54.21 PASS AC=1;AF=0.692;AN=2;DP=81;FS=0;MQ=60;set=variant-variant3-variant4-variant7-variant8-variant12-variant16-variant25-variant34-variant35-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:2,4:6:59:121,0,59:2,0,3,1 chr1 76378357 . ATAT A 551.29 PASS AC=1;AF=0.579;AN=2;DP=542;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant8-variant12-variant13-variant16-variant25-variant26-variant30-variant32-variant34-variant35-variant36-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:8,15:23:99:554,0,288:5,3,12,3 chr1 76378361 . T A 240.04 PASS AC=1;AF=0.558;AN=2;DP=579;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-filterInvariant9-variant10-variant11-variant15-variant16-variant17-filterInvariant22-variant24-variant27-variant28-variant29-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,8:23:99:261,0,688:12,3,5,3 chr1 76378363 . T A 239.97 PASS AC=1;AF=0.529;AN=2;DP=381;set=variant-variant2-variant3-variant5-variant6-variant9-variant15-variant22-variant24-variant28-variant29-variant35-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,7:25:99:261,0,688:13,5,4,3 chr1 76387748 . T A 429.93 PASS AC=1;AF=0.575;AN=2;DP=753;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant11-variant15-variant18-variant24-variant27-variant28-variant29-variant35-variant36-variant37-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,21:45:99:482,0,664:17,7,16,5 chr1 76397972 . C T 2883.09 PASS AC=1;AF=0.563;AN=2;DP=4408;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant11-variant15-variant18-variant21-variant24-variant27-variant28-variant29-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:83,85:168:99:2264,0,1970:42,41,49,36 chr1 76398249 . A T 206.22 PASS AC=1;AF=0.575;AN=2;DP=242;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant11-variant15-variant18-variant24-variant27-variant28-variant29-variant35-variant36-variant37-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,5:8:99:193,0,113:0,3,0,5 chr1 76398282 . T TTCTAAGAATTC 97.73 PASS AC=1;AF=0.75;AN=2;DP=76;FS=0;MQ=60;set=variant2-variant5-variant10-variant16-variant19-variant21-variant22-variant24-variant28-variant35-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,2:4:78:78,0,169:0,2,0,2 chr1 76540291 . C G 143.51 PASS AC=2;AF=0.632;AN=2;DP=190;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant18-variant21-variant22-variant23-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:99,12,0:0,0,2,2 chr1 76608777 . C T 417.52 PASS AC=2;AF=0.708;AN=2;DP=503;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:443,39,0:0,0,3,10 chr1 76771475 . G T 443.17 PASS AC=2;AF=0.813;AN=2;DP=2667;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:1861,177,0:0,0,39,20 chr1 76771495 . G C 2152.91 PASS AC=1;AF=0.529;AN=2;DP=1488;MQ=60;set=variant2-variant6-variant8-variant11-variant12-variant13-variant16-variant18-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:39,41:80:99:1074,0,963:25,14,28,13 chr1 77092972 . A G 377.97 PASS AC=1;AF=0.5;AN=2;DP=253;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant12-variant21-variant26-variant27-variant28-variant30-variant33-variant34-variant35-variant36-variant37-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:3,12:15:88:399,0,88:3,0,10,2 chr1 77098562 . A G 12223.8 PASS AC=2;AF=0.977;AN=2;DP=17186;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,390:390:99:11573,1167,0:0,0,190,200 chr1 77530101 . TAC T 1192.19 PASS AC=2;AF=0.706;AN=2;DP=1381;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,52:52:99:1860,157,0:0,0,34,18 chr1 77531223 . A C 2790.43 PASS AC=1;AF=0.5;AN=2;DP=1854;MQ=60;set=variant3-variant6-variant9-variant14-variant16-variant29-variant35-variant36-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:91,96:187:99:2540,0,2245:38,53,45,51 chr1 77554542 . G A 985.25 PASS AC=1;AF=0.579;AN=2;DP=1001;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant12-variant14-variant20-variant21-variant22-variant25-variant27-variant35-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:26,25:51:99:775,0,720:20,6,20,5 chr1 77555481 . C T 1094.39 PASS AC=2;AF=0.77;AN=2;DP=4190;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,115:115:99:3674,345,0:0,0,54,61 chr1 77555737 . C T 2296.93 PASS AC=1;AF=0.5;AN=2;DP=2209;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant9-variant12-variant21-variant22-variant25-variant27-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:86,87:173:99:2321,0,2367:59,27,56,31 chr1 77556766 . T A 2602.95 PASS AC=1;AF=0.589;AN=2;DP=5531;MQ=60;set=variant2-variant4-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:99,76:175:99:1508,0,2513:59,40,51,25 chr1 77558057 . G C 144.97 PASS AC=1;AF=0.5;AN=2;DP=917;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant12-variant14-variant21-variant22-variant25-variant27-variant28-variant34-variant35-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:15,32:47:99:786,0,360:9,6,17,15 chr1 77588131 . T C 44.17 PASS AC=1;AF=0.577;AN=2;DP=106;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant6-variant7-variant9-variant12-variant21-variant22-variant25-variant27-variant28-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:3,2:5:75:75,0,80:1,2,0,2 chr1 77595399 . AAAATAAAT AAAAT,A 98.18 PASS AC=0,2;AF=0.5,0.5;AN=2;DP=10;FS=0;FractionInformativeReads=0.5;set=variant16-variant35 GT:DP:GQ:SB 2/2:2:6:0,0,0,2 chr1 77620035 . T C 9960.51 PASS AC=2;AF=1;AN=2;DP=13635;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,317:317:99:9511,949,0:0,0,142,175 chr1 77627096 . G A 1673.78 PASS AC=2;AF=1;AN=2;DP=2297;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,52:52:99:1782,156,0:0,0,20,32 chr1 77634948 . G A 2024.33 PASS AC=2;AF=1;AN=2;DP=3376;FS=0;MQ=60;MQRankSum=0.231;ReadPosRankSum=-0.52;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,66:66:99:1811,198,0:0,0,37,29 chr1 77747738 . G T 158.28 PASS AC=1;AF=0.5;AN=2;DP=123;FractionInformativeReads=1;MQ=60;set=variant12-variant13-variant18-variant27-variant28-variant35 GT:AD:DP:GQ:PL:SB 0/1:16,9:25:99:228,0,467:9,7,6,3 chr1 77748664 . C T 2632.92 PASS AC=2;AF=0.646;AN=2;DP=2824;MQ=60;set=variant-variant3-variant5-variant8-variant11-variant12-variant13-variant17-variant18-variant20-variant22-variant23-variant27-variant28-variant32-variant33-variant34-variant35-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,117:117:99:3678,350,0:0,0,65,52 chr1 77748786 . A G 2926.04 PASS AC=2;AF=0.63;AN=2;DP=3110;MQ=60;set=variant-variant3-variant5-variant8-variant11-variant12-variant13-variant15-variant17-variant18-variant20-variant22-variant23-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,153:153:99:4342,459,0:0,0,74,79 chr1 77749322 . T C 230.06 PASS AC=1;AF=0.583;AN=2;DP=182;MQ=60;set=variant-variant20-variant22-variant35-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:15,9:24:99:171,0,446:4,11,4,5 chr1 77752544 . TAATTA T 88.36 PASS AC=1;AF=0.625;AN=2;DP=49;FS=0;FractionInformativeReads=1;MQ=60;set=variant22-variant35-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:5,7:12:99:279,0,181:3,2,4,3 chr1 77752921 . TG T 63.17 PASS AC=1;AF=0.6;AN=2;DP=40;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant20-variant35-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:4,3:7:95:95,0,140:1,3,0,3 chr1 77763071 . A G 575.17 PASS AC=2;AF=0.881;AN=2;DP=1502;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1410,123,0:0,0,30,11 chr1 77763542 . G A 2505.3 PASS AC=2;AF=1;AN=2;DP=3408;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,81:81:99:2392,243,0:0,0,38,43 chr1 77948729 . G T 227.91 PASS AC=1;AF=0.5;AN=2;DP=21;FractionInformativeReads=1;MQ=60;set=variant-variant35 GT:AD:DP:GQ:PL:SB 0/1:5,3:8:86:86,0,159:3,2,2,1 chr1 77948866 . A T 1301.71 PASS AC=1;AF=0.5;AN=2;DP=109;FractionInformativeReads=1;MQ=60;set=variant-variant35 GT:AD:DP:GQ:PL:SB 0/1:28,25:53:99:961,0,1511:14,14,16,9 chr1 77948868 . A G 1301.71 PASS AC=1;AF=0.5;AN=2;DP=107;FractionInformativeReads=1;MQ=60;set=variant-variant35 GT:AD:DP:GQ:PL:SB 0/1:28,25:53:99:961,0,1511:14,14,16,9 chr1 77949123 . G A 838.36 PASS AC=2;AF=0.587;AN=2;DP=814;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant11-variant12-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant31-variant32-variant35-variant36-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1487,108,0:0,0,15,21 chr1 77949129 . A T 838.36 PASS AC=2;AF=0.587;AN=2;DP=727;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant11-variant12-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant31-variant32-variant35-variant36-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:93:1334,93,0:0,0,8,20 chr1 78001881 . T C 672.23 PASS AC=2;AF=0.989;AN=2;DP=922;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.52;ReadPosRankSum=-1.283;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:814,81,0:0,0,10,17 chr1 78001947 . A G 367.63 PASS AC=2;AF=0.853;AN=2;DP=320;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:316,24,0:0,0,2,6 chr1 78024284 . T C 1566.53 PASS AC=2;AF=0.816;AN=2;DP=1570;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1199,114,0:0,0,26,12 chr1 78024345 . C CTAT 3973.66 PASS AC=2;AF=0.816;AN=2;DP=2848;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,73:73:99:3325,223,0:0,0,45,28 chr1 78024602 . A G 3079.28 PASS AC=2;AF=0.829;AN=2;DP=4546;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,140:140:99:4257,418,0:0,0,76,64 chr1 78025047 . G A 7309.15 PASS AC=2;AF=0.816;AN=2;DP=6517;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,158:158:99:7097,479,0:0,0,78,80 chr1 78025049 . C T 7309.15 PASS AC=2;AF=0.816;AN=2;DP=6527;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,156:156:99:7097,479,0:0,0,77,79 chr1 78025230 . GTATT G 3492.33 PASS AC=2;AF=0.811;AN=2;DP=3476;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,86:86:99:3802,259,0:0,0,39,47 chr1 78025454 . G T 14457.7 PASS AC=2;AF=0.816;AN=2;DP=11395;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,279:279:99:10586,841,0:0,0,143,136 chr1 78025459 . T C 5214.12 PASS AC=1;AF=0.605;AN=2;DP=5694;MQ=60;set=variant-variant3-variant5-variant12-variant14-variant15-variant17-variant18-variant22-variant23-variant25-variant27-variant28-variant30-variant31-variant35-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:129,150:279:99:3728,0,3097:67,62,76,74 chr1 78025551 . C T 8166.95 PASS AC=2;AF=0.811;AN=2;DP=8440;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,227:227:99:6844,678,0:0,0,91,136 chr1 78031994 . A G 414.75 PASS AC=2;AF=0.829;AN=2;DP=421;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:570,39,0:0,0,0,13 chr1 78033981 . AAAATG A 724.84 PASS AC=2;AF=0.814;AN=2;DP=765;set=variant-variant2-variant3-variant4-variant6-variant7-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:795,54,0:0,0,10,8 chr1 78045369 . G A 111.22 PASS AC=2;AF=0.828;AN=2;DP=347;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:219,21,0:0,0,1,6 chr1 78177213 . TACACAC TACAC,TAC,TACACACAC,T 1561.22 PASS AC=1,0,0,0;AF=0.795,0.08,0.034,0.023;AN=2;DP=2458;set=Intersection GT:DP:GQ:SB 0/1:47:99:16,10,20,1 chr1 78179032 . AT A 202.96 PASS AC=1;AF=0.611;AN=2;DP=485;MQ=60;set=variant-variant3-variant12-variant14-variant15-variant17-variant18-variant22-variant23-variant25-variant27-variant28-variant30-variant31-variant35-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,11:22:99:243,0,248:1,10,2,9 chr1 78184433 . G A 170.18 PASS AC=1;AF=0.571;AN=2;DP=104;MQ=60;set=variant-variant3-variant12-variant14-variant18-variant22-variant25-variant27-variant28-variant31-variant35-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,4:7:99:156,0,103:0,3,0,4 chr1 78281002 . T C 402.67 PASS AC=2;AF=0.806;AN=2;DP=643;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:672,54,0:0,0,2,16 chr1 78342409 . C T 2094.65 PASS AC=1;AF=0.5;AN=2;DP=619;MQ=60;set=variant7-variant16-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:74,76:150:99:2104,0,2002:30,44,28,48 chr1 78343510 . C T 1643.25 PASS AC=1;AF=0.5;AN=2;DP=855;set=variant18-variant27-variant35 GT:AD:DP:GQ:PL:SB 0/1:169,122:291:99:2190,0,4244:86,83,63,59 chr1 78383467 . G A 198.37 PASS AC=2;AF=0.869;AN=2;DP=745;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:766,60,0:0,0,3,17 chr1 78390046 . C CA,CAA 192.01 PASS AC=2,0;AF=0.825,0.013;AN=2;DP=1737;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:52:99:1,1,23,27 chr1 78399207 . C G 162.14 PASS AC=2;AF=0.882;AN=2;DP=834;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:402,36,0:0,0,3,9 chr1 78414310 . CA C,CAA 383.11 PASS AC=0,1;AF=0.352,0.148;AN=2;DP=9486;set=filterInvariant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-filterInvariant11-filterInvariant12-variant13-filterInvariant14-variant15-filterInvariant16-variant17-filterInvariant18-variant19-variant20-variant21-filterInvariant22-filterInvariant23-variant24-variant25-variant26-variant27-variant28-filterInvariant29-filterInvariant30-variant31-filterInvariant32-variant33-variant34-variant35-filterInvariant36-filterInvariant37-variant38-variant39-variant40-filterInvariant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:DP:GQ:SB 0/2:147:99:48,25,41,33 chr1 78430689 . A AG 2765.93 PASS AC=2;AF=1;AN=2;DP=3589;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,96:96:99:3514,289,0:0,0,50,46 chr1 78471060 . T TC 258.63 PASS AC=2;AF=0.897;AN=2;DP=342;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:287,24,0:0,0,1,7 chr1 78478675 . G A 642.14 PASS AC=2;AF=0.882;AN=2;DP=1296;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1140,99,0:0,0,22,11 chr1 78481640 . G A 642.32 PASS AC=2;AF=0.882;AN=2;DP=1996;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1476,135,0:0,0,29,16 chr1 78483422 . T A 3114.26 PASS AC=2;AF=0.882;AN=2;DP=8642;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,246:246:99:7301,733,0:0,0,108,138 chr1 78483452 . C CT,CTT 1096.43 PASS AC=1,0;AF=0.464,0.036;AN=2;DP=7713;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:172:94:11,18,53,90 chr1 78560583 . G A 1657.58 PASS AC=1;AF=0.611;AN=2;DP=693;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant8-variant9-variant12-variant16-variant19-variant20-variant26-variant27-variant30-variant31-variant33-variant35-variant36-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:15,23:38:99:674,0,360:9,6,17,6 chr1 78578177 . T C 2425.27 PASS AC=1;AF=0.595;AN=2;DP=3557;MQ=60;set=variant3-variant4-variant5-variant6-variant8-variant9-variant12-variant15-variant16-variant19-variant21-variant27-variant30-variant31-variant33-variant35-variant36-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:72,109:181:99:2737,0,1544:32,40,45,64 chr1 78585086 . T C 2447.93 PASS AC=1;AF=0.567;AN=2;DP=1135;MQ=60;set=variant4-variant5-variant6-variant8-variant9-variant12-variant16-variant19-variant27-variant30-variant31-variant33-variant35-variant36-variant42 GT:AD:DP:GQ:PL:SB 0/1:47,41:88:99:959,0,1214:32,15,22,19 chr1 78601465 . C CT 1887.77 PASS AC=1;AF=0.553;AN=2;DP=3469;MQ=60;set=variant2-variant4-variant5-variant6-variant8-variant9-variant12-variant16-variant17-variant19-variant27-variant30-variant31-variant33-variant35-variant36-variant37-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:93,99:192:99:2370,0,2237:43,50,48,51 chr1 78602292 . CTTTTT CTTTT,CTTTTTTT,C,CT,CTTTTTT,CTTTTTTTT,CTTT,CTT 532.37 PASS AC=0,0,1,0,0,0,0,0;AF=0.056,0.125,0.111,0.125,0.042,0.014,0.069,0.028;AN=2;DP=4313;set=variant-variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/3:100:99:14,23,22,41 chr1 78602461 . A T 5476.15 PASS AC=2;AF=1;AN=2;DP=7850;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,163:163:99:5105,488,0:0,0,94,69 chr1 78602491 . A T 7861.7 PASS AC=1;AF=0.563;AN=2;DP=3286;MQ=60;set=variant4-variant5-variant6-variant8-variant9-variant12-variant16-variant19-variant27-variant30-variant31-variant33-variant35-variant36-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:110,85:195:99:2061,0,2820:60,50,50,35 chr1 78602941 . C T 12464.1 PASS AC=1;AF=0.563;AN=2;DP=5652;MQ=60;set=variant4-variant5-variant6-variant8-variant9-variant12-variant16-variant19-variant27-variant30-variant31-variant33-variant35-variant36-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:191,178:369:99:4947,0,4864:90,101,81,97 chr1 78603067 . A G 13541.4 PASS AC=1;AF=0.563;AN=2;DP=5657;MQ=60;set=variant4-variant5-variant6-variant8-variant9-variant12-variant16-variant19-variant27-variant30-variant31-variant33-variant35-variant36-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:179,179:358:99:4335,0,4844:92,87,94,85 chr1 78603279 . A G 10334.3 PASS AC=1;AF=0.73;AN=2;DP=10312;set=variant-variant2-variant3-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:129,156:285:99:4366,0,3251:57,72,70,86 chr1 78603383 . G A 9199.09 PASS AC=2;AF=0.849;AN=2;DP=10058;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,226:226:99:6851,676,0:0,0,110,116 chr1 78603422 . AC A 8592.34 PASS AC=1;AF=0.563;AN=2;DP=3777;MQ=60;set=variant4-variant5-variant6-variant8-variant9-variant12-variant16-variant19-variant27-variant30-variant31-variant33-variant35-variant36-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:150,90:240:99:2619,0,4891:75,75,43,47 chr1 78603463 . T C 3270.62 PASS AC=1;AF=0.648;AN=2;DP=7417;MQ=60;set=variant2-variant3-variant5-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:98,157:255:99:4197,0,2476:50,48,76,81 chr1 78603687 . T TTTC 12258.5 PASS AC=1;AF=0.563;AN=2;DP=3532;MQ=60;set=variant4-variant5-variant6-variant8-variant9-variant12-variant16-variant19-variant27-variant30-variant31-variant33-variant35-variant36-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:132,96:228:99:3702,0,5035:56,76,48,48 chr1 78603708 . T C 10709.8 PASS AC=1;AF=0.563;AN=2;DP=3124;MQ=60;set=variant4-variant5-variant6-variant8-variant9-variant12-variant16-variant19-variant27-variant30-variant31-variant33-variant35-variant36-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:119,92:211:99:3282,0,4633:47,72,43,49 chr1 78603789 . C T 5782.36 PASS AC=1;AF=0.563;AN=2;DP=2612;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant6-variant8-variant9-variant12-variant16-variant19-variant27-variant30-variant31-variant33-variant35-variant36-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:88,102:190:99:2637,0,2318:37,51,44,58 chr1 78603846 . G A 5272.19 PASS AC=1;AF=0.563;AN=2;DP=2520;MQ=60;set=variant4-variant5-variant6-variant8-variant9-variant12-variant16-variant19-variant27-variant30-variant31-variant33-variant35-variant36-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:81,99:180:99:2408,0,1890:36,45,46,53 chr1 78604096 . C T 795.92 PASS AC=1;AF=0.563;AN=2;DP=379;MQ=60;set=variant4-variant5-variant6-variant8-variant9-variant12-variant16-variant19-variant27-variant30-variant31-variant33-variant35-variant36-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,7:19:99:159,0,320:4,8,2,5 chr1 79094593 . A G 1392.26 PASS AC=2;AF=0.977;AN=2;DP=2705;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,80:80:99:2252,238,0:0,0,40,40 chr1 79106967 . C T 1548.59 PASS AC=1;AF=0.675;AN=2;DP=747;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant9-variant12-variant14-variant15-variant16-variant19-variant23-variant25-variant27-variant32-variant35-variant36-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,20:39:99:535,0,597:5,14,5,15 chr1 79108069 . CAA C,CA 53.58 PASS AC=0,2;AF=0.625,0.25;AN=2;DP=17;FS=0;MQ=60;MQRankSum=0.727;ReadPosRankSum=-0.727;set=variant5-variant18-variant29-variant35 GT:DP:GQ:SB 2/2:3:9:0,0,2,1 chr1 79115905 . T C 1677.5 PASS AC=1;AF=0.5;AN=2;DP=936;FractionInformativeReads=1;MQ=60;set=variant10-variant17-variant19-variant21-variant24-variant27-variant35-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:56,47:103:99:1113,0,1489:39,17,28,19 chr1 79124961 . G T 156.21 PASS AC=1;AF=0.611;AN=2;DP=132;FractionInformativeReads=1;MQ=60;set=variant10-variant17-variant19-variant21-variant24-variant27-variant35-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:12,8:20:99:246,0,358:9,3,6,2 chr1 79128320 . A G 292.2 PASS AC=1;AF=0.588;AN=2;DP=514;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:3,11:14:82:363,0,82:3,0,10,1 chr1 79128570 . G GT 1498.57 PASS AC=1;AF=0.586;AN=2;DP=4270;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:54,53:107:99:1816,0,1856:25,29,22,31 chr1 79129694 . A G 1622.78 PASS AC=1;AF=0.563;AN=2;DP=999;MQ=60;set=variant17-variant19-variant21-variant24-variant27-variant35-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:55,58:113:99:1764,0,1539:16,39,19,39 chr1 79355596 . A G 4165.27 PASS AC=2;AF=0.786;AN=2;DP=5121;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,93:93:99:2921,279,0:0,0,50,43 chr1 79355911 . A C 832.82 PASS AC=2;AF=1;AN=2;DP=1524;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:809,78,0:0,0,12,14 chr1 79358743 . CA C,CAA,CAAA,CAAAA 531.01 PASS AC=0,1,0,0;AF=0.129,0.226,0.145,0.065;AN=2;DP=784;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant24-variant27-variant30-variant31-variant32-filterInvariant33-variant35-variant36-variant37-variant39-variant41-variant42-filterInvariant43-variant44 GT:DP:GQ:SB 0/2:18:59:5,2,8,3 chr1 79358811 . G A 678.99 PASS AC=1;AF=0.5;AN=2;DP=61;FS=0.975;FractionInformativeReads=1;MQ=60;MQRankSum=-1.306;QD=11.13;ReadPosRankSum=0.238;SOR=0.529;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:31,30:61:99:707,0,717:18,13,16,14 chr1 79383300 . CA C 469.04 PASS AC=2;AF=0.703;AN=2;DP=1114;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant25-variant27-variant28-variant31-variant32-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1475,120,0:0,0,25,15 chr1 79383458 . A T 1388.73 PASS AC=2;AF=0.743;AN=2;DP=3347;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,85:87:99:2404,211,0:1,1,41,44 chr1 79385807 . T C 421.62 PASS AC=1;AF=0.5;AN=2;DP=66;FractionInformativeReads=1;MQ=60;set=variant7-variant22-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,5:12:99:135,0,232:6,1,4,1 chr1 79392756 . C A 849.37 PASS AC=2;AF=0.743;AN=2;DP=2874;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,89:89:99:2792,267,0:0,0,31,58 chr1 79401927 . A G 940.12 PASS AC=2;AF=0.743;AN=2;DP=1790;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1180,123,0:0,0,24,17 chr1 79403751 . T G 1553.34 PASS AC=2;AF=0.714;AN=2;DP=4303;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,127:127:99:3916,381,0:0,0,70,57 chr1 79411888 . T C 867.81 PASS AC=2;AF=0.726;AN=2;DP=593;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant25-variant27-variant28-variant31-variant32-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:393,27,0:0,0,9,0 chr1 79411918 . A G 519.34 PASS AC=1;AF=0.5;AN=2;DP=178;FractionInformativeReads=1;MQ=60;set=variant7-variant22-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,11:28:99:278,0,546:14,3,7,4 chr1 79472141 . C A 570.93 PASS AC=2;AF=0.788;AN=2;DP=2084;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1502,138,0:0,0,33,13 chr1 81970883 . CCACACA CCA,CCACACACA,CCACA,C 124.73 PASS AC=0,0,1,0;AF=0.286,0.095,0.143,0.071;AN=2;DP=205;set=variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant14-variant15-variant17-variant19-variant20-variant23-variant24-variant25-variant26-variant31-variant35-variant37-variant39-variant41 GT:DP:GQ:SB 0/3:18:85:8,5,4,1 chr1 82227391 . T TA 901.28 PASS AC=1;AF=0.632;AN=2;DP=1457;MQ=60;set=variant-variant2-variant4-variant6-variant10-variant11-variant13-variant14-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,17:48:99:526,0,1109:21,10,14,3 chr1 82302600 . T C 6654.63 PASS AC=1;AF=0.726;AN=2;DP=11435;MQ=60;set=variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:195,184:379:99:4302,0,4850:88,107,87,97 chr1 82402364 . TAATC T 502.54 PASS AC=1;AF=0.556;AN=2;DP=916;MQ=60;set=variant-variant3-variant4-variant6-variant8-variant9-variant10-variant13-variant14-variant15-variant19-variant20-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,22:38:99:866,0,853:10,6,15,7 chr1 82415814 . T C 1316.62 PASS AC=2;AF=1;AN=2;DP=1907;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1256,114,0:0,0,28,10 chr1 82415982 . A T 1386.18 PASS AC=1;AF=0.5;AN=2;DP=136;FS=2.187;FractionInformativeReads=1;MQ=60;MQRankSum=-1.906;QD=10.19;ReadPosRankSum=-3.131;SOR=0.57;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:77,59:136:99:1414,0,1901:42,35,29,30 chr1 82416220 . G A 265.16 PASS AC=1;AF=0.707;AN=2;DP=1181;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,11:24:99:368,0,384:3,10,2,9 chr1 82417552 . T G 747.46 PASS AC=1;AF=0.703;AN=2;DP=579;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,11:20:99:350,0,257:6,3,9,2 chr1 82421596 . C T 2985.77 PASS AC=2;AF=1;AN=2;DP=4861;FS=0;MQ=60;MQRankSum=-0.763;ReadPosRankSum=-0.587;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,87:87:99:2696,261,0:0,0,50,37 chr1 82450153 . A G 596.72 PASS AC=1;AF=0.5;AN=2;DP=31;FS=2;FractionInformativeReads=1;MQ=60;MQRankSum=-0.31;QD=19.25;ReadPosRankSum=-0.186;SOR=0.324;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:11,20:31:99:625,0,356:10,1,16,4 chr1 82450365 . A G 1558.61 PASS AC=1;AF=0.5;AN=2;DP=139;FS=0.627;FractionInformativeReads=1;MQ=60;MQRankSum=0.432;QD=11.21;ReadPosRankSum=0.634;SOR=0.614;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:70,69:139:99:1587,0,1810:32,38,33,36 chr1 82451152 . G A 87.17 PASS AC=1;AF=0.5;AN=2;DP=8;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.922;QD=10.9;ReadPosRankSum=0.922;SOR=0.148;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:99:115,0,159:0,4,1,3 chr1 82456930 . T G 792.95 PASS AC=1;AF=0.5;AN=2;DP=378;FractionInformativeReads=1;set=variant-variant14-variant15-variant18-variant24-variant28-variant30-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:19,17:36:99:503,0,557:12,7,9,8 chr1 82457069 . C T 2988.95 PASS AC=1;AF=0.5;AN=2;DP=300;FS=2.501;FractionInformativeReads=1;MQ=60;MQRankSum=3.142;QD=9.96;ReadPosRankSum=-0.269;SOR=0.565;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:157,143:300:99:3017,0,3916:91,66,78,65 chr1 82457662 . G A 6658.85 PASS AC=2;AF=1;AN=2;DP=8855;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,202:202:99:6160,604,0:0,0,90,112 chr1 82459781 . C A 704.47 PASS AC=1;AF=0.5;AN=2;DP=584;MQ=60;set=variant-variant14-variant15-variant18-variant24-variant28-variant30-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:37,43:80:99:902,0,923:15,22,16,27 chr1 84332235 . A G 4149.43 PASS AC=2;AF=0.829;AN=2;DP=13511;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,346:346:99:10784,1036,0:0,0,195,151 chr1 84335412 . C T 735.28 PASS AC=2;AF=0.559;AN=2;DP=1070;FractionInformativeReads=1;MQ=60;set=variant7-variant10-variant11-variant12-variant13-variant18-variant20-variant23-variant25-variant27-variant33-variant35-variant37-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:2319,225,0:0,0,28,47 chr1 84394792 . G A 470.57 PASS AC=2;AF=0.545;AN=2;DP=768;FractionInformativeReads=1;MQ=60;set=variant10-variant11-variant12-variant20-variant23-variant25-variant27-variant33-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,66:66:99:2104,198,0:0,0,44,22 chr1 84640691 . T G 2281.91 PASS AC=2;AF=0.989;AN=2;DP=2996;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,63:63:99:1644,188,0:0,0,32,31 chr1 84640834 . T G 46.72 PASS AC=1;AF=0.64;AN=2;DP=263;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant6-variant9-variant10-variant11-variant12-variant14-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant31-variant33-variant35-variant36-variant37-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,7:19:99:177,0,326:3,9,2,5 chr1 84641304 . A C 498.97 PASS AC=1;AF=0.559;AN=2;DP=608;FractionInformativeReads=1;MQ=60;set=variant8-variant9-variant11-variant13-variant14-variant16-variant20-variant23-variant25-variant28-variant32-variant33-variant34-variant35-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,22:33:99:663,0,290:9,2,17,5 chr1 84662217 . A T 265.63 PASS AC=1;AF=0.5;AN=2;DP=202;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant9-variant10-variant12-variant25-variant33-variant35-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,10:19:99:285,0,271:7,2,8,2 chr1 84670439 . A AC 102.02 PASS AC=1;AF=0.657;AN=2;DP=593;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,9:16:99:344,0,472:3,4,3,6 chr1 84670457 . A G 76.67 PASS AC=1;AF=0.662;AN=2;DP=607;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,8:18:99:306,0,517:5,5,3,5 chr1 84670584 . T A 373.02 PASS AC=1;AF=0.657;AN=2;DP=1091;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,9:23:99:288,0,399:9,5,7,2 chr1 84670816 . A C 4326.47 PASS AC=1;AF=0.662;AN=2;DP=11253;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:162,191:353:99:4703,0,3916:85,77,108,83 chr1 84701251 . T C 14146.6 PASS AC=1;AF=0.845;AN=2;DP=15778;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:212,186:398:99:5115,0,5531:116,96,118,68 chr1 84702474 . C T 5033.59 PASS AC=1;AF=0.5;AN=2;DP=4710;MQ=60;set=variant-variant2-variant9-variant12-variant25-variant27-variant33-variant35-variant37-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:211,210:421:99:5273,0,5326:83,128,91,119 chr1 84764993 . C T 73.73 PASS AC=1;AF=0.55;AN=2;DP=198;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant14-variant16-variant19-variant20-variant23-variant26-variant29-variant33-variant35-variant37-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,8:15:99:193,0,233:5,2,5,3 chr1 84765340 . GTA GTATATA,GTATATATA,G,GTATA 77.65 PASS AC=2,0,0,0;AF=0.364,0.364,0.045,0.091;AN=2;DP=234;MQ=60;set=variant-variant7-variant10-filterInvariant12-variant21-variant27-variant31-variant35-variant36-variant39-variant43 GT:DP:GQ:SB 1/1:3:8:0,0,1,2 chr1 84768224 . TACACAC TACACACACAC,TACAC,TACACACAC,TAC,T 48.65 PASS AC=0,0,0,1,0;AF=0.025,0.075,0.05,0.225,0.25;AN=2;DP=281;set=variant5-variant7-variant9-variant10-variant11-variant12-variant18-variant22-variant23-variant25-variant27-variant28-variant30-variant31-variant32-variant34-variant35-filterInvariant37-variant38-variant44 GT:DP:GQ:SB 0/4:12:99:3,1,6,2 chr1 84768861 . C T 475.14 PASS AC=1;AF=0.5;AN=2;DP=201;FractionInformativeReads=1;MQ=60;set=variant12-variant22-variant35-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,19:48:99:513,0,847:15,14,11,8 chr1 84791239 . T C 147.98 PASS AC=2;AF=0.939;AN=2;DP=341;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:222,15,0:0,0,5,0 chr1 84810396 . A C 621.51 PASS AC=1;AF=0.886;AN=2;DP=658;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:7,9:16:99:306,0,226:6,1,8,1 chr1 84810815 . A G 4618.04 PASS AC=2;AF=0.977;AN=2;DP=5495;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,123:124:99:3804,331,0:1,0,57,66 chr1 84816123 . C T 1237.72 PASS AC=2;AF=0.966;AN=2;DP=2037;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1159,105,0:0,0,21,14 chr1 84853957 . A T 941.07 PASS AC=2;AF=0.977;AN=2;DP=2295;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1126,117,0:0,0,24,15 chr1 84873835 . A G 1517.6 PASS AC=1;AF=0.686;AN=2;DP=2079;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,39:65:99:885,0,677:16,10,23,16 chr1 84876711 . C CA 2151.3 PASS AC=1;AF=0.686;AN=2;DP=2162;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,34:77:99:1123,0,1517:13,30,5,29 chr1 84876731 . T G 1075.19 PASS AC=1;AF=0.686;AN=2;DP=1551;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,19:47:99:581,0,926:6,22,2,17 chr1 84878228 . C T 1458.16 PASS AC=1;AF=0.5;AN=2;DP=1015;MQ=60;set=variant2-variant5-variant6-variant7-variant13-variant15-variant23-variant25-variant30-variant34-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:39,34:73:99:981,0,1105:20,19,13,21 chr1 84878380 . A G 1010.64 PASS AC=2;AF=1;AN=2;DP=2168;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,56:57:99:1742,133,0:1,0,22,34 chr1 84880775 . T C 1010.5 PASS AC=2;AF=1;AN=2;DP=1678;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1636,129,0:0,0,6,37 chr1 84944989 . A G 606.02 PASS AC=1;AF=0.713;AN=2;DP=2255;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,29:65:99:702,0,1020:14,22,15,14 chr1 84946745 . C T 904.12 PASS AC=2;AF=0.989;AN=2;DP=1124;MQ=60;MQRankSum=-0.488;ReadPosRankSum=-0.387;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:682,57,0:0,0,4,15 chr1 84963000 . A G 858.28 PASS AC=1;AF=0.58;AN=2;DP=1121;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant13-variant14-variant15-variant16-variant18-variant21-variant24-variant26-variant28-variant30-variant32-variant34-variant35-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:22,19:41:99:550,0,623:15,7,14,5 chr1 84972099 . G T 374.53 PASS AC=1;AF=0.5;AN=2;DP=639;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant6-variant7-variant10-variant14-variant16-variant21-variant24-variant26-variant35-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:35,13:48:99:388,0,954:15,20,4,9 chr1 84982259 . T C 475.99 PASS AC=1;AF=0.577;AN=2;DP=774;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant13-variant14-variant15-variant16-variant18-variant21-variant24-variant26-variant28-variant30-variant31-variant32-variant34-variant35-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:19,11:30:99:203,0,371:9,10,6,5 chr1 84986213 . AT A 222.41 PASS AC=2;AF=0.955;AN=2;DP=1071;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:704,75,0:0,0,21,4 chr1 84991488 . T G 875.17 PASS AC=1;AF=0.5;AN=2;DP=606;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant7-variant10-variant14-variant16-variant21-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:39,37:76:99:896,0,922:20,19,21,16 chr1 84998445 . C G 284.64 PASS AC=1;AF=0.6;AN=2;DP=451;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant10-variant13-variant14-variant16-variant18-variant21-variant24-variant26-variant31-variant34-variant35-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:5,6:11:99:213,0,118:4,1,6,0 chr1 84998637 . T C 569.24 PASS AC=1;AF=0.5;AN=2;DP=112;FractionInformativeReads=1;MQ=60;set=variant18-variant35 GT:AD:DP:GQ:PL:SB 0/1:29,24:53:99:641,0,713:11,18,8,16 chr1 84999571 . T C 284.4 PASS AC=1;AF=0.6;AN=2;DP=278;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant10-variant13-variant14-variant16-variant18-variant21-variant24-variant26-variant31-variant34-variant35-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:10,8:18:99:262,0,305:3,7,1,7 chr1 85009864 . C T 1568.55 PASS AC=1;AF=0.5;AN=2;DP=297;FractionInformativeReads=1;MQ=60;set=variant18-variant35 GT:AD:DP:GQ:PL:SB 0/1:55,65:120:99:1492,0,1413:31,24,39,26 chr1 85014679 . G A 583.65 PASS AC=1;AF=0.5;AN=2;DP=75;FractionInformativeReads=1;MQ=60;set=variant18-variant35 GT:AD:DP:GQ:PL:SB 0/1:11,20:31:99:470,0,272:2,9,8,12 chr1 85014690 . C G 407.7 PASS AC=1;AF=0.5;AN=2;DP=29;FS=3.853;FractionInformativeReads=1;MQ=60;MQRankSum=-0.382;QD=14.06;ReadPosRankSum=1.461;SOR=0.184;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:11,18:29:99:436,0,286:2,9,7,11 chr1 85016112 . C T 1562.13 PASS AC=1;AF=0.667;AN=2;DP=360;FractionInformativeReads=1;MQ=60;set=variant2-variant10-variant18-variant35-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:38,30:68:99:606,0,858:18,20,16,14 chr1 85016177 . A G 808.73 PASS AC=1;AF=0.6;AN=2;DP=1919;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant9-variant10-variant13-variant14-variant15-variant16-variant18-variant21-variant24-variant26-variant28-variant30-variant31-variant32-variant34-variant35-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:36,42:78:99:904,0,884:13,23,22,20 chr1 85018648 . C T 1326.71 PASS AC=1;AF=0.667;AN=2;DP=261;FractionInformativeReads=1;MQ=60;set=variant2-variant10-variant18-variant35-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:21,18:39:99:512,0,499:12,9,12,6 chr1 85019924 . T TG 2572.61 PASS AC=1;AF=0.667;AN=2;DP=351;MQ=60;set=variant2-variant10-variant18-variant35-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:41,29:70:99:873,0,1296:22,19,16,13 chr1 85020637 . G T 5550.18 PASS AC=1;AF=0.667;AN=2;DP=1104;FractionInformativeReads=1;MQ=60;set=variant2-variant10-variant18-variant35-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:83,102:185:99:2733,0,2021:48,35,59,43 chr1 85020649 . C T 5941.71 PASS AC=1;AF=0.667;AN=2;DP=1196;MQ=60;set=variant2-variant10-variant18-variant35-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:92,102:194:99:2586,0,2258:50,42,57,45 chr1 85035839 . T A 523.7 PASS AC=1;AF=0.5;AN=2;DP=108;FractionInformativeReads=1;MQ=60;set=variant18-variant35 GT:AD:DP:GQ:PL:SB 0/1:24,21:45:99:547,0,626:8,16,7,14 chr1 85036239 . C G 1735.15 PASS AC=1;AF=0.6;AN=2;DP=2467;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant10-variant13-variant14-variant16-variant18-variant21-variant24-variant26-variant31-variant34-variant35-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:76,56:132:99:1338,0,1981:45,31,35,21 chr1 85039718 . C T 184.87 PASS AC=1;AF=0.5;AN=2;DP=52;FractionInformativeReads=1;MQ=60;set=variant18-variant35 GT:AD:DP:GQ:PL:SB 0/1:14,14:28:99:363,0,427:11,3,11,3 chr1 85039998 . CGCAGCGCCA C 953.31 PASS AC=1;AF=0.575;AN=2;DP=2950;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant10-variant13-variant16-variant18-variant21-variant24-variant26-variant31-variant34-variant35-variant36-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:53,59:112:99:2226,0,4859:19,34,22,37 chr1 85094275 . ATG A 238.03 PASS AC=1;AF=0.5;AN=2;DP=439;MQ=60;set=variant-variant5-variant6-variant7-variant10-variant16-variant21-variant24-variant26-variant31-variant35-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:7,19:26:99:474,0,191:3,4,11,8 chr1 85094292 . TGC T 328.42 PASS AC=1;AF=0.674;AN=2;DP=1238;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,7:30:99:174,0,657:14,9,3,4 chr1 85095078 . A T 415.28 PASS AC=1;AF=0.563;AN=2;DP=379;MQ=60;set=variant2-variant8-variant11-variant18-variant35-variant36-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:20,30:50:99:813,0,626:14,6,19,11 chr1 85095457 . G A 579.88 PASS AC=1;AF=0.571;AN=2;DP=321;FractionInformativeReads=1;MQ=60;set=variant2-variant8-variant11-variant18-variant35-variant36-variant41 GT:AD:DP:GQ:PL:SB 0/1:21,15:36:99:367,0,573:7,14,6,9 chr1 85096589 . T G 1089.07 PASS AC=1;AF=0.563;AN=2;DP=702;MQ=60;set=variant2-variant8-variant11-variant18-variant35-variant36-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:53,32:85:99:774,0,1424:20,33,12,20 chr1 85100559 . C T 167.11 PASS AC=1;AF=0.571;AN=2;DP=103;FractionInformativeReads=1;MQ=60;set=variant6-variant13-variant16-variant19-variant21-variant26-variant35 GT:AD:DP:GQ:PL:SB 0/1:8,8:16:99:188,0,218:7,1,5,3 chr1 85110325 . C A 1867.36 PASS AC=1;AF=0.93;AN=2;DP=2587;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,26:68:99:837,0,1194:26,16,22,4 chr1 85111124 . C A 3422.37 PASS AC=1;AF=0.528;AN=2;DP=5592;MQ=60;set=variant-variant2-variant3-variant7-variant10-variant13-variant19-variant21-variant23-variant24-variant26-variant31-variant33-variant34-variant35-variant37-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:184,152:336:99:3508,0,4538:95,89,79,73 chr1 85112260 . T C 652.64 PASS AC=1;AF=0.5;AN=2;DP=349;FractionInformativeReads=1;MQ=60;set=variant13-variant21-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:32,49:81:99:1109,0,700:14,18,26,23 chr1 85112510 . C T 2043.22 PASS AC=1;AF=0.5;AN=2;DP=720;FractionInformativeReads=1;MQ=60;set=variant13-variant21-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:88,87:175:99:2053,0,2115:40,48,39,48 chr1 85113203 . T C 4118.59 PASS AC=1;AF=0.881;AN=2;DP=5255;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:73,69:142:99:1941,0,1868:31,42,21,48 chr1 85115852 . G T 10433.3 PASS AC=1;AF=0.881;AN=2;DP=12804;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:157,116:273:99:2811,0,4025:82,75,64,52 chr1 85121299 . GT G 214.19 PASS AC=1;AF=0.5;AN=2;DP=158;MQ=60;set=variant13-variant21-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:26,11:37:99:219,0,642:11,15,4,7 chr1 85121983 . A G 232.08 PASS AC=1;AF=0.5;AN=2;DP=43;FS=0;FractionInformativeReads=1;MQ=60;set=variant21-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:2,10:12:55:329,0,55:1,1,8,2 chr1 85123819 . A G 66.22 PASS AC=2;AF=0.946;AN=2;DP=126;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.937;set=variant2-variant3-variant7-variant8-variant9-variant12-variant13-variant14-variant16-variant17-variant19-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:90,6,0:0,0,2,0 chr1 85128262 . A G 1127.31 PASS AC=1;AF=0.774;AN=2;DP=2735;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,44:76:99:1184,0,811:14,18,15,29 chr1 85128280 . T C 1810.49 PASS AC=1;AF=0.93;AN=2;DP=2175;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,35:61:99:901,0,698:8,18,12,23 chr1 85131641 . G C 43.71 PASS AC=1;AF=0.803;AN=2;DP=342;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,9:14:99:322,0,178:5,0,7,2 chr1 85131982 . T G 435.13 PASS AC=1;AF=0.93;AN=2;DP=601;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,3:7:97:97,0,142:0,4,0,3 chr1 85137188 . T C 558.48 PASS AC=1;AF=0.5;AN=2;DP=64;FractionInformativeReads=1;MQ=60;set=variant21-variant35 GT:AD:DP:GQ:PL:SB 0/1:12,15:27:99:392,0,306:4,8,5,10 chr1 85278013 . C T 570.59 PASS AC=1;AF=0.5;AN=2;DP=194;MQ=60;set=variant5-variant10-variant25-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:28,20:48:99:463,0,652:14,14,10,10 chr1 85278106 . CTTTTTT CTTT,CTT,CTTTT,C 164.13 PASS AC=1,0,0,0;AF=0.281,0.25,0.094,0.031;AN=2;DP=222;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant11-variant15-variant20-variant21-variant23-variant27-variant34-variant35-variant43 GT:DP:GQ:SB 0/1:8:83:0,3,0,5 chr1 85278156 . C T 49.51 PASS AC=1;AF=0.5;AN=2;DP=3;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.736;QD=16.5;ReadPosRankSum=0.736;SOR=0.223;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:1,2:3:36:78,0,36:0,1,1,1 chr1 85278665 . A G 772.18 PASS AC=1;AF=0.762;AN=2;DP=1336;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,14:39:99:336,0,581:9,16,3,11 chr1 85278952 . T TTAAG 9889.36 PASS AC=1;AF=0.762;AN=2;DP=7813;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:77,81:158:99:3379,0,3872:48,29,53,28 chr1 85279077 . C T 12731.2 PASS AC=2;AF=0.833;AN=2;DP=15838;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,356:356:99:10188,1064,0:0,0,180,176 chr1 85331808 . G GAGA 2843.91 PASS AC=2;AF=0.841;AN=2;DP=3291;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:3586,244,0:0,0,30,49 chr1 85391564 . A C 649.9 PASS AC=1;AF=0.5;AN=2;DP=78;FractionInformativeReads=1;MQ=60;set=variant9-variant35 GT:AD:DP:GQ:PL:SB 0/1:15,14:29:99:488,0,659:4,11,4,10 chr1 85391575 . AT A,ATT 36.32 PASS AC=0,1;AF=0.25,0.25;AN=2;DP=235;set=variant-filterInvariant2-variant15-variant19-variant23-filterInvariant25-filterInvariant26-variant35-variant37-variant43 GT:DP:GQ:SB 0/2:20:99:5,7,3,5 chr1 85391582 . T TTG 574.43 PASS AC=1;AF=0.5;AN=2;DP=52;FS=0;FractionInformativeReads=1;MQ=60;set=variant9-variant35 GT:AD:DP:GQ:PL:SB 0/1:12,8:20:99:315,0,527:4,8,3,5 chr1 85391899 . A G 1278.31 PASS AC=2;AF=0.989;AN=2;DP=1706;FS=0;MQ=60;MQRankSum=-1.279;ReadPosRankSum=-3.767;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:2002,186,0:0,0,40,22 chr1 85392064 . C G 2238.78 PASS AC=1;AF=0.5;AN=2;DP=199;FS=4.048;FractionInformativeReads=1;MQ=60;MQRankSum=-1.694;QD=11.25;ReadPosRankSum=0.199;SOR=0.925;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:106,93:199:99:2267,0,2550:52,54,52,41 chr1 85397286 . G C 849.67 PASS AC=1;AF=0.611;AN=2;DP=1335;MQ=60;set=variant-variant3-variant6-variant9-variant15-variant20-variant21-variant24-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:36,43:79:99:1021,0,808:15,21,16,27 chr1 85417779 . G A 158.16 PASS AC=1;AF=0.719;AN=2;DP=394;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant12-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:2,4:6:62:162,0,62:2,0,3,1 chr1 85418307 . C G 340.83 PASS AC=2;AF=0.719;AN=2;DP=1689;MQ=60;set=variant-variant3-variant4-variant6-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1202,99,0:0,0,7,26 chr1 85422061 . C T 1894.6 PASS AC=2;AF=0.688;AN=2;DP=4973;MQ=60;set=variant-variant3-variant4-variant6-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,171:172:99:4925,504,0:0,1,93,78 chr1 85424182 . A G 1120.24 PASS AC=2;AF=0.646;AN=2;DP=1323;MQ=60;set=variant-variant6-variant9-variant12-variant13-variant15-variant17-variant18-variant21-variant22-variant23-variant24-variant26-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,48:49:99:1375,100,0:1,0,29,19 chr1 85424479 . A G 46.72 PASS AC=2;AF=0.711;AN=2;DP=111;FS=0;FractionInformativeReads=1;MQ=60;set=variant6-variant9-variant12-variant13-variant15-variant18-variant21-variant22-variant23-variant24-variant26-variant31-variant33-variant35-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:483,33,0:0,0,1,10 chr1 85462582 . C G 1039.52 PASS AC=2;AF=0.707;AN=2;DP=3153;set=variant-variant3-variant4-variant5-variant6-variant9-variant10-variant12-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant30-variant31-variant33-variant35-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,139:139:99:4291,415,0:0,0,61,78 chr1 85462652 . G T 806.75 PASS AC=2;AF=0.707;AN=2;DP=1621;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant9-variant10-variant12-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant30-variant31-variant33-variant35-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,74:74:99:3258,226,0:0,0,28,46 chr1 85462665 . T G 776.79 PASS AC=2;AF=0.707;AN=2;DP=1440;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant9-variant10-variant12-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant30-variant31-variant33-variant35-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:3246,229,0:0,0,28,47 chr1 85462750 . T C 468.11 PASS AC=2;AF=0.955;AN=2;DP=963;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1465,147,0:0,0,19,30 chr1 85464736 . C G 107.65 PASS AC=2;AF=0.75;AN=2;DP=63;FS=0;FractionInformativeReads=1;MQ=60;set=variant6-variant15-variant17-variant21-variant22-variant23-variant31-variant35-variant36-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:132,9,0:0,0,2,1 chr1 85464843 . T A 94.28 PASS AC=2;AF=0.707;AN=2;DP=603;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant9-variant10-variant12-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant30-variant31-variant33-variant35-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:677,63,0:0,0,15,6 chr1 85465026 . G A 64.65 PASS AC=2;AF=0.652;AN=2;DP=575;MQ=60;set=variant-variant5-variant6-variant9-variant12-variant15-variant17-variant18-variant21-variant22-variant23-variant24-variant26-variant30-variant31-variant33-variant35-variant36-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:871,72,0:0,0,8,16 chr1 85484366 . A G 2332.16 PASS AC=2;AF=0.83;AN=2;DP=3228;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,87:87:99:2626,261,0:0,0,48,39 chr1 85484473 . C T 2514.43 PASS AC=1;AF=0.756;AN=2;DP=4328;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,33:92:99:797,0,1767:28,31,15,18 chr1 85488030 . G A 3432.72 PASS AC=2;AF=0.83;AN=2;DP=4963;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,135:136:99:3882,396,0:1,0,60,75 chr1 85488154 . G C 583.31 PASS AC=2;AF=0.955;AN=2;DP=988;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:927,69,0:0,0,1,22 chr1 85490350 . G A 5364.5 PASS AC=1;AF=0.5;AN=2;DP=2138;MQ=60;set=variant5-variant15-variant21-variant26-variant35 GT:AD:DP:GQ:PL:SB 0/1:182,225:407:99:5400,0,4125:99,83,112,113 chr1 85491062 . T C 2587.08 PASS AC=1;AF=0.5;AN=2;DP=1194;MQ=60;set=variant5-variant15-variant21-variant26-variant35 GT:AD:DP:GQ:PL:SB 0/1:115,119:234:99:2966,0,3045:62,53,60,59 chr1 85507074 . G T 196.77 PASS AC=2;AF=1;AN=2;DP=430;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.666;ReadPosRankSum=1.179;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:253,18,0:0,0,0,6 chr1 85513398 . C T 268.23 PASS AC=1;AF=0.545;AN=2;DP=91;MQ=60;set=variant3-variant4-variant5-variant9-variant10-variant12-variant16-variant25-variant26-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:2,3:5:72:112,0,72:0,2,0,3 chr1 85514282 . T C 87.14 PASS AC=1;AF=0.656;AN=2;DP=243;FractionInformativeReads=1;MQ=60;set=variant6-variant9-variant12-variant15-variant17-variant21-variant22-variant23-variant24-variant31-variant35-variant36-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,17:28:99:499,0,261:3,8,4,13 chr1 85527974 . G A 619.4 PASS AC=1;AF=0.886;AN=2;DP=1410;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:18,8:26:99:241,0,409:9,9,5,3 chr1 85528006 . C A 199.69 PASS AC=1;AF=0.625;AN=2;DP=927;MQ=60;set=variant-variant3-variant4-variant6-variant9-variant10-variant12-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant26-variant31-variant35-variant36-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,13:35:99:350,0,551:13,9,8,5 chr1 85537502 . T A 376.59 PASS AC=1;AF=0.86;AN=2;DP=483;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,4:7:99:159,0,169:2,1,3,1 chr1 85537522 . T C 713.3 PASS AC=1;AF=0.852;AN=2;DP=826;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:3,7:10:99:230,0,161:2,1,5,2 chr1 85538655 . A AAAG,AG,AAG 126.53 PASS AC=1,0,0;AF=0.231,0.5,0.115;AN=2;DP=159;set=variant-variant2-variant3-variant7-variant17-variant22-variant24-variant25-variant29-variant35-variant36-variant38-variant41 GT:DP:GQ:SB 0/1:5:54:1,1,2,1 chr1 85538879 . G A 356.14 PASS AC=1;AF=0.633;AN=2;DP=332;MQ=60;set=variant6-variant9-variant12-variant15-variant17-variant18-variant22-variant23-variant24-variant31-variant35-variant36-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,8:23:99:238,0,431:4,11,1,7 chr1 85559118 . CT C 1456.71 PASS AC=1;AF=0.708;AN=2;DP=2270;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant16-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,26:58:99:636,0,818:22,10,22,4 chr1 85559452 . A G 3058.4 PASS AC=1;AF=0.606;AN=2;DP=2848;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant9-variant11-variant12-variant13-variant16-variant19-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,30:77:99:828,0,1329:18,29,14,16 chr1 85560264 . G A 1038.59 PASS AC=1;AF=0.577;AN=2;DP=400;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant8-variant13-variant21-variant27-variant29-variant35-variant36-variant37-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:13,15:28:99:405,0,378:4,9,4,11 chr1 85560313 . T C 546.46 PASS AC=1;AF=0.621;AN=2;DP=399;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant9-variant11-variant12-variant13-variant16-variant19-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,5:13:99:168,0,258:1,7,0,5 chr1 85561546 . T C 1568.45 PASS AC=1;AF=0.621;AN=2;DP=1554;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant9-variant11-variant12-variant13-variant16-variant19-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,29:53:99:891,0,612:17,7,23,6 chr1 85563452 . AAAAG A 1087.73 PASS AC=1;AF=0.577;AN=2;DP=379;MQ=60;set=variant-variant5-variant8-variant13-variant21-variant27-variant29-variant35-variant36-variant37-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:12,25:37:99:1014,0,599:4,8,9,16 chr1 85564138 . A G 1552.49 PASS AC=1;AF=0.621;AN=2;DP=1204;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant9-variant11-variant12-variant13-variant16-variant19-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,20:42:99:556,0,619:16,6,15,5 chr1 85573705 . A AC,ACT 312.53 PASS AC=1,0;AF=0.603,0.132;AN=2;DP=547;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant16-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:DP:GQ:SB 0/1:13:99:5,1,5,2 chr1 85574021 . G A 548.36 PASS AC=1;AF=0.603;AN=2;DP=365;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant9-variant11-variant12-variant13-variant16-variant19-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,7:9:55:285,0,55:0,2,0,7 chr1 85583323 . T A 376.17 PASS AC=1;AF=0.525;AN=2;DP=339;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant8-variant10-variant12-variant15-variant17-variant18-variant21-variant27-variant29-variant30-variant32-variant35-variant36-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:13,11:24:99:349,0,454:10,3,10,1 chr1 85589939 . GT G 1542.07 PASS AC=1;AF=0.697;AN=2;DP=4780;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,67:117:99:2145,0,1511:17,33,31,36 chr1 85590031 . G A 1471.14 PASS AC=1;AF=0.545;AN=2;DP=426;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant8-variant13-variant21-variant27-variant29-variant35-variant36-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:30,15:45:99:453,0,991:6,24,2,13 chr1 85592126 . G T 640.93 PASS AC=2;AF=0.977;AN=2;DP=664;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:640,60,0:0,0,14,6 chr1 85594466 . G A 2024.6 PASS AC=1;AF=0.525;AN=2;DP=1192;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant8-variant10-variant12-variant13-variant17-variant18-variant21-variant27-variant29-variant30-variant32-variant35-variant36-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:38,28:66:99:694,0,955:18,20,10,18 chr1 85595645 . C T 1497.69 PASS AC=1;AF=0.684;AN=2;DP=4973;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:69,64:133:99:1657,0,1778:41,28,40,24 chr1 85595975 . T C 851.55 PASS AC=1;AF=0.694;AN=2;DP=2461;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,30:62:99:982,0,998:6,26,5,25 chr1 85598527 . TC T 1272.66 PASS AC=2;AF=1;AN=2;DP=2159;FS=0;MQRankSum=-0.675;ReadPosRankSum=-0.206;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:1831,180,0:0,0,42,18 chr1 85599563 . A C 2058.82 PASS AC=1;AF=0.548;AN=2;DP=1620;MQ=60;set=variant-variant5-variant8-variant10-variant12-variant13-variant17-variant18-variant21-variant27-variant29-variant30-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:43,49:92:99:1100,0,1227:22,21,25,24 chr1 85623859 . G A 360.85 PASS AC=1;AF=0.5;AN=2;DP=180;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant8-variant12-variant21-variant27-variant29-variant35-variant36-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:6,8:14:99:277,0,190:2,4,1,7 chr1 85624006 . C G 145.66 PASS AC=1;AF=0.559;AN=2;DP=151;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant8-variant12-variant14-variant18-variant19-variant21-variant25-variant27-variant29-variant33-variant35-variant36-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:2,6:8:67:243,0,67:1,1,6,0 chr1 85624549 . C T 5973.41 PASS AC=2;AF=1;AN=2;DP=6915;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,173:173:99:5020,518,0:0,0,86,87 chr1 85624864 . G A 2357.4 PASS AC=2;AF=1;AN=2;DP=3254;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:2352,237,0:0,0,31,48 chr1 85647713 . T C 1362.19 PASS AC=2;AF=1;AN=2;DP=1243;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:631,54,0:0,0,14,4 chr1 85648620 . C T 4029.58 PASS AC=2;AF=1;AN=2;DP=5395;FS=0;MQ=60;MQRankSum=0.243;ReadPosRankSum=0.043;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,138:138:99:4265,414,0:0,0,63,75 chr1 85648905 . T C 81 PASS AC=1;AF=0.737;AN=2;DP=798;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,15:26:99:388,0,299:3,8,5,10 chr1 85666327 . T C 1135.04 PASS AC=1;AF=0.5;AN=2;DP=894;MQ=60;set=variant-variant5-variant8-variant12-variant21-variant27-variant29-variant35-variant36-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:56,46:102:99:1175,0,1369:23,33,22,24 chr1 85725353 . GCCGGAAA G 621.21 PASS AC=1;AF=0.617;AN=2;DP=2409;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant10-variant11-variant14-variant15-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:35,37:72:99:1362,0,2121:14,21,13,24 chr1 85732065 . A G 1361.64 PASS AC=1;AF=0.662;AN=2;DP=3111;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,39:88:99:1010,0,1233:30,19,25,14 chr1 85732559 . CAAAAAAAAAA C,CAAAAAAAAA,CAAAAAAAA,CAAAAAAAAAAAA,CAAAAAAA,CAAAAA 576.09 PASS AC=0,0,1,0,0,0;AF=0.06,0.22,0.2,0.02,0.04,0.02;AN=2;DP=360;set=variant2-variant5-variant6-variant7-variant11-variant12-variant13-variant19-variant20-variant23-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant44 GT:DP:GQ:SB 0/3:10:53:3,1,6,0 chr1 85732739 . C T 2368.23 PASS AC=1;AF=0.5;AN=2;DP=2098;MQ=60;set=variant-variant5-variant8-variant12-variant13-variant27-variant29-variant35-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:103,108:211:99:2418,0,2546:61,42,58,50 chr1 85732941 . A C 4325.88 PASS AC=1;AF=0.662;AN=2;DP=10466;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:158,128:286:99:2885,0,3526:78,80,55,73 chr1 85733737 . TGTTAA T 319.57 PASS AC=1;AF=0.5;AN=2;DP=133;MQ=60;set=variant-variant5-variant8-variant12-variant13-variant27-variant29-variant35-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:4,10:14:99:408,0,242:2,2,1,9 chr1 85741684 . T C 162.18 PASS AC=1;AF=0.537;AN=2;DP=563;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant10-variant12-variant14-variant15-variant17-variant20-variant21-variant22-variant23-variant26-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:19,10:29:99:235,0,498:12,7,7,3 chr1 85741921 . G C 3889.75 PASS AC=2;AF=0.872;AN=2;DP=6147;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,151:151:99:4660,451,0:0,0,84,67 chr1 85742012 . G C 2178.77 PASS AC=1;AF=0.537;AN=2;DP=5124;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant10-variant12-variant14-variant15-variant17-variant20-variant21-variant22-variant23-variant26-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:115,100:215:99:2374,0,2808:57,58,45,55 chr1 85742264 . G C 1117.72 PASS AC=1;AF=0.5;AN=2;DP=1072;MQ=60;set=variant-variant5-variant8-variant12-variant13-variant27-variant29-variant35-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:67,59:126:99:1347,0,1599:36,31,28,31 chr1 85742338 . G C 3403.36 PASS AC=2;AF=0.872;AN=2;DP=5123;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,127:127:99:4291,380,0:0,0,70,57 chr1 85785550 . C CA 6742.14 PASS AC=1;AF=0.886;AN=2;DP=15466;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:190,177:367:99:6034,0,6537:96,94,93,84 chr1 85786166 . G A 2263.97 PASS AC=1;AF=0.5;AN=2;DP=652;FractionInformativeReads=1;MQ=60;set=variant3-variant9-variant10-variant30-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:52,35:87:99:994,0,1301:32,20,24,11 chr1 85786748 . GAAA GAA,G,GA,GAAAA 665.54 PASS AC=1,0,0,0;AF=0.397,0.026,0.09,0.026;AN=2;DP=6469;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-filterInvariant26-variant28-variant29-variant30-filterInvariant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:123:99:30,30,37,26 chr1 85787114 . A T 1901.62 PASS AC=2;AF=1;AN=2;DP=2974;FS=0;MQ=60;MQRankSum=0.073;ReadPosRankSum=1.635;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,67:67:99:1992,200,0:0,0,36,31 chr1 85870024 . C T 925.46 PASS AC=1;AF=0.5;AN=2;DP=853;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant8-variant12-variant25-variant26-variant27-variant29-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:48,34:82:99:875,0,1221:24,24,22,12 chr1 85930272 . GACAC G,GAC,GACACAC 821.22 PASS AC=0,1,1;AF=0.011,0.75,0.08;AN=2;DP=2144;set=Intersection GT:DP:GQ:SB 2/3:41:99:1,0,14,26 chr1 86046561 . C A 1668.37 PASS AC=2;AF=0.722;AN=2;DP=2633;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,103:103:99:3355,307,0:0,0,67,36 chr1 86046924 . G A 466.77 PASS AC=1;AF=0.676;AN=2;DP=1072;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,16:29:99:456,0,448:3,10,3,13 chr1 86118447 . A G 2691.81 PASS AC=2;AF=0.955;AN=2;DP=2589;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1261,120,0:0,0,27,13 chr1 86118587 . A T 1956.83 PASS AC=2;AF=0.563;AN=2;DP=1549;MQ=60;set=variant9-variant11-variant20-variant24-variant27-variant35-variant39-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,160:160:99:4772,478,0:0,0,90,70 chr1 86119269 . C T 359.05 PASS AC=1;AF=0.5;AN=2;DP=33;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.79;QD=10.88;ReadPosRankSum=-1.862;SOR=0.646;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:18,15:33:99:387,0,500:11,7,9,6 chr1 86119295 . A G 407.55 PASS AC=2;AF=0.583;AN=2;DP=441;FractionInformativeReads=1;MQ=60;set=variant9-variant11-variant14-variant20-variant23-variant24-variant27-variant35-variant36-variant37-variant39-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1329,126,0:0,0,25,17 chr1 86167957 . C T 1270.42 PASS AC=2;AF=0.849;AN=2;DP=1521;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:700,66,0:0,0,6,16 chr1 86173298 . C T 1180.39 PASS AC=2;AF=0.603;AN=2;DP=4058;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,149:149:99:4531,446,0:0,0,93,56 chr1 86174232 . G T 82.71 PASS AC=2;AF=0.611;AN=2;DP=260;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant6-variant8-variant9-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant23-variant24-variant25-variant27-variant29-variant32-variant33-variant35-variant36-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:435,42,0:0,0,6,8 chr1 86195047 . T C 2548.18 PASS AC=2;AF=0.591;AN=2;DP=5084;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,174:174:99:5023,520,0:0,0,89,85 chr1 86195106 . CT C 1420.63 PASS AC=2;AF=0.591;AN=2;DP=3801;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,114:114:99:3236,342,0:0,0,48,66 chr1 86202016 . C T 4884.14 PASS AC=2;AF=0.955;AN=2;DP=6517;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,160:160:99:4827,479,0:0,0,86,74 chr1 86210241 . G GT 386.51 PASS AC=2;AF=0.955;AN=2;DP=520;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:334,33,0:0,0,8,3 chr1 86210546 . G A 668.72 PASS AC=2;AF=0.943;AN=2;DP=898;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:749,69,0:0,0,7,16 chr1 86211325 . G A 625.13 PASS AC=2;AF=0.955;AN=2;DP=1182;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1153,105,0:0,0,10,25 chr1 86246849 . A C 865 PASS AC=2;AF=0.872;AN=2;DP=1515;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:1391,140,0:0,0,29,18 chr1 86249063 . C T 1208.39 PASS AC=2;AF=0.966;AN=2;DP=1127;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:931,84,0:0,0,19,9 chr1 86249911 . A G 2278.13 PASS AC=2;AF=0.966;AN=2;DP=3494;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:2058,204,0:0,0,38,30 chr1 86334070 . T A 775.41 PASS AC=1;AF=0.641;AN=2;DP=1433;MQ=60;set=variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,11:29:99:297,0,510:12,6,8,3 chr1 86334316 . T C 1373.01 PASS AC=1;AF=0.641;AN=2;DP=2202;MQ=60;set=variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,21:72:99:442,0,1341:17,34,7,14 chr1 86334423 . C T 148.58 PASS AC=1;AF=0.5;AN=2;DP=22;FS=4.154;FractionInformativeReads=1;MQ=60;MQRankSum=-1.068;QD=6.75;ReadPosRankSum=-0.467;SOR=0.525;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:13,9:22:99:177,0,382:4,9,5,4 chr1 86340193 . G T 43.52 PASS AC=1;AF=0.859;AN=2;DP=360;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:8,11:19:99:308,0,183:5,3,7,4 chr1 86340263 . G A 257.95 PASS AC=1;AF=0.5;AN=2;DP=32;FS=5.514;FractionInformativeReads=1;MQ=60;MQRankSum=-0.729;QD=8.06;ReadPosRankSum=-0.576;SOR=0.442;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:19,13:32:99:286,0,626:13,6,6,7 chr1 86340794 . T C 669.63 PASS AC=1;AF=0.863;AN=2;DP=478;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,9:17:99:319,0,181:5,3,9,0 chr1 86340892 . A G 1067.11 PASS AC=1;AF=0.641;AN=2;DP=1511;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,27:42:99:680,0,337:10,5,15,12 chr1 86361384 . C T 175.08 PASS AC=1;AF=0.886;AN=2;DP=520;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:5,6:11:99:141,0,154:2,3,4,2 chr1 86453409 . C T 529.33 PASS AC=1;AF=0.526;AN=2;DP=573;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant8-variant10-variant14-variant16-variant18-variant19-variant20-variant24-variant28-variant30-variant35-variant36-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,21:32:99:642,0,258:3,8,6,15 chr1 86482922 . A T 442.22 PASS AC=1;AF=0.548;AN=2;DP=782;MQ=60;set=variant2-variant3-variant4-variant6-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant35-variant37-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:25,21:46:99:549,0,636:10,15,9,12 chr1 86487981 . G A 1581.35 PASS AC=1;AF=0.756;AN=2;DP=3059;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:62,43:105:99:1458,0,3402:25,37,15,28 chr1 86487992 . A AACAG 2112.9 PASS AC=1;AF=0.756;AN=2;DP=2761;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,36:88:99:1360,0,3169:21,31,11,25 chr1 86488232 . G A 853.07 PASS AC=1;AF=0.55;AN=2;DP=1705;MQ=60;set=variant2-variant3-variant4-variant6-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant35-variant37-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:48,34:82:99:696,0,1185:28,20,18,16 chr1 86497769 . C G 53.54 PASS AC=1;AF=0.857;AN=2;DP=80;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant10-variant13-variant15-variant17-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:1,4:5:27:124,0,27:0,1,1,3 chr1 86554813 . G GA 250.86 PASS AC=1;AF=0.604;AN=2;DP=460;set=variant-variant2-variant5-variant6-variant7-variant9-variant11-variant12-variant16-variant17-variant22-variant24-variant26-variant29-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,5:18:85:85,0,308:6,7,3,2 chr1 86554821 . G A 579.6 PASS AC=2;AF=0.66;AN=2;DP=609;FractionInformativeReads=1;set=variant-variant2-variant5-variant6-variant7-variant9-variant11-variant12-variant16-variant17-variant22-variant24-variant26-variant27-variant29-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:888,84,0:0,0,15,13 chr1 86590915 . G A 3873.43 PASS AC=2;AF=0.989;AN=2;DP=4577;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,110:110:99:3919,330,0:0,0,48,62 chr1 86591837 . G A 3808.89 PASS AC=2;AF=0.726;AN=2;DP=5788;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,142:142:99:4468,425,0:0,0,58,84 chr1 86621992 . C A 605.87 PASS AC=2;AF=0.757;AN=2;DP=1696;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:2155,195,0:0,0,47,18 chr1 86813770 . G A 313.04 PASS AC=2;AF=0.568;AN=2;DP=471;MQ=60;set=variant5-variant6-variant7-variant8-variant9-variant10-variant15-variant17-variant19-variant20-variant21-variant22-variant25-variant27-variant29-variant31-variant33-variant35-variant37-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:663,60,0:0,0,15,5 chr1 86813829 . T C 943.25 PASS AC=1;AF=0.531;AN=2;DP=1083;FractionInformativeReads=1;MQ=60;set=variant5-variant6-variant8-variant9-variant10-variant15-variant17-variant20-variant21-variant22-variant25-variant27-variant31-variant33-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:34,28:62:99:622,0,850:21,13,18,10 chr1 86815022 . C G 1896.89 PASS AC=2;AF=0.795;AN=2;DP=2221;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:1831,171,0:0,0,29,28 chr1 86815319 . A G 3329.52 PASS AC=2;AF=0.795;AN=2;DP=5147;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,124:124:99:4073,372,0:0,0,78,46 chr1 86818572 . T C 3385.97 PASS AC=2;AF=0.795;AN=2;DP=3794;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,93:93:99:2690,278,0:0,0,46,47 chr1 86820267 . C T 3625.46 PASS AC=2;AF=0.795;AN=2;DP=4010;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,134:134:99:3862,401,0:0,0,70,64 chr1 86821194 . A ACT 358.01 PASS AC=2;AF=0.824;AN=2;DP=331;FS=0;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:270,18,0:0,0,0,6 chr1 86823286 . GA G,GAA 122.98 PASS AC=2,0;AF=0.565,0.13;AN=2;DP=223;MQ=60;set=variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-filterInvariant22-variant25-variant27-variant29-variant31-variant35-variant37-variant38-variant40-variant44 GT:DP:GQ:SB 1/1:10:3:1,0,6,3 chr1 86838158 . C T 735.25 PASS AC=2;AF=0.795;AN=2;DP=1496;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1268,129,0:0,0,23,20 chr1 86851420 . A G 364.42 PASS AC=2;AF=0.565;AN=2;DP=930;MQ=60;set=variant5-variant6-variant7-variant8-variant9-variant10-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant25-variant27-variant29-variant31-variant33-variant35-variant37-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1116,102,0:0,0,17,17 chr1 86852042 . A G 963.13 PASS AC=2;AF=0.565;AN=2;DP=947;MQ=60;set=variant5-variant6-variant7-variant8-variant9-variant10-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant25-variant27-variant29-variant31-variant33-variant35-variant37-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:1070,81,0:0,0,3,24 chr1 86852621 . A G 1448.73 PASS AC=2;AF=0.565;AN=2;DP=2704;MQ=60;set=variant5-variant6-variant7-variant8-variant9-variant10-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant25-variant27-variant29-variant31-variant33-variant35-variant37-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,109:110:99:3057,303,0:1,0,64,45 chr1 86890931 . T A 241.77 PASS AC=2;AF=0.734;AN=2;DP=235;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:211,18,0:0,0,5,1 chr1 86891005 . C A 654.91 PASS AC=1;AF=0.657;AN=2;DP=794;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,5:14:99:176,0,230:5,4,4,1 chr1 86891179 . T C 308.26 PASS AC=1;AF=0.556;AN=2;DP=739;MQ=60;set=variant5-variant6-variant7-variant8-variant9-variant10-variant15-variant17-variant18-variant19-variant20-variant25-variant29-variant31-variant35-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,17:31:99:461,0,302:7,7,7,10 chr1 86894371 . G T 1946.26 PASS AC=2;AF=0.684;AN=2;DP=2429;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,82:82:99:2388,245,0:0,0,33,49 chr1 86894496 . T C 196.93 PASS AC=2;AF=0.719;AN=2;DP=412;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:530,45,0:0,0,3,12 chr1 86896354 . G A 737.82 PASS AC=2;AF=0.852;AN=2;DP=690;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,15:15:44:508,44,0:0,0,13,2 chr1 86896541 . G A 562.18 PASS AC=2;AF=0.568;AN=2;DP=2367;FractionInformativeReads=1;MQ=60;set=variant5-variant6-variant7-variant8-variant9-variant10-variant15-variant17-variant19-variant20-variant21-variant22-variant25-variant27-variant29-variant31-variant33-variant35-variant37-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,109:109:99:3169,325,0:0,0,56,53 chr1 86897973 . T C 945.01 PASS AC=2;AF=0.852;AN=2;DP=659;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:475,33,0:0,0,10,1 chr1 86898315 . T C 478.73 PASS AC=1;AF=0.559;AN=2;DP=308;FractionInformativeReads=1;MQ=60;set=variant5-variant6-variant7-variant8-variant9-variant10-variant15-variant17-variant19-variant20-variant25-variant29-variant31-variant35-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,7:19:99:128,0,350:3,9,3,4 chr1 86906114 . T C 235.24 PASS AC=1;AF=0.75;AN=2;DP=286;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant16-variant19-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,8:15:99:271,0,173:2,5,1,7 chr1 86911392 . TA T 7550.79 PASS AC=1;AF=0.594;AN=2;DP=2404;MQ=60;set=variant-variant3-variant6-variant7-variant11-variant16-variant17-variant18-variant19-variant27-variant29-variant30-variant33-variant35-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:104,87:191:99:2938,0,3586:46,58,39,48 chr1 86911543 . C T 591.98 PASS AC=2;AF=0.872;AN=2;DP=501;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:555,39,0:0,0,2,11 chr1 86913265 . C T 1126.8 PASS AC=1;AF=0.563;AN=2;DP=1713;MQ=60;set=variant5-variant6-variant7-variant8-variant9-variant10-variant15-variant17-variant19-variant25-variant29-variant31-variant35-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,40:93:99:965,0,1412:25,28,21,19 chr1 86913564 . A AT 476.26 PASS AC=1;AF=0.594;AN=2;DP=487;MQ=60;set=variant-variant3-variant6-variant7-variant11-variant16-variant17-variant18-variant19-variant27-variant29-variant30-variant33-variant35-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:10,16:26:99:352,0,203:3,7,3,13 chr1 86920904 . A G 1812.81 PASS AC=1;AF=0.55;AN=2;DP=3388;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant15-variant17-variant18-variant19-variant25-variant29-variant31-variant34-variant35-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:87,96:183:99:2344,0,1892:48,39,50,46 chr1 86922161 . C T 2825.84 PASS AC=1;AF=0.594;AN=2;DP=1104;MQ=60;set=variant-variant3-variant6-variant7-variant11-variant16-variant17-variant19-variant27-variant29-variant30-variant33-variant35-variant37-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:40,35:75:99:943,0,1031:13,27,9,26 chr1 86934176 . T G 6450.4 PASS AC=1;AF=0.703;AN=2;DP=6545;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:85,69:154:99:1904,0,2369:42,43,30,39 chr1 86934250 . A G 48.09 PASS AC=1;AF=0.5;AN=2;DP=383;set=filterInvariant12-variant16-filterInvariant17-filterInvariant18-filterInvariant22-variant35-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:41,15:56:99:174,0,981:20,21,0,15 chr1 86939130 . C T 3048.82 PASS AC=2;AF=0.955;AN=2;DP=3948;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:2193,231,0:0,0,41,36 chr1 86939390 . G A 2203.56 PASS AC=2;AF=0.966;AN=2;DP=3089;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,89:89:99:2603,266,0:0,0,54,35 chr1 86947975 . A T 898.79 PASS AC=2;AF=0.604;AN=2;DP=1699;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant15-variant17-variant18-variant19-variant25-variant29-variant31-variant34-variant35-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,64:64:99:2138,192,0:0,0,39,25 chr1 86948169 . T C 142.62 PASS AC=1;AF=0.545;AN=2;DP=333;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant11-variant19-variant29-variant34-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:17,17:34:99:494,0,435:5,12,4,13 chr1 86952324 . A G 694.29 PASS AC=2;AF=0.814;AN=2;DP=3986;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,121:121:99:3942,363,0:0,0,55,66 chr1 86954880 . G A 179.86 PASS AC=1;AF=0.5;AN=2;DP=81;FractionInformativeReads=1;MQ=60;set=variant27-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:16,20:36:99:535,0,535:2,14,7,13 chr1 86956785 . C G 160.46 PASS AC=2;AF=0.869;AN=2;DP=569;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:38:430,38,0:0,0,11,2 chr1 86959173 . T C 1102.52 PASS AC=1;AF=0.826;AN=2;DP=4488;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,45:100:99:987,0,1220:31,24,24,21 chr1 86959748 . A T 163.95 PASS AC=1;AF=0.5;AN=2;DP=40;FractionInformativeReads=1;MQ=60;set=variant27-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:14,9:23:99:215,0,419:12,2,6,3 chr1 86959796 . C T 416.88 PASS AC=1;AF=0.813;AN=2;DP=1839;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,35:67:99:1020,0,882:24,8,26,9 chr1 86961210 . C T 958.87 PASS AC=1;AF=0.5;AN=2;DP=282;FractionInformativeReads=1;MQ=60;set=variant27-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:53,42:95:99:998,0,1431:33,20,27,15 chr1 86965419 . T C 987.41 PASS AC=1;AF=0.525;AN=2;DP=1608;MQ=60;set=variant2-variant6-variant7-variant8-variant10-variant11-variant14-variant16-variant17-variant22-variant24-variant26-variant27-variant28-variant31-variant32-variant35-variant37-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,37:77:99:859,0,1111:26,14,24,13 chr1 87012728 . C A 466.86 PASS AC=1;AF=0.5;AN=2;DP=109;FractionInformativeReads=1;MQ=60;set=variant16-variant27-variant35 GT:AD:DP:GQ:PL:SB 0/1:19,17:36:99:491,0,575:15,4,11,6 chr1 87029337 . C T 1102.02 PASS AC=1;AF=0.5;AN=2;DP=232;FractionInformativeReads=1;MQ=60;set=variant16-variant35 GT:AD:DP:GQ:PL:SB 0/1:52,73:125:99:1823,0,1092:27,25,42,31 chr1 87036746 . C A 2167.4 PASS AC=2;AF=0.813;AN=2;DP=7311;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,184:184:99:5233,548,0:0,0,107,77 chr1 87045587 . C T 98.42 PASS AC=1;AF=0.5;AN=2;DP=33;FS=0;FractionInformativeReads=1;MQ=60;set=variant16-variant35 GT:AD:DP:GQ:PL:SB 0/1:10,8:18:99:210,0,274:7,3,6,2 chr1 87045896 . TCCTACA T 3702.44 PASS AC=1;AF=0.769;AN=2;DP=7723;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:124,91:215:99:3211,0,4989:67,57,43,48 chr1 87045902 . ACCTACT ACCTACTCCTACT,A 4076.42 PASS AC=1,0;AF=0.333,0.167;AN=2;DP=613;MQ=60;set=variant16-variant35-variant41 GT:DP:GQ:SB 0/1:196:99:43,49,54,50 chr1 87458695 . G A 1852.51 PASS AC=2;AF=0.849;AN=2;DP=3220;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,64:64:99:1945,192,0:0,0,42,22 chr1 87538182 . TTG T 4143.25 PASS AC=2;AF=0.833;AN=2;DP=4193;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,84:84:99:3807,262,0:0,0,47,37 chr1 87538200 . G A 4467.46 PASS AC=2;AF=0.869;AN=2;DP=4499;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,94:94:99:4000,286,0:0,0,47,47 chr1 87549858 . A G 1652.72 PASS AC=2;AF=0.977;AN=2;DP=1503;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:896,84,0:0,0,20,8 chr1 87558066 . CCACATA C 232.96 PASS AC=2;AF=0.977;AN=2;DP=359;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:361,24,0:0,0,8,0 chr1 87563668 . G A 5792.32 PASS AC=2;AF=0.977;AN=2;DP=6951;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,161:162:99:5167,475,0:0,1,83,78 chr1 87563921 . T G 3950.02 PASS AC=2;AF=0.93;AN=2;DP=4163;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,106:106:99:3378,314,0:0,0,84,22 chr1 87564110 . G A 2407.57 PASS AC=2;AF=1;AN=2;DP=2687;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:2367,212,0:0,0,16,55 chr1 87570398 . G A 3460.82 PASS AC=2;AF=0.833;AN=2;DP=4279;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,120:120:99:3701,358,0:0,0,49,71 chr1 87572817 . C T 6264.43 PASS AC=2;AF=0.93;AN=2;DP=6954;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,175:175:99:6086,526,0:0,0,124,51 chr1 87573336 . ATATGTT A 779.4 PASS AC=2;AF=0.805;AN=2;DP=1124;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:655,45,0:0,0,9,6 chr1 87573963 . T C 2039.8 PASS AC=2;AF=0.833;AN=2;DP=3077;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,73:73:99:2281,219,0:0,0,32,41 chr1 87573988 . T C 1688.89 PASS AC=2;AF=0.93;AN=2;DP=2911;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:2078,204,0:0,0,31,37 chr1 87574217 . A G 3812.87 PASS AC=2;AF=0.833;AN=2;DP=4039;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,114:114:99:3941,340,0:0,0,83,31 chr1 87575680 . T C 1252.03 PASS AC=1;AF=0.5;AN=2;DP=482;FractionInformativeReads=1;MQ=60;set=variant4-variant8-variant31-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:43,45:88:99:1131,0,1064:15,28,15,30 chr1 87598117 . T G 5674.04 PASS AC=1;AF=0.8;AN=2;DP=4608;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,46:102:99:1333,0,1577:40,16,31,15 chr1 87599697 . G A 5011.79 PASS AC=2;AF=0.9;AN=2;DP=4501;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,117:117:99:3489,351,0:0,0,55,62 chr1 87633761 . C T 151.4 PASS AC=1;AF=0.886;AN=2;DP=1099;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:13,15:28:99:394,0,339:6,7,10,5 chr1 87633929 . A G 1296.73 PASS AC=1;AF=0.55;AN=2;DP=863;MQ=60;set=variant18-variant22-variant24-variant29-variant30-variant34-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,46:90:99:1012,0,1017:22,22,22,24 chr1 87634149 . C T 43.63 PASS AC=1;AF=0.571;AN=2;DP=192;FractionInformativeReads=1;MQ=60;set=filterInvariant18-variant22-variant24-variant29-variant30-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,15:31:99:343,0,419:7,9,6,9 chr1 87709224 . C A 838.2 PASS AC=1;AF=0.542;AN=2;DP=507;FractionInformativeReads=1;MQ=60;set=variant9-variant14-variant21-variant26-variant30-variant31-variant34-variant35-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,26:39:99:751,0,301:8,5,19,7 chr1 87716226 . T A 1119.01 PASS AC=1;AF=0.536;AN=2;DP=1268;MQ=60;set=variant2-variant4-variant7-variant9-variant10-variant11-variant13-variant17-variant33-variant35-variant37-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:51,33:84:99:745,0,1263:21,30,17,16 chr1 87794519 . C G 2281.72 PASS AC=2;AF=1;AN=2;DP=2488;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:2237,203,0:0,0,41,27 chr1 87811065 . G A 1415.58 PASS AC=2;AF=0.667;AN=2;DP=317;FractionInformativeReads=1;MQ=60;set=variant7-variant35-variant36 GT:AD:DP:GQ:PL:SB 1/1:0,90:90:99:2796,270,0:0,0,34,56 chr1 89225976 . T C 448.14 PASS AC=2;AF=0.711;AN=2;DP=2074;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1213,117,0:0,0,19,20 chr1 89236029 . T A 494.97 PASS AC=2;AF=0.671;AN=2;DP=1644;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1466,138,0:0,0,31,15 chr1 89252013 . A AT 51.25 PASS AC=2;AF=0.714;AN=2;DP=48;FS=0;MQ=60;set=variant5-variant7-variant9-variant17-variant22-variant23-variant35 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:113,12,0:0,0,1,3 chr1 89271574 . T C 2228.04 PASS AC=2;AF=0.671;AN=2;DP=3857;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,118:118:99:4030,353,0:0,0,81,37 chr1 89280965 . A G 652.41 PASS AC=2;AF=0.671;AN=2;DP=1532;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1317,117,0:0,0,26,13 chr1 89301123 . C T 3017.96 PASS AC=2;AF=0.711;AN=2;DP=8158;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,212:212:99:6466,635,0:0,0,74,138 chr1 89322982 . G A 4460.96 PASS AC=2;AF=1;AN=2;DP=6386;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,166:166:99:5071,497,0:0,0,79,87 chr1 89414776 . A T 661.2 PASS AC=1;AF=0.5;AN=2;DP=60;FS=2.212;FractionInformativeReads=1;MQ=60;MQRankSum=1.338;QD=11.02;ReadPosRankSum=-2.048;SOR=0.38;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:30,30:60:99:689,0,732:19,11,16,14 chr1 89473175 . T C 1983.13 PASS AC=1;AF=0.613;AN=2;DP=4032;MQ=60;set=variant-variant2-variant4-variant7-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,74:139:99:1919,0,1577:35,30,44,30 chr1 89474818 . A G 1222.41 PASS AC=1;AF=0.614;AN=2;DP=1668;MQ=60;set=variant-variant2-variant9-variant12-variant14-variant16-variant17-variant18-variant20-variant23-variant24-variant27-variant28-variant29-variant31-variant33-variant35-variant36-variant37-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,60:95:99:1562,0,716:15,20,26,34 chr1 89475135 . C T 996.18 PASS AC=1;AF=0.614;AN=2;DP=1667;FractionInformativeReads=1;set=variant-variant2-variant9-variant12-variant14-variant16-variant17-variant18-variant20-variant23-variant24-variant27-variant28-variant29-variant31-variant33-variant35-variant36-variant37-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,48:84:99:1083,0,765:20,16,25,23 chr1 89478854 . C G 1106.18 PASS AC=2;AF=0.817;AN=2;DP=833;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:696,66,0:0,0,15,7 chr1 89478868 . G A 1045.19 PASS AC=1;AF=0.542;AN=2;DP=295;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant15-variant22-variant30-variant31-variant33-variant34-variant35-variant36-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:13,16:29:99:431,0,358:10,3,12,4 chr1 89479063 . G A 1861.69 PASS AC=1;AF=0.625;AN=2;DP=3331;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:71,49:120:99:1141,0,1714:33,38,19,30 chr1 89479074 . C T 1715.66 PASS AC=1;AF=0.625;AN=2;DP=3036;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:69,46:115:99:1017,0,1735:31,38,17,29 chr1 89479758 . T C 3665.2 PASS AC=2;AF=0.829;AN=2;DP=4213;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,111:111:99:3243,331,0:0,0,69,42 chr1 89486037 . C T 2180.33 PASS AC=2;AF=0.826;AN=2;DP=3851;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,121:121:99:3942,361,0:0,0,81,40 chr1 89517918 . C T 269.73 PASS AC=2;AF=0.837;AN=2;DP=535;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:654,51,0:0,0,15,2 chr1 89518065 . C G 1702.61 PASS AC=2;AF=0.837;AN=2;DP=7166;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,153:153:99:4775,459,0:0,0,93,60 chr1 89518120 . A G 1893.05 PASS AC=1;AF=0.607;AN=2;DP=4833;set=variant2-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:98,72:170:99:1789,0,2418:47,51,39,33 chr1 89518173 . T A 1232.25 PASS AC=2;AF=0.837;AN=2;DP=5742;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,140:140:99:5732,424,0:0,0,61,79 chr1 89518195 . G A 1285.72 PASS AC=2;AF=0.837;AN=2;DP=4864;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,117:117:99:5109,352,0:0,0,49,68 chr1 89520329 . GAAAAAC G 410.86 PASS AC=1;AF=0.641;AN=2;DP=1316;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:30,20:50:99:728,0,2186:18,12,14,6 chr1 89520574 . C A 780.66 PASS AC=2;AF=0.829;AN=2;DP=3219;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,74:74:99:2389,221,0:0,0,29,45 chr1 89520636 . G A 344.06 PASS AC=2;AF=0.829;AN=2;DP=1406;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:1186,81,0:0,0,5,22 chr1 89520643 . C T 310.54 PASS AC=2;AF=0.829;AN=2;DP=1278;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:81:1191,81,0:0,0,5,20 chr1 89520658 . C T 197.34 PASS AC=1;AF=0.636;AN=2;DP=485;set=variant2-variant8-variant9-variant10-variant12-variant14-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant33-variant35-variant37-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,14:22:99:386,0,269:0,8,4,10 chr1 89521841 . G C 2436.69 PASS AC=1;AF=0.63;AN=2;DP=4991;set=variant2-variant8-variant9-variant10-variant12-variant14-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant33-variant34-variant35-variant37-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:122,94:216:99:2181,0,3210:43,79,31,63 chr1 89522512 . C T 1958.88 PASS AC=1;AF=0.609;AN=2;DP=5268;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:90,89:179:99:2172,0,2219:56,34,55,34 chr1 89522646 . G C 2129.28 PASS AC=2;AF=0.829;AN=2;DP=8201;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,206:206:99:6605,617,0:0,0,94,112 chr1 89523927 . C T 345.93 PASS AC=1;AF=0.636;AN=2;DP=999;FractionInformativeReads=1;MQ=60;set=variant2-variant8-variant9-variant10-variant12-variant14-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant27-filterInvariant28-variant29-variant33-variant35-variant37-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,21:49:99:455,0,746:10,18,7,14 chr1 89525812 . C G 661.21 PASS AC=1;AF=0.63;AN=2;DP=1081;FractionInformativeReads=1;set=variant2-variant8-variant9-variant10-variant12-variant14-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant33-variant34-variant35-variant37-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,21:61:99:803,0,2217:23,17,12,9 chr1 89525820 . C T 655.21 PASS AC=1;AF=0.63;AN=2;DP=1160;FractionInformativeReads=1;set=variant2-variant8-variant9-variant10-variant12-variant14-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant33-variant34-variant35-variant37-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,22:63:99:800,0,2239:23,18,12,10 chr1 89526132 . G A 464.67 PASS AC=1;AF=0.5;AN=2;DP=37;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.41;QD=12.56;ReadPosRankSum=2.173;SOR=0.818;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:19,18:37:99:493,0,591:11,8,11,7 chr1 89574026 . G A 2249.91 PASS AC=1;AF=0.743;AN=2;DP=3027;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:55,40:95:99:883,0,1339:20,35,16,24 chr1 89575677 . T C 126.78 PASS AC=1;AF=0.75;AN=2;DP=297;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:99:153,0,117:2,2,1,3 chr1 89579941 . T C 4046.9 PASS AC=1;AF=0.73;AN=2;DP=6028;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:107,75:182:99:1713,0,2641:49,58,39,36 chr1 89582690 . G C 2703.63 PASS AC=1;AF=0.73;AN=2;DP=3927;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:53,39:92:99:897,0,1450:34,19,18,21 chr1 89583544 . T C 286.76 PASS AC=1;AF=0.736;AN=2;DP=362;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:11,4:15:99:132,0,360:2,9,0,4 chr1 89597755 . T C 2223.05 PASS AC=1;AF=0.716;AN=2;DP=2356;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:31,29:60:99:763,0,719:14,17,18,11 chr1 89607479 . G T 2770.83 PASS AC=1;AF=0.716;AN=2;DP=3015;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:35,44:79:99:1760,0,1983:11,24,15,29 chr1 89607486 . T C 2721.22 PASS AC=1;AF=0.743;AN=2;DP=2704;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:31,42:73:99:1667,0,1898:9,22,13,29 chr1 89615979 . C T 1021.21 PASS AC=1;AF=0.716;AN=2;DP=976;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:18,17:35:99:486,0,499:13,5,12,5 chr1 89618472 . GA G,GAA 553.25 PASS AC=1,0;AF=0.56,0.036;AN=2;DP=2880;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-filterInvariant11-variant12-variant13-filterInvariant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-filterInvariant40-variant41-variant42-variant43-filterInvariant44 GT:DP:GQ:SB 0/1:70:99:17,16,21,16 chr1 89637578 . G A 9008.28 PASS AC=1;AF=0.743;AN=2;DP=13315;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:168,203:371:99:4482,0,3658:82,86,99,104 chr1 89647386 . G A 3838.67 PASS AC=1;AF=0.744;AN=2;DP=4531;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,55:114:99:1281,0,1375:32,27,31,24 chr1 89647546 . T TC 912.44 PASS AC=1;AF=0.744;AN=2;DP=1242;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,15:34:99:497,0,660:7,12,3,12 chr1 89650850 . A T 588.02 PASS AC=1;AF=0.588;AN=2;DP=2526;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,30:68:99:899,0,975:20,18,15,15 chr1 89652071 . T C 672.78 PASS AC=1;AF=0.574;AN=2;DP=3065;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,27:80:99:950,0,13457:28,25,12,15 chr1 89652072 . C T 672.78 PASS AC=1;AF=0.574;AN=2;DP=3054;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,26:80:99:947,0,13627:29,25,12,14 chr1 89652078 . A T 708.75 PASS AC=1;AF=0.574;AN=2;DP=3065;FractionInformativeReads=1;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,26:80:99:971,0,13585:28,26,13,13 chr1 89652087 . C T 795.74 PASS AC=1;AF=0.574;AN=2;DP=3040;FractionInformativeReads=1;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,28:86:99:1085,0,14236:29,29,14,14 chr1 89652088 . C G 795.74 PASS AC=1;AF=0.574;AN=2;DP=3012;FractionInformativeReads=1;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,29:87:99:1076,0,14508:29,29,15,14 chr1 89652090 . T G 753.75 PASS AC=1;AF=0.574;AN=2;DP=3002;FractionInformativeReads=1;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,29:90:99:1031,0,14632:30,31,15,14 chr1 89652094 . G A 711.76 PASS AC=1;AF=0.574;AN=2;DP=2965;FractionInformativeReads=1;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,27:88:99:983,0,14708:30,31,14,13 chr1 89652097 . C T 714.77 PASS AC=1;AF=0.574;AN=2;DP=2971;FractionInformativeReads=1;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,26:90:99:980,0,14708:32,32,14,12 chr1 89652102 . A T 720.81 PASS AC=1;AF=0.574;AN=2;DP=2974;FractionInformativeReads=1;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:66,27:93:99:932,0,14590:32,34,15,12 chr1 89661228 . T G 2628.11 PASS AC=1;AF=0.731;AN=2;DP=5006;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,62:126:99:1681,0,1761:19,45,17,45 chr1 89664276 . T C 523.83 PASS AC=1;AF=0.75;AN=2;DP=484;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,9:18:99:205,0,299:8,1,6,3 chr1 89726592 . G A 543.94 PASS AC=2;AF=0.795;AN=2;DP=1135;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,29:30:51:1011,51,0:1,0,7,22 chr1 89727870 . A T 501.16 PASS AC=1;AF=0.607;AN=2;DP=545;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant13-variant15-variant34-variant35-variant36-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:19,21:40:99:660,0,524:14,5,16,5 chr1 89730723 . C T 678.67 PASS AC=1;AF=0.722;AN=2;DP=2069;MQ=60;set=variant-variant2-variant4-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,36:73:99:901,0,1008:10,27,11,25 chr1 89731959 . G A 531.94 PASS AC=1;AF=0.722;AN=2;DP=1085;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,18:33:99:563,0,457:12,3,15,3 chr1 89732237 . G A 901.73 PASS AC=1;AF=0.607;AN=2;DP=1264;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant13-variant15-variant34-variant35-variant36-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:42,45:87:99:1121,0,1007:16,26,18,27 chr1 89733273 . T C 543.95 PASS AC=1;AF=0.722;AN=2;DP=1395;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,25:44:99:629,0,552:4,15,8,17 chr1 89735314 . G A 4552.23 PASS AC=1;AF=0.65;AN=2;DP=1066;MQ=60;set=variant3-variant5-variant6-variant13-variant15-variant34-variant35-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:53,42:95:99:1195,0,1659:24,29,20,22 chr1 89737152 . GA G 15431.5 PASS AC=1;AF=0.65;AN=2;DP=3045;MQ=60;set=variant3-variant5-variant6-variant13-variant15-variant34-variant35-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:139,151:290:99:4302,0,3779:77,62,87,64 chr1 89737161 . CA C 3772.57 PASS AC=2;AF=0.767;AN=2;DP=13137;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,284:285:99:8445,833,0:0,1,164,120 chr1 89844035 . T C 1473.61 PASS AC=1;AF=0.5;AN=2;DP=648;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant29-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:46,66:112:99:1667,0,1002:24,22,38,28 chr1 89845926 . GT G 1404.85 PASS AC=2;AF=0.92;AN=2;DP=2639;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1532,153,0:0,0,33,18 chr1 89846291 . C T 79.55 PASS AC=1;AF=0.5;AN=2;DP=92;FractionInformativeReads=1;MQ=60;set=variant4-variant14-variant16-variant25-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:4,6:10:99:199,0,134:0,4,1,5 chr1 89847051 . T C 82.47 PASS AC=1;AF=0.5;AN=2;DP=7;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.55;QD=11.78;ReadPosRankSum=-0.937;SOR=0.495;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:4,3:7:99:111,0,158:4,0,3,0 chr1 89847372 . G T 1246.92 PASS AC=2;AF=0.791;AN=2;DP=6303;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,158:158:99:4810,473,0:0,0,84,74 chr1 89847411 . C T 1318.78 PASS AC=2;AF=0.791;AN=2;DP=6406;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,166:167:99:4925,486,0:1,0,82,84 chr1 89847444 . A G 1338.45 PASS AC=2;AF=0.791;AN=2;DP=6234;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,171:171:99:5212,511,0:0,0,79,92 chr1 89849201 . C G 3125.44 PASS AC=2;AF=0.92;AN=2;DP=4350;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,113:113:99:3148,338,0:0,0,59,54 chr1 89849268 . T C 1264.87 PASS AC=1;AF=0.5;AN=2;DP=521;MQ=60;set=variant3-variant4-variant29-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:49,45:94:99:1048,0,1233:22,27,22,23 chr1 89849350 . G A 2628.18 PASS AC=2;AF=0.92;AN=2;DP=3295;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:2241,213,0:0,0,37,34 chr1 89849441 . T G 2189.15 PASS AC=2;AF=0.92;AN=2;DP=3720;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:2255,213,0:0,0,32,39 chr1 89849742 . A T 840.11 PASS AC=2;AF=0.92;AN=2;DP=2217;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,61:61:99:1858,183,0:0,0,26,35 chr1 89851100 . G GT 46.7 PASS AC=2;AF=0.907;AN=2;DP=276;set=variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant22-variant23-variant25-variant26-variant27-variant29-variant31-variant35-variant36-variant37-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:124,15,0:0,0,1,4 chr1 89885854 . G A 883.42 PASS AC=2;AF=0.92;AN=2;DP=2484;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1686,167,0:0,0,26,30 chr1 89885896 . A G 920.47 PASS AC=1;AF=0.5;AN=2;DP=246;FractionInformativeReads=1;set=variant3-variant4-variant29-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:21,24:45:99:966,0,773:8,13,10,14 chr1 89885906 . G A 1007.21 PASS AC=1;AF=0.5;AN=2;DP=228;FractionInformativeReads=1;set=variant3-variant4-variant29-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:22,22:44:99:879,0,807:9,13,10,12 chr1 89888530 . C T 3329.3 PASS AC=2;AF=0.92;AN=2;DP=5591;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,136:136:99:4329,407,0:0,0,92,44 chr1 89888552 . T A 4753.13 PASS AC=2;AF=0.92;AN=2;DP=7437;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,188:188:99:5727,564,0:0,0,118,70 chr1 89888585 . C G 8758.22 PASS AC=2;AF=0.92;AN=2;DP=9590;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,248:248:99:11008,749,0:0,0,144,104 chr1 89888588 . G T 8709.61 PASS AC=2;AF=0.92;AN=2;DP=9715;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,251:251:99:11156,758,0:0,0,145,106 chr1 89889456 . T C 782.39 PASS AC=1;AF=0.5;AN=2;DP=297;FractionInformativeReads=1;set=variant3-variant4-variant29-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:31,11:42:99:207,0,727:16,15,6,5 chr1 90058242 . GT GTT,G 1168.65 PASS AC=2,0;AF=0.6,0.033;AN=2;DP=1674;set=variant3-variant4-variant5-variant6-filterInvariant8-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-filterInvariant25-variant26-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43 GT:DP:GQ:SB 1/1:43:29:2,2,26,13 chr1 90058936 . CAA CA,C,CAAA 336.11 PASS AC=1,1,0;AF=0.5,0.116,0.012;AN=2;DP=2533;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 2/1:51:99:4,3,37,7 chr1 90060824 . C T 8606.3 PASS AC=2;AF=0.966;AN=2;DP=9805;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,203:203:99:6974,608,0:0,0,65,138 chr1 90098715 . G C 473.69 PASS AC=2;AF=0.657;AN=2;DP=2222;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,78:78:99:2393,234,0:0,0,40,38 chr1 90171835 . C T 3105.3 PASS AC=2;AF=1;AN=2;DP=3488;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,87:87:99:2621,261,0:0,0,52,35 chr1 90178743 . A G 1919.41 PASS AC=2;AF=1;AN=2;DP=4181;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,97:97:99:3253,290,0:0,0,48,49 chr1 90179532 . A G 1156.48 PASS AC=1;AF=0.5;AN=2;DP=1027;MQ=60;set=variant2-variant3-variant4-variant18-variant27-variant29-variant31-variant33-variant34-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:59,32:91:99:786,0,1653:35,24,15,17 chr1 90182591 . A G 4290.72 PASS AC=1;AF=0.5;AN=2;DP=5699;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant15-variant18-variant26-variant27-variant29-variant31-variant33-variant34-variant35-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:173,182:355:99:4857,0,4272:79,94,83,99 chr1 90185106 . C G 816.84 PASS AC=1;AF=0.603;AN=2;DP=1232;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,18:34:99:570,0,479:3,13,3,15 chr1 90286636 . TGCTGCC T 26183.2 PASS AC=2;AF=0.977;AN=2;DP=25638;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,667:667:99:29442,2014,0:0,0,300,367 chr1 90459744 . A G 1629.27 PASS AC=2;AF=0.966;AN=2;DP=2868;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1785,168,0:0,0,31,25 chr1 90470915 . T A 856.7 PASS AC=1;AF=0.73;AN=2;DP=2870;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,22:51:99:620,0,845:13,16,14,8 chr1 90486412 . T G 1806.11 PASS AC=1;AF=0.757;AN=2;DP=5789;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:82,86:168:99:2139,0,1873:42,40,42,44 chr1 90493026 . G A 665.68 PASS AC=1;AF=0.73;AN=2;DP=3221;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,39:80:99:911,0,1051:17,24,22,17 chr1 90493918 . G GA 556.2 PASS AC=1;AF=0.757;AN=2;DP=1631;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,18:29:99:427,0,228:4,7,8,10 chr1 91177647 . A C 411.41 PASS AC=1;AF=0.667;AN=2;DP=1797;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,35:61:99:1024,0,689:15,11,19,16 chr1 91182880 . G T 521.06 PASS AC=1;AF=0.567;AN=2;DP=477;MQ=60;set=variant5-variant7-variant10-variant17-variant18-variant22-variant23-variant26-variant32-variant33-variant35-variant36-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:16,5:21:99:125,0,562:5,11,2,3 chr1 91381679 . G A 3060.94 PASS AC=1;AF=0.545;AN=2;DP=2092;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant8-variant9-variant14-variant17-variant21-variant28-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:102,80:182:99:1903,0,2529:49,53,42,38 chr1 91383589 . T G 1660.97 PASS AC=1;AF=0.545;AN=2;DP=787;MQ=60;set=variant3-variant4-variant5-variant8-variant9-variant14-variant17-variant21-variant28-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:38,37:75:99:907,0,951:24,14,22,15 chr1 91402917 . T TA 199.18 PASS AC=1;AF=0.55;AN=2;DP=179;MQ=60;set=variant3-variant5-variant8-variant9-variant14-variant17-variant21-variant28-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:14,6:20:99:102,0,332:14,0,6,0 chr1 91447985 . C T 3650.43 PASS AC=2;AF=0.932;AN=2;DP=4190;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:2456,236,0:0,0,31,48 chr1 91728053 . G A 2749.48 PASS AC=2;AF=1;AN=2;DP=4134;FS=0;MQ=60;MQRankSum=-0.942;ReadPosRankSum=1.428;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,92:92:99:2553,275,0:0,0,43,49 chr1 91728202 . T C 431.9 PASS AC=2;AF=1;AN=2;DP=550;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:346,27,0:0,0,1,8 chr1 91731454 . G T 100.99 PASS AC=1;AF=0.5;AN=2;DP=18;FS=0;FractionInformativeReads=1;MQ=60;set=variant11-variant35 GT:AD:DP:GQ:PL:SB 0/1:7,4:11:99:139,0,275:7,0,4,0 chr1 91739208 . C T 1111.35 PASS AC=2;AF=1;AN=2;DP=1414;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:719,66,0:0,0,14,8 chr1 91739414 . G A 1334.73 PASS AC=2;AF=1;AN=2;DP=1151;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:465,48,0:0,0,6,10 chr1 91740105 . T G 2313.23 PASS AC=2;AF=1;AN=2;DP=3132;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.253;ReadPosRankSum=-0.506;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2109,210,0:0,0,45,25 chr1 91740542 . AT ATT,ATTT,A 92.15 PASS AC=0,1,0;AF=0.143,0.286,0.143;AN=2;DP=82;FS=0;MQ=60;set=variant2-variant16-variant20-variant24-variant25-variant35-variant36 GT:DP:GQ:SB 0/2:5:18:0,1,1,3 chr1 91781304 . T C 868.94 PASS AC=2;AF=1;AN=2;DP=617;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:721,54,0:0,0,17,1 chr1 91781413 . T G 945.9 PASS AC=2;AF=0.782;AN=2;DP=2365;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,69:69:99:2100,206,0:0,0,36,33 chr1 91813184 . C T 793.44 PASS AC=2;AF=1;AN=2;DP=1019;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:340,30,0:0,0,2,8 chr1 91841301 . T C 864.65 PASS AC=2;AF=1;AN=2;DP=1520;FS=0;MQ=60;MQRankSum=-0.289;ReadPosRankSum=-0.144;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1382,123,0:0,0,10,31 chr1 91846374 . C A 2901.57 PASS AC=2;AF=1;AN=2;DP=4109;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,98:98:99:2837,293,0:0,0,48,50 chr1 91846595 . T TA 220.74 PASS AC=2;AF=1;AN=2;DP=711;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:796,66,0:0,0,7,15 chr1 91846654 . A T 196.77 PASS AC=2;AF=1;AN=2;DP=161;FS=0;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant24-variant25-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:135,9,0:0,0,0,3 chr1 91851253 . T C 2751.93 PASS AC=2;AF=1;AN=2;DP=3664;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,83:83:99:2390,248,0:0,0,41,42 chr1 91859795 . T C 6540.7 PASS AC=2;AF=1;AN=2;DP=6846;FS=0;MQ=60;MQRankSum=0.152;ReadPosRankSum=0.59;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,183:183:99:5007,548,0:0,0,92,91 chr1 91870410 . G C 3112.18 PASS AC=2;AF=0.594;AN=2;DP=3218;MQ=60;set=variant3-variant5-variant11-variant15-variant23-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,213:213:99:6425,638,0:0,0,107,106 chr1 91966406 . G A 809.36 PASS AC=1;AF=0.5;AN=2;DP=689;FractionInformativeReads=1;MQ=60;set=variant6-variant8-variant12-variant14-variant19-variant22-variant24-variant28-variant30-variant33-variant35-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,25:58:99:746,0,1049:25,8,17,8 chr1 91973557 . T G 1416.26 PASS AC=2;AF=1;AN=2;DP=2427;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1564,147,0:0,0,16,33 chr1 91980447 . A G 3854.16 PASS AC=1;AF=0.817;AN=2;DP=4743;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:63,57:120:99:1427,0,1489:38,25,37,20 chr1 91981484 . G A 634.45 PASS AC=1;AF=0.5;AN=2;DP=232;FractionInformativeReads=1;MQ=60;set=variant12-variant14-variant28-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:36,20:56:99:497,0,950:12,24,6,14 chr1 91989569 . GTTT G 202.61 PASS AC=1;AF=0.5;AN=2;DP=131;set=variant12-variant14-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:16,14:30:99:540,0,581:12,4,10,4 chr1 91989572 . T G 1373.56 PASS AC=1;AF=0.955;AN=2;DP=1530;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:14,16:30:99:431,0,541:10,4,12,4 chr1 91990988 . A AGT 1562.6 PASS AC=1;AF=0.5;AN=2;DP=167;MQ=60;set=variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:42,46:88:99:1804,0,1655:23,19,26,20 chr1 91991267 . AT A 523.48 PASS AC=1;AF=0.5;AN=2;DP=322;MQ=60;set=variant12-variant14-variant28-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:44,36:80:99:841,0,1030:12,32,11,25 chr1 91991268 . T A 2034.93 PASS AC=1;AF=0.943;AN=2;DP=3088;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:38,41:79:99:875,0,891:13,25,10,31 chr1 92100981 . A G 246.05 PASS AC=1;AF=0.5;AN=2;DP=121;FractionInformativeReads=1;MQ=60;set=variant11-variant13-variant21-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:21,11:32:99:312,0,499:7,14,2,9 chr1 92107937 . C T 969.91 PASS AC=1;AF=0.5;AN=2;DP=224;MQ=60;set=variant11-variant13-variant35 GT:AD:DP:GQ:PL:SB 0/1:55,29:84:99:647,0,1534:37,18,19,10 chr1 92108119 . A G 755.36 PASS AC=1;AF=0.5;AN=2;DP=155;MQ=60;set=variant11-variant13-variant35 GT:AD:DP:GQ:PL:SB 0/1:40,20:60:99:471,0,1230:14,26,9,11 chr1 92108899 . C T 2668.59 PASS AC=2;AF=0.81;AN=2;DP=9765;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,202:202:99:6071,604,0:0,0,92,110 chr1 92147961 . CTT CT,CTTT,CTTTTT,C,CTTTT 354.5 PASS AC=1,0,0,0,0;AF=0.212,0.227,0.076,0.015,0.03;AN=2;DP=1913;set=variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-filterInvariant20-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant33-variant34-filterInvariant35-filterInvariant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:50:90:21,15,8,6 chr1 92148227 . C G 5403.88 PASS AC=2;AF=0.767;AN=2;DP=5251;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,133:133:99:4031,399,0:0,0,62,71 chr1 92174260 . A G 6407.95 PASS AC=1;AF=0.898;AN=2;DP=8474;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:114,109:223:99:2403,0,2832:56,58,51,58 chr1 92174415 . G A 218.9 PASS AC=1;AF=0.5;AN=2;DP=294;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant14-variant23-variant31-variant34-variant35-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,17:42:99:415,0,781:5,20,6,11 chr1 92185657 . C T 2081.28 PASS AC=1;AF=0.671;AN=2;DP=2448;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:42,49:91:99:1210,0,1142:18,24,19,30 chr1 92195601 . G A 629.49 PASS AC=1;AF=0.586;AN=2;DP=978;MQ=60;set=variant3-variant4-variant6-variant10-variant11-variant12-variant13-variant14-variant16-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:19,14:33:99:325,0,485:8,11,5,9 chr1 92200593 . A G 1232.4 PASS AC=1;AF=0.724;AN=2;DP=1733;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,34:60:99:933,0,990:8,18,11,23 chr1 92200597 . G A 1163.5 PASS AC=1;AF=0.611;AN=2;DP=1093;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant14-variant15-variant16-variant17-variant18-variant19-variant23-variant28-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,26:58:99:688,0,1329:9,23,8,18 chr1 92200627 . T C 636.52 PASS AC=2;AF=0.977;AN=2;DP=1082;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1501,108,0:0,0,5,31 chr1 92200634 . C T 242.86 PASS AC=1;AF=0.525;AN=2;DP=405;MQ=60;set=variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant21-variant22-variant23-variant24-variant27-variant32-variant34-variant35-variant36-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,17:28:99:539,0,370:1,10,3,14 chr1 92224067 . C T 465.64 PASS AC=1;AF=0.524;AN=2;DP=737;MQ=60;set=variant2-variant3-variant12-variant13-variant14-variant15-variant16-variant19-variant22-variant23-variant24-variant30-variant31-variant32-variant35-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,18:40:99:397,0,595:15,7,9,9 chr1 92262874 . T C 205.52 PASS AC=1;AF=0.676;AN=2;DP=1716;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,28:60:99:601,0,857:22,10,17,11 chr1 92414916 . C T 77.94 PASS AC=1;AF=0.672;AN=2;DP=409;MQ=60;set=variant-variant4-variant5-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,3:10:67:67,0,172:4,3,3,0 chr1 92414993 . T C 772.68 PASS AC=1;AF=0.829;AN=2;DP=1335;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,14:23:99:472,0,275:6,3,12,2 chr1 92415049 . G C 1784.45 PASS AC=1;AF=0.594;AN=2;DP=703;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant22-variant26-variant28-variant29-variant34-variant35-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,21:49:99:540,0,761:19,9,13,8 chr1 92415118 . C A 1727.51 PASS AC=1;AF=0.829;AN=2;DP=2881;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,45:86:99:1085,0,956:24,17,22,23 chr1 92428495 . C A 1249.44 PASS AC=2;AF=0.895;AN=2;DP=1350;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1171,114,0:0,0,14,24 chr1 92446112 . T C 436.35 PASS AC=1;AF=0.826;AN=2;DP=554;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,8:16:99:228,0,234:6,2,6,2 chr1 92446398 . T A 3255.89 PASS AC=1;AF=0.833;AN=2;DP=3401;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,30:81:99:743,0,1208:26,25,17,13 chr1 92447004 . A G 669.12 PASS AC=1;AF=0.837;AN=2;DP=799;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,12:25:99:417,0,387:4,9,4,8 chr1 92457843 . C T 1518.79 PASS AC=1;AF=0.837;AN=2;DP=1919;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,20:45:99:519,0,694:16,9,14,6 chr1 92457969 . CAAA CAA,CA,C 250.7 PASS AC=0,0,1;AF=0.415,0.171,0.073;AN=2;DP=1726;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:DP:GQ:SB 0/3:31:99:6,6,7,12 chr1 92467741 . A C 1115.58 PASS AC=1;AF=0.5;AN=2;DP=337;FractionInformativeReads=1;MQ=60;set=variant5-variant22-variant29-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:25,35:60:99:889,0,600:9,16,14,21 chr1 92545968 . G T 3591.26 PASS AC=1;AF=0.75;AN=2;DP=306;FractionInformativeReads=1;MQ=60;MQRankSum=1.739;ReadPosRankSum=-0.194;set=variant16-variant35 GT:AD:DP:GQ:PL:SB 0/1:93,91:184:99:2175,0,2162:53,40,53,38 chr1 92568263 . A G 600.67 PASS AC=2;AF=0.821;AN=2;DP=1478;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:1009,87,0:0,0,8,21 chr1 92573670 . G A 923.61 PASS AC=1;AF=0.591;AN=2;DP=1028;MQ=60;set=variant-variant6-variant9-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant24-variant27-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,19:42:99:479,0,672:8,15,5,14 chr1 92605215 . CTT C 331.52 PASS AC=2;AF=0.821;AN=2;DP=1113;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:970,66,0:0,0,7,15 chr1 92605350 . G T 157.4 PASS AC=2;AF=0.986;AN=2;DP=204;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.322;ReadPosRankSum=-1.517;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:186,18,0:0,0,2,4 chr1 92646021 . G A 1277.57 PASS AC=2;AF=0.821;AN=2;DP=3259;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:2422,225,0:0,0,39,36 chr1 92647223 . A G 770.78 PASS AC=2;AF=0.859;AN=2;DP=1976;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2328,210,0:0,0,35,35 chr1 92647532 . C A 3328.25 PASS AC=2;AF=0.977;AN=2;DP=4440;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,108:108:99:3122,322,0:0,0,55,53 chr1 92649292 . A T 399.36 PASS AC=2;AF=0.859;AN=2;DP=504;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:437,39,0:0,0,10,3 chr1 92649312 . G GTT,GT 257.65 PASS AC=1,0;AF=0.457,0.3;AN=2;DP=647;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:14:99:5,1,6,2 chr1 92649335 . A G 462.7 PASS AC=2;AF=0.859;AN=2;DP=1202;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:1087,90,0:0,0,18,12 chr1 92650349 . C T 1792.76 PASS AC=2;AF=0.859;AN=2;DP=2924;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,84:84:99:2987,251,0:0,0,16,68 chr1 92711067 . A T 653.43 PASS AC=1;AF=0.697;AN=2;DP=1535;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,22:51:99:495,0,784:20,9,12,10 chr1 92712266 . C T 2020.3 PASS AC=2;AF=1;AN=2;DP=2533;FS=0;MQRankSum=-0.65;ReadPosRankSum=1.66;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:2006,186,0:0,0,23,39 chr1 92712598 . GAA G 1128.69 PASS AC=1;AF=0.682;AN=2;DP=2957;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,51:105:99:1976,0,2039:28,26,28,23 chr1 92735359 . T C 496.3 PASS AC=1;AF=0.682;AN=2;DP=1985;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,43:71:99:1102,0,610:10,18,15,28 chr1 92755943 . G A 181.76 PASS AC=1;AF=0.721;AN=2;DP=414;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,10:14:99:391,0,141:0,4,1,9 chr1 92764828 . T A 576.54 PASS AC=2;AF=1;AN=2;DP=1315;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,31:31:93:1070,93,0:0,0,10,21 chr1 92765848 . A T 907.3 PASS AC=1;AF=0.682;AN=2;DP=2473;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,45:79:99:1153,0,756:14,20,20,25 chr1 92799151 . C T 892.82 PASS AC=1;AF=0.866;AN=2;DP=626;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,8:14:99:318,0,224:1,5,1,7 chr1 92852504 . A G 1851.13 PASS AC=1;AF=0.866;AN=2;DP=1923;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,26:57:99:651,0,802:21,10,19,7 chr1 92941357 . A G 1676.83 PASS AC=1;AF=0.803;AN=2;DP=2073;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,33:62:99:885,0,688:15,14,18,15 chr1 92944314 . CAGAGAGAGAG CAGAGAGAGAGAGAGAG,CAGAG,CAGAGAGAGAGAGAGAGAGAG,CAGAGAGAG,CAGAGAGAGAGAGAG,C,CAGAGAG,CAGAGAGAGAGAG,CAGAGAGAGAGAGAGAGAGAGAG 433.03 PASS AC=1,0,0,1,0,0,0,0,0;AF=0.244,0.037,0.037,0.207,0.085,0.024,0.037,0.049,0.024;AN=2;DP=1845;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 4/1:21:99:0,2,0,19 chr1 92946479 . G A 2506.75 PASS AC=1;AF=0.829;AN=2;DP=3915;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,52:100:99:1336,0,1316:29,19,28,24 chr1 92952217 . CA C 740.54 PASS AC=2;AF=1;AN=2;DP=1214;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:1212,90,0:0,0,25,5 chr1 92974595 . G A 4722.73 PASS AC=1;AF=0.829;AN=2;DP=5738;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:91,56:147:99:1404,0,2257:41,50,26,30 chr1 92975050 . A AT 496.42 PASS AC=1;AF=0.586;AN=2;DP=1225;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-filterInvariant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,16:27:99:287,0,174:2,9,3,13 chr1 92975244 . T A 3311.87 PASS AC=1;AF=0.784;AN=2;DP=3192;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,52:110:99:1208,0,1414:31,27,27,25 chr1 92975262 . C A 3391.2 PASS AC=1;AF=0.784;AN=2;DP=3355;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,53:108:99:1302,0,1355:31,24,27,26 chr1 92975493 . A G 5741.01 PASS AC=1;AF=0.795;AN=2;DP=5927;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,62:130:99:1529,0,1726:40,28,38,24 chr1 92975938 . T C 12963.7 PASS AC=1;AF=0.784;AN=2;DP=12412;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:187,162:349:99:4179,0,4943:103,84,83,79 chr1 92976023 . T G 13045.3 PASS AC=1;AF=0.829;AN=2;DP=14186;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:208,185:393:99:4425,0,5337:106,102,94,91 chr1 92976590 . G A 1497.69 PASS AC=1;AF=0.829;AN=2;DP=2300;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,42:77:99:1160,0,839:21,14,24,18 chr1 92977275 . A G 1616.84 PASS AC=1;AF=0.829;AN=2;DP=1602;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,17:39:99:564,0,593:16,6,14,3 chr1 92978722 . TA T 3169.12 PASS AC=1;AF=0.792;AN=2;DP=3418;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,57:100:99:1315,0,909:31,12,43,14 chr1 92979092 . ATATATATATATATATATATATATATATATATG A 54.23 PASS AC=1;AF=0.667;AN=2;DP=27;FractionInformativeReads=1;MQ=60;set=variant29-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:1,5:6:24:199,0,24:1,0,4,1 chr1 92979354 . A G 3584.46 PASS AC=1;AF=0.829;AN=2;DP=6177;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:74,78:152:99:1944,0,1678:39,35,34,44 chr1 92979681 . TTA T 130.95 PASS AC=1;AF=0.846;AN=2;DP=407;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,9:19:99:321,0,359:1,9,2,7 chr1 93029453 . A G 546.35 PASS AC=1;AF=0.829;AN=2;DP=696;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,12:18:99:361,0,125:2,4,3,9 chr1 93071048 . G T 1391.68 PASS AC=2;AF=0.884;AN=2;DP=1428;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:837,75,0:0,0,7,18 chr1 93073228 . C A 647.8 PASS AC=1;AF=0.538;AN=2;DP=624;MQ=60;set=variant2-variant3-variant5-variant8-variant10-variant14-variant22-variant29-variant35-variant36-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:22,24:46:99:574,0,448:10,12,11,13 chr1 93087855 . C T 598.8 PASS AC=1;AF=0.5;AN=2;DP=412;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant14-variant22-variant29-variant35-variant36-variant40 GT:AD:DP:GQ:PL:SB 0/1:26,26:52:99:591,0,621:15,11,15,11 chr1 93089823 . T C 2648.6 PASS AC=2;AF=0.884;AN=2;DP=2892;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,64:64:99:1789,191,0:0,0,28,36 chr1 93128514 . TA TAA,TAAA,T 248.87 PASS AC=1,0,0;AF=0.605,0.013,0.013;AN=2;DP=987;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:23:1:1,2,5,15 chr1 93128854 . A G 1035.94 PASS AC=2;AF=0.884;AN=2;DP=1329;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,29:29:86:763,86,0:0,0,16,13 chr1 93160002 . G A 499.4 PASS AC=1;AF=0.538;AN=2;DP=493;set=variant2-variant3-variant5-variant8-variant10-variant14-variant22-variant29-variant35-variant36-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,25:33:99:775,0,162:3,5,5,20 chr1 93160902 . T C 4266.85 PASS AC=2;AF=0.884;AN=2;DP=4836;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,104:104:99:3057,310,0:0,0,43,61 chr1 93163385 . A G 2269.55 PASS AC=1;AF=0.784;AN=2;DP=2057;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,29:48:99:793,0,464:12,7,21,8 chr1 93163633 . C T 773.56 PASS AC=2;AF=0.893;AN=2;DP=580;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:700,57,0:0,0,3,16 chr1 93167610 . C T 106.77 PASS AC=2;AF=0.902;AN=2;DP=322;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:324,27,0:0,0,7,2 chr1 93167854 . A G 1320.16 PASS AC=2;AF=0.895;AN=2;DP=1552;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:997,99,0:0,0,13,20 chr1 93306317 . G A 1665.5 PASS AC=1;AF=0.731;AN=2;DP=6441;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:89,72:161:99:1607,0,2151:45,44,38,34 chr1 93307908 . T A 10364.8 PASS AC=2;AF=0.878;AN=2;DP=11874;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,282:282:99:8895,844,0:0,0,142,140 chr1 93308035 . G GA 2983.02 PASS AC=1;AF=0.5;AN=2;DP=4202;MQ=60;set=variant-variant2-variant3-variant5-variant8-variant10-variant29-variant31-variant34-variant35-variant36-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:161,109:270:99:2484,0,4089:77,84,51,58 chr1 93308168 . T TA 2521.14 PASS AC=1;AF=0.75;AN=2;DP=7769;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:98,103:201:99:3221,0,3044:41,57,47,56 chr1 93308798 . G A 1984.78 PASS AC=2;AF=0.886;AN=2;DP=2915;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:2097,186,0:0,0,20,42 chr1 93308853 . C A 1291.37 PASS AC=2;AF=0.884;AN=2;DP=1660;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1132,108,0:0,0,11,25 chr1 93311065 . GAAAA GAA,GA,GAAA,G 132.86 PASS AC=1,0,0,0;AF=0.309,0.118,0.088,0.059;AN=2;DP=657;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant10-variant11-variant12-filterInvariant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:DP:GQ:SB 0/1:10:82:1,4,4,1 chr1 93311098 . GAA GAAA,GA,G 127.11 PASS AC=1,0,0;AF=0.389,0.056,0.056;AN=2;DP=153;MQ=60;set=variant2-variant8-variant10-variant21-variant29-variant31-variant35-variant37-variant39 GT:DP:GQ:SB 0/1:10:78:0,5,1,4 chr1 93312142 . A G 388.94 PASS AC=1;AF=0.5;AN=2;DP=367;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant8-variant10-variant29-variant31-variant35-variant36-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:17,22:39:99:651,0,463:4,13,5,17 chr1 93312192 . C CT 31.1 PASS AC=1;AF=0.5;AN=2;DP=60;FS=0;MQ=60;set=variant-variant10-variant31-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:2,6:8:32:136,0,32:0,2,1,5 chr1 93312592 . C T 253.66 PASS AC=1;AF=0.5;AN=2;DP=206;FractionInformativeReads=1;set=variant-variant2-variant3-variant5-variant8-variant10-variant29-variant31-variant34-variant35-variant36-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,11:17:99:377,0,139:4,2,9,2 chr1 93426866 . T C 2951.9 PASS AC=2;AF=1;AN=2;DP=4185;FS=0;MQ=60;MQRankSum=-1.022;ReadPosRankSum=1.89;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,116:116:99:5443,367,0:0,0,74,42 chr1 93426869 . G C 1854.4 PASS AC=2;AF=0.878;AN=2;DP=4138;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,128:128:99:5661,394,0:0,0,80,48 chr1 93426874 . G T 1854.4 PASS AC=1;AF=0.5;AN=2;DP=1520;MQ=60;set=variant-variant2-variant3-variant5-variant8-variant10-variant29-variant31-variant35-variant36-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:76,64:140:99:1336,0,1738:44,32,39,25 chr1 93545157 . G A 2958.15 PASS AC=2;AF=0.966;AN=2;DP=4527;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,101:101:99:3524,302,0:0,0,50,51 chr1 93580581 . G C 4494.87 PASS AC=2;AF=1;AN=2;DP=5718;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,114:114:99:3279,340,0:0,0,60,54 chr1 93580992 . C T 1810.69 PASS AC=2;AF=0.857;AN=2;DP=3198;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:2424,229,0:0,0,51,26 chr1 93581024 . T C 926.9 PASS AC=2;AF=0.713;AN=2;DP=4637;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,109:109:99:3429,326,0:0,0,70,39 chr1 93583818 . CTT CT,C,CTTTTT 144.68 PASS AC=1,0,0;AF=0.636,0.045,0.015;AN=2;DP=402;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:8:18:2,0,6,0 chr1 93602194 . C T 994.85 PASS AC=2;AF=0.905;AN=2;DP=4249;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,102:102:99:3145,305,0:0,0,64,38 chr1 93603183 . C CAT,CATGTGTATATATATACACACAT 5183.81 PASS AC=2,0;AF=0.893,0.012;AN=2;DP=10546;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:271:99:0,0,136,135 chr1 93616202 . T C 8289.29 PASS AC=2;AF=0.75;AN=2;DP=24902;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,624:625:99:19490,1827,0:0,1,310,314 chr1 93617403 . T G 2444.27 PASS AC=2;AF=0.775;AN=2;DP=9739;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,222:222:99:6697,665,0:0,0,99,123 chr1 93617546 . T C 6700.16 PASS AC=2;AF=0.881;AN=2;DP=7640;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,188:188:99:5874,562,0:0,0,100,88 chr1 93620393 . G A 2481.89 PASS AC=2;AF=0.713;AN=2;DP=7273;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,187:189:99:6152,517,0:1,1,56,131 chr1 93621483 . A G 272.85 PASS AC=2;AF=0.75;AN=2;DP=1023;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:640,51,0:0,0,12,5 chr1 93646207 . T C 4171.66 PASS AC=2;AF=0.75;AN=2;DP=11363;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,315:315:99:9692,941,0:0,0,159,156 chr1 93646418 . C T 3003.28 PASS AC=2;AF=0.569;AN=2;DP=10421;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant31-variant33-variant35-variant37-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,346:346:99:10139,1032,0:0,0,144,202 chr1 93648816 . A G 1565.08 PASS AC=2;AF=0.881;AN=2;DP=1873;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1532,123,0:0,0,35,6 chr1 93649732 . A G 484.29 PASS AC=2;AF=0.763;AN=2;DP=804;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:767,60,0:0,0,3,17 chr1 93659350 . A T 1043.39 PASS AC=2;AF=0.89;AN=2;DP=1006;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:589,54,0:0,0,6,12 chr1 93672723 . A C 1818.47 PASS AC=2;AF=0.857;AN=2;DP=2385;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:1739,162,0:0,0,36,18 chr1 93676314 . A G 303.31 PASS AC=2;AF=0.75;AN=2;DP=1072;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:960,81,0:0,0,21,6 chr1 93676578 . A G 398.69 PASS AC=2;AF=0.713;AN=2;DP=963;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:888,72,0:0,0,4,20 chr1 93711782 . T A 1084.44 PASS AC=2;AF=0.653;AN=2;DP=2680;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:1837,194,0:0,0,27,38 chr1 93811569 . A G 1682.11 PASS AC=2;AF=0.775;AN=2;DP=5999;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,150:150:99:4682,450,0:0,0,80,70 chr1 93826600 . A AGGG,AGG,AGGGG 2132.74 PASS AC=2,0,0;AF=0.613,0.088,0.05;AN=2;DP=5808;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:81:99:2,0,66,13 chr1 93827456 . T A 8583.64 PASS AC=2;AF=0.881;AN=2;DP=9354;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,210:210:99:6710,630,0:0,0,77,133 chr1 93827995 . C CT,CTT 908.7 PASS AC=2,0;AF=0.714,0.024;AN=2;DP=2007;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-filterInvariant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:27:54:1,0,11,15 chr1 93998640 . AT A 1364.17 PASS AC=2;AF=0.684;AN=2;DP=2811;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:2652,214,0:0,0,21,50 chr1 94012287 . G A 462.99 PASS AC=2;AF=0.85;AN=2;DP=400;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:356,27,0:0,0,8,1 chr1 94041787 . G GAC 3454.94 PASS AC=2;AF=0.909;AN=2;DP=3792;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,83:83:99:3630,252,0:0,0,28,55 chr1 94054382 . T C 376.29 PASS AC=2;AF=0.73;AN=2;DP=1196;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1159,102,0:0,0,23,11 chr1 94312482 . T TC 1637.7 PASS AC=2;AF=1;AN=2;DP=5512;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,119:119:99:4412,358,0:0,0,62,57 chr1 94312528 . G GC 1548.51 PASS AC=2;AF=1;AN=2;DP=4706;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,104:104:99:4277,311,0:0,0,49,55 chr1 94312533 . G GC 1387.08 PASS AC=2;AF=1;AN=2;DP=3709;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,84:84:99:3890,262,0:0,0,32,52 chr1 94312542 . G GC 1267.73 PASS AC=2;AF=1;AN=2;DP=3320;FS=0;MQ=60;MQRankSum=-1.091;ReadPosRankSum=-1.561;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:3645,244,0:0,0,29,46 chr1 94312544 . G GC 1267.73 PASS AC=2;AF=1;AN=2;DP=3156;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:3375,226,0:0,0,29,43 chr1 94312554 . A AG 1087.73 PASS AC=2;AF=1;AN=2;DP=2896;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:3240,217,0:0,0,30,41 chr1 94312558 . G GC 952.73 PASS AC=2;AF=0.716;AN=2;DP=2201;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:3330,223,0:0,0,28,42 chr1 94312566 . G T 916.77 PASS AC=2;AF=0.716;AN=2;DP=2098;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:2970,199,0:0,0,26,39 chr1 94312567 . T C 916.77 PASS AC=2;AF=0.716;AN=2;DP=2091;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,64:64:99:2970,199,0:0,0,26,38 chr1 94312571 . G GC 952.73 PASS AC=2;AF=0.716;AN=2;DP=2044;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:2925,196,0:0,0,26,36 chr1 94312573 . G GC 907.73 PASS AC=2;AF=0.716;AN=2;DP=2000;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:2835,190,0:0,0,27,33 chr1 94312576 . G GC 817.73 PASS AC=2;AF=1;AN=2;DP=2478;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:2700,181,0:0,0,27,32 chr1 94312579 . G GC,GT 817.73 PASS AC=2,0;AF=0.602,0.398;AN=2;DP=2357;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:DP:GQ:SB 1/1:56:99:0,0,25,31 chr1 94312584 . G GC 582.7 PASS AC=2;AF=1;AN=2;DP=2235;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:2507,168,0:0,0,26,29 chr1 94471075 . A G 4479.85 PASS AC=2;AF=0.915;AN=2;DP=5345;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,159:159:99:4785,477,0:0,0,72,87 chr1 94476555 . G A 109.23 PASS AC=2;AF=0.819;AN=2;DP=590;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:41:478,41,0:0,0,2,12 chr1 94480037 . C T 371.57 PASS AC=1;AF=0.594;AN=2;DP=1754;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,31:69:99:926,0,1104:22,16,22,9 chr1 94487354 . G A 2004.63 PASS AC=1;AF=0.706;AN=2;DP=4669;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:71,81:152:99:1976,0,1843:38,33,48,33 chr1 94495407 . C T 491.68 PASS AC=1;AF=0.603;AN=2;DP=1403;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,15:35:99:570,0,809:6,14,5,10 chr1 94495417 . C T 403.42 PASS AC=1;AF=0.603;AN=2;DP=1260;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,15:31:99:582,0,702:4,12,5,10 chr1 94495487 . G A 73.33 PASS AC=1;AF=0.609;AN=2;DP=410;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant35-variant36-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,6:11:99:193,0,139:2,3,1,5 chr1 94495930 . T C 310.28 PASS AC=2;AF=0.977;AN=2;DP=1584;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,33:33:98:1119,98,0:0,0,24,9 chr1 94496253 . G A 673.91 PASS AC=1;AF=0.618;AN=2;DP=1924;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,32:60:99:970,0,920:3,25,7,25 chr1 94497178 . G A 482.4 PASS AC=1;AF=0.692;AN=2;DP=1899;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,26:49:99:620,0,584:15,8,17,9 chr1 94511533 . G A 952.23 PASS AC=2;AF=0.713;AN=2;DP=3046;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,80:81:99:2823,236,0:1,0,17,63 chr1 94544135 . A AC 259.88 PASS AC=2;AF=0.803;AN=2;DP=933;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:930,90,0:0,0,6,24 chr1 94544234 . T C 1390.66 PASS AC=2;AF=0.583;AN=2;DP=2157;set=variant3-variant4-variant5-variant8-variant9-variant10-variant12-variant14-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant31-variant33-variant35-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,123:123:99:3674,369,0:0,0,65,58 chr1 94544805 . T TCA 343.19 PASS AC=2;AF=0.583;AN=2;DP=462;MQ=60;set=variant3-variant4-variant5-variant8-variant9-variant10-variant12-variant14-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant31-variant33-variant35-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:60:626,60,0:0,0,12,6 chr1 94549029 . A G 1595.09 PASS AC=1;AF=0.563;AN=2;DP=2176;MQ=60;set=variant3-variant4-variant5-variant8-variant9-variant10-variant12-variant14-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant31-variant33-variant35-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:44,75:119:99:1896,0,989:15,29,32,43 chr1 94549083 . T C 507.26 PASS AC=1;AF=0.782;AN=2;DP=1780;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,45:68:99:1255,0,606:7,16,16,29 chr1 94568491 . A G 164.46 PASS AC=1;AF=0.591;AN=2;DP=846;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant10-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant29-variant32-variant35-variant38-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,12:29:99:389,0,546:14,3,10,2 chr1 94574053 . C A 617.46 PASS AC=1;AF=0.603;AN=2;DP=1487;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant14-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:31,25:56:99:578,0,858:15,16,15,10 chr1 94576968 . T C 751.04 PASS AC=1;AF=0.603;AN=2;DP=1748;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant14-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:28,36:64:99:883,0,728:18,10,23,13 chr1 94578548 . T C 1516.64 PASS AC=2;AF=0.989;AN=2;DP=2134;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,63:63:99:1928,188,0:0,0,41,22 chr1 94638168 . GAT GATAT,GATATAT,GATATATAT,G,GATATATATAT 444.91 PASS AC=1,0,1,0,0;AF=0.464,0.214,0.036,0.012,0.024;AN=2;DP=2286;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-filterInvariant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/3:17:99:0,2,6,9 chr1 94638439 . A C 4211.32 PASS AC=1;AF=0.538;AN=2;DP=6706;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant16-variant18-variant19-variant20-variant22-variant23-variant26-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:141,114:255:99:2831,0,3794:68,73,47,67 chr1 94638711 . C T 761.59 PASS AC=1;AF=0.538;AN=2;DP=1188;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant16-variant18-variant19-variant20-variant22-variant23-variant26-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:22,19:41:99:515,0,571:12,10,9,10 chr1 94639337 . A G 8972.4 PASS AC=2;AF=0.989;AN=2;DP=11704;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,256:256:99:7930,765,0:0,0,119,137 chr1 94639447 . C T 6647.57 PASS AC=2;AF=0.966;AN=2;DP=8763;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,209:209:99:6877,627,0:0,0,102,107 chr1 94643531 . T C 1592.9 PASS AC=1;AF=0.575;AN=2;DP=2739;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant21-variant24-variant26-variant27-variant30-variant32-variant35 GT:AD:DP:GQ:PL:SB 0/1:84,64:148:99:1421,0,2042:50,34,38,26 chr1 94667430 . G GA 304.72 PASS AC=2;AF=0.965;AN=2;DP=881;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:313,33,0:0,0,7,4 chr1 94667970 . T C 1811.79 PASS AC=1;AF=0.531;AN=2;DP=2309;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant6-variant8-variant9-variant18-variant20-variant22-variant23-variant26-variant31-variant33-variant35-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:63,67:130:99:1842,0,1788:24,39,27,40 chr1 94668046 . C T 3666.02 PASS AC=2;AF=0.966;AN=2;DP=5264;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,121:121:99:3973,361,0:0,0,63,58 chr1 94670784 . T C 810.22 PASS AC=1;AF=0.538;AN=2;DP=1100;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant16-variant18-variant19-variant20-variant22-variant23-variant26-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:18,31:49:99:836,0,462:5,13,13,18 chr1 94674723 . G A 1529.26 PASS AC=2;AF=0.989;AN=2;DP=2119;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1167,123,0:0,0,26,15 chr1 94883977 . AGCC A,AGCCGCCGCCGCCGCC,AGCCGCCGCC 40.27 PASS AC=1,0,0;AF=0.469,0.016,0.016;AN=2;DP=2966;MQ=60;set=filterInvariant-filterInvariant4-filterInvariant6-variant7-filterInvariant8-filterInvariant9-filterInvariant10-variant12-filterInvariant13-variant15-variant16-filterInvariant17-filterInvariant18-filterInvariant21-variant22-variant23-filterInvariant24-variant25-filterInvariant26-variant27-filterInvariant28-filterInvariant29-variant30-filterInvariant31-variant32-variant35-variant37-variant39-filterInvariant40-filterInvariant42-filterInvariant43-filterInvariant44 GT:DP:GQ:SB 0/1:92:99:42,31,10,9 chr1 94924046 . A G 252.34 PASS AC=1;AF=0.621;AN=2;DP=695;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant32-variant35-variant36-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,8:17:99:220,0,235:6,3,5,3 chr1 94930345 . G A 1180.53 PASS AC=1;AF=0.621;AN=2;DP=3375;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant32-variant35-variant36-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,30:77:99:658,0,1240:22,25,15,15 chr1 94941376 . G A 241.6 PASS AC=2;AF=0.868;AN=2;DP=399;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:400,30,0:0,0,1,9 chr1 94980671 . C G 3614.65 PASS AC=2;AF=1;AN=2;DP=4755;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,115:115:99:3261,344,0:0,0,60,55 chr1 94984052 . TAA TA,TAAA,T 789.96 PASS AC=1,0,0;AF=0.489,0.023,0.068;AN=2;DP=5960;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-filterInvariant33-variant34-variant35-variant36-filterInvariant37-variant38-variant39-filterInvariant40-variant41-variant42-filterInvariant43-variant44 GT:DP:GQ:SB 0/1:89:99:15,21,19,34 chr1 94995585 . G A 894.36 PASS AC=1;AF=0.529;AN=2;DP=627;set=variant2-variant3-variant5-variant6-variant8-variant9-variant18-variant20-variant25-variant26-variant28-variant31-variant33-variant35-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,15:39:99:558,0,948:23,1,14,1 chr1 94995629 . CAAAAA CAA,CA,CAAA,C 1218.1 PASS AC=1,0,0,0;AF=0.295,0.321,0.064,0.026;AN=2;DP=4254;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:74:52:6,8,58,2 chr1 95001600 . A C 4122.38 PASS AC=2;AF=1;AN=2;DP=4923;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,133:133:99:3978,398,0:0,0,71,62 chr1 95007008 . C A 240.14 PASS AC=1;AF=0.5;AN=2;DP=17;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.01;QD=14.13;ReadPosRankSum=-1.876;SOR=1.179;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:9,8:17:99:268,0,273:7,2,7,1 chr1 95211525 . G A 732.89 PASS AC=2;AF=0.8;AN=2;DP=3207;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:2262,204,0:0,0,25,43 chr1 95285887 . C G 412.62 PASS AC=1;AF=0.553;AN=2;DP=296;MQ=60;set=variant3-variant4-variant8-variant11-variant12-variant15-variant16-variant17-variant20-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:4,6:10:99:159,0,150:2,2,3,3 chr1 95285897 . C CCCCAGA 638.77 PASS AC=1;AF=0.65;AN=2;DP=370;MQ=60;set=variant3-variant4-variant5-variant9-variant13-variant21-variant23-variant25-variant26-variant28-variant30-variant33-variant34-variant35-variant36-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,5:10:99:195,0,175:1,4,2,3 chr1 95286085 . G A 2098.89 PASS AC=1;AF=0.595;AN=2;DP=2345;MQ=60;set=variant3-variant4-variant5-variant9-variant13-variant21-variant23-variant25-variant26-variant28-variant30-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:79,64:143:99:1479,0,1878:42,37,36,28 chr1 95286094 . G T 3039.37 PASS AC=2;AF=1;AN=2;DP=4872;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,151:151:99:5256,455,0:0,0,81,70 chr1 95286658 . C A 2370.54 PASS AC=1;AF=0.811;AN=2;DP=3063;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,35:83:99:740,0,1322:23,25,17,18 chr1 95286675 . GTCCCAAATGTAAA G 3070.16 PASS AC=1;AF=0.811;AN=2;DP=2936;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,31:78:99:1161,0,2526:24,23,14,17 chr1 95290003 . C T 1831.44 PASS AC=1;AF=0.811;AN=2;DP=2044;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,38:62:99:976,0,653:18,6,23,15 chr1 95290305 . T C 693.43 PASS AC=2;AF=1;AN=2;DP=956;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.657;ReadPosRankSum=0.538;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:488,42,0:0,0,4,10 chr1 95290315 . A G 170.27 PASS AC=1;AF=0.65;AN=2;DP=357;MQ=60;set=variant3-variant4-variant5-variant9-variant13-variant21-variant23-variant25-variant26-variant28-variant30-variant33-variant34-variant35-variant36-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,6:13:99:231,0,146:3,4,0,6 chr1 95291366 . A G 3052.93 PASS AC=2;AF=0.989;AN=2;DP=3859;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,85:85:99:2645,255,0:0,0,47,38 chr1 95291479 . A C 1351.66 PASS AC=1;AF=0.5;AN=2;DP=1867;MQ=60;set=variant3-variant4-variant8-variant11-variant12-variant15-variant16-variant17-variant20-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:52,37:89:99:887,0,1402:22,30,16,21 chr1 95293005 . A G 3430.09 PASS AC=1;AF=0.5;AN=2;DP=3635;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant8-variant11-variant12-variant15-variant16-variant17-variant20-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant39 GT:AD:DP:GQ:PL:SB 0/1:103,103:206:99:2479,0,2489:64,39,61,42 chr1 95294089 . T C 2076.06 PASS AC=1;AF=0.5;AN=2;DP=2756;MQ=60;set=variant3-variant4-variant8-variant11-variant12-variant15-variant16-variant17-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant41 GT:AD:DP:GQ:PL:SB 0/1:74,58:132:99:1444,0,1962:34,40,25,33 chr1 95305440 . A G 5763.57 PASS AC=2;AF=0.682;AN=2;DP=5155;MQ=60;set=variant3-variant4-variant5-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,208:208:99:6191,622,0:0,0,113,95 chr1 95330372 . G A 2928.94 PASS AC=1;AF=0.732;AN=2;DP=4080;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,50:103:99:1241,0,1337:33,20,28,22 chr1 95332864 . C T 721.36 PASS AC=1;AF=0.569;AN=2;DP=1630;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:39,33:72:99:771,0,952:23,16,18,15 chr1 95333068 . G T 1286.98 PASS AC=2;AF=0.732;AN=2;DP=1850;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1488,132,0:0,0,16,28 chr1 95358096 . A G 3071.2 PASS AC=1;AF=0.721;AN=2;DP=2913;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,51:87:99:1352,0,841:14,22,19,32 chr1 95360825 . A AT 2117.54 PASS AC=2;AF=0.989;AN=2;DP=4137;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,66:66:99:1762,198,0:0,0,22,44 chr1 95362927 . TAAAAA T,TA,TAAAAAA,TAAA,TAAAA,TAA 3416.45 PASS AC=0,1,0,1,0,0;AF=0.209,0.302,0.07,0.174,0.035,0.023;AN=2;DP=5420;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 2/4:87:99:4,3,46,34 chr1 95363001 . T C 2272.26 PASS AC=1;AF=0.583;AN=2;DP=1100;MQ=60;set=variant7-variant10-variant21-variant28-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:98,113:211:99:3021,0,2631:58,40,64,49 chr1 95365257 . AT A 225.4 PASS AC=1;AF=0.721;AN=2;DP=759;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,9:27:99:229,0,512:7,11,2,7 chr1 95367108 . ACC A,AC 353.37 PASS AC=1,0;AF=0.598,0.232;AN=2;DP=439;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:DP:GQ:SB 0/1:10:99:4,1,5,0 chr1 95367136 . G A 794.03 PASS AC=2;AF=1;AN=2;DP=930;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:960,87,0:0,0,21,8 chr1 95367416 . C T 662.97 PASS AC=1;AF=0.583;AN=2;DP=279;MQ=60;set=variant7-variant10-variant21-variant28-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:31,19:50:99:467,0,839:14,17,10,9 chr1 95367649 . T C 2740.86 PASS AC=1;AF=0.721;AN=2;DP=3286;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,56:100:99:1450,0,1002:23,21,32,24 chr1 95367669 . G A 1015.68 PASS AC=1;AF=0.583;AN=2;DP=593;FractionInformativeReads=1;MQ=60;set=variant7-variant10-variant21-variant28-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:65,42:107:99:877,0,1722:36,29,22,20 chr1 95367894 . A C 1601.44 PASS AC=1;AF=0.893;AN=2;DP=1635;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,15:37:99:390,0,616:7,15,5,10 chr1 95369211 . T G 2421.36 PASS AC=1;AF=0.93;AN=2;DP=3343;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,36:69:99:896,0,793:10,23,15,21 chr1 95392593 . C T 936.76 PASS AC=1;AF=0.545;AN=2;DP=925;MQ=60;set=variant7-variant8-variant9-variant17-variant24-variant29-variant31-variant35-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,46:95:99:1142,0,1329:19,30,17,29 chr1 95427041 . ATT AT,A 82.87 PASS AC=2,0;AF=0.5,0.225;AN=2;DP=908;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:22:66:0,0,7,15 chr1 95428414 . G A 542.69 PASS AC=1;AF=0.591;AN=2;DP=998;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,6:15:99:141,0,313:8,1,4,2 chr1 95428455 . CT C,CTT 130.61 PASS AC=0,1;AF=0.044,0.471;AN=2;DP=2041;set=filterInvariant-filterInvariant2-variant4-variant5-filterInvariant6-variant7-variant8-variant9-filterInvariant10-variant13-variant14-filterInvariant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant31-filterInvariant32-variant33-variant34-variant35-filterInvariant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:DP:GQ:SB 0/2:50:99:10,6,25,9 chr1 95449033 . T C 507.59 PASS AC=1;AF=0.557;AN=2;DP=1195;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant29-variant31-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,15:25:99:391,0,282:2,8,6,9 chr1 95583090 . G C 968.05 PASS AC=2;AF=1;AN=2;DP=1897;FS=0;MQ=60;MQRankSum=-0.657;ReadPosRankSum=1.614;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1326,135,0:0,0,24,21 chr1 95583394 . A C 152.99 PASS AC=2;AF=1;AN=2;DP=488;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:533,39,0:0,0,8,5 chr1 95615554 . G A 193.26 PASS AC=2;AF=1;AN=2;DP=6;FS=0;FractionInformativeReads=1;MQ=60;QD=32.21;SOR=3.912;set=variant35 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:221,18,0:0,0,6,0 chr1 95658345 . AT A 3474.27 PASS AC=2;AF=1;AN=2;DP=6724;MQ=60;MQRankSum=-1.635;ReadPosRankSum=2.418;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,141:141:99:4465,424,0:0,0,59,82 chr1 95658500 . C T 4133.04 PASS AC=1;AF=0.55;AN=2;DP=6069;MQ=60;set=variant5-variant8-variant11-variant12-variant15-variant16-variant19-variant23-variant27-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:133,141:274:99:3731,0,3544:80,53,81,60 chr1 95658770 . T C 3052.01 PASS AC=1;AF=0.604;AN=2;DP=5921;MQ=60;set=variant-variant2-variant3-variant5-variant8-variant11-variant12-variant15-variant16-variant19-variant22-variant23-variant27-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:127,121:248:99:3196,0,3377:48,79,41,80 chr1 95659685 . CCCT C 2859.37 PASS AC=1;AF=0.5;AN=2;DP=161;FS=2.776;FractionInformativeReads=0.988;MQ=60;MQRankSum=-0.033;QD=17.76;ReadPosRankSum=1.078;SOR=0.507;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:84,75:159:99:2897,0,4476:47,37,38,37 chr1 95660024 . AC A 1798.99 PASS AC=1;AF=0.55;AN=2;DP=1861;MQ=60;set=variant5-variant8-variant11-variant12-variant15-variant16-variant19-variant23-variant27-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,35:73:99:1164,0,1306:12,26,10,25 chr1 95661696 . G A 3428.49 PASS AC=1;AF=0.5;AN=2;DP=323;FS=0;FractionInformativeReads=0.997;MQ=60;MQRankSum=3.66;QD=10.61;ReadPosRankSum=-2.439;SOR=0.713;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:173,149:322:99:3457,0,4235:81,92,69,80 chr1 95696709 . T G 361.15 PASS AC=1;AF=0.5;AN=2;DP=56;FractionInformativeReads=1;MQ=60;set=variant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,10:18:99:389,0,257:1,7,0,10 chr1 95699594 . A G 106.77 PASS AC=1;AF=0.898;AN=2;DP=894;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:8,8:16:99:312,0,507:5,3,3,5 chr1 95699604 . G C 106.77 PASS AC=1;AF=0.909;AN=2;DP=974;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:8,10:18:99:388,0,501:5,3,5,5 chr1 95705615 . G A 1390.44 PASS AC=2;AF=0.943;AN=2;DP=1679;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1435,138,0:0,0,16,30 chr1 95709821 . T C 5035.81 PASS AC=2;AF=1;AN=2;DP=6731;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,161:161:99:4608,482,0:0,0,86,75 chr1 95709939 . T G 4372.54 PASS AC=1;AF=0.909;AN=2;DP=5318;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:54,74:128:99:1916,0,1338:28,26,32,42 chr1 95712458 . C A 3344.31 PASS AC=1;AF=0.5;AN=2;DP=708;FractionInformativeReads=1;MQ=60;set=variant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:107,137:244:99:3373,0,2560:50,57,69,68 chr1 95712797 . G A 514.8 PASS AC=1;AF=0.898;AN=2;DP=740;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:4,8:12:99:240,0,105:1,3,2,6 chr1 96457465 . C T 192.31 PASS AC=2;AF=0.81;AN=2;DP=570;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:569,48,0:0,0,9,7 chr1 96488174 . A G 2329.88 PASS AC=2;AF=0.594;AN=2;DP=6387;MQ=60;set=variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant17-variant19-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,211:211:99:6631,633,0:0,0,121,90 chr1 96488206 . G A 2085.05 PASS AC=1;AF=0.5;AN=2;DP=1715;MQ=60;set=variant8-variant13-variant17-variant22-variant25-variant30-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:144,100:244:99:2477,0,3665:76,68,56,44 chr1 96488261 . A T 8830.38 PASS AC=2;AF=0.943;AN=2;DP=10501;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,275:275:99:8103,823,0:0,0,147,128 chr1 96488283 . T C 8993.11 PASS AC=2;AF=1;AN=2;DP=11077;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,286:286:99:8647,854,0:0,0,154,132 chr1 96488369 . T C 2353.09 PASS AC=1;AF=0.5;AN=2;DP=1743;FractionInformativeReads=1;MQ=60;set=variant8-variant13-variant17-variant22-variant25-variant30-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:140,122:262:99:2910,0,3665:62,78,50,72 chr1 96488492 . T C 466.05 PASS AC=2;AF=0.606;AN=2;DP=1224;MQ=60;set=variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant17-variant19-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,46:48:95:1829,95,0:1,1,3,43 chr1 97279217 . CTTTTTTTTTTT CTTTTTTTTTT,CTTTTTT,C,CTTTTTTTTTTTT,CTTTTT,CTTTTTTTTTTTTTTTTTTTTT,CTTTT,CTTTTTTTTTTTTT,CTTTTTTTTT 163.08 PASS AC=1,0,0,1,0,0,0,0,0;AF=0.063,0.3,0.013,0.075,0.05,0.013,0.013,0.013,0.013;AN=2;DP=7235;set=filterInvariant-variant2-variant3-filterInvariant4-filterInvariant5-variant6-variant7-variant8-variant9-variant10-filterInvariant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-filterInvariant26-filterInvariant27-variant28-filterInvariant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-filterInvariant39-filterInvariant40-variant41-variant43-variant44 GT:DP:GQ:SB 1/4:104:99:7,8,43,46 chr1 97543752 . G A 5959.73 PASS AC=1;AF=0.553;AN=2;DP=5422;MQ=60;set=variant4-variant5-variant8-variant10-variant11-variant16-variant18-variant20-variant21-variant25-variant29-variant32-variant33-variant35-variant37-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:178,138:316:99:5203,0,9481:100,78,81,57 chr1 97543764 . C T 3477.31 PASS AC=1;AF=0.597;AN=2;DP=9566;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant29-variant32-variant33-variant35-variant37-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:192,143:335:99:5281,0,9870:108,84,81,62 chr1 97547831 . G A 2073.89 PASS AC=2;AF=1;AN=2;DP=1848;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.034;ReadPosRankSum=-1.152;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:1986,171,0:0,0,41,16 chr1 97700589 . C T 779.81 PASS AC=2;AF=0.542;AN=2;DP=691;MQ=60;set=variant2-variant14-variant23-variant24-variant26-variant29-variant31-variant33-variant35-variant36-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2249,209,0:0,0,22,48 chr1 97771947 . C A 222.1 PASS AC=1;AF=0.54;AN=2;DP=580;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:7,6:13:99:190,0,197:2,5,1,5 chr1 97981242 . T C 106.77 PASS AC=2;AF=0.74;AN=2;DP=150;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant6-variant8-variant9-variant11-variant15-variant16-variant17-variant21-variant22-variant27-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:315,21,0:0,0,6,1 chr1 97981243 . G A 94.73 PASS AC=2;AF=0.75;AN=2;DP=45;FS=0;FractionInformativeReads=1;MQ=60;set=variant8-variant11-variant21-variant22-variant35-variant36-variant37-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:315,21,0:0,0,6,1 chr1 97981395 . T C 1096.47 PASS AC=2;AF=0.571;AN=2;DP=1039;FractionInformativeReads=1;MQ=60;set=variant2-variant8-variant9-variant11-variant14-variant20-variant21-variant22-variant29-variant30-variant35-variant36-variant37-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,82:82:99:2425,246,0:0,0,46,36 chr1 98039541 . A G 1247.85 PASS AC=1;AF=0.5;AN=2;DP=752;FractionInformativeReads=1;MQ=60;set=variant5-variant7-variant18-variant19-variant21-variant23-variant28-variant33-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:34,39:73:99:1001,0,866:13,21,13,26 chr1 98165091 . T C 1577.04 PASS AC=1;AF=0.5;AN=2;DP=847;FractionInformativeReads=1;MQ=60;set=variant5-variant7-variant18-variant21-variant28-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:55,78:133:99:1965,0,1339:19,36,32,46 chr1 98185527 . A G 9765.81 PASS AC=2;AF=1;AN=2;DP=13996;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,319:319:99:9211,955,0:0,0,156,163 chr1 98185705 . TTC T 306.89 PASS AC=1;AF=0.5;AN=2;DP=518;set=variant-variant6-variant12-variant24-variant27-variant29-variant35-variant36-variant39 GT:AD:DP:GQ:PL:SB 0/1:21,22:43:99:667,0,784:8,13,9,13 chr1 98185722 . A T 462.47 PASS AC=1;AF=0.5;AN=2;DP=513;set=variant5-variant7-variant18-variant21-variant28-variant34-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:31,14:45:99:491,0,1289:13,18,6,8 chr1 98185724 . A T 346.17 PASS AC=1;AF=0.5;AN=2;DP=433;set=variant5-variant7-variant18-variant28-variant34-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:32,14:46:99:492,0,1289:14,18,6,8 chr1 98186077 . T C 11197.5 PASS AC=2;AF=1;AN=2;DP=14686;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,307:307:99:9583,918,0:0,0,177,130 chr1 98186229 . T C 5494.11 PASS AC=1;AF=0.5;AN=2;DP=2992;MQ=60;set=variant5-variant7-variant18-variant21-variant28-variant34-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:164,209:373:99:5315,0,4054:72,92,93,116 chr1 98348885 . G A 2346.7 PASS AC=1;AF=0.875;AN=2;DP=3429;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:49,25:74:99:469,0,1133:23,26,12,13 chr1 98349390 . C CA,CAA 458.52 PASS AC=2,0;AF=0.864,0.045;AN=2;DP=1432;MQ=60;set=Intersection GT:DP:GQ:SB 1/1:27:56:1,0,12,14 chr1 98510326 . G T 190.09 PASS AC=1;AF=0.5;AN=2;DP=30;FractionInformativeReads=1;MQ=60;set=variant28-variant35 GT:AD:DP:GQ:PL:SB 0/1:10,10:20:99:211,0,338:9,1,6,4 chr1 98510679 . G GAAAC 2683.96 PASS AC=1;AF=0.5;AN=2;DP=505;MQ=60;set=variant7-variant28-variant35 GT:AD:DP:GQ:PL:SB 0/1:103,70:173:99:2662,0,4701:62,41,42,28 chr1 98510847 . C T 1543.99 PASS AC=1;AF=0.5;AN=2;DP=337;FractionInformativeReads=1;MQ=60;set=variant28-variant35 GT:AD:DP:GQ:PL:SB 0/1:110,85:195:99:2172,0,2923:46,64,39,46 chr1 98511733 . G GCCGCTGCCGCTGCTACCGCTGCCGCTGCTACCGCTGCCGCTGCTA,GCCGCTGCCGCTGCTACCGCTGCCGCTGCTA,GCCGCTGCCGCTGCTA,GCCGCTGCCGCTGCTACCGCTGCCGCTGCTACCGCTGCCGCTGCTACCGCTGCCGCTGCTA 434.47 PASS AC=0,0,2,0;AF=0.067,0.167,0.267,0.067;AN=2;DP=1435;set=variant-variant3-variant5-variant7-variant8-variant15-variant16-variant19-variant21-variant25-variant27-variant30-variant32-variant35-variant37 GT:DP:GQ:SB 3/3:40:99:0,0,18,22 chr1 99127205 . A G 247.45 PASS AC=1;AF=0.942;AN=2;DP=910;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,8:22:99:178,0,338:9,5,3,5 chr1 99127392 . T C 2891.74 PASS AC=2;AF=1;AN=2;DP=4498;FS=0;FractionInformativeReads=1;MQRankSum=1.447;ReadPosRankSum=0.688;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,125:125:99:3660,374,0:0,0,73,52 chr1 99150635 . G A 2324.93 PASS AC=1;AF=0.93;AN=2;DP=3443;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,34:75:99:852,0,954:18,23,14,20 chr1 99225627 . G A 3372.65 PASS AC=2;AF=0.989;AN=2;DP=4857;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,129:129:99:3721,384,0:0,0,67,62 chr1 99355825 . AT A 211.33 PASS AC=1;AF=0.568;AN=2;DP=698;MQ=60;set=variant-variant4-variant5-variant6-variant8-variant9-variant11-variant13-variant14-variant20-variant21-variant22-variant23-variant25-variant29-variant35-variant36-variant37-variant38-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,18:34:99:463,0,411:10,6,12,6 chr1 99356958 . A G 9680.75 PASS AC=2;AF=0.854;AN=2;DP=9636;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,228:228:99:7373,683,0:0,0,84,144 chr1 99358358 . G T 968.14 PASS AC=2;AF=0.7;AN=2;DP=4593;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,126:126:99:3629,377,0:0,0,64,62 chr1 99387628 . T TA 1588.11 PASS AC=2;AF=0.811;AN=2;DP=2635;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1633,171,0:0,0,18,38 chr1 99418911 . TTGTGTGTGTGTG T,TTGTGTGTGTGTGTGTG,TTGTGTGTGTGTGTGTGTGTG,TTGTGTGTGTGTGTG,TTGTGTGTGTG,TTGTGTGTG,TTGTGTGTGTGTGTGTGTG 1198.19 PASS AC=0,0,0,0,0,1,0;AF=0.214,0.161,0.089,0.071,0.018,0.125,0.036;AN=2;DP=1202;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant14-variant16-variant17-variant18-variant20-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant44 GT:DP:GQ:SB 0/6:17:99:1,7,1,8 chr1 99418948 . T TGTGTGA,TGTGA,TGTGTGTGA,TGA 362.04 PASS AC=0,0,0,1;AF=0.38,0.2,0.02,0.1;AN=2;DP=599;set=variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant42 GT:DP:GQ:SB 0/4:18:99:1,9,1,7 chr1 99470269 . T C 1884.67 PASS AC=1;AF=0.545;AN=2;DP=2171;MQ=60;set=variant3-variant4-variant6-variant9-variant10-variant12-variant13-variant16-variant18-variant22-variant23-variant24-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:82,58:140:99:1335,0,2000:31,51,21,37 chr1 99470696 . G A 151.6 PASS AC=1;AF=0.5;AN=2;DP=86;FractionInformativeReads=1;MQ=60;set=variant3-variant10-variant18-variant22-variant33-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:9,4:13:80:80,0,277:4,5,3,1 chr1 99764303 . T C 1074.6 PASS AC=1;AF=0.721;AN=2;DP=1491;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:24,20:44:99:490,0,697:17,7,14,6 chr1 100111956 . A G 1082.62 PASS AC=1;AF=0.545;AN=2;DP=1628;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant9-variant13-variant15-variant16-variant17-variant26-variant28-variant30-variant32-variant33-variant34-variant35-variant37-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:57,50:107:99:1222,0,1469:22,35,19,31 chr1 100133438 . CT C 52.55 PASS AC=1;AF=0.614;AN=2;DP=348;MQ=60;set=variant-variant2-variant9-variant11-variant12-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant29-variant31-variant32-variant33-variant35-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:5,9:14:89:178,0,89:1,4,1,8 chr1 100152443 . T C 1131.61 PASS AC=2;AF=0.656;AN=2;DP=2544;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant9-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,69:69:99:2223,207,0:0,0,39,30 chr1 100160177 . A T 1646.34 PASS AC=2;AF=0.676;AN=2;DP=5307;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,166:167:99:5131,457,0:1,0,57,109 chr1 100182884 . C T 2070.9 PASS AC=1;AF=0.559;AN=2;DP=712;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant7-variant10-variant11-variant13-variant15-variant17-variant19-variant27-variant28-variant29-variant34-variant35-variant36-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,15:37:99:507,0,639:16,6,14,1 chr1 100185282 . G T 555.98 PASS AC=1;AF=0.567;AN=2;DP=169;FractionInformativeReads=1;MQ=60;set=variant4-variant7-variant10-variant11-variant15-variant17-variant19-variant27-variant28-variant29-variant34-variant35-variant36-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,3:11:99:99,0,239:1,7,0,3 chr1 100194305 . C G 2592.48 PASS AC=1;AF=0.614;AN=2;DP=1417;MQ=60;set=variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant15-variant17-variant19-variant22-variant26-variant27-variant28-variant29-variant34-variant35-variant36-variant37-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,37:75:99:1031,0,980:11,27,10,27 chr1 100203501 . C T 554.21 PASS AC=1;AF=0.6;AN=2;DP=323;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant7-variant10-variant11-variant13-variant15-variant17-variant19-variant22-variant26-variant27-variant28-variant29-variant34-variant35-variant37-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,4:17:99:129,0,358:9,4,4,0 chr1 100203571 . A G 1750.63 PASS AC=1;AF=0.625;AN=2;DP=1009;FractionInformativeReads=1;set=variant4-variant6-variant7-variant10-variant11-variant13-variant15-variant17-variant19-variant22-variant26-variant27-variant28-variant29-variant34-variant35-variant37-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,19:37:99:474,0,526:13,5,12,7 chr1 100203597 . G A 2208.45 PASS AC=1;AF=0.625;AN=2;DP=1366;MQ=60;set=variant4-variant6-variant7-variant10-variant11-variant13-variant15-variant17-variant19-variant22-variant26-variant27-variant28-variant29-variant34-variant35-variant37-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,30:63:99:762,0,826:21,12,21,9 chr1 100203648 . C T 3169.78 PASS AC=1;AF=0.625;AN=2;DP=1887;MQ=60;set=variant4-variant6-variant7-variant10-variant11-variant13-variant15-variant17-variant19-variant22-variant26-variant27-variant28-variant29-variant34-variant35-variant37-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,47:103:99:1098,0,1298:29,27,26,21 chr1 100203693 . G A 3254.98 PASS AC=1;AF=0.625;AN=2;DP=2009;MQ=60;set=variant4-variant6-variant7-variant10-variant11-variant13-variant15-variant17-variant19-variant22-variant26-variant27-variant28-variant29-variant34-variant35-variant37-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:66,47:113:99:989,0,1648:34,32,23,24 chr1 100214391 . T A 5526.17 PASS AC=1;AF=0.625;AN=2;DP=2602;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant7-variant10-variant11-variant13-variant15-variant17-variant19-variant22-variant26-variant27-variant28-variant29-variant34-variant35-variant37-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:79,45:124:99:1335,0,2295:55,24,31,14 chr1 100214487 . C T 10967 PASS AC=1;AF=0.625;AN=2;DP=7374;MQ=60;set=variant4-variant6-variant7-variant10-variant11-variant13-variant15-variant17-variant19-variant22-variant26-variant27-variant28-variant29-variant34-variant35-variant37-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:191,159:350:99:3845,0,4536:106,85,93,66 chr1 100214634 . C T 832.97 PASS AC=1;AF=0.5;AN=2;DP=876;MQ=60;set=variant6-variant7-variant10-variant11-variant13-variant22-variant26-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:53,50:103:99:1577,0,1586:12,41,8,42 chr1 100316589 . A G 2000.36 PASS AC=2;AF=0.621;AN=2;DP=5003;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,131:133:99:4113,348,0:1,1,58,73 chr1 100316765 . C T 1140.97 PASS AC=2;AF=0.817;AN=2;DP=1867;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1476,132,0:0,0,12,32 chr1 100329889 . G C 3488.97 PASS AC=2;AF=0.813;AN=2;DP=3360;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,97:97:99:2985,290,0:0,0,63,34 chr1 100335883 . A G 341.62 PASS AC=1;AF=0.594;AN=2;DP=941;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant9-variant11-variant12-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,11:32:99:325,0,670:17,4,9,2 chr1 100336361 . C T 1972.52 PASS AC=2;AF=0.817;AN=2;DP=2489;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:1671,174,0:0,0,32,26 chr1 100340225 . G A 1813.63 PASS AC=2;AF=0.817;AN=2;DP=2967;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:2011,203,0:0,0,40,28 chr1 100340827 . T C 961.94 PASS AC=1;AF=0.5;AN=2;DP=278;FractionInformativeReads=1;MQ=60;set=variant11-variant13-variant35 GT:AD:DP:GQ:PL:SB 0/1:34,56:90:99:1452,0,934:19,15,26,30 chr1 100342227 . C T 732.03 PASS AC=2;AF=0.657;AN=2;DP=1651;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:1557,144,0:0,0,14,34 chr1 100343153 . A G 818.06 PASS AC=1;AF=0.586;AN=2;DP=1456;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant6-variant9-variant11-variant12-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant31-variant32-variant33-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,21:41:99:527,0,515:14,6,13,8 chr1 100345409 . C G 238.16 PASS AC=2;AF=0.657;AN=2;DP=863;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,24:25:65:819,65,0:1,0,18,6 chr1 100346741 . T C 1368.33 PASS AC=2;AF=0.657;AN=2;DP=2854;set=variant-variant2-variant3-variant6-variant7-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,87:87:99:2765,260,0:0,0,48,39 chr1 100350383 . G A 431.14 PASS AC=2;AF=0.662;AN=2;DP=548;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:50:580,50,0:0,0,2,15 chr1 100353675 . G A 5773.43 PASS AC=2;AF=0.775;AN=2;DP=7653;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,195:195:99:5672,583,0:0,0,90,105 chr1 100357141 . T A 637.43 PASS AC=2;AF=0.657;AN=2;DP=1194;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1150,111,0:0,0,25,12 chr1 100358200 . G A 1269.9 PASS AC=2;AF=0.775;AN=2;DP=1259;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:1261,96,0:0,0,4,28 chr1 100366446 . GTT G,GTTT,GTTTT,GT 1463.34 PASS AC=1,0,0,0;AF=0.659,0.037,0.012,0.024;AN=2;DP=2606;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-filterInvariant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:56:99:7,14,10,25 chr1 100376448 . G A 433.99 PASS AC=1;AF=0.606;AN=2;DP=1683;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant9-variant11-variant12-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,23:43:99:830,0,1046:8,12,10,13 chr1 100376456 . T A 421.46 PASS AC=1;AF=0.606;AN=2;DP=1558;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant9-variant11-variant12-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,20:41:99:798,0,1078:8,13,8,12 chr1 100387479 . G T 956.19 PASS AC=1;AF=0.583;AN=2;DP=2052;MQ=60;set=variant-variant2-variant3-variant6-variant9-variant11-variant12-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,34:64:99:836,0,847:18,12,19,15 chr1 100387939 . C T 1870.73 PASS AC=1;AF=0.731;AN=2;DP=2170;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,21:39:99:642,0,438:7,11,7,14 chr1 100388235 . C T 724.1 PASS AC=1;AF=0.606;AN=2;DP=2055;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant9-variant11-variant12-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,25:64:99:561,0,1105:23,16,13,12 chr1 100388503 . A C 3284.57 PASS AC=1;AF=0.594;AN=2;DP=8111;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant9-variant11-variant12-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:115,131:246:99:3237,0,2784:74,41,76,55 chr1 100388748 . T C 6176.29 PASS AC=1;AF=0.591;AN=2;DP=13377;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant9-variant11-variant12-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:211,191:402:99:4663,0,5384:100,111,91,100 chr1 100533960 . G A 791.68 PASS AC=1;AF=0.607;AN=2;DP=842;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant6-variant9-variant11-variant12-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant31-variant33-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,19:34:99:622,0,405:12,3,15,4 chr1 100547994 . T C 3443.38 PASS AC=1;AF=0.607;AN=2;DP=6688;set=variant-variant2-variant3-variant6-variant9-variant11-variant12-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant31-variant33-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:118,105:223:99:2567,0,3076:57,61,57,48 chr1 100549698 . TA T,TAA 261.7 PASS AC=1,0;AF=0.474,0.026;AN=2;DP=7053;set=filterInvariant-variant2-filterInvariant3-filterInvariant4-filterInvariant5-variant7-filterInvariant8-variant9-filterInvariant10-variant11-variant13-variant14-filterInvariant15-filterInvariant16-filterInvariant17-variant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-variant23-variant24-filterInvariant25-filterInvariant26-filterInvariant27-variant29-filterInvariant31-filterInvariant33-variant34-filterInvariant35-variant36-filterInvariant37-filterInvariant38-filterInvariant39-filterInvariant40-variant41-filterInvariant42-filterInvariant44 GT:DP:GQ:SB 0/1:160:99:55,73,13,19 chr1 100572876 . T A 222.64 PASS AC=1;AF=0.5;AN=2;DP=28;FractionInformativeReads=1;MQ=60;set=variant7-variant13-variant35 GT:AD:DP:GQ:PL:SB 0/1:2,5:7:75:226,0,75:1,1,5,0 chr1 100572883 . C G 238.37 PASS AC=1;AF=0.5;AN=2;DP=35;FS=0;FractionInformativeReads=1;MQ=60;set=variant7-variant13-variant35 GT:AD:DP:GQ:PL:SB 0/1:2,6:8:75:226,0,75:1,1,5,1 chr1 100575933 . G A 1699.44 PASS AC=1;AF=0.603;AN=2;DP=4096;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant11-variant12-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant31-variant33-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:74,64:138:99:1457,0,1808:41,33,36,28 chr1 100598866 . G A 3559.77 PASS AC=2;AF=0.919;AN=2;DP=5812;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,129:129:99:5754,388,0:0,0,45,84 chr1 100598867 . C T 3559.77 PASS AC=2;AF=0.919;AN=2;DP=5711;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,127:127:99:5754,388,0:0,0,44,83 chr1 100617887 . C T 758.58 PASS AC=2;AF=0.955;AN=2;DP=1295;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:787,69,0:0,0,15,8 chr1 100643910 . G A 1982.22 PASS AC=2;AF=0.932;AN=2;DP=2542;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,69:69:99:2633,207,0:0,0,9,60 chr1 100661987 . GAAAAAAAAAA GAAA,GA,GAA,G,GAAAAAAA,GAAAAA,GAAAA 210.27 PASS AC=0,0,0,0,0,0,1;AF=0.188,0.083,0.063,0.042,0.021,0.063,0.042;AN=2;DP=837;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant14-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-filterInvariant26-variant27-variant35-filterInvariant39-variant40-variant44 GT:DP:GQ:SB 0/7:11:99:1,5,3,2 chr1 100671628 . TAAA TAA,TA,T 72.05 PASS AC=2,0,0;AF=0.467,0.333,0.033;AN=2;DP=91;FS=0;MQ=60;set=variant-variant3-variant9-variant11-variant12-variant19-variant21-variant22-variant26-variant30-variant31-variant35-variant36-variant42-variant44 GT:DP:GQ:SB 1/1:4:12:0,0,3,1 chr1 100671866 . T A 529.77 PASS AC=1;AF=0.607;AN=2;DP=1429;set=variant-variant2-variant3-variant6-variant9-variant10-variant11-variant12-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant33-variant35-variant36-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,20:37:99:585,0,448:7,10,9,11 chr1 100672060 . T C 3056.75 PASS AC=2;AF=0.92;AN=2;DP=4885;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,109:109:99:3239,326,0:0,0,58,51 chr1 100680593 . C CT 68.81 PASS AC=1;AF=0.649;AN=2;DP=618;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,15:21:92:294,0,92:0,6,2,13 chr1 100700887 . T A 49.5 PASS AC=1;AF=0.5;AN=2;DP=3;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.736;QD=16.5;ReadPosRankSum=0.736;SOR=1.179;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:1,2:3:37:78,0,37:1,0,2,0 chr1 100715454 . G A 168.68 PASS AC=2;AF=0.872;AN=2;DP=2467;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:1504,141,0:0,0,15,33 chr1 100731819 . C CA 1087.73 PASS AC=2;AF=0.907;AN=2;DP=1701;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:2114,141,0:0,0,27,19 chr1 100731820 . G A 1096.77 PASS AC=2;AF=0.907;AN=2;DP=1724;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:2114,141,0:0,0,28,19 chr1 100732450 . T C 1160.03 PASS AC=2;AF=0.907;AN=2;DP=2046;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,54:55:99:1503,155,0:1,0,24,30 chr1 100732526 . C G 554.22 PASS AC=2;AF=0.907;AN=2;DP=989;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,31:31:93:1028,93,0:0,0,8,23 chr1 100733207 . G GT,GTT 1677.46 PASS AC=2,0;AF=0.761,0.193;AN=2;DP=3656;set=Intersection GT:DP:GQ:SB 1/1:66:64:2,3,26,35 chr1 100733552 . T C 722.08 PASS AC=2;AF=0.907;AN=2;DP=880;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:917,72,0:0,0,21,3 chr1 100742670 . A G 645.73 PASS AC=2;AF=0.907;AN=2;DP=693;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:920,66,0:0,0,21,1 chr1 100750733 . AGTTTT A 4442.73 PASS AC=2;AF=0.907;AN=2;DP=4370;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,101:101:99:4429,305,0:0,0,70,31 chr1 100758155 . T C 5671.07 PASS AC=2;AF=0.907;AN=2;DP=6637;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,149:149:99:4637,446,0:0,0,100,49 chr1 100817529 . AGTGTGTGTGTGTGT AGTGTGTGTGTGT,AGTGTGTGTGTGTGTGT,A,AGTGTGTGTGTGTGTGTGT,AGTGT,AGTGTGTGT,AGTGTGTGTGT 73.55 PASS AC=0,2,0,0,0,0,0;AF=0.333,0.2,0.05,0.033,0.017,0.017,0.017;AN=2;DP=550;set=variant-variant3-variant4-variant5-filterInvariant6-variant9-variant10-variant12-variant14-variant15-variant17-variant18-variant20-variant21-variant23-variant25-filterInvariant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant39-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 2/2:11:33:0,0,1,10 chr1 100818286 . A T 4050.45 PASS AC=2;AF=0.932;AN=2;DP=4270;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,112:112:99:3475,334,0:0,0,60,52 chr1 100818464 . T C 5085.1 PASS AC=2;AF=0.989;AN=2;DP=7771;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,198:198:99:5957,594,0:0,0,91,107 chr1 100961779 . ATTT AT,ATT,A 304.03 PASS AC=2,0,0;AF=0.886,0.011,0.045;AN=2;DP=944;FS=0;set=Intersection GT:DP:GQ:SB 1/1:16:46:0,0,2,14 chr1 100963418 . T G 269.73 PASS AC=2;AF=0.976;AN=2;DP=635;FS=0;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:407,33,0:0,0,9,2 chr1 100970346 . T C 1756.82 PASS AC=2;AF=0.636;AN=2;DP=2616;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2110,210,0:0,0,40,30 chr1 100984092 . T C 4008.71 PASS AC=2;AF=0.942;AN=2;DP=4552;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,103:104:99:3300,301,0:1,0,30,73 chr1 100984519 . T C 14096 PASS AC=2;AF=0.942;AN=2;DP=16396;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,389:390:99:11984,1155,0:1,0,177,212 chr1 101003659 . A G 512.99 PASS AC=2;AF=0.977;AN=2;DP=565;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:386,33,0:0,0,9,2 chr1 101004010 . C T 1481.58 PASS AC=2;AF=1;AN=2;DP=3287;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,101:101:99:3005,302,0:0,0,45,56 chr1 101004142 . CAT C 132.62 PASS AC=1;AF=0.611;AN=2;DP=171;set=variant9-variant12-variant17-variant18-variant20-variant23-variant24-variant29-variant35 GT:AD:DP:GQ:PL:SB 0/1:2,4:6:59:126,0,59:1,1,0,4 chr1 101005855 . T C 3493.63 PASS AC=2;AF=0.917;AN=2;DP=4555;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,110:110:99:3596,330,0:0,0,71,39 chr1 101007055 . C T 6699.73 PASS AC=2;AF=0.917;AN=2;DP=8432;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,206:206:99:6468,618,0:0,0,91,115 chr1 101189027 . C G 401.11 PASS AC=2;AF=1;AN=2;DP=612;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:310,24,0:0,0,0,8 chr1 101194965 . G GT 429.23 PASS AC=1;AF=0.731;AN=2;DP=3014;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,25:64:99:477,0,893:14,25,10,15 chr1 101199979 . A G 190.31 PASS AC=2;AF=0.977;AN=2;DP=289;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:169,12,0:0,0,4,0 chr1 101203827 . G A 4164.88 PASS AC=2;AF=0.932;AN=2;DP=5866;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,142:142:99:4203,425,0:0,0,68,74 chr1 101204644 . A G 899.48 PASS AC=2;AF=0.703;AN=2;DP=1240;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1491,102,0:0,0,0,34 chr1 101339863 . T C 1115.57 PASS AC=1;AF=0.5;AN=2;DP=71;FS=4.753;FractionInformativeReads=1;MQ=60;MQRankSum=-1.71;QD=15.71;ReadPosRankSum=1.606;SOR=1.26;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:31,40:71:99:1144,0,806:15,16,25,15 chr1 101354479 . T C 2643.19 PASS AC=1;AF=0.538;AN=2;DP=1136;MQ=60;set=variant7-variant8-variant11-variant13-variant14-variant16-variant24-variant25-variant26-variant35-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:55,42:97:99:1064,0,1315:21,34,14,28 chr1 101360684 . G C 1257.14 PASS AC=1;AF=0.714;AN=2;DP=2437;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,36:69:99:868,0,827:13,20,17,19 chr1 101372607 . C A 320.22 PASS AC=2;AF=1;AN=2;DP=371;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:491,36,0:0,0,1,11 chr1 101441384 . GTTTTTT GTTT,GTT,GT,GTTTT,GTTTTT,G 455.21 PASS AC=0,0,0,2,0,0;AF=0.237,0.421,0.158,0.053,0.013,0.013;AN=2;DP=443;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 4/4:9:25:0,0,7,2 chr1 101442211 . T C 9802.03 PASS AC=1;AF=0.538;AN=2;DP=3920;set=variant7-variant8-variant11-variant13-variant14-variant16-variant24-variant25-variant26-variant35-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:166,133:299:99:3262,0,4261:88,78,76,57 chr1 101442570 . A AT 5111.44 PASS AC=1;AF=0.565;AN=2;DP=9882;MQ=60;set=variant2-variant3-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant16-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant30-variant35-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:192,190:382:99:5612,0,5699:104,88,108,82 chr1 101443395 . C T 1407.48 PASS AC=1;AF=0.538;AN=2;DP=310;FractionInformativeReads=1;set=variant7-variant8-variant11-variant13-variant14-variant16-variant24-variant25-variant26-variant35-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:7,3:10:83:83,0,250:0,7,0,3 chr1 101443582 . C T 297.58 PASS AC=1;AF=0.565;AN=2;DP=576;FractionInformativeReads=1;set=variant2-variant3-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant16-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant30-variant35-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,9:25:99:209,0,474:12,4,5,4 chr1 101443701 . A G 1456.88 PASS AC=1;AF=0.565;AN=2;DP=2676;MQ=60;set=variant2-variant3-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant16-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant30-variant35-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,50:110:99:1464,0,1633:38,22,37,13 chr1 101444992 . CAAAAAA CAAAAA,CAAAA,C,CA,CAAAAAAA 452.53 PASS AC=0,0,0,1,0;AF=0.238,0.107,0.012,0.167,0.036;AN=2;DP=8564;set=variant-variant2-filterInvariant3-filterInvariant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-filterInvariant15-variant16-variant17-variant18-variant19-variant21-filterInvariant22-variant23-variant24-variant25-variant26-variant27-filterInvariant28-variant29-variant30-filterInvariant31-variant32-variant33-filterInvariant34-variant35-filterInvariant36-variant37-variant39-variant40-filterInvariant41-filterInvariant42-variant43-variant44 GT:DP:GQ:SB 0/4:158:99:41,25,54,38 chr1 101445821 . C T 8770.99 PASS AC=1;AF=0.538;AN=2;DP=3581;MQ=60;set=variant7-variant8-variant11-variant13-variant14-variant16-variant24-variant25-variant26-variant35-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:164,104:268:99:2627,0,4263:77,87,49,55 chr1 101446276 . A G 6914.39 PASS AC=1;AF=0.538;AN=2;DP=3001;MQ=60;set=variant7-variant8-variant11-variant13-variant14-variant16-variant24-variant25-variant26-variant35-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:108,106:214:99:2795,0,2893:49,59,47,59 chr1 101447384 . A T 532.84 PASS AC=1;AF=0.565;AN=2;DP=848;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant6-variant7-variant8-variant10-variant11-variant13-filterInvariant14-variant16-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant30-variant35-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,9:27:99:202,0,478:6,12,4,5 chr1 101473779 . T C 1011.13 PASS AC=1;AF=0.538;AN=2;DP=316;FractionInformativeReads=1;MQ=60;set=variant7-variant8-variant11-variant13-variant14-variant16-variant24-variant25-variant26-variant35-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,12:25:99:333,0,394:10,3,9,3 chr1 101475901 . T C 106.43 PASS AC=1;AF=0.583;AN=2;DP=164;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant6-variant7-variant8-variant10-variant11-variant13-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,3:5:76:120,0,76:0,2,0,3 chr1 101476786 . G A 134.13 PASS AC=1;AF=0.575;AN=2;DP=597;MQ=60;set=variant2-variant3-variant6-variant7-variant10-variant11-variant13-variant14-variant16-variant19-variant21-variant22-variant24-variant25-variant26-variant35-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,7:30:99:141,0,560:13,10,5,2 chr1 101476800 . CA C 132.49 PASS AC=1;AF=0.571;AN=2;DP=703;MQ=60;set=variant2-variant3-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant16-variant19-variant21-variant22-variant24-variant25-variant26-variant35-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,7:31:99:135,0,688:13,11,5,2 chr1 101476814 . C T 198.6 PASS AC=1;AF=0.568;AN=2;DP=809;MQ=60;set=variant2-variant3-variant6-variant7-variant8-variant10-variant11-filterInvariant13-variant14-variant16-variant19-variant21-variant22-variant24-variant25-variant26-filterInvariant30-variant35-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,9:32:99:180,0,585:12,11,6,3 chr1 101487373 . AACACACAC AACACACACACACAC,AACACACACAC,AACACACACACAC,AAC,A,AACAC 212.43 PASS AC=0,0,0,2,0,0;AF=0.054,0.162,0.284,0.257,0.014,0.014;AN=2;DP=718;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:DP:GQ:SB 4/4:15:47:0,0,0,15 chr1 101704532 . G T 4197.29 PASS AC=1;AF=0.611;AN=2;DP=2256;MQ=60;set=variant2-variant4-variant7-variant8-variant12-variant14-variant16-variant19-variant23-variant24-variant25-variant26-variant27-variant31-variant33-variant35-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:71,84:155:99:2232,0,1847:46,25,52,32 chr1 101706145 . A C 63.95 PASS AC=1;AF=0.5;AN=2;DP=306;MQ=60;set=filterInvariant27-filterInvariant30-filterInvariant32-filterInvariant33-filterInvariant35-variant42-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:35,13:48:82:82,0,733:6,29,12,1 chr1 102252432 . G A 1189.38 PASS AC=1;AF=0.5;AN=2;DP=1102;set=variant-variant10-variant13-variant18-variant29-variant30-variant31-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:65,64:129:99:1673,0,1732:28,37,29,35 chr1 102268924 . T C 1723.14 PASS AC=1;AF=0.5;AN=2;DP=759;FractionInformativeReads=1;MQ=60;set=variant-variant15-variant30-variant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:68,80:148:99:2064,0,1583:36,32,48,32 chr1 102269548 . C CT 3221.65 PASS AC=1;AF=0.583;AN=2;DP=9476;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant10-variant12-variant14-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant31-variant32-variant35-variant36-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:179,155:334:99:3084,0,3789:80,99,78,77 chr1 102270082 . C G 1799.75 PASS AC=1;AF=0.5;AN=2;DP=147;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.099;QD=12.24;ReadPosRankSum=1.401;SOR=0.72;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:74,73:147:99:1828,0,1816:37,37,36,37 chr1 102271774 . G A 4761.87 PASS AC=1;AF=0.617;AN=2;DP=4830;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant27-variant31-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:87,66:153:99:1512,0,2233:40,47,29,37 chr1 102296144 . T G 395.78 PASS AC=1;AF=0.531;AN=2;DP=523;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant9-variant11-variant14-variant15-variant18-variant19-variant28-variant33-variant34-variant35-variant37-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,18:34:99:480,0,458:11,5,13,5 chr1 102296279 . T C 1613.81 PASS AC=1;AF=0.531;AN=2;DP=1565;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant9-variant11-variant14-variant15-variant18-variant19-variant28-variant33-variant34-variant35-variant37-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,48:107:99:1075,0,1403:30,29,27,21 chr1 102462171 . G A 30.91 PASS AC=1;AF=0.625;AN=2;DP=44;FS=0;FractionInformativeReads=1;MQ=60;set=variant9-variant35-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:6,7:13:99:224,0,236:6,0,7,0 chr1 102462446 . GTCAGT G 3952.57 PASS AC=1;AF=0.587;AN=2;DP=3916;MQ=60;set=variant2-variant5-variant6-variant7-variant9-variant13-variant14-variant15-variant17-variant18-variant20-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:95,80:175:99:3061,0,5352:44,51,32,48 chr1 103352451 . A G 1250.73 PASS AC=1;AF=0.743;AN=2;DP=4226;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:76,65:141:99:1615,0,1772:36,40,32,33 chr1 103354135 . G C 844.97 PASS AC=1;AF=0.5;AN=2;DP=112;MQ=60;set=variant30-variant35 GT:AD:DP:GQ:PL:SB 0/1:31,32:63:99:787,0,819:17,14,20,12 chr1 103354138 . A G 1371.61 PASS AC=2;AF=0.884;AN=2;DP=2337;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:2565,195,0:0,0,38,27 chr1 103354428 . A G 1759.29 PASS AC=1;AF=0.845;AN=2;DP=3598;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,46:94:99:1117,0,1118:25,23,21,25 chr1 103354939 . CTG CTGTGTGTGTGTG,CTGTGTGTGTGTGTGTG,CTGTG,CTGTGTGTGTG,C,CTGTGTGTGTGTGTGTGTGTG,CTGTGTGTGTGTGTG 1303.42 PASS AC=1,0,0,0,1,0,0;AF=0.646,0.073,0.061,0.024,0.024,0.012,0.012;AN=2;DP=1457;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 5/1:43:99:0,0,31,12 chr1 103356168 . A C 61.77 PASS AC=1;AF=0.889;AN=2;DP=262;FS=0;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,3:4:34:115,0,34:0,1,0,3 chr1 103379870 . A C 303.44 PASS AC=1;AF=0.5;AN=2;DP=364;MQ=60;set=variant-variant8-variant23-variant28-variant29-variant30-variant32-variant33-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:16,17:33:99:312,0,320:8,8,8,9 chr1 103379918 . G A 598.41 PASS AC=1;AF=0.724;AN=2;DP=1565;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,14:32:99:396,0,427:7,11,4,10 chr1 103380379 . TA TAA,T,TAAA 131.63 PASS AC=1,0,0;AF=0.817,0.037,0.012;AN=2;DP=965;set=variant-variant2-variant3-variant4-variant5-variant6-filterInvariant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:23:40:1,4,7,11 chr1 103380393 . G A 110.37 PASS AC=1;AF=0.5;AN=2;DP=124;MQ=60;set=variant-variant28-variant29-variant30-variant32-variant33-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:12,12:24:99:211,0,229:3,9,5,7 chr1 103381224 . G T 800.23 PASS AC=1;AF=0.5;AN=2;DP=65;FS=2.052;FractionInformativeReads=1;MQ=60;MQRankSum=0.059;QD=12.31;ReadPosRankSum=1.441;SOR=0.984;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:30,35:65:99:828,0,735:14,16,14,21 chr1 103399917 . GA G,GAA 288.89 PASS AC=1,0;AF=0.333,0.167;AN=2;DP=85;FractionInformativeReads=1;MQ=60;set=variant30-variant35-variant37 GT:DP:GQ:SB 0/1:29:99:10,5,7,7 chr1 103400491 . G A 859.25 PASS AC=2;AF=0.907;AN=2;DP=1070;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:1198,81,0:0,0,18,9 chr1 103400492 . A T 859.25 PASS AC=2;AF=0.907;AN=2;DP=1090;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:1198,81,0:0,0,18,9 chr1 103405793 . G A 766.86 PASS AC=1;AF=0.538;AN=2;DP=507;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant6-variant14-variant16-variant17-variant20-variant23-variant27-variant30-variant32-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:26,21:47:99:511,0,769:20,6,15,6 chr1 103427381 . A G 1054.11 PASS AC=1;AF=0.559;AN=2;DP=1724;MQ=60;set=variant-variant2-variant4-variant6-variant16-variant17-variant23-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:65,52:117:99:1172,0,1658:32,33,28,24 chr1 103428389 . G A 885.57 PASS AC=2;AF=0.932;AN=2;DP=1692;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:1107,90,0:0,0,6,24 chr1 103444497 . A G 628.88 PASS AC=1;AF=0.559;AN=2;DP=899;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant16-variant17-variant23-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:27,31:58:99:816,0,653:12,15,11,20 chr1 103444679 . T G 514.67 PASS AC=1;AF=0.788;AN=2;DP=2172;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,37:60:99:921,0,528:10,13,19,18 chr1 103445223 . G A 402.72 PASS AC=1;AF=0.559;AN=2;DP=851;MQ=60;set=variant-variant2-variant4-variant6-variant16-variant17-variant23-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:21,24:45:99:560,0,532:10,11,9,15 chr1 103449598 . G C 520.72 PASS AC=2;AF=0.932;AN=2;DP=675;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:658,63,0:0,0,13,8 chr1 103455217 . C T 626.36 PASS AC=2;AF=0.886;AN=2;DP=1689;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:917,84,0:0,0,8,20 chr1 103461508 . T A 908.01 PASS AC=2;AF=0.92;AN=2;DP=1651;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1279,132,0:0,0,26,18 chr1 103462473 . A G 58.54 PASS AC=2;AF=0.932;AN=2;DP=183;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:84,6,0:0,0,1,1 chr1 103463976 . G T 41.49 PASS AC=2;AF=0.952;AN=2;DP=164;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant10-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:271,21,0:0,0,1,6 chr1 103467596 . A G 326.29 PASS AC=1;AF=0.5;AN=2;DP=238;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant16-variant17-variant30-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:10,14:24:99:425,0,253:3,7,4,10 chr1 103467615 . C T 508.82 PASS AC=2;AF=0.92;AN=2;DP=837;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:675,54,0:0,0,2,16 chr1 103468609 . A G 1912.5 PASS AC=2;AF=0.92;AN=2;DP=2534;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,64:64:99:2014,192,0:0,0,41,23 chr1 103468767 . A T 696.28 PASS AC=1;AF=0.5;AN=2;DP=509;MQ=60;set=variant-variant2-variant4-variant6-variant16-variant17-variant30-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:28,24:52:99:683,0,732:9,19,10,14 chr1 103471456 . CCAT C 837.72 PASS AC=2;AF=0.86;AN=2;DP=3705;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:2598,181,0:0,0,29,31 chr1 103483514 . C T 354.05 PASS AC=1;AF=0.775;AN=2;DP=1521;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,29:46:99:749,0,422:5,12,10,19 chr1 103487394 . CT C 434.22 PASS AC=2;AF=0.932;AN=2;DP=1460;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1232,135,0:0,0,10,35 chr1 103496620 . G T 4430.2 PASS AC=2;AF=0.932;AN=2;DP=7047;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,154:154:99:4597,462,0:0,0,80,74 chr1 103496805 . GAA GA,GAAA,GAAAAA,G 493.06 PASS AC=2,0,0,0;AF=0.837,0.058,0.012,0.012;AN=2;DP=1618;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:26:68:0,1,5,20 chr1 103540489 . A G 159.14 PASS AC=1;AF=0.545;AN=2;DP=122;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant16-variant17-variant22-variant30-variant35-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:7,4:11:99:147,0,227:1,6,0,4 chr1 103544191 . C T 1074.65 PASS AC=1;AF=0.5;AN=2;DP=895;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant16-variant17-variant30-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:56,65:121:99:1653,0,1364:36,20,39,26 chr1 103544434 . A G 118.33 PASS AC=1;AF=0.5;AN=2;DP=181;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant16-variant17-variant30-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:8,12:20:99:436,0,218:2,6,2,10 chr1 103548319 . C G 571.35 PASS AC=1;AF=0.75;AN=2;DP=326;MQ=60;set=variant3-variant5-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,2:5:75:75,0,122:3,0,2,0 chr1 103573547 . G A 1875.83 PASS AC=2;AF=0.966;AN=2;DP=3369;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:1956,183,0:0,0,37,25 chr1 104076462 . C T 87.49 PASS AC=2;AF=0.8;AN=2;DP=1583;MQ=60;set=filterInvariant-variant3-variant4-variant6-variant7-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1259,117,0:0,0,24,15 chr1 104076495 . A G 66.73 PASS AC=2;AF=0.8;AN=2;DP=1614;MQ=60;set=filterInvariant-variant3-variant4-variant6-variant7-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1164,125,0:0,0,19,23 chr1 104076537 . A T 85.73 PASS AC=2;AF=0.8;AN=2;DP=1244;MQ=60;set=filterInvariant-variant3-variant4-variant6-variant7-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1117,114,0:0,0,15,23 chr1 104077271 . GT GTT,G 68.17 PASS AC=0,1;AF=0.109,0.457;AN=2;DP=1042;set=filterInvariant-filterInvariant3-variant4-filterInvariant7-variant12-variant13-variant15-variant17-filterInvariant19-variant20-variant22-variant23-filterInvariant26-variant28-variant30-variant31-filterInvariant32-variant35-variant37-variant40-variant41-variant43-filterInvariant44 GT:DP:GQ:SB 0/2:58:99:19,11,20,8 chr1 104080169 . G C 269.9 PASS AC=2;AF=0.8;AN=2;DP=1810;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1749,159,0:0,0,22,31 chr1 104084226 . A G 698.02 PASS AC=2;AF=0.8;AN=2;DP=1442;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1635,147,0:0,0,15,34 chr1 104086145 . A G 1442.86 PASS AC=2;AF=1;AN=2;DP=2833;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,64:64:99:1889,192,0:0,0,24,40 chr1 104089773 . C G 241.62 PASS AC=2;AF=0.818;AN=2;DP=476;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant9-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:756,57,0:0,0,1,18 chr1 104096692 . T C 257.84 PASS AC=2;AF=0.8;AN=2;DP=895;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:923,75,0:0,0,7,18 chr1 104108280 . CCAGT C 484.39 PASS AC=1;AF=0.625;AN=2;DP=139;MQ=60;set=variant12-variant13-variant15-variant23-variant28-variant31-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,5:13:99:186,0,464:3,5,0,5 chr1 104116312 . A G 812.48 PASS AC=1;AF=0.607;AN=2;DP=1180;set=variant4-variant12-variant13-variant15-variant17-variant20-variant22-variant23-variant28-variant31-variant35-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:46,39:85:99:1126,0,1211:31,15,24,15 chr1 104116565 . A T 1197.67 PASS AC=1;AF=0.542;AN=2;DP=1345;set=variant3-variant12-variant18-variant21-variant24-variant26-variant29-variant32-variant35-variant37-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:69,50:119:99:1147,0,1699:28,41,18,32 chr1 104162351 . A G 247.59 PASS AC=1;AF=0.5;AN=2;DP=289;set=variant13-variant28-filterInvariant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:67,27:94:99:413,0,1581:30,37,11,16 chr1 104166496 . T C 801.27 DRAGENHardSNP AC=1;AF=0.543;AN=2;DP=4857;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:73,64:137:99:1372,0,1626:44,29,46,18 chr1 104256478 . T A 148.54 PASS AC=2;AF=0.921;AN=2;DP=232;FractionInformativeReads=1;set=variant4-variant6-filterInvariant11-variant13-variant16-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:426,30,0:0,0,10,0 chr1 104256520 . A G 211.46 PASS AC=1;AF=0.5;AN=2;DP=34;FS=0;FractionInformativeReads=1;set=variant13-variant28-variant35 GT:AD:DP:GQ:PL:SB 0/1:11,5:16:99:177,0,399:11,0,5,0 chr1 107946262 . G A 1083.74 PASS AC=2;AF=0.588;AN=2;DP=851;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:1021,84,0:0,0,23,5 chr1 107951101 . A G 5790.35 PASS AC=2;AF=1;AN=2;DP=5821;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,142:142:99:4532,426,0:0,0,84,58 chr1 107951532 . A G 7895.03 PASS AC=2;AF=0.989;AN=2;DP=9001;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,199:199:99:6779,596,0:0,0,125,74 chr1 107952605 . T G 1963.92 PASS AC=2;AF=0.966;AN=2;DP=2518;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1451,114,0:0,0,28,10 chr1 107952914 . G A 8488.71 PASS AC=2;AF=0.989;AN=2;DP=10125;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,229:229:99:7308,683,0:0,0,119,110 chr1 107979396 . A C 2480.5 PASS AC=2;AF=1;AN=2;DP=3812;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,113:113:99:3527,339,0:0,0,46,67 chr1 108113702 . A G 366.53 PASS AC=2;AF=0.909;AN=2;DP=673;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:809,63,0:0,0,16,5 chr1 108115145 . T C 12389.6 PASS AC=2;AF=0.919;AN=2;DP=13703;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,297:297:99:9166,890,0:0,0,164,133 chr1 108185301 . C G 1998.27 PASS AC=2;AF=0.531;AN=2;DP=1346;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant8-variant10-variant11-variant12-variant13-variant17-variant20-variant21-variant23-variant32-variant35-variant37-variant38-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,97:97:99:4302,292,0:0,0,51,46 chr1 108185309 . G A 2084.77 PASS AC=2;AF=0.531;AN=2;DP=1406;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant8-variant10-variant11-variant12-variant13-variant17-variant20-variant21-variant23-variant32-variant35-variant37-variant38-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,101:101:99:4445,304,0:0,0,53,48 chr1 108299775 . ATGTGTGTGTG ATGTGTGTG,ATGTGTG,ATG,ATGTGTGTGTGTG,A 1047.28 PASS AC=2,0,0,0,0;AF=0.6,0.125,0.025,0.013,0.013;AN=2;DP=1734;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-filterInvariant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:DP:GQ:SB 1/1:38:63:1,1,29,7 chr1 108299809 . G A,GTGTATA 2780.56 PASS AC=1,0;AF=0.675,0.075;AN=2;DP=1341;set=variant16-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant3-variant8-variant32-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:73:99:27,13,22,11 chr1 108307636 . G C 250.09 PASS AC=1;AF=0.5;AN=2;DP=101;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant22-variant23-variant25-variant26-variant35 GT:AD:DP:GQ:PL:SB 0/1:6,10:16:99:395,0,205:6,0,10,0 chr1 108307642 . C T 495.3 PASS AC=2;AF=0.863;AN=2;DP=678;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:724,51,0:0,0,16,1 chr1 108307727 . T A 1741.59 PASS AC=2;AF=0.847;AN=2;DP=2390;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:1712,185,0:0,0,37,25 chr1 108313258 . C T 2058.87 PASS AC=2;AF=0.85;AN=2;DP=2708;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,78:78:99:2250,234,0:0,0,38,40 chr1 108315305 . C T 1780.01 PASS AC=2;AF=1;AN=2;DP=1875;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1515,138,0:0,0,33,13 chr1 108507541 . GGCCGCC GGCC,G 437.99 PASS AC=2,0;AF=0.775,0.038;AN=2;DP=2135;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:32:97:0,0,4,28 chr1 108507636 . G A 138.41 PASS AC=2;AF=0.77;AN=2;DP=560;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:400,36,0:0,0,3,9 chr1 108676624 . A C 5597.89 PASS AC=2;AF=1;AN=2;DP=6698;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,146:146:99:4643,438,0:0,0,94,52 chr1 108677973 . A C 1091.77 PASS AC=1;AF=0.55;AN=2;DP=1161;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant6-variant9-variant11-variant16-variant17-variant18-variant20-variant21-variant24-variant28-variant32-variant34-variant35-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,35:60:99:886,0,571:11,14,14,21 chr1 108678732 . T C 4515.98 PASS AC=1;AF=0.531;AN=2;DP=4904;MQ=60;set=variant3-variant5-variant6-variant9-variant16-variant17-variant18-variant20-variant21-variant24-variant28-variant32-variant34-variant35-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:159,146:305:99:3365,0,3755:68,91,66,80 chr1 108679532 . C T 475.64 PASS AC=1;AF=0.531;AN=2;DP=511;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant6-variant9-variant16-variant17-variant18-variant20-variant21-variant24-variant28-variant32-variant34-variant35-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,15:29:99:419,0,482:1,13,6,9 chr1 108681600 . T C 1122.2 PASS AC=1;AF=0.531;AN=2;DP=1061;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant6-variant9-variant16-variant17-variant18-variant20-variant21-variant24-variant28-variant32-variant34-variant35-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,32:61:99:769,0,796:21,8,21,11 chr1 108700316 . G C 559.7 PASS AC=1;AF=0.533;AN=2;DP=583;FractionInformativeReads=1;MQ=60;set=variant5-variant6-variant9-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant28-variant34-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,25:42:99:637,0,449:4,13,7,18 chr1 108724518 . A G 3257.27 PASS AC=2;AF=0.8;AN=2;DP=4053;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,85:85:99:2622,255,0:0,0,45,40 chr1 108724693 . G A 372.92 PASS AC=2;AF=0.808;AN=2;DP=608;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:627,51,0:0,0,2,15 chr1 108728347 . T C 239.03 PASS AC=1;AF=0.533;AN=2;DP=236;MQ=60;set=variant5-variant6-variant9-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant28-variant34-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,10:11:9:252,0,9:1,0,6,4 chr1 108728484 . T C 488.75 PASS AC=1;AF=0.533;AN=2;DP=1123;MQ=60;set=variant5-variant6-variant9-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant28-variant34-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,34:82:99:650,0,990:25,23,17,17 chr1 108734993 . G C 346.05 PASS AC=2;AF=0.684;AN=2;DP=336;FractionInformativeReads=1;MQ=60;set=variant5-variant6-variant9-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant28-variant32-variant34-variant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:767,60,0:0,0,18,2 chr1 108735388 . T A 1740.36 PASS AC=2;AF=0.694;AN=2;DP=2370;MQ=60;set=variant5-variant6-variant9-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant28-variant32-variant34-variant35-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,200:200:99:5661,598,0:0,0,91,109 chr1 108741065 . T C 265.71 PASS AC=2;AF=0.553;AN=2;DP=361;FractionInformativeReads=1;MQ=60;set=variant5-variant6-variant9-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant28-variant32-variant34-variant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:543,39,0:0,0,13,0 chr1 108742123 . C G 181.56 PASS AC=2;AF=0.65;AN=2;DP=1015;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant6-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1042,102,0:0,0,14,20 chr1 108742632 . C T 4124.07 PASS AC=1;AF=0.5;AN=2;DP=968;MQ=60;set=variant32-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:149,210:359:99:4978,0,3528:85,64,115,95 chr1 108742892 . T G 880.64 PASS AC=2;AF=0.553;AN=2;DP=1138;MQ=60;set=variant5-variant6-variant9-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant28-variant32-variant34-variant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:1960,180,0:0,0,29,31 chr1 108742904 . CGCGCAGG C 943.02 PASS AC=2;AF=0.553;AN=2;DP=1086;MQ=60;set=variant5-variant6-variant9-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant28-variant32-variant34-variant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:2102,143,0:0,0,25,22 chr1 108742954 . A C 803.21 PASS AC=2;AF=0.553;AN=2;DP=1019;MQ=60;set=variant5-variant6-variant9-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant28-variant32-variant34-variant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:2161,179,0:0,0,35,25 chr1 108743042 . C A 1386.53 PASS AC=2;AF=0.553;AN=2;DP=1427;MQ=60;set=variant5-variant6-variant9-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant28-variant32-variant34-variant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,93:93:99:4113,283,0:0,0,48,45 chr1 108743059 . G C 778.36 PASS AC=2;AF=0.676;AN=2;DP=2841;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,94:94:99:4113,283,0:0,0,47,47 chr1 108743140 . C G 841.8 PASS AC=2;AF=0.553;AN=2;DP=1577;MQ=60;set=variant5-variant6-variant9-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant28-variant32-variant34-variant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,85:85:99:2630,254,0:0,0,39,46 chr1 108743178 . C G 778.83 PASS AC=2;AF=0.553;AN=2;DP=1454;MQ=60;set=variant5-variant6-variant9-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant28-variant32-variant34-variant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:2168,215,0:0,0,37,35 chr1 108771721 . T C 2647.26 PASS AC=1;AF=0.5;AN=2;DP=5759;set=variant2-variant5-filterInvariant6-filterInvariant8-variant15-variant16-filterInvariant17-variant19-variant21-variant22-variant23-variant28-filterInvariant29-variant33-variant34-variant35-variant39-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:101,90:191:99:1721,0,2322:39,62,39,51 chr1 109008061 . G A 439.39 PASS AC=2;AF=1;AN=2;DP=66;FS=0;FractionInformativeReads=1;set=variant10-variant32-variant35-variant38 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:915,72,0:0,0,0,24 chr1 109013458 . C T 315.69 PASS AC=2;AF=0.927;AN=2;DP=323;FS=0;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:344,24,0:0,0,1,7 chr1 109102744 . A AGGCGGCGGCGGC,AGGC 377.33 PASS AC=0,1;AF=0.333,0.167;AN=2;DP=392;set=variant-variant5-variant7-variant12-variant17-variant27-variant29-variant31-variant32-variant33-variant35-variant42 GT:DP:GQ:SB 0/2:40:99:6,6,11,17 chr1 109103207 . G T 544.75 PASS AC=1;AF=0.5;AN=2;DP=823;MQ=60;set=variant-variant5-variant7-variant12-variant13-variant17-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:23,36:59:99:1064,0,599:6,17,10,26 chr1 109143457 . A G 391.05 PASS AC=1;AF=0.5;AN=2;DP=231;FractionInformativeReads=1;MQ=60;set=variant-variant7-variant12-variant13-variant17-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:11,7:18:99:208,0,247:4,7,1,6 chr1 109154974 . G A 331.14 PASS AC=1;AF=0.5;AN=2;DP=466;FractionInformativeReads=1;MQ=60;set=variant-variant7-variant12-variant13-variant17-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:23,21:44:99:635,0,756:4,19,5,16 chr1 109158746 . CTTT CT,CTT,C 65.16 PASS AC=0,2,0;AF=0.159,0.636,0.023;AN=2;DP=160;set=variant3-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant17-variant19-variant21-variant22-variant25-variant26-variant31-variant35-variant37-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 2/2:8:23:0,0,8,0 chr1 109170746 . C T 588.81 PASS AC=1;AF=0.841;AN=2;DP=2148;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:30,32:62:99:1089,0,900:24,6,28,4 chr1 109173710 . G A 1234.93 PASS AC=1;AF=0.5;AN=2;DP=1054;MQ=60;set=variant-variant7-variant12-variant17-variant27-variant29-variant31-variant32-variant33-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:55,51:106:99:1199,0,1283:33,22,31,20 chr1 109179167 . A T 1096.51 PASS AC=1;AF=0.5;AN=2;DP=1233;MQ=60;set=variant-variant5-variant7-variant12-variant13-variant17-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:43,41:84:99:1088,0,1392:26,17,18,23 chr1 109179412 . TG T 1777.94 PASS AC=1;AF=0.5;AN=2;DP=1176;MQ=60;set=variant-variant7-variant12-variant13-variant17-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:34,39:73:99:1367,0,1149:15,19,17,22 chr1 109179771 . T C 1305.82 PASS AC=1;AF=0.5;AN=2;DP=1273;MQ=60;set=variant-variant7-variant12-variant13-variant17-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:45,59:104:99:1451,0,1064:23,22,29,30 chr1 109180038 . A T 2353.57 PASS AC=1;AF=0.5;AN=2;DP=2463;MQ=60;set=variant-variant7-variant12-variant13-variant17-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:106,101:207:99:2192,0,2188:47,59,46,55 chr1 109180280 . T C 782.15 PASS AC=1;AF=0.5;AN=2;DP=74;FS=0.883;FractionInformativeReads=1;MQ=60;MQRankSum=-2.133;QD=10.57;ReadPosRankSum=-1.765;SOR=0.84;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:39,35:74:99:810,0,966:22,17,21,14 chr1 109181304 . C G 3600.45 PASS AC=1;AF=0.5;AN=2;DP=3210;MQ=60;set=variant-variant7-variant12-variant17-variant27-variant29-variant31-variant32-variant33-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:151,136:287:99:3395,0,3636:75,76,62,74 chr1 109181309 . C CAT 16504.8 PASS AC=2;AF=1;AN=2;DP=13849;FS=0;MQ=60;MQRankSum=2.088;ReadPosRankSum=1.156;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,278:278:99:12353,843,0:0,0,135,143 chr1 109181853 . CT C,CTT 108.79 PASS AC=1,0;AF=0.375,0.125;AN=2;DP=580;MQ=60;set=variant3-variant8-filterInvariant11-variant12-filterInvariant19-filterInvariant21-filterInvariant22-filterInvariant24-filterInvariant33-filterInvariant34-filterInvariant35-filterInvariant40 GT:DP:GQ:SB 0/1:32:79:8,17,1,6 chr1 109235180 . C G 1327.47 PASS AC=1;AF=0.5;AN=2;DP=266;MQ=60;set=variant27-variant32-variant35 GT:AD:DP:GQ:PL:SB 0/1:39,55:94:99:1585,0,1010:19,20,27,28 chr1 109240112 . TA T 756.02 PASS AC=1;AF=0.615;AN=2;DP=2292;MQ=60;set=variant-variant3-variant4-variant7-variant8-variant9-variant12-variant13-variant17-variant19-variant20-variant26-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,63:90:99:1348,0,431:3,24,16,47 chr1 109240160 . CTTTTTTTTTTTT C 1539.87 PASS AC=2;AF=0.989;AN=2;DP=1437;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1446,103,0:0,0,1,33 chr1 109255513 . G T 3254.12 PASS AC=2;AF=0.932;AN=2;DP=3958;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,86:86:99:2741,257,0:0,0,51,35 chr1 109260357 . G A 1441.06 PASS AC=1;AF=0.784;AN=2;DP=2967;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:63,42:105:99:1012,0,1532:37,26,27,15 chr1 109261321 . T TA 382.61 PASS AC=1;AF=0.568;AN=2;DP=311;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant7-variant8-variant9-variant10-variant13-variant14-variant17-variant20-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,8:13:99:258,0,148:4,1,8,0 chr1 109265029 . G T 1129.25 PASS AC=1;AF=0.764;AN=2;DP=3589;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,49:94:99:1198,0,1147:20,25,24,25 chr1 109265326 . G C 127.38 PASS AC=1;AF=0.784;AN=2;DP=807;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,13:22:99:445,0,248:2,7,1,12 chr1 109268573 . T C 3889.99 PASS AC=2;AF=0.821;AN=2;DP=5010;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,140:140:99:4715,420,0:0,0,66,74 chr1 109270402 . G A 2417.25 PASS AC=2;AF=0.689;AN=2;DP=2601;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:2413,213,0:0,0,51,20 chr1 109273456 . A G 3296.02 PASS AC=2;AF=0.707;AN=2;DP=4093;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,103:103:99:3051,309,0:0,0,44,59 chr1 109273610 . G A 637.41 PASS AC=2;AF=0.695;AN=2;DP=916;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:853,81,0:0,0,9,18 chr1 109289236 . C A 693.35 PASS AC=2;AF=0.818;AN=2;DP=1625;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1382,114,0:0,0,31,7 chr1 109289353 . C G 3730.71 PASS AC=2;AF=0.818;AN=2;DP=6147;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,176:176:99:5198,528,0:0,0,94,82 chr1 109289487 . C T 3506.18 PASS AC=2;AF=0.818;AN=2;DP=5136;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,139:139:99:4516,417,0:0,0,63,76 chr1 109299453 . C G 902.1 PASS AC=2;AF=0.826;AN=2;DP=1254;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:830,81,0:0,0,9,18 chr1 109301250 . G C 1527.8 PASS AC=2;AF=0.818;AN=2;DP=3048;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,63:63:99:1764,189,0:0,0,27,36 chr1 109321824 . G T 2029.55 PASS AC=2;AF=0.818;AN=2;DP=2133;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1483,135,0:0,0,32,13 chr1 109338861 . G C 1915.94 PASS AC=2;AF=0.658;AN=2;DP=3089;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:2139,227,0:0,0,40,36 chr1 109342742 . C G 569.93 PASS AC=1;AF=0.5;AN=2;DP=130;FractionInformativeReads=1;MQ=60;set=variant17-variant32-variant35 GT:AD:DP:GQ:PL:SB 0/1:18,15:33:99:374,0,454:12,6,10,5 chr1 109358755 . A AT 8409.33 PASS AC=2;AF=0.645;AN=2;DP=9190;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,233:233:99:7070,700,0:0,0,116,117 chr1 109366286 . C T 3947.68 PASS AC=1;AF=0.621;AN=2;DP=4158;MQ=60;set=variant-variant4-variant5-variant6-variant8-variant9-variant12-variant13-variant14-variant18-variant19-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:90,67:157:99:1482,0,2126:43,47,32,35 chr1 109366370 . C T 2462.52 PASS AC=1;AF=0.744;AN=2;DP=3898;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:63,34:97:99:916,0,1703:23,40,12,22 chr1 109372876 . G A 205.04 PASS AC=2;AF=0.803;AN=2;DP=637;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:608,54,0:0,0,14,4 chr1 109372968 . T G 591.42 PASS AC=2;AF=0.795;AN=2;DP=1844;FractionInformativeReads=1;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:1907,176,0:0,0,41,18 chr1 109377157 . TA T,TAA 1312.12 PASS AC=2,0;AF=0.907,0.07;AN=2;DP=1988;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:37:99:0,0,23,14 chr1 109391486 . G A 2670.67 PASS AC=2;AF=1;AN=2;DP=2802;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:2028,186,0:0,0,40,22 chr1 109394564 . T C 1759.64 PASS AC=1;AF=0.5;AN=2;DP=500;FractionInformativeReads=1;MQ=60;set=variant17-variant19-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:48,75:123:99:1975,0,1096:23,25,41,34 chr1 109395105 . C T 1533.14 PASS AC=1;AF=0.857;AN=2;DP=5950;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:79,78:157:99:2022,0,1972:41,38,41,37 chr1 109399473 . G T 75.41 PASS AC=1;AF=0.5;AN=2;DP=27;FS=0;FractionInformativeReads=1;MQ=60;set=variant17-variant19-variant35 GT:AD:DP:GQ:PL:SB 0/1:4,7:11:99:235,0,104:2,2,4,3 chr1 109399660 . A G 409.45 PASS AC=1;AF=0.583;AN=2;DP=750;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant26-variant33-variant34-variant35-variant36-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:16,21:37:99:534,0,369:7,9,10,11 chr1 109428249 . G A 521.23 PASS AC=1;AF=0.63;AN=2;DP=1188;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant9-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant26-variant29-variant33-variant34-variant35-variant36-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:29,35:64:99:758,0,600:14,15,15,20 chr1 109444298 . A G 334.08 PASS AC=1;AF=0.5;AN=2;DP=98;FS=0;FractionInformativeReads=1;MQ=60;set=variant17-variant19-variant29-variant35 GT:AD:DP:GQ:PL:SB 0/1:13,10:23:99:378,0,508:13,0,10,0 chr1 109461131 . A G 434.98 PASS AC=1;AF=0.5;AN=2;DP=115;FractionInformativeReads=1;MQ=60;set=variant17-variant19-variant29-variant35 GT:AD:DP:GQ:PL:SB 0/1:13,17:30:99:488,0,335:10,3,13,4 chr1 109465165 . ACTT A 1484.18 PASS AC=1;AF=0.62;AN=2;DP=2692;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant26-variant29-variant33-variant34-variant35-variant36-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:60,55:115:99:2074,0,2824:26,34,22,33 chr1 109466982 . G A 3623.14 PASS AC=1;AF=0.5;AN=2;DP=1378;FractionInformativeReads=1;set=variant17-variant19-variant29-variant35 GT:AD:DP:GQ:PL:SB 0/1:195,144:339:99:3612,0,5165:79,116,53,91 chr1 109467069 . G A 1022.37 PASS AC=1;AF=0.542;AN=2;DP=1366;MQ=60;set=variant4-variant6-variant9-variant13-variant16-variant17-variant19-variant29-variant33-variant35-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:74,49:123:99:1141,0,2085:22,52,17,32 chr1 109472773 . G A 2110.52 PASS AC=2;AF=0.6;AN=2;DP=1495;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant11-variant12-variant14-variant15-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant34-variant35-variant36-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,69:69:99:2220,206,0:0,0,37,32 chr1 109472813 . T C 1540.18 PASS AC=1;AF=0.594;AN=2;DP=1106;MQ=60;set=variant3-variant5-variant6-variant7-variant11-variant13-variant15-variant20-variant22-variant23-variant24-variant25-variant27-variant34-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:45,21:66:99:505,0,1173:23,22,9,12 chr1 109472921 . T G 712.51 PASS AC=1;AF=0.5;AN=2;DP=407;FractionInformativeReads=1;MQ=60;set=variant17-variant18-variant19-variant29-variant35 GT:AD:DP:GQ:PL:SB 0/1:56,50:106:99:1278,0,1230:25,31,21,29 chr1 109473605 . T C 278.06 PASS AC=1;AF=0.5;AN=2;DP=116;FractionInformativeReads=1;MQ=60;set=variant17-variant19-variant29-variant35 GT:AD:DP:GQ:PL:SB 0/1:14,12:26:99:300,0,444:12,2,8,4 chr1 109473826 . G A 2839.46 PASS AC=1;AF=0.625;AN=2;DP=5096;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant26-variant29-variant33-variant34-variant35-variant36-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:96,106:202:99:2546,0,2400:54,42,61,45 chr1 109474221 . C T 2167.56 PASS AC=1;AF=0.625;AN=2;DP=3866;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant26-variant29-variant33-variant34-variant35-variant36-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:74,72:146:99:1940,0,2133:43,31,43,29 chr1 109474250 . TA TAAA,TAA,TAAAA,T 1116.05 PASS AC=1,0,0,0;AF=0.218,0.141,0.013,0.218;AN=2;DP=7731;set=variant2-variant3-variant4-variant5-filterInvariant6-filterInvariant7-filterInvariant8-variant9-variant10-variant12-variant13-variant14-filterInvariant15-variant16-variant17-variant18-variant19-filterInvariant20-variant21-variant22-filterInvariant23-filterInvariant24-variant26-filterInvariant27-filterInvariant28-variant29-filterInvariant30-filterInvariant31-filterInvariant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-filterInvariant40-filterInvariant42-variant44 GT:DP:GQ:SB 0/1:140:99:52,39,27,22 chr1 109477653 . G A 1262.67 PASS AC=1;AF=0.625;AN=2;DP=1761;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant26-variant29-variant33-variant34-variant35-variant36-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:22,39:61:99:927,0,489:9,13,16,23 chr1 109477765 . C T 172.82 PASS AC=1;AF=0.5;AN=2;DP=79;FractionInformativeReads=1;MQ=60;set=variant17-variant19-variant29-variant35 GT:AD:DP:GQ:PL:SB 0/1:6,7:13:99:190,0,219:1,5,1,6 chr1 109479978 . G T 1366.75 PASS AC=1;AF=0.625;AN=2;DP=3557;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant26-variant29-variant33-variant34-variant35-variant36-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:121,60:181:99:1477,0,3026:63,58,33,27 chr1 109482220 . C T 266 PASS AC=1;AF=0.588;AN=2;DP=634;FractionInformativeReads=1;set=variant2-variant3-variant4-variant5-variant9-variant12-variant13-variant16-variant17-variant18-variant19-variant21-variant26-variant33-variant35-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:12,21:33:99:622,0,296:9,3,15,6 chr1 109482826 . C T 974.29 PASS AC=1;AF=0.595;AN=2;DP=2269;MQ=60;set=variant2-variant3-variant5-variant6-variant9-variant12-variant13-variant16-variant17-variant18-variant19-variant21-variant26-variant29-variant31-variant33-variant34-variant35-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,37:81:99:815,0,1039:23,21,17,20 chr1 109483975 . T C 904.86 PASS AC=1;AF=0.542;AN=2;DP=1122;MQ=60;set=variant2-variant3-variant5-variant12-variant13-variant17-variant18-variant21-variant26-variant29-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:35,55:90:99:1398,0,796:21,14,34,21 chr1 109486196 . A G 1414.81 PASS AC=2;AF=0.676;AN=2;DP=6804;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,170:171:99:5060,486,0:1,0,89,81 chr1 109486240 . TA T 1587.68 PASS AC=2;AF=0.636;AN=2;DP=5696;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant34-variant35-variant36-variant37-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,153:153:99:5268,460,0:0,0,75,78 chr1 109486269 . C A 1478.2 PASS AC=1;AF=0.5;AN=2;DP=481;MQ=60;set=variant13-variant17-variant29-variant35 GT:AD:DP:GQ:PL:SB 0/1:66,69:135:99:1687,0,1351:32,34,27,42 chr1 109490457 . T C 631.53 PASS AC=2;AF=0.676;AN=2;DP=2015;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:1834,177,0:0,0,26,33 chr1 109493134 . G GTTA 127.38 PASS AC=1;AF=0.667;AN=2;DP=86;FS=0;set=variant2-variant6-variant7-variant15-variant21-variant23-variant24-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:3,5:8:99:198,0,102:1,2,2,3 chr1 109513497 . C T 13751.1 PASS AC=1;AF=0.826;AN=2;DP=15643;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:202,186:388:99:5005,0,5138:110,92,96,90 chr1 109524584 . C A 408.8 PASS AC=1;AF=0.531;AN=2;DP=388;FractionInformativeReads=1;set=variant3-variant5-variant6-variant7-variant11-variant15-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant33-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:10,7:17:99:185,0,350:1,9,2,5 chr1 109529322 . T TAA 1562.01 PASS AC=2;AF=0.989;AN=2;DP=1314;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:1429,96,0:0,0,7,25 chr1 109534940 . G A 1338.7 PASS AC=2;AF=0.989;AN=2;DP=1645;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-filterInvariant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:935,105,0:0,0,20,15 chr1 109545046 . C T 492.87 PASS AC=2;AF=0.989;AN=2;DP=675;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.424;ReadPosRankSum=-0.193;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:761,63,0:0,0,4,17 chr1 109606778 . CAAAAAAAAAA C,CAAAAAAAAAAAAAA,CAAAAAAAAAAAAA,CAAAAAAAAAAAAAAA,CAAAAAAAAAAAA,CAAAAAAAA,CAAAAAAAAA,CAAAAAAAAAAA 1106.46 PASS AC=0,2,0,0,0,0,0,0;AF=0.1,0.086,0.129,0.071,0.171,0.014,0.014,0.071;AN=2;DP=719;set=variant-variant2-variant3-variant4-variant5-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43 GT:DP:GQ:SB 2/2:6:24:0,0,6,0 chr1 109618257 . C T 1462.45 PASS AC=2;AF=0.989;AN=2;DP=1828;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1368,129,0:0,0,32,12 chr1 109618308 . G A 2126.95 PASS AC=1;AF=0.71;AN=2;DP=2113;MQ=60;set=variant2-variant4-variant6-variant8-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:39,35:74:99:1045,0,1129:27,12,26,9 chr1 109650484 . GA G,GAA 146.43 PASS AC=1,0;AF=0.261,0.239;AN=2;DP=998;MQ=60;set=variant-filterInvariant4-variant5-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant10-variant11-variant12-variant14-variant15-variant17-filterInvariant18-filterInvariant20-variant24-variant25-variant27-variant33-variant34-variant35-variant40-variant43-variant44 GT:DP:GQ:SB 0/1:44:99:17,13,10,4 chr1 109656038 . AAGAGAGAGAGAGAGAGAGAGAGAG AAGAGAGAGAGAGAGAGAG,AAGAGAGAGAGAGAGAGAGAGAGAGAG,AAGAGAGAGAGAGAGAGAGAGAG,A,AAGAG,AAGAGAGAGAGAG,AAGAGAGAGAGAGAGAGAGAGAGAGAGAG,AAGAGAGAGAGAGAGAG,AAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG,AAGAGAGAGAGAGAGAGAGAG,AAGAGAG,AAGAGAGAGAGAGAG,AAGAGAGAGAG 128.24 PASS AC=0,0,0,0,0,1,0,1,0,0,0,0,0;AF=0.159,0.023,0.091,0.023,0.068,0.068,0.023,0.159,0.023,0.023,0.023,0.023,0.023;AN=2;DP=526;set=variant-variant2-variant6-variant7-filterInvariant8-variant9-variant10-variant12-variant13-variant16-variant18-variant21-variant22-variant23-filterInvariant24-variant28-variant29-variant30-variant32-variant33-variant35-variant41 GT:DP:GQ:SB 6/8:22:99:0,0,18,4 chr1 109704361 . A G 684.32 PASS AC=1;AF=0.538;AN=2;DP=544;MQ=60;set=variant11-variant12-variant13-variant17-variant19-variant25-variant26-variant29-variant32-variant33-variant35-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:19,21:40:99:807,0,673:17,2,21,0 chr1 109704390 . C G 2226.07 PASS AC=2;AF=0.989;AN=2;DP=3139;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,67:67:99:2740,202,0:0,0,61,6 chr1 109704618 . A G 5408.79 PASS AC=2;AF=1;AN=2;DP=7181;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,175:175:99:5356,524,0:0,0,71,104 chr1 109714750 . T C 254.34 PASS AC=1;AF=0.639;AN=2;DP=1217;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,22:37:99:670,0,376:3,12,4,18 chr1 109714919 . A G 73.25 PASS AC=1;AF=0.643;AN=2;DP=399;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,10:16:99:312,0,133:4,2,8,2 chr1 109716533 . T G 515.59 PASS AC=1;AF=0.5;AN=2;DP=38;FS=3.368;FractionInformativeReads=1;MQ=60;MQRankSum=0.763;QD=13.57;ReadPosRankSum=-0.881;SOR=0.223;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:17,21:38:99:544,0,489:3,14,7,14 chr1 109727475 . T C 323.3 PASS AC=2;AF=0.953;AN=2;DP=567;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:489,36,0:0,0,11,1 chr1 109727653 . CT C 626.92 PASS AC=1;AF=0.563;AN=2;DP=988;MQ=60;set=variant7-variant11-variant12-variant14-variant15-variant17-variant19-variant22-variant25-variant28-variant29-variant32-variant33-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:27,33:60:99:1004,0,774:11,16,17,16 chr1 109727832 . A G 294.12 PASS AC=1;AF=0.575;AN=2;DP=312;FractionInformativeReads=1;MQ=60;set=variant7-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant22-variant24-variant25-variant28-variant29-variant32-variant33-variant35-variant37-variant38-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:9,11:20:99:331,0,256:1,8,4,7 chr1 109732080 . C T 857.2 PASS AC=1;AF=0.77;AN=2;DP=916;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,16:29:99:548,0,466:6,7,4,12 chr1 109732387 . G C 230.85 PASS AC=1;AF=0.531;AN=2;DP=496;FractionInformativeReads=1;MQ=60;set=variant7-variant11-variant12-variant14-variant15-variant17-variant19-variant22-variant25-variant28-variant29-variant32-variant33-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:14,19:33:99:535,0,392:3,11,6,13 chr1 109734157 . T C 1830.47 PASS AC=1;AF=0.77;AN=2;DP=1964;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,38:72:99:1010,0,918:12,22,11,27 chr1 109734225 . G T 1031.33 PASS AC=1;AF=0.77;AN=2;DP=926;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,14:38:99:498,0,893:13,11,4,10 chr1 109734541 . C T 1434.12 PASS AC=1;AF=0.814;AN=2;DP=2416;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,26:62:99:598,0,1004:12,24,9,17 chr1 109735298 . T C 5745 PASS AC=1;AF=0.763;AN=2;DP=6918;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:105,99:204:99:2517,0,2559:58,47,56,43 chr1 109735416 . A C 4164.01 PASS AC=1;AF=0.763;AN=2;DP=6004;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:86,96:182:99:2286,0,2264:38,48,42,54 chr1 109735504 . T C 1263.74 PASS AC=1;AF=0.763;AN=2;DP=2248;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,39:72:99:1136,0,869:10,23,10,29 chr1 109737063 . C T 2169.67 PASS AC=1;AF=0.763;AN=2;DP=2952;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,28:86:99:628,0,1615:35,23,17,11 chr1 109737090 . G A 2999.2 PASS AC=1;AF=0.763;AN=2;DP=4122;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:77,43:120:99:948,0,1878:41,36,24,19 chr1 109737132 . T C 3718.04 PASS AC=1;AF=0.769;AN=2;DP=5484;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:93,57:150:99:1209,0,2380:46,47,29,28 chr1 109737172 . C T 3670.25 PASS AC=1;AF=0.763;AN=2;DP=5256;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:87,56:143:99:1222,0,2328:40,47,28,28 chr1 109737314 . T C 1235.95 PASS AC=1;AF=0.763;AN=2;DP=1765;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,23:50:99:906,0,1584:8,19,8,15 chr1 109737320 . G A 1138.05 PASS AC=1;AF=0.763;AN=2;DP=1628;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,24:49:99:909,0,1546:7,18,8,16 chr1 109741516 . A C 542.07 PASS AC=2;AF=0.898;AN=2;DP=677;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:531,39,0:0,0,3,10 chr1 109741530 . T C 94.17 PASS AC=1;AF=0.591;AN=2;DP=145;FractionInformativeReads=1;MQ=60;set=variant6-variant10-variant15-variant17-variant19-variant24-variant28-variant33-variant35-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:5,5:10:99:195,0,154:1,4,1,4 chr1 109742452 . C T 151.77 PASS AC=1;AF=0.78;AN=2;DP=436;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,9:18:99:284,0,288:7,2,7,2 chr1 109742485 . G A 450.06 PASS AC=1;AF=0.78;AN=2;DP=852;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,13:26:99:396,0,437:11,2,11,2 chr1 109743622 . C T 531.89 PASS AC=1;AF=0.6;AN=2;DP=1420;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant34-variant35-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,26:53:99:929,0,760:6,21,2,24 chr1 109745618 . T C 2059.21 PASS AC=2;AF=0.898;AN=2;DP=2583;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:2009,177,0:0,0,22,37 chr1 109771063 . T C 4837.82 PASS AC=2;AF=0.738;AN=2;DP=5683;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,139:139:99:4156,417,0:0,0,59,80 chr1 109771881 . G T 755.12 PASS AC=2;AF=1;AN=2;DP=715;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:733,54,0:0,0,17,1 chr1 109778577 . T C 3158.67 PASS AC=2;AF=0.738;AN=2;DP=3725;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,100:100:99:2942,299,0:0,0,57,43 chr1 109779556 . T A 3082.84 PASS AC=2;AF=1;AN=2;DP=4031;FS=0;MQ=60;MQRankSum=-0.258;ReadPosRankSum=-0.258;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,74:74:99:2302,222,0:0,0,32,42 chr1 109779621 . T TC 2449.43 PASS AC=2;AF=0.779;AN=2;DP=2442;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1456,117,0:0,0,14,25 chr1 109792735 . A ACGC 901.58 PASS AC=2;AF=0.738;AN=2;DP=4781;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,133:135:99:4377,375,0:1,1,84,49 chr1 109794123 . G C 3911.63 PASS AC=1;AF=0.5;AN=2;DP=337;FS=4.168;FractionInformativeReads=1;MQ=60;MQRankSum=1.54;QD=11.61;ReadPosRankSum=1.03;SOR=0.915;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:169,168:337:99:3940,0,4035:86,83,94,74 chr1 109794252 . T C 2720.95 PASS AC=2;AF=0.955;AN=2;DP=9677;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,244:244:99:7966,732,0:0,0,112,132 chr1 109795026 . T C 3965.83 PASS AC=2;AF=0.955;AN=2;DP=6691;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,184:184:99:5763,550,0:0,0,90,94 chr1 109795608 . T C 5077.79 PASS AC=2;AF=0.966;AN=2;DP=8514;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:2,238:240:99:7409,670,0:1,1,112,126 chr1 109804646 . G A 130.23 PASS AC=1;AF=0.625;AN=2;DP=624;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,15:27:99:517,0,380:2,10,2,13 chr1 109806442 . C A 2052.83 PASS AC=1;AF=0.676;AN=2;DP=2611;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,30:72:99:866,0,1294:10,32,6,24 chr1 109806834 . C T 3060.93 PASS AC=1;AF=0.625;AN=2;DP=8327;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:124,168:292:99:4182,0,2776:68,56,87,81 chr1 109807099 . G A 1068.95 PASS AC=1;AF=0.625;AN=2;DP=4159;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,75:136:99:1965,0,1605:31,30,33,42 chr1 109807283 . A T 1188.46 PASS AC=1;AF=0.571;AN=2;DP=628;MQ=60;set=variant4-variant5-variant24-variant27-variant31-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:46,59:105:99:1757,0,1144:23,23,27,32 chr1 109813020 . G A 205.43 PASS AC=1;AF=0.706;AN=2;DP=1426;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,18:41:99:449,0,582:15,8,13,5 chr1 109813236 . TTCCCAGTCTTGGGG T 905.95 PASS AC=1;AF=0.697;AN=2;DP=3725;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:72,61:133:99:2327,0,10364:34,38,22,39 chr1 109815074 . G A 1514.98 PASS AC=1;AF=0.5;AN=2;DP=366;FractionInformativeReads=1;MQ=60;set=variant27-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:68,64:132:99:1574,0,1739:31,37,22,42 chr1 109815133 . G A 1202.58 PASS AC=1;AF=0.5;AN=2;DP=296;MQ=60;set=variant27-variant34-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:49,45:94:99:1163,0,1347:17,32,16,29 chr1 109815211 . C A 1194.82 PASS AC=1;AF=0.5;AN=2;DP=273;FractionInformativeReads=1;MQ=60;set=variant27-variant34-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:44,32:76:99:1191,0,1802:25,19,20,12 chr1 109815214 . T TG 1151.17 PASS AC=1;AF=0.5;AN=2;DP=279;FractionInformativeReads=1;MQ=60;set=variant27-variant34-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:47,31:78:99:1199,0,1820:26,21,20,11 chr1 109815252 . A G 767.43 PASS AC=1;AF=0.625;AN=2;DP=2176;FractionInformativeReads=1;set=variant2-variant4-variant5-variant16-variant17-variant18-variant21-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:69,47:116:99:1082,0,1807:40,29,28,19 chr1 109815368 . T C 1524.79 PASS AC=1;AF=0.5;AN=2;DP=617;FractionInformativeReads=1;MQ=60;set=variant27-variant34-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:81,86:167:99:2132,0,1982:40,41,42,44 chr1 109815746 . A G 2720.17 PASS AC=1;AF=0.5;AN=2;DP=826;FractionInformativeReads=1;MQ=60;set=variant27-variant34-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:116,109:225:99:2765,0,3013:66,50,65,44 chr1 109816176 . A C 5403.31 PASS AC=2;AF=1;AN=2;DP=8342;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,252:253:99:7867,748,0:1,0,100,152 chr1 109817192 . A G 1361.93 PASS AC=1;AF=0.563;AN=2;DP=2025;set=variant2-variant4-variant5-variant13-variant19-variant21-variant23-variant26-variant27-variant29-variant30-variant31-variant34-variant35-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,81:146:99:2124,0,1704:38,27,43,38 chr1 109817245 . C T 3238.47 PASS AC=1;AF=0.763;AN=2;DP=4905;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:69,68:137:99:1581,0,2071:36,33,38,30 chr1 109817479 . G C 1633.16 PASS AC=1;AF=0.591;AN=2;DP=1425;MQ=60;set=variant16-variant17-variant18-variant25-variant27-variant31-variant32-variant34-variant35-variant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:62,87:149:99:2302,0,1521:27,35,40,47 chr1 109817590 . G T 1023.27 PASS AC=1;AF=0.567;AN=2;DP=1176;MQ=60;set=variant2-variant4-variant5-variant19-variant21-variant23-variant26-variant27-variant29-variant30-variant31-variant34-variant35-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,46:93:99:1254,0,1207:22,25,16,30 chr1 109817838 . T C 616.36 PASS AC=1;AF=0.845;AN=2;DP=1360;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,17:32:99:439,0,495:9,6,8,9 chr1 109818128 . C T 2118.46 PASS AC=1;AF=0.5;AN=2;DP=296;FractionInformativeReads=1;MQ=60;set=variant27-variant35 GT:AD:DP:GQ:PL:SB 0/1:78,70:148:99:1717,0,1937:42,36,40,30 chr1 109818158 . C CT 5905 PASS AC=1;AF=0.845;AN=2;DP=5974;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:83,93:176:99:3151,0,2781:45,38,48,45 chr1 109818263 . G A 3778.69 PASS AC=2;AF=1;AN=2;DP=4873;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,127:127:99:3929,379,0:0,0,54,73 chr1 109818306 . G T 2623.24 PASS AC=1;AF=0.833;AN=2;DP=3009;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,39:86:99:1076,0,1359:15,32,11,28 chr1 109822143 . G A 1926.43 PASS AC=1;AF=0.81;AN=2;DP=1494;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,21:38:99:708,0,492:13,4,18,3 chr1 109822166 . G A 2741.34 PASS AC=1;AF=0.81;AN=2;DP=2639;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,39:63:99:1185,0,680:18,6,28,11 chr1 109823147 . CAAGTTTAACTGACCTCGA C 2528.11 PASS AC=1;AF=0.5;AN=2;DP=181;FS=2.668;FractionInformativeReads=0.983;MQ=60;MQRankSum=1.237;QD=13.97;ReadPosRankSum=5.668;SOR=0.844;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:108,70:178:99:2565,0,19008:55,53,32,38 chr1 109825360 . C T 942.79 PASS AC=2;AF=1;AN=2;DP=1851;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1147,99,0:0,0,16,17 chr1 109825591 . C T 1546.82 PASS AC=1;AF=0.587;AN=2;DP=3384;MQ=60;set=variant2-variant8-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant25-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:99,83:182:99:2307,0,2507:55,44,48,35 chr1 109825834 . G A 1396.37 PASS AC=1;AF=0.5;AN=2;DP=121;FS=5.831;FractionInformativeReads=1;MQ=60;MQRankSum=-1.339;QD=11.54;ReadPosRankSum=1.354;SOR=0.348;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:65,56:121:99:1425,0,1800:21,44,24,32 chr1 109836835 . A G 1426.86 PASS AC=1;AF=0.609;AN=2;DP=3969;FractionInformativeReads=1;MQ=60;set=variant2-variant8-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant25-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:67,94:161:99:2396,0,2443:27,40,46,48 chr1 109836842 . C G 5697.38 PASS AC=1;AF=0.722;AN=2;DP=5934;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:92,62:154:99:1456,0,3621:42,50,23,39 chr1 109838116 . C T 273.85 PASS AC=2;AF=1;AN=2;DP=603;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:271,24,0:0,0,2,6 chr1 109838833 . T C 660.75 PASS AC=2;AF=1;AN=2;DP=1224;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:1133,90,0:0,0,25,5 chr1 109838918 . C T 2531.13 PASS AC=2;AF=0.943;AN=2;DP=4861;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,119:119:99:3319,355,0:0,0,66,53 chr1 109839063 . AT A,ATT 332.92 PASS AC=0,1;AF=0.386,0.136;AN=2;DP=1044;set=variant2-variant4-variant5-filterInvariant7-variant10-variant11-filterInvariant14-variant15-filterInvariant16-filterInvariant17-filterInvariant19-variant23-variant25-variant26-variant27-variant29-variant30-filterInvariant35-variant36-variant41-variant42-variant44 GT:DP:GQ:SB 0/2:38:82:11,19,3,5 chr1 109839392 . A G 975.91 PASS AC=2;AF=0.864;AN=2;DP=2844;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:1972,177,0:0,0,37,22 chr1 109839433 . A G 1151.54 PASS AC=2;AF=1;AN=2;DP=4179;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,86:86:99:2582,257,0:0,0,49,37 chr1 109839954 . G C 247.98 PASS AC=2;AF=0.907;AN=2;DP=1063;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:768,63,0:0,0,4,17 chr1 109840918 . C T 3232.15 PASS AC=1;AF=0.563;AN=2;DP=802;FractionInformativeReads=1;MQ=60;set=variant9-variant13-variant16-variant18-variant27-variant32-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:50,52:102:99:1079,0,1327:23,27,22,30 chr1 109855135 . TAA TA,T,TAAA,TAAAA 2159.05 PASS AC=1,0,0,0;AF=0.636,0.045,0.125,0.011;AN=2;DP=4447;set=Intersection GT:DP:GQ:SB 0/1:73:99:19,20,18,16 chr1 109855404 . G A 9147.68 PASS AC=1;AF=0.821;AN=2;DP=11589;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:174,131:305:99:2993,0,4149:88,86,62,69 chr1 109856306 . G A 3944.01 PASS AC=1;AF=0.697;AN=2;DP=3783;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant28-variant30-variant31-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,52:120:99:1279,0,1624:35,33,32,20 chr1 109856384 . CAA C 6252.42 PASS AC=1;AF=0.821;AN=2;DP=5974;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:75,89:164:99:3305,0,2649:32,43,46,43 chr1 109856842 . TG TGG,T 1213.9 PASS AC=0,1;AF=0.265,0.353;AN=2;DP=1013;MQ=60;set=variant3-variant4-variant9-variant11-variant12-variant13-variant16-variant18-variant19-variant22-variant27-variant32-variant34-variant35-variant37-variant39-variant40 GT:DP:GQ:SB 0/2:54:99:14,10,13,17 chr1 109883576 . C CAT 2347.54 PASS AC=1;AF=0.821;AN=2;DP=3391;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,38:93:99:1430,0,2464:21,34,12,26 chr1 109884775 . T G 2120.88 PASS AC=1;AF=0.793;AN=2;DP=2531;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,32:64:99:720,0,864:14,18,15,17 chr1 109897103 . A G 3472.46 PASS AC=1;AF=0.814;AN=2;DP=6288;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:63,65:128:99:1523,0,1509:33,30,35,30 chr1 109898263 . A ACC,C 461.51 PASS AC=1,0;AF=0.703,0.095;AN=2;DP=705;MQ=60;set=variant3-variant5-variant6-variant7-variant8-variant10-variant11-variant2-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-filterInvariant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:DP:GQ:SB 0/1:16:99:1,7,2,6 chr1 109898267 . GC GCC,G,GCCC 569.21 PASS AC=1,0,0;AF=0.534,0.155,0.052;AN=2;DP=443;set=variant-variant2-variant4-variant5-variant6-variant7-variant12-variant13-variant14-variant15-variant17-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant33-variant35-variant36-variant3-variant37-variant38-variant40-variant41-variant42-variant44 GT:DP:GQ:SB 0/1:16:99:1,7,2,6 chr1 109910013 . C T 1581.93 PASS AC=1;AF=0.563;AN=2;DP=556;MQ=60;set=variant9-variant13-variant16-variant18-variant27-variant32-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:31,34:65:99:747,0,766:17,14,17,17 chr1 109940503 . G C 1385.8 PASS AC=1;AF=0.538;AN=2;DP=766;MQ=60;set=variant9-variant13-variant15-variant16-variant18-variant21-variant27-variant32-variant34-variant35-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:31,32:63:99:718,0,833:9,22,15,17 chr1 109943893 . C T 5712.37 PASS AC=1;AF=0.793;AN=2;DP=5329;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,46:114:99:1387,0,2120:19,49,11,35 chr1 109944078 . T C 4468.35 PASS AC=1;AF=0.821;AN=2;DP=4038;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,41:96:99:1217,0,1692:38,17,29,12 chr1 109955010 . C A 306.83 PASS AC=1;AF=0.868;AN=2;DP=363;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,5:9:99:191,0,156:0,4,0,5 chr1 109958035 . T C 994.84 PASS AC=1;AF=0.821;AN=2;DP=1648;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,27:50:99:655,0,642:6,17,10,17 chr1 110009434 . A C 1710.74 PASS AC=1;AF=0.817;AN=2;DP=3173;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,63:119:99:1569,0,1574:38,18,39,24 chr1 110009654 . AC A 3479.38 PASS AC=1;AF=0.788;AN=2;DP=6355;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:101,122:223:99:3200,0,2525:44,57,57,65 chr1 110018148 . C T 640.43 PASS AC=2;AF=0.966;AN=2;DP=1921;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,31:31:92:1001,92,0:0,0,24,7 chr1 110022896 . A C 475.05 PASS AC=1;AF=0.567;AN=2;DP=648;FractionInformativeReads=1;MQ=60;set=variant5-variant9-variant13-variant14-variant15-variant16-variant18-variant21-variant27-variant32-variant34-variant35-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:14,35:49:99:953,0,354:5,9,21,14 chr1 110023432 . G A 741.96 PASS AC=1;AF=0.567;AN=2;DP=914;FractionInformativeReads=1;MQ=60;set=variant5-variant9-variant13-variant14-variant15-variant16-variant18-variant21-variant27-variant32-variant34-variant35-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:35,20:55:99:455,0,1098:13,22,9,11 chr1 110023610 . G A 1652.32 PASS AC=1;AF=0.619;AN=2;DP=1244;MQ=60;set=variant5-variant9-variant13-variant14-variant15-variant16-variant18-variant21-variant23-variant27-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,40:64:99:1006,0,565:15,9,20,20 chr1 110026485 . G C 552.71 PASS AC=1;AF=0.5;AN=2;DP=33;FS=0;FractionInformativeReads=0.97;MQ=60;MQRankSum=-0.019;QD=16.75;ReadPosRankSum=-0.32;SOR=0.2;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:16,16:32:99:581,0,566:16,0,15,1 chr1 110030895 . GTC G 950.37 PASS AC=1;AF=0.556;AN=2;DP=1021;MQ=60;set=variant5-variant9-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant27-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:28,19:47:99:704,0,1078:18,10,14,5 chr1 110030945 . A G 2546.63 PASS AC=1;AF=0.591;AN=2;DP=1957;FractionInformativeReads=1;MQ=60;set=variant5-variant9-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant23-variant27-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,37:82:99:1043,0,980:24,21,25,12 chr1 110035159 . T C 789.89 PASS AC=1;AF=0.553;AN=2;DP=1437;MQ=60;set=variant5-variant9-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant27-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:52,53:105:99:1184,0,1149:27,25,30,23 chr1 110035318 . AT A 902.55 PASS AC=1;AF=0.636;AN=2;DP=841;MQ=60;set=variant5-variant9-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant23-variant27-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,25:47:99:609,0,498:13,9,14,11 chr1 110036998 . G C 3658.81 PASS AC=1;AF=0.533;AN=2;DP=1470;MQ=60;set=variant9-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant32-variant34-variant35-variant38-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,48:90:99:1341,0,1211:13,29,16,32 chr1 110037838 . T G 955.73 PASS AC=1;AF=0.595;AN=2;DP=2107;MQ=60;set=variant5-variant9-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant23-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:62,43:105:99:938,0,1498:23,39,20,23 chr1 110040310 . A G 676.86 PASS AC=1;AF=0.579;AN=2;DP=1199;MQ=60;set=variant5-variant9-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant23-variant32-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,30:70:99:803,0,1107:20,20,18,12 chr1 110040452 . TATGGGG T 818.78 PASS AC=1;AF=0.579;AN=2;DP=1295;MQ=60;set=variant5-variant9-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant23-variant32-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,36:93:99:1332,0,6338:27,30,18,18 chr1 110040460 . C CA 818.93 PASS AC=1;AF=0.579;AN=2;DP=1263;MQ=60;set=variant5-variant9-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant23-variant32-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,36:92:99:1334,0,6294:26,30,18,18 chr1 110040680 . C T 659.84 PASS AC=1;AF=0.679;AN=2;DP=1680;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant28-variant31-variant33-variant35-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:27,42:69:99:1094,0,638:14,13,21,21 chr1 110041037 . CAG C 841.73 PASS AC=1;AF=0.714;AN=2;DP=1990;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant28-variant31-variant33-variant35-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:47,41:88:99:1415,0,1765:23,24,22,19 chr1 110041477 . TAAAA TAA,TAAAAA,TAAA,T 450.41 PASS AC=0,0,1,0;AF=0.318,0.045,0.288,0.015;AN=2;DP=1010;set=variant-filterInvariant4-variant5-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant27-variant29-variant30-variant31-variant32-filterInvariant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/3:25:99:5,7,6,7 chr1 110042079 . A G 242.08 PASS AC=1;AF=0.595;AN=2;DP=478;set=variant5-variant9-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant23-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,9:25:99:312,0,555:1,15,0,9 chr1 110047110 . C G 82.72 PASS AC=1;AF=0.6;AN=2;DP=163;FractionInformativeReads=1;MQ=60;set=variant5-variant9-variant13-variant15-variant16-variant18-variant19-variant21-variant29-variant35-variant36-variant38-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,7:13:99:154,0,186:4,2,3,4 chr1 110048436 . C A 676.37 PASS AC=1;AF=0.583;AN=2;DP=760;FractionInformativeReads=1;MQ=60;set=variant5-variant9-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant23-variant29-variant32-variant35-variant36-variant38-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,17:46:99:456,0,585:14,15,11,6 chr1 110048527 . G A 739.95 PASS AC=1;AF=0.583;AN=2;DP=855;FractionInformativeReads=1;MQ=60;set=variant5-variant9-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant23-variant29-variant32-variant35-variant36-variant38-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,16:43:99:414,0,777:14,13,9,7 chr1 110052139 . A G 938.53 PASS AC=1;AF=0.688;AN=2;DP=1945;MQ=60;set=variant4-variant5-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,17:64:99:313,0,1145:16,31,6,11 chr1 110087207 . T C 775.79 PASS AC=1;AF=0.5;AN=2;DP=210;FractionInformativeReads=1;MQ=60;set=variant14-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:26,35:61:99:1090,0,626:14,12,22,13 chr1 110091447 . G A 1205.97 PASS AC=1;AF=0.5;AN=2;DP=772;MQ=60;set=variant3-variant14-variant15-variant26-variant31-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:71,63:134:99:1320,0,1770:30,41,28,35 chr1 110136458 . A G 17752.6 PASS AC=1;AF=0.681;AN=2;DP=18413;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant14-variant15-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:285,263:548:99:6548,0,7168:141,144,136,127 chr1 110145758 . ACCTGGGGGGTCTTCTAACTACTGG A 758.76 PASS AC=1;AF=0.611;AN=2;DP=1486;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant10-variant12-variant14-variant15-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,22:50:99:826,0,5898:22,6,18,4 chr1 110148974 . C T 1288.4 PASS AC=1;AF=0.614;AN=2;DP=3205;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant10-variant12-variant14-variant15-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,38:93:99:938,0,1391:33,22,25,13 chr1 110163076 . A G 256.95 PASS AC=1;AF=0.671;AN=2;DP=1224;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant10-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,14:34:99:387,0,648:5,15,4,10 chr1 110168888 . C G 1221.66 PASS AC=1;AF=0.756;AN=2;DP=5322;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:75,77:152:99:1788,0,1839:41,34,40,37 chr1 110169957 . A G 2112.79 PASS AC=1;AF=0.768;AN=2;DP=10170;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:150,157:307:99:3839,0,3539:73,77,76,81 chr1 110170896 . T C 897.79 PASS AC=1;AF=0.756;AN=2;DP=4189;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,47:106:99:1246,0,1559:33,26,28,19 chr1 110171705 . A C 719.77 PASS AC=1;AF=0.756;AN=2;DP=3311;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,39:79:99:1038,0,1094:24,16,26,13 chr1 110172346 . T TG 462.29 PASS AC=1;AF=0.768;AN=2;DP=2044;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,35:60:99:927,0,613:16,9,22,13 chr1 110172362 . C T 445.98 PASS AC=1;AF=0.629;AN=2;DP=1634;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant10-variant12-variant14-variant15-variant17-variant19-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,36:65:99:888,0,754:19,10,22,14 chr1 110198727 . C G 738.74 PASS AC=1;AF=0.609;AN=2;DP=2933;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,53:113:99:1332,0,1530:36,24,35,18 chr1 110199172 . CTGTGTGTGTGTG CTGTGTGTGTGTGTGTG,CTGTGTGTGTG,CTGTGTGTGTGTGTG,CTGTGTGTGTGTGTGTGTGTGTG,CTGTGTGTGTGTGTGTGTGTGTGTGTG,CTGTGTGTG,CTGTGTG,CTGTG,CTGTGTGTGTGTGTGTGTG,CTGTGTGTGTGTGTGTGTGTG,C,CTGTGTGTGTGTGTGTGTGTGTGTG,CTG 426.42 PASS AC=0,0,1,0,0,0,1,0,0,0,0,0,0;AF=0.125,0.138,0.075,0.038,0.013,0.125,0.05,0.075,0.025,0.013,0.025,0.013,0.013;AN=2;DP=3084;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 7/3:34:99:1,1,12,20 chr1 110199225 . TG T,GG,TGG 537.15 PASS AC=1,0,0;AF=0.477,0.091,0.045;AN=2;DP=657;set=variant3-variant8-variant10-variant11-variant13-variant15-variant18-variant19-variant22-variant23-variant5-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant40-variant43 GT:DP:GQ:SB 0/1:21:99:9,1,8,3 chr1 110200360 . T C 1953.53 PASS AC=1;AF=0.571;AN=2;DP=6439;set=variant-variant5-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant20-variant21-variant23-variant24-variant27-variant30-variant34-variant35-variant36-variant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:144,174:318:99:4391,0,3536:66,78,80,94 chr1 110201580 . C T 5961.37 PASS AC=2;AF=0.966;AN=2;DP=10086;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,256:256:99:7611,767,0:0,0,122,134 chr1 110201699 . T C 2763.56 PASS AC=2;AF=0.893;AN=2;DP=3320;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,91:91:99:3123,273,0:0,0,38,53 chr1 110201809 . G T 4909.9 PASS AC=2;AF=0.919;AN=2;DP=3892;FractionInformativeReads=1;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,106:106:99:4749,322,0:0,0,60,46 chr1 110201812 . A G 4980.87 PASS AC=2;AF=0.919;AN=2;DP=4015;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,107:107:99:4786,325,0:0,0,60,47 chr1 110204463 . G GT,GTT 119.84 PASS AC=1,0;AF=0.5,0.056;AN=2;DP=166;MQ=60;set=variant-variant5-variant13-variant16-variant18-variant29-variant35-variant36-variant37 GT:DP:GQ:SB 0/1:14:99:1,8,0,5 chr1 110207482 . C T 687.49 PASS AC=1;AF=0.5;AN=2;DP=240;FractionInformativeReads=1;MQ=60;set=variant-variant13-variant16-variant18-variant35-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:17,23:40:99:590,0,490:13,4,15,8 chr1 110208188 . A AACG 127.47 PASS AC=1;AF=0.5;AN=2;DP=14;FS=0;MQ=60;set=variant35-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:1,4:5:37:165,0,37:0,1,2,2 chr1 110210671 . G T 1470.71 PASS AC=1;AF=0.5;AN=2;DP=1600;MQ=60;set=variant-variant13-variant16-variant18-variant35-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:139,136:275:99:3070,0,2820:77,62,71,65 chr1 110210780 . C G 2730.11 PASS AC=2;AF=0.898;AN=2;DP=7796;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,227:227:99:7282,680,0:0,0,93,134 chr1 110210818 . C T 148.61 PASS AC=1;AF=0.645;AN=2;DP=2492;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant10-variant11-variant12-variant14-variant15-variant17-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:72,31:103:99:508,0,1816:32,40,13,18 chr1 110211681 . G C 198.56 PASS AC=1;AF=0.708;AN=2;DP=1571;set=variant-variant5-filterInvariant10-filterInvariant11-filterInvariant12-variant13-variant16-variant17-variant18-filterInvariant20-filterInvariant21-variant23-variant24-variant26-variant27-variant29-variant34-filterInvariant35-variant36-variant37-variant40-variant41-filterInvariant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:112,16:128:99:284,0,2864:47,65,1,15 chr1 110211835 . T C 1190.53 PASS AC=2;AF=0.672;AN=2;DP=2255;set=variant-variant2-variant3-variant4-variant6-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,66:66:99:2741,198,0:0,0,64,2 chr1 110211956 . C T 2213.07 PASS AC=1;AF=0.5;AN=2;DP=2206;set=variant-variant13-variant16-variant18-variant35-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:197,161:358:99:3795,0,5102:111,86,94,67 chr1 110224329 . C G 90.48 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=52;FS=0;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:6,6:12:99:162,0,145:5,1,6,0 chr1 110231592 . T C 2234.3 PASS AC=2;AF=0.962;AN=2;DP=705;MQ=60;set=variant3-variant5-variant8-variant12-variant14-variant15-variant26-variant28-variant29-variant30-variant31-variant35-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,73:73:99:2897,219,0:0,0,51,22 chr1 110231777 . G A 6927.79 PASS AC=2;AF=0.955;AN=2;DP=2609;MQRankSum=1.519;ReadPosRankSum=1.235;set=variant3-variant8-variant12-variant14-variant15-variant26-variant28-variant29-variant31-variant35-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,257:257:99:7863,769,0:0,0,120,137 chr1 110233138 . G C 2560.14 PASS AC=2;AF=0.962;AN=2;DP=679;FractionInformativeReads=1;set=variant3-variant5-variant8-variant12-variant14-variant15-variant26-variant28-variant29-variant30-variant31-variant35-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:1746,140,0:0,0,15,32 chr1 110252010 . T C 2780.01 PASS AC=2;AF=0.818;AN=2;DP=4014;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,97:97:99:2900,291,0:0,0,54,43 chr1 110252091 . G A 535.17 PASS AC=1;AF=0.558;AN=2;DP=1203;set=variant-variant2-variant7-variant8-variant10-variant12-variant13-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant31-variant32-variant33-variant35-variant36-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:36,23:59:99:727,0,1220:6,30,2,21 chr1 110255117 . T G 118.19 PASS AC=1;AF=0.5;AN=2;DP=873;set=filterInvariant-filterInvariant2-filterInvariant14-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant31-filterInvariant32-variant35-filterInvariant37-variant42 GT:AD:DP:GQ:PL:SB 0/1:51,20:71:99:189,0,1111:34,17,1,19 chr1 110255174 . T G 993.51 PASS AC=1;AF=0.5;AN=2;DP=1534;set=variant2-variant8-variant10-variant12-variant13-variant18-variant19-variant20-variant23-variant24-variant25-variant31-variant35-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:55,59:114:99:1403,0,1409:27,28,29,30 chr1 110259016 . G T 445.02 PASS AC=1;AF=0.522;AN=2;DP=1571;MQ=60;set=variant2-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant19-variant20-variant22-variant23-variant24-variant25-variant28-variant31-variant32-variant33-variant35-variant36-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:32,41:73:99:872,0,755:16,16,21,20 chr1 110259362 . G A 629.25 PASS AC=1;AF=0.523;AN=2;DP=1267;MQ=60;set=variant2-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant19-variant20-variant23-variant24-variant25-variant28-variant31-variant32-variant33-variant35-variant36-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:30,23:53:99:588,0,864:15,15,11,12 chr1 110277403 . T C 1133.46 PASS AC=1;AF=0.5;AN=2;DP=1886;MQ=60;set=variant2-variant4-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant19-variant20-variant22-variant23-variant24-variant25-variant31-variant33-variant35-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:58,65:123:99:1408,0,1329:29,29,31,34 chr1 110278256 . T A,G 119.29 PASS AC=1,0;AF=0.475,0.15;AN=2;DP=166;set=variant2-variant4-variant6-variant7-variant13-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant28-variant31-variant33-variant35-variant37-variant40-variant42 GT:DP:GQ:SB 0/1:8:99:1,3,1,3 chr1 110278257 . T G 119.29 PASS AC=1;AF=0.594;AN=2;DP=133;set=variant2-variant4-variant13-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant28-variant33-variant35-variant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:99:147,0,157:1,3,1,3 chr1 110278972 . C T 956.1 PASS AC=1;AF=0.614;AN=2;DP=1200;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant28-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,17:26:99:497,0,323:5,4,8,9 chr1 110279027 . C T 683.14 PASS AC=1;AF=0.5;AN=2;DP=996;MQ=60;set=variant2-variant4-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant19-variant20-variant22-variant23-variant24-variant25-variant31-variant33-variant35-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:27,27:54:99:880,0,793:20,7,16,11 chr1 110279053 . GT G 1080.93 PASS AC=1;AF=0.667;AN=2;DP=3299;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,38:76:99:956,0,952:29,9,24,14 chr1 110279701 . C T 572.29 PASS AC=1;AF=0.5;AN=2;DP=1281;MQ=60;set=variant2-variant4-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant19-variant20-variant22-variant23-variant24-variant25-variant31-variant33-variant35-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:32,33:65:99:885,0,874:22,10,21,12 chr1 110279821 . C A 3203.75 PASS AC=1;AF=0.569;AN=2;DP=3239;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant31-variant32-variant33-variant35-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,58:122:99:1317,0,1633:34,30,29,29 chr1 110279914 . C T 810.36 PASS AC=1;AF=0.525;AN=2;DP=1723;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant19-variant20-variant22-variant23-variant24-variant25-variant31-variant33-variant35-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:42,34:76:99:917,0,1000:17,25,16,18 chr1 110281941 . G A 535.18 PASS AC=1;AF=0.654;AN=2;DP=2306;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,17:52:99:440,0,836:21,14,11,6 chr1 110282972 . G T 1244.63 PASS AC=1;AF=0.654;AN=2;DP=8843;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:117,119:236:99:2985,0,2857:46,71,49,70 chr1 110283785 . C T 355.34 PASS AC=1;AF=0.671;AN=2;DP=493;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,11:18:99:385,0,244:0,7,1,10 chr1 110284212 . C G 165.16 PASS AC=1;AF=0.5;AN=2;DP=190;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant8-variant10-variant12-variant19-variant20-variant24-variant25-variant31-variant33-variant35-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:6,9:15:99:266,0,187:4,2,7,2 chr1 110292856 . G C 464.42 PASS AC=1;AF=0.529;AN=2;DP=990;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant6-variant8-variant12-variant13-variant19-variant20-variant23-variant25-variant31-variant33-variant35-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:25,19:44:99:511,0,619:13,12,13,6 chr1 110295772 . T C 754.36 PASS AC=1;AF=0.679;AN=2;DP=3914;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,54:99:99:1251,0,1098:22,23,25,29 chr1 110295890 . C G 70.68 PASS AC=1;AF=0.679;AN=2;DP=1424;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,10:33:99:331,0,604:10,13,0,10 chr1 110300356 . AC A 419.96 PASS AC=1;AF=0.5;AN=2;DP=90;FractionInformativeReads=1;MQ=60;set=variant29-variant35 GT:AD:DP:GQ:PL:SB 0/1:32,24:56:99:795,0,1121:17,15,11,13 chr1 110300441 . G A 848.04 PASS AC=1;AF=0.6;AN=2;DP=2630;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,37:83:99:955,0,1210:28,18,22,15 chr1 110300504 . A G 2808.06 PASS AC=2;AF=0.977;AN=2;DP=4432;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,116:116:99:3578,348,0:0,0,66,50 chr1 110301766 . AGTGTGTGTGT AGT,AGTGTGT,AGTGTGTGTGTGT,AGTGTGTGT,AGTGT,A 464.39 PASS AC=0,1,0,1,0,0;AF=0.216,0.239,0.034,0.33,0.114,0.011;AN=2;DP=1690;set=Intersection GT:DP:GQ:SB 2/4:38:99:0,0,29,9 chr1 110302450 . C T 1081.02 PASS AC=1;AF=0.5;AN=2;DP=452;FractionInformativeReads=1;MQ=60;set=variant14-variant15-variant26-variant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:47,54:101:99:1327,0,925:24,23,24,30 chr1 110466338 . C A 10561.2 PASS AC=2;AF=0.736;AN=2;DP=16683;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:3,482:485:99:14070,1421,0:0,3,227,255 chr1 110466709 . T C 4700.31 PASS AC=2;AF=1;AN=2;DP=9366;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,263:263:99:7865,788,0:0,0,112,151 chr1 110467745 . A G 1909.4 PASS AC=2;AF=1;AN=2;DP=3241;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,67:67:99:2188,201,0:0,0,44,23 chr1 110469319 . T C 911.15 PASS AC=2;AF=1;AN=2;DP=1252;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1372,108,0:0,0,8,28 chr1 110472728 . A G 3419.93 PASS AC=2;AF=1;AN=2;DP=5377;FS=0;MQRankSum=2.111;ReadPosRankSum=1.659;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,142:142:99:4352,425,0:0,0,69,73 chr1 110527452 . G GC 1977.62 PASS AC=2;AF=1;AN=2;DP=3304;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:3065,229,0:0,0,32,44 chr1 110558276 . A AC 2300.26 PASS AC=2;AF=1;AN=2;DP=2429;FS=0;MQ=60;MQRankSum=1.299;ReadPosRankSum=-1.245;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,63:63:99:2453,190,0:0,0,21,42 chr1 110564996 . CAAAAAAA CAAAAAA,CAAAAA,C 199.97 PASS AC=1,0,0;AF=0.467,0.017,0.017;AN=2;DP=3062;set=filterInvariant4-filterInvariant5-filterInvariant7-variant8-filterInvariant11-filterInvariant12-filterInvariant13-filterInvariant14-variant15-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant19-variant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-variant35-filterInvariant36-variant37-filterInvariant38-filterInvariant39-filterInvariant40-filterInvariant41-filterInvariant44 GT:DP:GQ:SB 0/1:97:99:33,28,21,15 chr1 110592048 . CTT CT,C 219.47 PASS AC=0,1;AF=0.382,0.132;AN=2;DP=1161;set=variant-variant2-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-filterInvariant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:32:99:12,8,9,3 chr1 110656011 . G A 1054.25 PASS AC=1;AF=0.548;AN=2;DP=1618;set=variant-variant6-variant7-variant8-variant9-variant11-variant12-variant16-variant17-variant21-variant23-variant24-variant31-variant33-variant34-variant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,47:100:99:1131,0,1313:28,25,20,27 chr1 110693263 . C T 1202 PASS AC=1;AF=0.611;AN=2;DP=2591;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant9-variant12-variant14-variant16-variant19-variant20-variant21-variant22-variant26-variant27-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:61,46:107:99:1122,0,1520:32,29,20,26 chr1 110693447 . T C 609.96 PASS AC=1;AF=0.841;AN=2;DP=1762;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:30,21:51:99:517,0,767:11,19,7,14 chr1 110765535 . C G 358.85 PASS AC=1;AF=0.7;AN=2;DP=1147;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:26,14:40:99:510,0,850:21,5,12,2 chr1 110881083 . ACT A 201.24 PASS AC=1;AF=0.55;AN=2;DP=476;MQ=60;set=variant-variant10-variant15-variant22-variant23-variant35-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:16,28:44:99:1086,0,561:10,6,20,8 chr1 110882444 . A G 3056.91 PASS AC=1;AF=0.798;AN=2;DP=5430;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,73:134:99:1822,0,1419:28,33,33,40 chr1 110888948 . G A 472.46 PASS AC=1;AF=0.55;AN=2;DP=556;MQ=60;set=variant-variant10-variant15-variant22-variant23-variant35-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:28,17:45:99:404,0,689:14,14,9,8 chr1 110906247 . CA CAA,C 260.72 PASS AC=0,1;AF=0.25,0.25;AN=2;DP=3855;set=filterInvariant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-filterInvariant12-variant14-variant15-variant16-variant17-filterInvariant18-variant19-variant20-variant21-filterInvariant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-filterInvariant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:112:99:60,12,35,5 chr1 110917734 . G C 152.6 PASS AC=1;AF=0.625;AN=2;DP=60;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant10-variant22-variant23-variant35-variant38-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:3,4:7:99:110,0,112:3,0,3,1 chr1 110922140 . G A 180.3 PASS AC=1;AF=0.6;AN=2;DP=147;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant10-variant18-variant20-variant22-variant23-variant25-variant28-variant29-variant30-variant34-variant35-variant38-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:4,6:10:99:240,0,107:1,3,2,4 chr1 110949566 . G T 283.55 PASS AC=1;AF=0.571;AN=2;DP=179;FractionInformativeReads=1;MQ=60;set=variant-variant10-variant22-variant23-variant35-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:16,20:36:99:500,0,438:12,4,13,7 chr1 110949720 . C T 527.24 PASS AC=1;AF=0.708;AN=2;DP=2084;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,20:51:99:505,0,787:13,18,7,13 chr1 110949857 . A T 872.21 PASS AC=1;AF=0.708;AN=2;DP=2905;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,29:83:99:707,0,1692:36,18,19,10 chr1 110950462 . G A 2756.85 PASS AC=1;AF=0.563;AN=2;DP=1600;MQ=60;set=variant-variant10-variant22-variant23-variant35-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:112,97:209:99:2476,0,3233:60,52,44,53 chr1 110993990 . G A 1707.48 PASS AC=1;AF=0.5;AN=2;DP=1222;FractionInformativeReads=1;MQ=60;set=variant-variant9-variant10-variant22-variant28-variant35-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:88,80:168:99:2022,0,2258:33,55,29,51 chr1 110998766 . T A 346.42 PASS AC=1;AF=0.625;AN=2;DP=578;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant15-variant17-variant18-variant19-variant20-variant22-variant25-variant28-variant29-variant30-variant32-variant34-variant35-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,13:25:99:383,0,334:10,2,10,3 chr1 110998854 . G A 1426.26 PASS AC=1;AF=0.621;AN=2;DP=1883;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant17-variant18-variant19-variant20-variant22-variant25-variant28-variant29-variant30-variant32-variant34-variant35-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,34:71:99:903,0,856:19,18,23,11 chr1 111059825 . G A 1345.88 PASS AC=1;AF=0.577;AN=2;DP=892;MQ=60;set=variant4-variant12-variant19-variant25-variant26-variant27-variant29-variant32-variant35-variant37-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,40:66:99:1170,0,590:16,10,30,10 chr1 111060669 . T C 1565.12 PASS AC=1;AF=0.776;AN=2;DP=6554;MQ=60;set=variant-variant2-variant4-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:95,84:179:99:2153,0,2443:42,53,34,50 chr1 111060752 . C T 1639.56 PASS AC=1;AF=0.538;AN=2;DP=1800;MQ=60;set=variant5-variant6-variant9-variant11-variant17-variant18-variant21-variant22-variant26-variant30-variant35-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:67,66:133:99:1463,0,1986:32,35,29,37 chr1 111061011 . C A 1427.18 PASS AC=1;AF=0.571;AN=2;DP=1116;FractionInformativeReads=1;MQ=60;set=variant4-variant12-variant19-variant25-variant26-variant27-variant29-variant32-variant35-variant37-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,60:88:99:1623,0,657:14,14,28,32 chr1 111061062 . T C 1258.06 PASS AC=1;AF=0.776;AN=2;DP=3036;MQ=60;set=variant-variant2-variant4-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,44:67:99:1244,0,580:15,8,22,22 chr1 111144526 . T G 376.77 PASS AC=2;AF=1;AN=2;DP=1048;FS=0;MQ=60;MQRankSum=1.542;ReadPosRankSum=-1.735;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:746,63,0:0,0,17,4 chr1 111173886 . G A 196.77 PASS AC=2;AF=0.919;AN=2;DP=506;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:441,39,0:0,0,10,3 chr1 111215090 . T TGG 4598.1 PASS AC=1;AF=0.611;AN=2;DP=3967;MQ=60;set=variant3-variant5-variant7-variant10-variant12-variant15-variant20-variant22-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant35-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:127,101:228:99:2489,0,4921:71,56,66,35 chr1 111215472 . A C 3554.35 PASS AC=1;AF=0.813;AN=2;DP=3384;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,41:80:99:1238,0,1141:10,29,13,28 chr1 111390624 . ATT A,AT,ATTTT,ATTT 45.42 PASS AC=0,1,0,0;AF=0.106,0.439,0.015,0.015;AN=2;DP=747;set=variant2-variant3-variant4-variant5-variant7-variant8-filterInvariant9-variant10-variant11-variant12-variant13-variant15-variant17-variant19-variant20-variant21-variant22-variant23-filterInvariant24-variant25-variant26-variant27-variant28-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:DP:GQ:SB 0/2:30:99:3,6,14,7 chr1 111436857 . T G 2446.77 PASS AC=1;AF=0.739;AN=2;DP=5768;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:67,63:130:99:2456,0,3371:40,27,34,29 chr1 111436858 . C T 2446.77 PASS AC=1;AF=0.739;AN=2;DP=5788;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:65,65:130:99:2456,0,3371:39,26,35,30 chr1 111437129 . A C 539.19 PASS AC=1;AF=0.649;AN=2;DP=1684;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,25:49:99:634,0,618:14,10,9,16 chr1 111437176 . G GA 678.17 PASS AC=1;AF=0.739;AN=2;DP=1209;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:19,13:32:99:328,0,491:9,10,3,10 chr1 111437421 . C A 1466.73 PASS AC=1;AF=0.784;AN=2;DP=1941;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:28,15:43:99:402,0,844:23,5,11,4 chr1 111441829 . C T 5138.69 PASS AC=1;AF=0.739;AN=2;DP=8626;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:103,109:212:99:2611,0,2627:52,51,58,51 chr1 111441858 . G A 2869.88 PASS AC=1;AF=0.5;AN=2;DP=1785;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant15-variant16-variant22-variant29-variant31-variant32-variant35 GT:AD:DP:GQ:PL:SB 0/1:105,108:213:99:2683,0,2798:50,55,51,57 chr1 111442529 . A AAC 5980.9 PASS AC=1;AF=0.784;AN=2;DP=4820;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:50,48:98:99:1865,0,2030:16,34,13,35 chr1 111442555 . G C 3345.2 PASS AC=1;AF=0.784;AN=2;DP=2893;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:41,30:71:99:897,0,1131:12,29,5,25 chr1 111489901 . A C 2975.33 PASS AC=1;AF=0.526;AN=2;DP=6631;MQ=60;set=variant2-variant3-variant5-variant7-variant12-variant15-variant16-variant17-variant18-variant22-variant25-variant26-variant29-variant31-variant32-variant35-variant36-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:162,137:299:99:2899,0,6095:88,74,79,58 chr1 111489902 . A C 4235.34 PASS AC=1;AF=0.5;AN=2;DP=1387;MQ=60;set=variant15-variant18-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:166,136:302:99:2856,0,6852:89,77,79,57 chr1 111492807 . G A 685.84 PASS AC=1;AF=0.559;AN=2;DP=586;MQ=60;set=variant3-variant6-variant9-variant15-variant16-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant30-variant32-variant35-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,12:29:99:331,0,477:4,13,3,9 chr1 111661413 . T C 425.54 PASS AC=2;AF=0.654;AN=2;DP=2071;MQ=60;set=variant2-variant6-variant7-variant8-variant9-variant13-variant16-variant18-variant19-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,81:81:99:2310,242,0:0,0,42,39 chr1 111663040 . A G 156.5 PASS AC=2;AF=0.607;AN=2;DP=249;set=variant6-variant9-variant16-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant37-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:64:612,64,0:0,0,17,5 chr1 111680215 . C T 4188.23 PASS AC=2;AF=0.635;AN=2;DP=10549;set=variant2-variant6-variant7-variant8-variant9-variant13-variant16-variant18-variant19-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,354:354:99:10714,1059,0:0,0,168,186 chr1 111682758 . G GC 4128.56 PASS AC=2;AF=0.575;AN=2;DP=6142;MQ=60;set=variant6-variant7-variant9-variant13-variant16-variant19-variant21-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant37-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,301:301:99:9685,905,0:0,0,152,149 chr1 111726026 . G A 348.03 PASS AC=2;AF=0.654;AN=2;DP=840;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant7-variant8-variant9-variant13-variant16-variant18-variant19-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1152,111,0:0,0,24,13 chr1 111726213 . A G 251.83 PASS AC=2;AF=0.716;AN=2;DP=1409;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1270,120,0:0,0,17,23 chr1 111727469 . CTT CTTT,CT,C 318.24 PASS AC=0,0,1;AF=0.132,0.382,0.013;AN=2;DP=7551;set=filterInvariant-variant2-variant3-variant4-filterInvariant5-variant6-variant7-variant8-variant9-variant10-filterInvariant12-variant13-variant14-filterInvariant15-variant16-variant17-variant18-variant20-variant22-filterInvariant23-variant24-variant25-filterInvariant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-filterInvariant36-variant37-variant39-variant41-variant42-variant43-filterInvariant44 GT:DP:GQ:SB 0/3:142:99:46,57,12,27 chr1 111730901 . C T 1012.85 PASS AC=2;AF=0.618;AN=2;DP=1403;MQ=60;set=variant6-variant7-variant9-variant13-variant16-variant19-variant23-variant27-variant28-variant29-variant30-variant32-variant35-variant36-variant37-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,81:81:99:2462,243,0:0,0,32,49 chr1 111731940 . G A 1536.37 PASS AC=1;AF=0.5;AN=2;DP=130;FS=0.64;FractionInformativeReads=1;MQ=60;MQRankSum=-1.36;QD=11.82;ReadPosRankSum=-1.96;SOR=0.695;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:65,65:130:99:1565,0,1722:32,33,33,32 chr1 111737183 . C T 609.37 PASS AC=2;AF=0.75;AN=2;DP=1426;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1182,108,0:0,0,25,11 chr1 111741160 . T C 1064.46 PASS AC=1;AF=0.5;AN=2;DP=86;FS=1.766;FractionInformativeReads=1;MQ=60;MQRankSum=0.471;QD=12.38;ReadPosRankSum=1.965;SOR=0.913;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:44,42:86:99:1093,0,1163:25,19,26,16 chr1 111742714 . A C 284.76 PASS AC=2;AF=0.951;AN=2;DP=435;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:390,36,0:0,0,8,4 chr1 111742761 . T C 340.68 PASS AC=2;AF=0.909;AN=2;DP=816;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:604,54,0:0,0,11,7 chr1 111742838 . G C 540.13 PASS AC=2;AF=0.909;AN=2;DP=1870;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1371,120,0:0,0,28,12 chr1 111768576 . G A 5644.59 PASS AC=1;AF=0.58;AN=2;DP=3977;set=variant-variant2-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant33-variant35-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:94,84:178:99:1650,0,2286:56,38,49,35 chr1 111770423 . T G 3588.33 PASS AC=1;AF=0.725;AN=2;DP=4916;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:63,70:133:99:1918,0,1455:33,30,38,32 chr1 111772303 . CAAAAA C,CAAAA,CAAAAAAAAAAA,CAAAAAA,CAAAAAAAAAAAA,CAA,CAAA 304.32 PASS AC=0,0,0,0,0,0,1;AF=0.111,0.056,0.167,0.056,0.056,0.056,0.056;AN=2;DP=87;set=variant7-variant8-variant9-variant10-variant13-variant15-variant23-variant27-variant35 GT:DP:GQ:SB 0/7:13:99:6,2,5,0 chr1 111773568 . G C 1203.62 PASS AC=1;AF=0.603;AN=2;DP=2616;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant33-variant35-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,61:104:99:1609,0,1095:15,28,21,40 chr1 111773830 . A T 822.41 PASS AC=1;AF=0.603;AN=2;DP=1815;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant33-variant35-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,27:58:99:686,0,858:17,14,10,17 chr1 111778187 . A G 2318.79 PASS AC=1;AF=0.625;AN=2;DP=1931;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant33-variant35-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,33:76:99:843,0,1062:22,21,22,11 chr1 111778241 . C T 2770.55 PASS AC=2;AF=0.989;AN=2;DP=3577;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,85:85:99:2754,255,0:0,0,45,40 chr1 111778468 . G A 931.16 PASS AC=1;AF=0.577;AN=2;DP=1926;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant24-variant26-variant27-variant30-variant31-variant32-variant34-variant35-variant37-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,38:78:99:988,0,1170:14,26,14,24 chr1 111778824 . T C 822.72 PASS AC=1;AF=0.737;AN=2;DP=1046;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,15:30:99:444,0,489:2,13,3,12 chr1 111783982 . C A,T 251.8 PASS AC=1,0;AF=0.435,0.145;AN=2;DP=2187;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant43 GT:DP:GQ:SB 0/1:81:99:20,14,27,20 chr1 111783996 . A G 1045.41 PASS AC=2;AF=1;AN=2;DP=3606;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,87:87:99:2675,261,0:0,0,53,34 chr1 111784138 . T C 814.93 PASS AC=1;AF=0.563;AN=2;DP=2072;MQ=60;set=variant-variant2-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant33-variant35-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:44,40:84:99:1013,0,1076:20,24,18,22 chr1 111784148 . T G 2812.63 PASS AC=2;AF=1;AN=2;DP=3694;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,80:80:99:3008,240,0:0,0,34,46 chr1 111784158 . T C 815.34 PASS AC=1;AF=0.563;AN=2;DP=1833;MQ=60;set=variant-variant2-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant33-variant35-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:36,38:74:99:941,0,812:16,20,15,23 chr1 111784227 . C T 605.26 PASS AC=1;AF=0.563;AN=2;DP=1061;MQ=60;set=variant-variant2-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant33-variant35-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:20,18:38:99:524,0,514:8,12,6,12 chr1 111785246 . C CAT 2648.13 PASS AC=1;AF=0.583;AN=2;DP=1606;MQ=60;set=variant-variant2-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant33-variant35-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:24,33:57:99:1147,0,803:7,17,12,21 chr1 111785929 . C A 1094.56 PASS AC=1;AF=0.571;AN=2;DP=2545;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,52:88:99:1408,0,1356:13,23,24,28 chr1 111785930 . T C 2402.04 PASS AC=1;AF=0.671;AN=2;DP=3319;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,36:87:99:952,0,2066:24,27,13,23 chr1 111786012 . T A 1557.5 PASS AC=1;AF=0.583;AN=2;DP=1508;MQ=60;set=variant-variant2-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant33-variant35-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:43,19:62:99:406,0,1103:18,25,8,11 chr1 111825883 . T C 1644.34 PASS AC=2;AF=0.633;AN=2;DP=2496;FractionInformativeReads=1;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant23-variant24-variant25-variant27-variant28-variant31-variant33-variant34-variant35-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,98:98:99:2951,294,0:0,0,54,44 chr1 111826007 . C T 1043.34 PASS AC=1;AF=0.6;AN=2;DP=1618;set=variant-variant2-variant5-variant6-variant8-variant9-variant12-variant14-variant18-variant23-variant24-variant25-variant28-variant31-variant33-variant34-variant35-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:37,49:86:99:1144,0,881:17,20,19,30 chr1 111826106 . C T 55.46 PASS AC=1;AF=0.5;AN=2;DP=178;FractionInformativeReads=1;set=variant2-variant5-variant8-variant12-variant14-variant18-variant24-variant28-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:7,6:13:99:156,0,251:1,6,2,4 chr1 111833270 . C T 597.61 PASS AC=2;AF=0.724;AN=2;DP=527;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant14-variant15-variant16-variant18-variant19-variant23-variant24-variant27-variant28-variant31-variant33-variant34-variant35-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:1025,75,0:0,0,24,1 chr1 111833441 . G A 3642.99 PASS AC=2;AF=0.717;AN=2;DP=4689;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant14-variant15-variant16-variant18-variant19-variant23-variant24-variant25-variant27-variant28-variant31-variant33-variant34-variant35-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,173:173:99:5103,518,0:0,0,82,91 chr1 111833488 . C CCT 3386.9 PASS AC=2;AF=0.717;AN=2;DP=3374;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant14-variant15-variant16-variant18-variant19-variant23-variant24-variant25-variant27-variant28-variant31-variant33-variant34-variant35-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,115:115:99:5034,346,0:0,0,46,69 chr1 111833517 . G A 1810.55 PASS AC=2;AF=0.717;AN=2;DP=2195;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant14-variant15-variant16-variant18-variant19-variant23-variant24-variant25-variant27-variant28-variant31-variant33-variant34-variant35-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,82:82:99:2607,245,0:0,0,26,56 chr1 111854005 . C G 428.67 PASS AC=2;AF=0.989;AN=2;DP=463;FractionInformativeReads=1;MQ=60;MQRankSum=0.597;ReadPosRankSum=-0.278;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:222,15,0:0,0,5,0 chr1 111854096 . A G 1691.87 PASS AC=2;AF=0.989;AN=2;DP=2289;MQ=60;MQRankSum=1.902;ReadPosRankSum=0.216;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:1457,141,0:0,0,32,15 chr1 111854207 . T C 3636.3 PASS AC=2;AF=0.838;AN=2;DP=4369;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,99:99:99:3228,297,0:0,0,58,41 chr1 111854223 . C T 3865.25 PASS AC=2;AF=0.713;AN=2;DP=4468;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,109:109:99:3290,326,0:0,0,56,53 chr1 111854755 . A C 293.72 PASS AC=2;AF=0.989;AN=2;DP=601;FS=0;MQ=60;MQRankSum=-1.01;ReadPosRankSum=1.491;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:500,39,0:0,0,10,3 chr1 111893788 . GTTTTT GTTT,GTT,G,GTTTT,GTTTTTT,GT 117.88 PASS AC=1,0,0,0,0,0;AF=0.114,0.171,0.2,0.071,0.014,0.014;AN=2;DP=1243;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant12-variant13-variant14-filterInvariant15-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-filterInvariant31-variant32-variant33-variant34-variant35-variant36-variant39-variant41-variant43-variant44 GT:DP:GQ:SB 0/1:29:99:11,8,5,5 chr1 111957097 . C G 1133.92 PASS AC=1;AF=0.75;AN=2;DP=1841;FractionInformativeReads=1;set=variant2-variant3-variant4-variant6-variant8-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,32:64:99:947,0,797:18,14,19,13 chr1 111957311 . G C 1621.67 PASS AC=1;AF=0.55;AN=2;DP=1715;FractionInformativeReads=1;MQ=60;set=variant8-variant14-variant18-variant19-variant22-variant35-variant36-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:85,94:179:99:2547,0,2071:42,43,49,45 chr1 111957693 . A G 1449.04 PASS AC=1;AF=0.75;AN=2;DP=4171;set=variant2-variant3-variant4-variant6-variant8-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:78,85:163:99:2010,0,1957:33,45,40,45 chr1 111964144 . G C,T 1728.03 PASS AC=1,0;AF=0.5,0.042;AN=2;DP=1391;MQ=60;set=variant8-variant13-variant14-variant19-variant22-variant25-variant29-variant35-variant36-variant39-variant41-variant44 GT:DP:GQ:SB 0/1:154:99:27,42,47,38 chr1 111968121 . C T 1248.11 PASS AC=1;AF=0.5;AN=2;DP=708;MQ=60;set=variant8-variant14-variant18-variant19-variant22-variant35-variant36-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,35:71:99:844,0,1008:20,16,17,18 chr1 111968316 . G A 213.97 PASS AC=1;AF=0.667;AN=2;DP=257;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant8-variant11-variant13-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant35-variant36-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,3:7:91:91,0,133:0,4,0,3 chr1 111968327 . T C 187.23 PASS AC=1;AF=0.692;AN=2;DP=247;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant8-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,2:4:75:75,0,75:0,2,0,2 chr1 111969294 . A G 2351.11 PASS AC=1;AF=0.685;AN=2;DP=4524;MQ=60;set=variant3-variant4-variant6-variant8-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:81,71:152:99:1700,0,2182:42,39,34,37 chr1 111969432 . C G 646.66 PASS AC=1;AF=0.5;AN=2;DP=382;FractionInformativeReads=1;MQ=60;set=variant8-variant14-variant19-variant35-variant36-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,23:54:99:665,0,881:7,24,6,17 chr1 111969719 . A G 2643.83 PASS AC=1;AF=0.685;AN=2;DP=5455;MQ=60;set=variant3-variant4-variant6-variant8-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:121,98:219:99:2144,0,3028:59,62,48,50 chr1 111970431 . TACACACACACACACACACAC TACACACACACACACACACACAC,TACACACACACACACACAC,TACACACACACACACAC,TACACACACACACACACACACACACACACAC,TACACACACACAC,TACACACACACACAC,TACACACACACACACACACACACACACAC,TACACACACAC,TACACACACACACACACACACACACACACACACAC,TACACACACACACACACACACACAC,TACACACACACACACACACACACACACACACAC,TACACACACACACACACACACACACAC,T,TACACACAC 100.39 PASS AC=0,0,0,1,0,0,0,0,0,0,0,0,0,0;AF=0.132,0.118,0.103,0.059,0.015,0.029,0.044,0.015,0.029,0.074,0.015,0.015,0.044,0.015;AN=2;DP=2081;set=variant-variant5-variant6-variant7-variant8-variant9-filterInvariant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant32-filterInvariant33-filterInvariant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-filterInvariant44 GT:DP:GQ:SB 0/4:14:99:1,6,1,6 chr1 111983152 . A G 269.08 PASS AC=1;AF=0.5;AN=2;DP=220;FractionInformativeReads=1;MQ=60;set=variant8-variant14-variant19-variant22-variant35-variant36-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,15:34:99:349,0,479:7,12,6,9 chr1 111983611 . CTA C 1546.23 PASS AC=1;AF=0.5;AN=2;DP=124;MQ=60;set=variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:32,40:72:99:1584,0,1241:15,17,18,22 chr1 111985229 . G T 1496.34 PASS AC=1;AF=0.685;AN=2;DP=2803;MQ=60;set=variant3-variant4-variant6-variant8-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,62:99:99:1550,0,716:22,15,37,25 chr1 111991845 . C A 3165.86 PASS AC=1;AF=0.667;AN=2;DP=6060;MQ=60;set=variant3-variant4-variant6-variant8-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:117,112:229:99:2720,0,3148:50,67,52,60 chr1 111992095 . C T 2268.78 PASS AC=1;AF=0.635;AN=2;DP=3839;MQ=60;set=variant3-variant4-variant6-variant8-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant35-variant36-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:72,73:145:99:1639,0,1994:31,41,34,39 chr1 112004523 . GA G,GAA 77.98 PASS AC=1,0;AF=0.371,0.129;AN=2;DP=1256;set=filterInvariant-variant2-variant5-filterInvariant7-variant8-variant9-variant10-variant11-variant12-filterInvariant13-filterInvariant15-variant16-variant17-filterInvariant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-filterInvariant37-variant38-variant39-variant40-variant41-variant42-filterInvariant43-filterInvariant44 GT:DP:GQ:SB 0/1:38:99:19,6,11,2 chr1 112020222 . GC G 335.87 PASS AC=1;AF=0.885;AN=2;DP=498;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,8:19:99:299,0,430:1,10,7,1 chr1 112020224 . C A 344.88 PASS AC=1;AF=0.882;AN=2;DP=494;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,8:19:99:299,0,430:1,10,7,1 chr1 112020238 . A C 238.57 PASS AC=2;AF=0.977;AN=2;DP=612;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:969,69,0:0,0,13,10 chr1 112026152 . C T 967.42 PASS AC=1;AF=0.593;AN=2;DP=2321;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant35-variant36-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:36,38:74:99:1015,0,825:18,18,21,17 chr1 112026198 . T A 3009.88 PASS AC=1;AF=0.55;AN=2;DP=1912;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant10-variant12-variant18-variant19-variant20-variant24-variant28-variant30-variant31-variant32-variant35-variant36-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:39,42:81:99:1011,0,928:20,19,20,22 chr1 112028577 . A T 822.33 PASS AC=1;AF=0.662;AN=2;DP=1762;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,29:57:99:899,0,776:5,23,7,22 chr1 112029193 . A G 794.17 PASS AC=1;AF=0.821;AN=2;DP=2898;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,43:87:99:993,0,1038:23,21,24,19 chr1 112029325 . A G 1414.5 PASS AC=1;AF=0.821;AN=2;DP=4505;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,51:100:99:1434,0,1178:19,30,24,27 chr1 112032347 . G A 369.77 PASS AC=1;AF=0.713;AN=2;DP=2946;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,38:74:99:918,0,949:13,23,14,24 chr1 112033456 . G GA 683.01 PASS AC=1;AF=0.713;AN=2;DP=2711;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,36:73:99:1020,0,1034:15,22,14,22 chr1 112033515 . T C 491.2 PASS AC=1;AF=0.7;AN=2;DP=1241;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,23:38:99:884,0,814:2,13,8,15 chr1 112033519 . A G 491.2 PASS AC=1;AF=0.7;AN=2;DP=1149;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,20:34:99:862,0,817:2,12,7,13 chr1 112042131 . T C 411.89 PASS AC=1;AF=0.821;AN=2;DP=2154;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,22:58:99:478,0,843:22,14,11,11 chr1 112042149 . C T 495.79 PASS AC=1;AF=0.649;AN=2;DP=2110;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,21:58:99:464,0,910:21,16,11,10 chr1 112042195 . T C 537.16 PASS AC=1;AF=0.821;AN=2;DP=2812;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,27:71:99:624,0,1028:22,22,13,14 chr1 112042236 . G A 482.74 PASS AC=1;AF=0.821;AN=2;DP=2472;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,29:69:99:719,0,978:20,20,16,13 chr1 112042383 . G A 457.95 PASS AC=1;AF=0.821;AN=2;DP=1633;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,21:52:99:640,0,804:16,15,10,11 chr1 112042632 . A G 1593.61 PASS AC=1;AF=0.821;AN=2;DP=6084;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,51:119:99:1419,0,1687:33,35,24,27 chr1 112045463 . T A 121.41 PASS AC=1;AF=0.814;AN=2;DP=517;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,10:12:56:252,0,56:2,0,6,4 chr1 112106444 . G A 2653.75 PASS AC=2;AF=0.907;AN=2;DP=5624;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,151:151:99:4558,451,0:0,0,73,78 chr1 112237915 . A T 420.52 PASS AC=2;AF=0.734;AN=2;DP=372;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant17-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:456,36,0:0,0,10,2 chr1 112240038 . CTT CTTT,C,CT 381.84 PASS AC=1,0,0;AF=0.167,0.091,0.242;AN=2;DP=3646;MQ=60;set=variant2-variant3-variant4-variant5-variant6-filterInvariant7-variant8-filterInvariant9-filterInvariant10-filterInvariant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant24-variant25-variant26-filterInvariant27-variant28-variant29-filterInvariant30-variant34-variant35-variant38-variant39-variant40-variant41-variant43-variant44 GT:DP:GQ:SB 0/1:88:99:14,7,32,35 chr1 112251983 . C G 2432.25 PASS AC=2;AF=0.719;AN=2;DP=2411;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant17-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,116:116:99:3495,348,0:0,0,47,69 chr1 112257193 . T C 6550.89 PASS AC=2;AF=0.719;AN=2;DP=7034;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant17-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,236:236:99:7507,707,0:0,0,93,143 chr1 112257784 . C T 140.31 PASS AC=2;AF=0.733;AN=2;DP=370;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant17-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant35-variant36-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:181,18,0:0,0,2,4 chr1 112258252 . A G 7006.46 PASS AC=2;AF=0.706;AN=2;DP=9078;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant17-variant18-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,290:290:99:8871,868,0:0,0,128,162 chr1 112266055 . G GC 398.78 PASS AC=2;AF=0.93;AN=2;DP=1730;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:1779,144,0:0,0,27,21 chr1 112266300 . A G 1141.9 PASS AC=2;AF=0.764;AN=2;DP=2122;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:1735,164,0:0,0,26,29 chr1 112266366 . T C 1082.59 PASS AC=2;AF=0.764;AN=2;DP=1903;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1423,126,0:0,0,22,20 chr1 112267187 . GCACACACA GCACACACACA,GCACACA,GCACA,G 405.53 PASS AC=0,1,0,0;AF=0.045,0.364,0.136,0.045;AN=2;DP=839;set=variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant26-variant28-variant29-variant30-filterInvariant31-variant32-variant34-variant35-variant37-variant38-variant39-filterInvariant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:26:99:7,5,7,7 chr1 112267354 . C T 1092.85 PASS AC=2;AF=0.743;AN=2;DP=1376;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:966,87,0:0,0,11,18 chr1 112268047 . G C,GC 1716.56 PASS AC=2,0;AF=0.833,0.048;AN=2;DP=2402;MQ=60;set=variant3-variant5-variant2-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant4-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:74:99:0,0,34,40 chr1 112268284 . G A 2117.6 PASS AC=2;AF=0.736;AN=2;DP=2660;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,88:88:99:2505,263,0:0,0,39,49 chr1 112268425 . C G 256.97 PASS AC=2;AF=0.951;AN=2;DP=379;FS=0;FractionInformativeReads=1;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:394,33,0:0,0,2,9 chr1 112268666 . T C 260.51 PASS AC=2;AF=0.94;AN=2;DP=702;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:799,69,0:0,0,16,7 chr1 112269872 . G A 1208.62 PASS AC=2;AF=0.93;AN=2;DP=6615;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,168:168:99:5383,502,0:0,0,85,83 chr1 112281899 . G T 2557.08 PASS AC=1;AF=0.5;AN=2;DP=818;MQ=60;set=variant8-variant19-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:84,129:213:99:2920,0,1820:45,39,59,70 chr1 112298829 . T C 67.47 PASS AC=1;AF=0.596;AN=2;DP=564;MQ=60;set=variant-variant3-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant22-variant23-variant30-variant31-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,14:21:99:417,0,127:2,5,4,10 chr1 112298875 . G C 91.49 PASS AC=1;AF=0.5;AN=2;DP=27;FractionInformativeReads=1;MQ=60;set=variant19-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:1,8:9:16:164,0,16:0,1,4,4 chr1 112303077 . A AT 1034.07 PASS AC=1;AF=0.5;AN=2;DP=701;MQ=60;set=variant8-variant19-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:69,77:146:99:1553,0,1362:42,27,43,34 chr1 112303237 . T A 1709.8 PASS AC=1;AF=0.5;AN=2;DP=465;MQ=60;set=variant8-variant19-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:57,41:98:99:1034,0,1532:22,35,14,27 chr1 112303791 . A T 2438.75 PASS AC=1;AF=0.5;AN=2;DP=747;FractionInformativeReads=1;MQ=60;set=variant8-variant19-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:100,92:192:99:2371,0,2497:53,47,45,47 chr1 112304126 . G T 3581.75 PASS AC=2;AF=1;AN=2;DP=3586;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1901,168,0:0,0,18,38 chr1 112305406 . TA T 406.51 PASS AC=1;AF=0.5;AN=2;DP=5558;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-filterInvariant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-filterInvariant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-filterInvariant35-filterInvariant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:77,23:100:99:216,0,1393:38,39,14,9 chr1 112305437 . T TTTAAGGGGAGG 1315.89 PASS AC=1;AF=0.5;AN=2;DP=401;MQ=60;set=variant8-variant19-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:40,42:82:99:1681,0,1958:18,22,18,24 chr1 112308953 . T C 1492.65 PASS AC=1;AF=0.596;AN=2;DP=2587;MQ=60;set=variant-variant3-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant22-variant23-variant30-variant31-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,56:117:99:1397,0,1687:30,31,28,28 chr1 112308972 . G A 1438.6 PASS AC=1;AF=0.596;AN=2;DP=2685;MQ=60;set=variant-variant3-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant22-variant23-variant30-variant31-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,53:118:99:1344,0,1819:32,33,25,28 chr1 112309926 . A G 4846.8 PASS AC=1;AF=0.5;AN=2;DP=1388;MQ=60;set=variant8-variant19-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:154,168:322:99:4148,0,3709:82,72,87,81 chr1 112313430 . GT G 2960.16 PASS AC=1;AF=0.596;AN=2;DP=8114;MQ=60;set=variant-variant3-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant22-variant23-variant30-variant31-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:179,167:346:99:3577,0,3657:96,83,83,84 chr1 112315450 . A C 3835.19 PASS AC=1;AF=0.596;AN=2;DP=5496;MQ=60;set=variant-variant3-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant22-variant23-variant30-variant31-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:103,111:214:99:2743,0,2766:37,66,43,68 chr1 112316030 . CT CTT,C 2124.21 PASS AC=1,0;AF=0.567,0.033;AN=2;DP=4021;set=variant-variant8-variant12-variant15-variant16-variant17-variant18-variant19-variant23-variant31-variant35-variant37-variant39-variant40-variant42 GT:DP:GQ:SB 0/1:194:99:24,52,39,79 chr1 112316047 . C CT,CTT 1770.97 PASS AC=1,0;AF=0.674,0.07;AN=2;DP=8133;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:112:99:5,39,21,47 chr1 112317512 . C A 818.86 PASS AC=1;AF=0.596;AN=2;DP=2083;MQ=60;set=variant-variant3-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant22-variant23-variant30-variant31-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,40:86:99:825,0,1144:23,23,22,18 chr1 112524680 . C G 3781.33 PASS AC=1;AF=0.5;AN=2;DP=599;FractionInformativeReads=1;MQ=60;set=variant7-variant35 GT:AD:DP:GQ:PL:SB 0/1:184,138:322:99:3509,0,4870:105,79,79,59 chr1 112938917 . C T 541.71 PASS AC=1;AF=0.583;AN=2;DP=570;MQ=60;set=variant-variant3-variant5-variant6-variant13-variant15-variant21-variant22-variant24-variant25-variant28-variant32-variant35-variant36-variant37-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,18:38:99:377,0,488:12,8,10,8 chr1 112954766 . G C 3396.6 PASS AC=1;AF=0.805;AN=2;DP=4388;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,56:100:99:1531,0,1200:28,16,38,18 chr1 112954964 . G A 2074.52 PASS AC=1;AF=0.805;AN=2;DP=3231;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,39:76:99:1031,0,1047:10,27,14,25 chr1 112954994 . A G 1009.99 PASS AC=1;AF=0.92;AN=2;DP=2140;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:25,22:47:99:565,0,837:4,21,7,15 chr1 112991698 . T C 2594.14 PASS AC=1;AF=0.805;AN=2;DP=3277;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,58:107:99:1367,0,1071:25,24,29,29 chr1 112992009 . TAAGACAGCA TA,T 85.92 PASS AC=0,1;AF=0.25,0.25;AN=2;DP=34;MQ=60;set=variant18-variant30-variant35-variant39 GT:DP:GQ:SB 0/2:6:73:0,4,0,2 chr1 112992022 . C T 94.73 PASS AC=1;AF=0.5;AN=2;DP=24;FS=0;FractionInformativeReads=1;MQ=60;set=variant18-variant30-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:3,1:4:75:75,0,521:0,3,0,1 chr1 112999227 . G A 809.01 PASS AC=1;AF=0.92;AN=2;DP=5547;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:56,60:116:99:1479,0,1536:28,28,31,29 chr1 113000946 . GGTCA G 4509.33 PASS AC=1;AF=0.909;AN=2;DP=8715;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:95,89:184:99:3404,0,5320:50,45,46,43 chr1 113002127 . TA T 8573.62 PASS AC=1;AF=0.793;AN=2;DP=10379;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:97,129:226:99:3902,0,2762:47,50,66,63 chr1 113063125 . A G 1598.49 PASS AC=2;AF=0.655;AN=2;DP=3899;MQ=60;set=variant-variant3-variant6-variant8-variant9-variant10-variant14-variant15-variant17-variant18-variant21-variant22-variant25-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,152:152:99:4666,455,0:0,0,70,82 chr1 113063933 . CTTTT CT,CTTTTT,CTTT,CTT,CTTTTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTT,C 1535.24 PASS AC=1,0,0,0,0,0,0,1;AF=0.269,0.013,0.218,0.064,0.013,0.013,0.013,0.026;AN=2;DP=5982;set=variant-filterInvariant2-variant5-variant6-filterInvariant7-variant8-variant10-filterInvariant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-filterInvariant20-variant21-variant22-filterInvariant23-variant24-variant25-filterInvariant26-variant27-variant28-variant30-variant31-variant32-filterInvariant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:DP:GQ:SB 8/1:141:99:15,3,33,90 chr1 113064468 . G A 2205.12 PASS AC=2;AF=0.579;AN=2;DP=2962;MQ=60;set=variant-variant6-variant10-variant14-variant15-variant17-variant18-variant21-variant22-variant25-variant30-variant34-variant35-variant36-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,182:182:99:5783,545,0:0,0,115,67 chr1 113067792 . A G 483.85 PASS AC=2;AF=0.575;AN=2;DP=1064;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant10-variant14-variant15-variant17-variant18-variant21-variant22-variant25-variant30-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:1671,162,0:0,0,28,26 chr1 113083439 . C T 910.48 PASS AC=2;AF=0.641;AN=2;DP=2119;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant6-variant8-variant9-variant10-variant13-variant14-variant15-variant17-variant18-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,61:61:99:1831,183,0:0,0,38,23 chr1 113098534 . C T 2075.27 PASS AC=2;AF=0.579;AN=2;DP=2291;MQ=60;set=variant-variant6-variant10-variant14-variant15-variant17-variant18-variant21-variant22-variant25-variant30-variant34-variant35-variant36-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,117:117:99:3524,350,0:0,0,59,58 chr1 113113167 . GTATATATATATATA G 396.96 PASS AC=2;AF=0.972;AN=2;DP=171;FS=0;MQ=60;MQRankSum=0.898;ReadPosRankSum=1.271;set=variant-variant6-variant10-variant14-variant15-variant17-variant18-variant21-variant22-variant25-variant34-variant35-variant36-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:888,60,0:0,0,14,6 chr1 113212984 . CTTTTTTTT CTTTTTTTTTTTT,CTTTTTTTTTT,C,CTTTTTTTTTTT,CTTTTTTT,CTTTTTTTTT,CTTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTT 1051.6 PASS AC=0,0,0,0,1,0,0,0,0,0;AF=0.039,0.197,0.013,0.118,0.105,0.066,0.026,0.013,0.013,0.013;AN=2;DP=8834;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-filterInvariant30-variant31-variant32-variant33-variant34-variant35-filterInvariant36-variant37-variant38-filterInvariant39-variant40-variant41-filterInvariant43-variant44 GT:DP:GQ:SB 0/5:168:99:27,59,19,63 chr1 113239478 . T C 661.87 PASS AC=1;AF=0.768;AN=2;DP=3491;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,44:89:99:1028,0,1088:16,29,23,21 chr1 113242488 . C T 1449.51 PASS AC=1;AF=0.725;AN=2;DP=6827;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:102,74:176:99:1694,0,2810:41,61,35,39 chr1 113244433 . T C 288.36 PASS AC=1;AF=0.884;AN=2;DP=1599;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,20:43:99:554,0,549:6,17,6,14 chr1 113245535 . T C 43.43 PASS AC=1;AF=0.5;AN=2;DP=307;MQ=60;set=filterInvariant4-variant5-variant21-variant22-variant23-variant29-filterInvariant31-variant32-filterInvariant35 GT:AD:DP:GQ:PL:SB 0/1:27,16:43:99:308,0,1062:3,24,16,0 chr1 113246229 . T A 611.05 PASS AC=1;AF=0.686;AN=2;DP=1721;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,25:47:99:795,0,694:20,2,22,3 chr1 113247713 . G A 870.96 PASS AC=1;AF=0.545;AN=2;DP=1010;MQ=60;set=variant-variant10-variant21-variant22-variant30-variant34-variant35-variant36-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,40:88:99:1010,0,1240:23,25,20,20 chr1 113248365 . A G 1217.7 PASS AC=1;AF=0.716;AN=2;DP=3506;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,57:109:99:1777,0,1622:16,36,24,33 chr1 113248791 . C A 749.63 PASS AC=1;AF=0.56;AN=2;DP=1761;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant8-variant9-variant10-variant12-variant13-variant17-variant21-variant22-variant24-variant26-variant28-variant30-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,37:88:99:928,0,1267:22,29,17,20 chr1 113249486 . C G 505.28 PASS AC=1;AF=0.56;AN=2;DP=1439;MQ=60;set=variant-variant2-variant3-variant8-variant9-variant10-variant12-variant13-variant17-variant21-variant22-variant24-variant26-variant28-variant30-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,34:72:99:790,0,967:19,19,17,17 chr1 113249504 . C T 459.88 PASS AC=1;AF=0.56;AN=2;DP=1421;MQ=60;set=variant-variant2-variant3-variant8-variant9-variant10-variant12-variant13-variant17-variant21-variant22-variant24-variant26-variant28-variant30-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,32:74:99:796,0,1068:21,21,16,16 chr1 113249524 . G C 519.77 PASS AC=1;AF=0.56;AN=2;DP=1443;MQ=60;set=variant-variant2-variant3-variant8-variant9-variant10-variant12-variant13-variant17-variant21-variant22-variant24-variant26-variant28-variant30-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,34:76:99:805,0,1122:19,23,17,17 chr1 113252614 . C A 929.41 PASS AC=1;AF=0.652;AN=2;DP=2630;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant29-variant31-variant33-variant35-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,35:89:99:923,0,1370:33,21,21,14 chr1 113254267 . G C 818.78 PASS AC=2;AF=0.869;AN=2;DP=1178;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1159,105,0:0,0,11,24 chr1 113254484 . A G 230.3 PASS AC=2;AF=1;AN=2;DP=615;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:807,72,0:0,0,16,8 chr1 113255389 . C T 215.28 PASS AC=2;AF=0.989;AN=2;DP=872;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:718,60,0:0,0,15,5 chr1 113454424 . T C 735.91 PASS AC=2;AF=0.625;AN=2;DP=781;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant11-variant15-variant17-variant18-variant20-variant23-variant24-variant29-variant31-variant32-variant35-variant36-variant38-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1788,135,0:0,0,40,5 chr1 113454571 . A G 2571.54 PASS AC=2;AF=0.63;AN=2;DP=5059;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant10-variant11-variant15-variant17-variant18-variant20-variant23-variant24-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,242:242:99:7239,725,0:0,0,121,121 chr1 113455099 . G A 4658.17 PASS AC=2;AF=0.684;AN=2;DP=10481;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:3,273:276:99:8067,765,0:2,1,127,146 chr1 113456546 . A T 2615.55 PASS AC=2;AF=0.684;AN=2;DP=5626;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,151:151:99:5149,452,0:0,0,69,82 chr1 113471629 . C CT 216.78 PASS AC=2;AF=0.563;AN=2;DP=1320;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant10-variant11-variant15-filterInvariant16-variant17-variant18-variant20-variant23-variant24-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant43 GT:AD:DP:GQ:PL:SB 1/1:5,48:53:31:1040,31,0:3,2,29,19 chr1 113498283 . A C 1339.42 PASS AC=2;AF=0.619;AN=2;DP=1732;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant11-variant15-variant17-variant18-variant20-variant23-variant24-variant29-variant30-variant31-variant32-variant35-variant36-variant38-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,99:99:99:4408,298,0:0,0,48,51 chr1 113498284 . G A 1339.42 PASS AC=2;AF=0.619;AN=2;DP=1717;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant11-variant15-variant17-variant18-variant20-variant23-variant24-variant29-variant30-variant31-variant32-variant35-variant36-variant38-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,98:98:99:4408,298,0:0,0,47,51 chr1 113616382 . G GA 459.36 PASS AC=1;AF=0.676;AN=2;DP=1093;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,15:22:99:466,0,184:1,6,4,11 chr1 113636924 . T C 525.76 PASS AC=2;AF=0.943;AN=2;DP=691;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:524,36,0:0,0,12,0 chr1 113657092 . A C 3055.09 PASS AC=2;AF=0.955;AN=2;DP=5575;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,111:111:99:3511,333,0:0,0,65,46 chr1 113658887 . G A 3585.29 PASS AC=2;AF=0.826;AN=2;DP=4665;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,118:118:99:3576,354,0:0,0,65,53 chr1 113659065 . ACT A 5088.47 PASS AC=2;AF=0.826;AN=2;DP=5943;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,115:115:99:5156,346,0:0,0,48,67 chr1 113662249 . G C 160.11 PASS AC=1;AF=0.593;AN=2;DP=535;MQ=60;set=variant2-variant4-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant21-variant22-variant24-variant27-variant28-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,7:16:99:264,0,300:1,8,1,6 chr1 113666345 . G GTT 122.45 PASS AC=1;AF=0.5;AN=2;DP=43;FS=0;MQ=60;set=variant3-variant16-variant35 GT:AD:DP:GQ:PL:SB 0/1:7,4:11:94:94,0,194:7,0,4,0 chr1 113666351 . G T 96.49 PASS AC=2;AF=0.725;AN=2;DP=529;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:447,33,0:0,0,11,0 chr1 113666353 . G T 96.49 PASS AC=1;AF=0.617;AN=2;DP=422;set=variant-variant2-variant3-variant4-variant6-variant7-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant21-variant24-variant25-variant27-variant28-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,7:11:94:194,0,94:4,0,7,0 chr1 113933278 . C A 1159.83 PASS AC=2;AF=1;AN=2;DP=1345;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,22:22:65:839,65,0:0,0,19,3 chr1 114137013 . C CAT 496.09 PASS AC=2;AF=0.85;AN=2;DP=433;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:29:378,29,0:0,0,8,1 chr1 114161116 . C A 236.23 PASS AC=2;AF=0.826;AN=2;DP=1135;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:494,57,0:0,0,9,10 chr1 114196364 . T G 337.67 PASS AC=2;AF=0.538;AN=2;DP=1811;MQ=60;set=variant-variant2-variant3-variant6-variant8-variant9-variant11-variant13-variant14-variant15-variant17-variant21-variant23-variant24-variant25-variant28-variant29-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,85:85:99:2690,255,0:0,0,44,41 chr1 114196495 . A G 788.41 PASS AC=2;AF=0.538;AN=2;DP=3416;MQ=60;set=variant-variant2-variant3-variant6-variant8-variant9-variant11-variant13-variant14-variant15-variant17-variant21-variant23-variant24-variant25-variant28-variant29-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,149:149:99:4587,447,0:0,0,78,71 chr1 114224782 . AT ATT,ATTT,A 498.3 PASS AC=1,0,0;AF=0.476,0.085,0.012;AN=2;DP=2718;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:80:99:26,13,22,19 chr1 114240319 . T TA 2043.5 PASS AC=2;AF=0.826;AN=2;DP=5313;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,141:141:99:5246,427,0:0,0,56,85 chr1 114242122 . T C 169.61 PASS AC=2;AF=0.611;AN=2;DP=683;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant21-variant23-variant24-variant27-variant28-variant29-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:765,66,0:0,0,13,9 chr1 114242250 . C T 979.16 PASS AC=1;AF=0.523;AN=2;DP=1977;MQ=60;set=variant-variant3-variant6-variant8-variant9-variant11-variant13-variant14-variant15-variant17-variant21-variant23-variant24-variant28-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,45:99:99:990,0,1248:29,25,24,21 chr1 114243198 . T C 150.2 PASS AC=1;AF=0.5;AN=2;DP=42;FractionInformativeReads=1;MQ=60;set=variant11-variant13-variant14-variant35 GT:AD:DP:GQ:PL:SB 0/1:3,8:11:99:216,0,100:3,0,6,2 chr1 114246453 . C T 223.27 PASS AC=2;AF=0.826;AN=2;DP=740;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:476,39,0:0,0,11,2 chr1 114247446 . G A 245.09 PASS AC=1;AF=0.5;AN=2;DP=169;FractionInformativeReads=1;MQ=60;set=variant8-variant17-variant29-variant32-variant33-variant35-variant37-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:6,6:12:99:142,0,197:1,5,1,5 chr1 114249382 . C T 878.68 PASS AC=2;AF=0.826;AN=2;DP=2457;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1665,149,0:0,0,14,36 chr1 114267347 . C T 867.58 PASS AC=2;AF=0.837;AN=2;DP=2741;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:1882,186,0:0,0,40,22 chr1 114280717 . A C 163.58 PASS AC=2;AF=0.744;AN=2;DP=1651;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1143,105,0:0,0,25,10 chr1 114302047 . AGGC A 108.54 PASS AC=2;AF=1;AN=2;DP=624;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:636,45,0:0,0,6,9 chr1 114307237 . AT A,ATT 139.17 PASS AC=1,0;AF=0.256,0.244;AN=2;DP=5971;set=filterInvariant-filterInvariant2-variant3-variant4-variant5-filterInvariant6-variant7-filterInvariant8-variant9-variant10-filterInvariant11-variant12-variant13-filterInvariant14-variant15-variant16-filterInvariant17-filterInvariant18-variant19-filterInvariant20-filterInvariant21-variant22-variant24-variant25-variant26-filterInvariant27-variant28-variant30-variant31-variant32-filterInvariant33-variant34-filterInvariant35-filterInvariant36-filterInvariant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:125:99:68,37,13,7 chr1 114309172 . C T 539.83 PASS AC=2;AF=0.8;AN=2;DP=494;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:542,42,0:0,0,1,13 chr1 114339956 . C CTAAA 436.29 PASS AC=2;AF=0.837;AN=2;DP=1273;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:57:814,57,0:0,0,13,3 chr1 114357211 . G A 2103.48 PASS AC=2;AF=0.845;AN=2;DP=4414;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,98:98:99:3422,293,0:0,0,57,41 chr1 114357750 . G A 52.74 PASS AC=2;AF=0.924;AN=2;DP=153;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:225,15,0:0,0,0,5 chr1 114372332 . TA T 608.67 PASS AC=2;AF=0.703;AN=2;DP=1772;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-filterInvariant18-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:991,110,0:0,0,13,24 chr1 114377093 . A G 1549.49 PASS AC=2;AF=0.845;AN=2;DP=2542;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1626,159,0:0,0,18,35 chr1 114377568 . A G 3643.61 PASS AC=2;AF=0.92;AN=2;DP=4977;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,107:107:99:2856,320,0:0,0,49,58 chr1 114400195 . G GA 35.14 PASS AC=2;AF=0.741;AN=2;DP=211;MQ=60;set=variant-variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant21-variant23-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:195,21,0:0,0,6,1 chr1 114401231 . A G 411.31 PASS AC=2;AF=0.703;AN=2;DP=821;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:810,81,0:0,0,11,16 chr1 114401904 . T G 580.95 PASS AC=2;AF=0.703;AN=2;DP=842;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1300,105,0:0,0,25,10 chr1 114424601 . C T 1333.39 PASS AC=2;AF=1;AN=2;DP=2508;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.643;ReadPosRankSum=1.244;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:1858,180,0:0,0,28,32 chr1 114472218 . A G 337.51 PASS AC=1;AF=0.72;AN=2;DP=1555;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,19:37:99:613,0,510:3,15,5,14 chr1 114512939 . A T 1923.76 PASS AC=1;AF=0.72;AN=2;DP=1972;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,20:49:99:423,0,861:6,23,6,14 chr1 114515717 . G A 4114.76 PASS AC=1;AF=0.613;AN=2;DP=5905;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant32-variant35-variant36-variant37-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:131,104:235:99:2463,0,3281:71,60,57,47 chr1 114519351 . T G 1351.74 PASS AC=1;AF=0.625;AN=2;DP=1338;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant35-variant36-variant37-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:16,27:43:99:687,0,392:8,8,14,13 chr1 114519857 . AT A 87.68 DRAGENHardINDEL AC=1;AF=0.5;AN=2;DP=163;FS=0.857;FractionInformativeReads=0.914;MQ=60;MQRankSum=-0.565;QD=0.54;ReadPosRankSum=1.7;SOR=0.823;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:126,23:149:99:125,0,2678:72,54,14,9 chr1 114524980 . TG T 34.17 PASS AC=1;AF=0.833;AN=2;DP=175;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant10-variant12-variant14-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:99:119,0,118:1,3,0,4 chr1 114632071 . G A 205.61 PASS AC=1;AF=0.525;AN=2;DP=413;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant11-variant12-variant14-variant15-variant17-variant19-variant20-variant23-variant25-variant30-variant31-variant35-variant36-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,16:25:99:398,0,249:6,3,8,8 chr1 114632155 . T G 216.08 PASS AC=1;AF=0.5;AN=2;DP=28;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.558;QD=7.72;ReadPosRankSum=-0.168;SOR=0.693;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:18,10:28:99:244,0,503:9,9,5,5 chr1 114633310 . C T 2455.97 PASS AC=1;AF=0.524;AN=2;DP=3159;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant6-variant11-variant12-variant14-variant15-variant17-variant19-variant20-variant25-variant30-variant31-variant33-variant35-variant36-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,71:138:99:1920,0,1802:34,33,29,42 chr1 114634367 . C CT 3534.96 PASS AC=2;AF=0.864;AN=2;DP=7284;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:13,159:172:99:4000,237,0:7,6,90,69 chr1 114641685 . A G 2527.95 PASS AC=1;AF=0.75;AN=2;DP=3357;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,47:83:99:1160,0,763:22,14,29,18 chr1 114680310 . G A 1892.1 PASS AC=1;AF=0.563;AN=2;DP=2860;MQ=60;set=variant4-variant7-variant8-variant9-variant11-variant13-variant16-variant25-variant26-variant29-variant33-variant35-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:108,89:197:99:2344,0,2755:58,50,48,41 chr1 114682001 . A C 317.41 PASS AC=1;AF=0.643;AN=2;DP=297;FractionInformativeReads=1;MQ=60;set=variant4-variant7-variant8-variant9-variant11-variant13-variant25-variant26-variant29-variant33-variant35-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,10:23:99:309,0,323:9,4,5,5 chr1 114682632 . G T 145.33 PASS AC=1;AF=0.533;AN=2;DP=1124;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant13-variant16-variant18-variant29-variant30-variant32-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:52,34:86:99:792,0,1246:22,30,14,20 chr1 114682780 . G C 201.22 PASS AC=2;AF=0.872;AN=2;DP=493;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:400,36,0:0,0,3,9 chr1 114936079 . T A 1892.71 PASS AC=1;AF=0.528;AN=2;DP=2226;set=variant3-variant8-variant12-variant13-variant14-variant16-variant18-variant20-variant21-variant23-variant26-variant28-variant30-variant31-variant32-variant35-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:52,70:122:99:1730,0,1400:24,28,35,35 chr1 114938090 . A AT 2931.84 PASS AC=1;AF=0.565;AN=2;DP=4049;MQ=60;set=variant3-variant4-variant7-variant8-variant12-variant13-variant14-variant16-variant18-variant20-variant21-variant23-variant26-variant27-variant28-variant30-variant31-variant32-variant35-variant36-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:106,62:168:99:1354,0,2705:62,44,37,25 chr1 114938289 . T G 2707.57 PASS AC=1;AF=0.528;AN=2;DP=2276;MQ=60;set=variant3-variant8-variant12-variant13-variant14-variant16-variant18-variant20-variant21-variant23-variant26-variant28-variant30-variant31-variant32-variant35-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:60,80:140:99:2321,0,1693:22,38,26,54 chr1 114939633 . G A 4416.48 PASS AC=1;AF=0.5;AN=2;DP=881;FractionInformativeReads=1;MQ=60;set=variant15-variant20-variant35 GT:AD:DP:GQ:PL:SB 0/1:128,114:242:99:3056,0,3491:59,69,55,59 chr1 114940215 . T TG 471.3 PASS AC=1;AF=0.528;AN=2;DP=1020;set=variant3-variant8-variant12-variant13-variant14-variant16-variant18-variant20-variant21-variant23-variant26-variant28-variant30-variant31-variant32-variant35-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:35,29:64:99:709,0,1074:7,28,10,19 chr1 114940632 . CAA CA,C 893.9 PASS AC=1,0;AF=0.767,0.023;AN=2;DP=2348;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:49:99:5,17,9,18 chr1 114948281 . A G 5382.8 PASS AC=2;AF=0.886;AN=2;DP=8416;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,217:217:99:6861,651,0:0,0,94,123 chr1 114951390 . T A 1039.44 PASS AC=1;AF=0.526;AN=2;DP=995;MQ=60;set=variant3-variant7-variant8-variant12-variant13-variant14-variant16-variant18-variant20-variant21-variant23-variant26-variant28-variant30-variant31-variant32-variant35-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:38,22:60:99:466,0,836:20,18,13,9 chr1 114969925 . GA G 1342.13 PASS AC=1;AF=0.526;AN=2;DP=1708;MQ=60;set=variant3-variant7-variant8-variant12-variant13-variant14-variant16-variant18-variant20-variant21-variant23-variant26-variant28-variant30-variant31-variant32-variant35-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:54,37:91:99:879,0,1403:21,33,18,19 chr1 114973429 . T C 1872.89 PASS AC=1;AF=0.58;AN=2;DP=2840;MQ=60;set=variant3-variant4-variant7-variant8-variant10-variant12-variant13-variant14-variant16-variant18-variant20-variant21-variant23-variant26-variant27-variant28-variant30-variant31-variant32-variant35-variant36-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:75,59:134:99:1335,0,1650:36,39,31,28 chr1 115006230 . TAA TA,T 231.02 PASS AC=1,0;AF=0.545,0.023;AN=2;DP=532;MQ=60;set=variant3-variant4-variant7-variant8-variant10-variant12-variant13-variant14-variant16-variant20-variant21-variant23-variant26-variant27-variant28-variant31-variant35-variant36-variant37-variant39-variant41-variant42 GT:DP:GQ:SB 0/1:10:50:1,3,0,6 chr1 115112597 . A T 368.79 PASS AC=1;AF=0.5;AN=2;DP=181;FractionInformativeReads=1;MQ=60;set=variant16-variant18-variant20-variant30-variant31-variant32-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:12,15:27:99:394,0,306:8,4,10,5 chr1 115125970 . T TA 4029.34 PASS AC=1;AF=0.5;AN=2;DP=2504;MQ=60;set=variant16-variant18-variant20-variant30-variant31-variant32-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:165,138:303:99:4258,0,5231:84,81,63,75 chr1 115126114 . AAC A,AACAC,AACACAC,AACACACAC 60.97 PASS AC=0,1,0,0;AF=0.257,0.203,0.027,0.014;AN=2;DP=4053;set=filterInvariant-filterInvariant3-variant4-filterInvariant5-variant7-variant8-filterInvariant9-variant10-variant11-variant12-filterInvariant15-variant16-filterInvariant17-variant18-variant20-filterInvariant21-filterInvariant22-filterInvariant23-variant24-filterInvariant25-variant27-filterInvariant28-variant30-variant31-variant32-variant33-variant34-variant35-filterInvariant36-variant37-filterInvariant38-variant39-filterInvariant40-filterInvariant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:85:99:9,37,14,25 chr1 115126428 . CA C,CAA,CAAA 68.09 PASS AC=1,0,0;AF=0.379,0.106,0.03;AN=2;DP=1102;set=variant-variant3-variant4-variant5-variant8-variant9-variant10-variant12-variant13-variant14-filterInvariant15-variant16-variant17-variant18-variant20-variant21-filterInvariant22-variant23-variant24-variant25-variant26-variant27-filterInvariant29-variant31-filterInvariant32-variant33-variant34-variant35-variant36-variant38-variant41-variant42-variant43 GT:DP:GQ:SB 0/1:30:99:14,6,9,1 chr1 115126456 . A AAC 623.66 PASS AC=2;AF=0.652;AN=2;DP=2363;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,59:61:99:2113,120,0:1,1,38,21 chr1 115128087 . A G 3480.88 PASS AC=2;AF=0.884;AN=2;DP=4542;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,108:108:99:3319,324,0:0,0,49,59 chr1 115144703 . A G 4419.43 PASS AC=2;AF=0.989;AN=2;DP=5457;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,104:104:99:3198,311,0:0,0,56,48 chr1 115165472 . T A 219.8 PASS AC=2;AF=0.893;AN=2;DP=467;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:402,27,0:0,0,9,0 chr1 115168097 . T C 2232.96 PASS AC=1;AF=0.565;AN=2;DP=2862;MQ=60;set=variant3-variant4-variant5-variant6-variant9-variant11-variant15-variant16-variant19-variant20-variant22-variant24-variant25-variant26-variant28-variant31-variant32-variant33-variant35-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,82:139:99:2236,0,1326:25,32,38,44 chr1 115197384 . TA T 989.34 PASS AC=1;AF=0.5;AN=2;DP=7951;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-filterInvariant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:76,79:155:99:1053,0,1039:29,47,23,56 chr1 115212572 . A G 1891.32 PASS AC=1;AF=0.5;AN=2;DP=1367;FractionInformativeReads=1;MQ=60;set=variant16-variant18-variant20-variant30-variant31-variant32-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:77,104:181:99:2510,0,1735:37,40,54,50 chr1 115219836 . C G 609.36 PASS AC=1;AF=0.5;AN=2;DP=346;FractionInformativeReads=1;MQ=60;set=variant16-variant18-variant20-variant30-variant31-variant32-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:21,17:38:99:724,0,1469:18,3,15,2 chr1 115219844 . G A 591.08 PASS AC=1;AF=0.5;AN=2;DP=397;FractionInformativeReads=1;MQ=60;set=variant16-variant18-variant20-variant30-variant31-variant32-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:27,22:49:99:774,0,1550:19,8,18,4 chr1 115222434 . G A 202.45 PASS AC=2;AF=0.91;AN=2;DP=396;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:344,24,0:0,0,0,8 chr1 115223156 . A T 545.34 PASS AC=1;AF=0.5;AN=2;DP=410;MQ=60;set=variant16-variant18-variant20-variant30-variant31-variant32-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:30,21:51:99:583,0,834:8,22,5,16 chr1 115238016 . CAA CA,CAAA,C 708.48 PASS AC=2,0,0;AF=0.636,0.057,0.045;AN=2;DP=2106;set=Intersection GT:DP:GQ:SB 1/1:49:22:3,2,33,11 chr1 115238239 . T C 1702.23 PASS AC=1;AF=0.5;AN=2;DP=133;FS=0.647;FractionInformativeReads=1;MQ=60;MQRankSum=-0.542;QD=12.8;ReadPosRankSum=0.52;SOR=0.782;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:66,67:133:99:1730,0,1697:29,37,28,39 chr1 115248756 . C T 2206.21 PASS AC=1;AF=0.5;AN=2;DP=200;FS=3.991;FractionInformativeReads=1;MQ=60;MQRankSum=-1.825;QD=11.03;ReadPosRankSum=-1.113;SOR=0.815;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:106,94:200:99:2234,0,2651:55,51,43,51 chr1 115249843 . G A 3468.11 PASS AC=1;AF=0.5;AN=2;DP=3478;MQ=60;set=variant-variant2-variant4-variant5-variant11-variant12-variant13-variant17-variant23-variant24-variant25-variant27-variant29-variant31-variant35-variant36-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:89,89:178:99:2532,0,2438:42,47,40,49 chr1 115256669 . G A 566.72 PASS AC=2;AF=0.762;AN=2;DP=1518;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1524,137,0:0,0,13,33 chr1 115260019 . AT A 4225.27 PASS AC=1;AF=0.5;AN=2;DP=691;MQ=60;set=variant29-variant35 GT:AD:DP:GQ:PL:SB 0/1:161,182:343:99:4523,0,3856:90,71,91,91 chr1 115276978 . GA G,GAA 287.9 PASS AC=1,0;AF=0.474,0.026;AN=2;DP=455;MQ=60;set=variant-variant2-variant4-variant5-variant11-variant12-variant13-variant17-variant23-variant24-variant25-variant27-variant29-variant31-variant35-variant36-variant39-variant41-variant44 GT:DP:GQ:SB 0/1:14:92:3,2,6,3 chr1 115280605 . A C 4136.12 PASS AC=1;AF=0.5;AN=2;DP=707;set=variant29-variant35 GT:AD:DP:GQ:PL:SB 0/1:199,168:367:99:3984,0,4727:112,87,102,66 chr1 115284056 . G T 812.15 PASS AC=1;AF=0.525;AN=2;DP=1369;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant10-variant11-variant12-variant13-variant17-variant23-variant24-variant25-variant27-variant29-variant31-variant35-variant36-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:25,32:57:99:868,0,568:15,10,22,10 chr1 115300685 . C T 178.37 PASS AC=1;AF=0.5;AN=2;DP=610;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant11-variant12-variant13-variant17-variant23-variant24-variant25-variant27-variant29-variant31-variant35-variant36-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:22,12:34:99:332,0,670:9,13,4,8 chr1 115313028 . T TA 1863.86 PASS AC=1;AF=0.521;AN=2;DP=2562;MQ=60;set=variant-variant2-variant4-variant5-variant11-variant12-variant13-variant16-variant17-variant18-variant20-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant35-variant36-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:51,47:98:99:1137,0,1271:32,19,31,16 chr1 115397950 . CT C 40.38 PASS AC=1;AF=0.611;AN=2;DP=466;MQ=60;set=variant-variant3-variant4-variant5-variant11-variant12-variant13-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant27-variant29-variant30-variant31-variant32-variant35-variant36-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,8:20:99:180,0,289:7,5,5,3 chr1 115398044 . GC G 1490.87 PASS AC=2;AF=1;AN=2;DP=2147;FS=0;MQ=60;MQRankSum=0;ReadPosRankSum=1.26;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1580,153,0:0,0,34,17 chr1 115399940 . T G 604.97 PASS AC=1;AF=0.577;AN=2;DP=1246;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant11-variant12-variant13-variant14-variant17-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant31-variant34-variant35-variant36-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,16:47:99:313,0,712:14,17,8,8 chr1 115401136 . G A 900.98 PASS AC=2;AF=1;AN=2;DP=1671;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.612;ReadPosRankSum=1.325;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1425,138,0:0,0,30,16 chr1 115417175 . A G 742.72 PASS AC=1;AF=0.5;AN=2;DP=145;FractionInformativeReads=1;MQ=60;set=variant20-variant35 GT:AD:DP:GQ:PL:SB 0/1:45,32:77:99:711,0,1117:19,26,16,16 chr1 115420905 . T C 446.73 PASS AC=1;AF=0.577;AN=2;DP=1119;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant11-variant12-variant13-variant14-variant17-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant31-variant34-variant35-variant36-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,17:60:99:288,0,1218:18,25,9,8 chr1 115437986 . G A 293.09 PASS AC=1;AF=0.5;AN=2;DP=696;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant11-variant12-variant13-variant17-variant23-variant25-variant29-variant31-variant35-variant36-variant39 GT:AD:DP:GQ:PL:SB 0/1:23,21:44:99:500,0,496:12,11,12,9 chr1 115452848 . G A 197.63 PASS AC=1;AF=0.5;AN=2;DP=208;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant7-variant8-variant11-variant12-variant13-variant16-variant20-variant22-variant23-variant25-variant26-variant28-variant32-variant33-variant35-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,2:6:69:69,0,156:4,0,2,0 chr1 115524216 . C T 84.86 PASS AC=1;AF=0.597;AN=2;DP=306;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant8-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,5:7:70:201,0,70:0,2,0,5 chr1 115537933 . A G 1864.48 PASS AC=1;AF=0.635;AN=2;DP=6179;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,86:150:99:2158,0,1742:27,37,41,45 chr1 115576023 . A G 6104.4 PASS AC=2;AF=0.966;AN=2;DP=7743;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,176:176:99:5003,525,0:0,0,95,81 chr1 115590794 . GTA GTATA,G 566.89 PASS AC=1,0;AF=0.52,0.02;AN=2;DP=1418;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant11-variant12-variant13-variant17-variant19-variant20-variant22-variant23-variant25-variant26-variant28-filterInvariant29-variant32-variant33-variant35-variant37-variant38-variant41-variant43 GT:DP:GQ:SB 0/1:32:99:4,10,6,12 chr1 115590920 . C CTATT 494.16 PASS AC=2;AF=0.975;AN=2;DP=298;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:270,18,0:0,0,3,3 chr1 115590998 . T C 610.02 PASS AC=1;AF=0.649;AN=2;DP=2228;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,26:51:99:686,0,563:15,10,16,10 chr1 115591053 . T G 1001.17 PASS AC=1;AF=0.5;AN=2;DP=1717;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant23-variant24-variant25-variant29-variant30-variant31-variant35-variant36-variant37-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:29,35:64:99:802,0,1144:16,13,21,14 chr1 115591058 . T C 812.86 PASS AC=1;AF=0.542;AN=2;DP=1796;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant11-variant12-variant13-variant17-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant32-variant33-variant35-variant37-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:38,30:68:99:641,0,1411:22,16,16,14 chr1 115591163 . A G 1141.97 PASS AC=1;AF=0.578;AN=2;DP=2755;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:33,39:72:99:1057,0,946:17,16,25,14 chr1 115592610 . GAC G 8388.47 PASS AC=1;AF=0.583;AN=2;DP=10313;MQ=60;set=variant-variant2-variant3-variant4-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant23-variant24-variant25-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:225,192:417:99:7264,0,8604:111,114,99,93 chr1 115592820 . T C 2964.15 PASS AC=1;AF=0.542;AN=2;DP=5246;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant11-variant12-variant13-variant17-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant32-variant33-variant35-variant37-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:114,87:201:99:2178,0,3173:53,61,42,45 chr1 115601615 . A G 2210.3 PASS AC=2;AF=0.943;AN=2;DP=2592;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:2247,213,0:0,0,24,47 chr1 115615358 . T C 220.49 PASS AC=1;AF=0.661;AN=2;DP=602;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant24-variant25-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:15,17:32:99:556,0,451:11,4,15,2 chr1 115631924 . C T 2391.46 PASS AC=2;AF=0.966;AN=2;DP=4717;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,137:137:99:4162,407,0:0,0,73,64 chr1 115829313 . G A 2025.67 PASS AC=2;AF=0.594;AN=2;DP=7072;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,254:254:99:7841,759,0:0,0,112,142 chr1 116206423 . G A 3099.41 PASS AC=1;AF=0.5;AN=2;DP=2650;FractionInformativeReads=1;MQ=60;set=variant5-variant15-variant27-variant29-variant31-variant33-variant35-variant36-variant41 GT:AD:DP:GQ:PL:SB 0/1:153,175:328:99:4201,0,3634:90,63,95,80 chr1 116224925 . G A 346.57 PASS AC=2;AF=0.744;AN=2;DP=1121;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:997,84,0:0,0,22,6 chr1 116224940 . C A 550.68 PASS AC=2;AF=0.744;AN=2;DP=1588;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1393,123,0:0,0,31,10 chr1 116225180 . A C 603.51 PASS AC=2;AF=0.744;AN=2;DP=1404;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:1276,90,0:0,0,2,28 chr1 116228220 . C T 186.16 PASS AC=1;AF=0.692;AN=2;DP=1374;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,20:35:99:560,0,311:6,9,5,15 chr1 116234313 . A G 625.63 PASS AC=2;AF=0.737;AN=2;DP=2092;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:2233,212,0:0,0,31,40 chr1 116234416 . G A 1514.09 PASS AC=1;AF=0.571;AN=2;DP=1143;MQ=60;set=variant2-variant3-variant5-variant7-variant11-variant12-variant15-variant17-variant19-variant25-variant27-variant29-variant30-variant33-variant34-variant35-variant37-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,38:68:99:1023,0,837:15,15,20,18 chr1 116234505 . A G 773.41 PASS AC=2;AF=0.737;AN=2;DP=2159;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:2441,237,0:0,0,43,36 chr1 116235182 . GA G 4080.29 PASS AC=1;AF=0.571;AN=2;DP=1836;MQ=60;set=variant2-variant3-variant5-variant7-variant11-variant12-variant15-variant17-variant19-variant25-variant27-variant29-variant30-variant33-variant34-variant35-variant37-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,45:95:99:1456,0,1676:23,27,21,24 chr1 116235277 . C T 2121.99 PASS AC=1;AF=0.571;AN=2;DP=1374;MQ=60;set=variant2-variant3-variant5-variant7-variant11-variant12-variant15-variant17-variant19-variant25-variant27-variant29-variant30-variant33-variant34-variant35-variant37-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,28:67:99:778,0,1063:18,21,14,14 chr1 116235749 . G T 1008.58 PASS AC=1;AF=0.5;AN=2;DP=382;FractionInformativeReads=1;MQ=60;set=variant5-variant11-variant15-variant27-variant35 GT:AD:DP:GQ:PL:SB 0/1:38,34:72:99:1178,0,1308:7,31,3,31 chr1 116236351 . T G 4982.11 PASS AC=1;AF=0.635;AN=2;DP=8071;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant25-variant27-variant29-variant30-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:138,153:291:99:4028,0,3604:70,68,81,72 chr1 116237023 . G T 1219.13 PASS AC=1;AF=0.575;AN=2;DP=871;MQ=60;set=variant2-variant3-variant5-variant7-variant12-variant15-variant17-variant19-variant25-variant27-variant29-variant30-variant33-variant34-variant35-variant37-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,18:40:99:524,0,635:10,12,8,10 chr1 116237496 . T A 1447.81 PASS AC=1;AF=0.609;AN=2;DP=1160;MQ=60;set=variant2-variant3-variant5-variant7-variant11-variant12-variant13-variant15-variant17-variant19-variant25-variant27-variant29-variant30-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,20:49:99:495,0,837:18,11,12,8 chr1 116238478 . C T 638.95 PASS AC=1;AF=0.635;AN=2;DP=1283;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant25-variant27-variant29-variant30-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,27:53:99:626,0,601:13,13,13,14 chr1 116239368 . G A 963.53 PASS AC=1;AF=0.635;AN=2;DP=1690;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant25-variant27-variant29-variant30-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,41:63:99:1199,0,551:10,12,23,18 chr1 116239633 . T G 9289.75 PASS AC=1;AF=0.611;AN=2;DP=5681;set=variant4-variant6-variant7-variant14-variant15-variant18-variant21-variant23-variant24-variant26-variant28-variant31-variant32-variant34-variant35-variant36-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:121,166:287:99:3991,0,2875:58,63,78,88 chr1 116239751 . A G 1746.15 PASS AC=1;AF=0.654;AN=2;DP=2904;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant25-variant27-variant29-variant30-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,47:100:99:1434,0,1715:16,37,15,32 chr1 116239841 . A T 1619.04 PASS AC=1;AF=0.635;AN=2;DP=3316;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant25-variant27-variant29-variant30-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,60:112:99:1613,0,1335:28,24,35,25 chr1 116239995 . A T 2643.75 PASS AC=1;AF=0.635;AN=2;DP=6147;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant25-variant27-variant29-variant30-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:85,130:215:99:3255,0,1994:42,43,64,66 chr1 116240026 . G A 9787.36 PASS AC=1;AF=0.611;AN=2;DP=4698;set=variant4-variant6-variant7-variant14-variant15-variant18-variant21-variant23-variant24-variant26-variant28-variant31-variant32-variant34-variant35-variant36-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:155,90:245:99:1962,0,3875:80,75,44,46 chr1 116240199 . A T 1262.03 PASS AC=1;AF=0.575;AN=2;DP=1266;MQ=60;set=variant2-variant3-variant5-variant7-variant12-variant15-variant17-variant19-variant25-variant27-variant29-variant30-variant33-variant34-variant35-variant37-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,28:63:99:861,0,991:12,23,6,22 chr1 116240921 . C T 518.6 PASS AC=1;AF=0.635;AN=2;DP=765;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant25-variant27-variant29-variant30-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,14:29:99:508,0,582:0,15,0,14 chr1 116242737 . CAT C 8176.54 PASS AC=1;AF=0.575;AN=2;DP=3358;MQ=60;set=variant2-variant3-variant5-variant7-variant12-variant15-variant17-variant19-variant25-variant27-variant29-variant30-variant33-variant34-variant35-variant37-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:88,66:154:99:2480,0,3904:46,42,36,30 chr1 116242844 . AT A,ATT 4645.78 PASS AC=1,0;AF=0.589,0.018;AN=2;DP=4600;MQ=60;set=variant2-variant3-variant5-filterInvariant6-variant7-filterInvariant8-variant11-variant12-variant13-variant15-variant17-filterInvariant18-variant19-filterInvariant20-filterInvariant24-variant25-variant27-variant29-variant30-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant44 GT:DP:GQ:SB 0/1:144:99:27,32,36,49 chr1 116243230 . C G 2248.67 PASS AC=2;AF=0.711;AN=2;DP=4863;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,154:154:99:4537,459,0:0,0,82,72 chr1 116243380 . G A 979.63 PASS AC=2;AF=0.711;AN=2;DP=3143;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,90:90:99:2876,269,0:0,0,35,55 chr1 116243877 . G A 606.68 PASS AC=1;AF=0.625;AN=2;DP=1526;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant10-variant11-variant13-variant14-variant15-variant17-variant19-variant25-variant27-variant29-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,26:68:99:655,0,1274:28,14,16,10 chr1 116245809 . C T 289.6 PASS AC=2;AF=0.7;AN=2;DP=854;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant14-variant15-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:1084,90,0:0,0,5,25 chr1 116247790 . G A 779.38 PASS AC=2;AF=0.64;AN=2;DP=1787;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant15-variant18-variant21-variant23-variant24-variant26-variant27-variant28-variant31-variant32-variant34-variant35-variant36-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,81:81:99:2441,241,0:0,0,55,26 chr1 116260532 . A T 912.98 PASS AC=2;AF=0.722;AN=2;DP=2826;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,75:76:99:2766,217,0:1,0,30,45 chr1 116260544 . C T 3964.75 PASS AC=1;AF=0.579;AN=2;DP=1346;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant7-variant15-variant17-variant19-variant25-variant27-variant29-variant30-variant33-variant34-variant35-variant37-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,37:67:99:906,0,718:14,16,14,23 chr1 116260604 . G A 451.95 PASS AC=2;AF=0.708;AN=2;DP=1376;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1220,111,0:0,0,13,24 chr1 116268178 . GAAAA GAA,GA,GAAA,G,GAAAAA 187.7 PASS AC=1,0,0,1,0;AF=0.328,0.207,0.017,0.086,0.034;AN=2;DP=1868;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant21-variant23-variant24-variant25-variant28-variant29-variant30-variant33-variant35-variant37-variant38-variant39-variant40-variant41 GT:DP:GQ:SB 4/1:33:99:0,2,12,19 chr1 116268283 . C T 324.84 PASS AC=2;AF=0.722;AN=2;DP=916;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:896,87,0:0,0,11,18 chr1 116283343 . A G 1910 PASS AC=2;AF=0.869;AN=2;DP=3358;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,108:108:99:3092,323,0:0,0,60,48 chr1 116283526 . G A 882.94 PASS AC=2;AF=0.869;AN=2;DP=1334;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1489,123,0:0,0,6,35 chr1 116287634 . A G 1135.48 PASS AC=2;AF=0.667;AN=2;DP=1062;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant14-variant15-variant18-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1495,135,0:0,0,12,33 chr1 116287651 . G A 795.79 PASS AC=2;AF=0.667;AN=2;DP=787;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant14-variant15-variant18-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:913,87,0:0,0,8,21 chr1 116310818 . G C 282.99 PASS AC=2;AF=0.615;AN=2;DP=627;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant14-variant15-variant18-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant33-variant35-variant36-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:59:707,59,0:0,0,19,1 chr1 116310967 . T C 5107.94 PASS AC=2;AF=0.615;AN=2;DP=4482;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant14-variant15-variant18-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant33-variant35-variant36-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,166:166:99:5141,498,0:0,0,88,78 chr1 116311198 . T C 1594.43 PASS AC=2;AF=0.966;AN=2;DP=2757;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,63:64:99:1885,150,0:0,1,28,35 chr1 116311366 . GCACACA GCACACACACACACA,GCACACACACACA,G 318.35 PASS AC=2,0,0;AF=0.477,0.136,0.023;AN=2;DP=471;set=variant2-variant4-variant5-variant6-variant7-variant11-variant14-variant15-variant18-variant21-variant23-variant24-variant27-variant28-variant29-variant31-variant33-variant35-variant36-variant40-variant41-variant44 GT:DP:GQ:SB 1/1:17:49:0,0,3,14 chr1 116380029 . T C 3489.23 PASS AC=1;AF=0.724;AN=2;DP=2913;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant32-variant33-variant35-variant36-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,57:122:99:1459,0,1763:26,39,22,35 chr1 116380172 . C T 1396.97 PASS AC=1;AF=0.667;AN=2;DP=1568;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant19-variant20-variant21-variant23-variant25-variant27-variant28-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,15:45:99:414,0,830:12,18,5,10 chr1 116382318 . A G 1931.12 PASS AC=2;AF=0.895;AN=2;DP=2477;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1942,167,0:0,0,29,27 chr1 116382511 . A T 2523.41 PASS AC=2;AF=1;AN=2;DP=2842;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,78:78:99:2708,234,0:0,0,50,28 chr1 116382778 . T C 4069.38 PASS AC=2;AF=1;AN=2;DP=5118;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,121:121:99:3827,363,0:0,0,56,65 chr1 116383300 . T C 2991.08 PASS AC=2;AF=1;AN=2;DP=4151;FS=0;MQ=60;MQRankSum=-0.297;ReadPosRankSum=1.242;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,93:93:99:3045,277,0:0,0,29,64 chr1 116383333 . C A 1131.95 PASS AC=1;AF=0.583;AN=2;DP=1037;MQ=60;set=variant4-variant5-variant6-variant9-variant10-variant12-variant14-variant15-variant19-variant20-variant28-variant30-variant34-variant35-variant37-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,27:55:99:842,0,803:7,21,8,19 chr1 116383364 . AT ATTT,A,ATT,ATTTT 512.1 PASS AC=0,0,0,1;AF=0.2,0.029,0.214,0.243;AN=2;DP=1687;set=variant-filterInvariant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant29-variant30-filterInvariant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant43-variant44 GT:DP:GQ:SB 0/4:35:56:4,5,8,18 chr1 116384090 . G A 6262.12 PASS AC=2;AF=0.925;AN=2;DP=7512;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,207:208:99:6540,613,0:1,0,101,106 chr1 116384580 . C T 8655.27 PASS AC=1;AF=0.648;AN=2;DP=6866;MQ=60;set=variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant19-variant20-variant21-variant23-variant25-variant28-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:145,131:276:99:3647,0,4031:49,96,46,85 chr1 116384773 . A G 2713.84 PASS AC=1;AF=0.741;AN=2;DP=3199;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant32-variant33-variant35-variant36-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:85,48:133:99:1064,0,2246:43,42,23,25 chr1 116385122 . T C 2095.62 PASS AC=1;AF=0.648;AN=2;DP=1405;MQ=60;set=variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant19-variant20-variant21-variant23-variant25-variant28-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,21:62:99:495,0,1143:19,22,8,13 chr1 116385171 . C T 849.65 PASS AC=1;AF=0.741;AN=2;DP=1477;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant32-variant33-variant35-variant36-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,45:66:99:1205,0,422:9,12,20,25 chr1 116385288 . C T 1524.92 PASS AC=1;AF=0.648;AN=2;DP=1008;MQ=60;set=variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant19-variant20-variant21-variant23-variant25-variant28-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,14:39:99:317,0,714:11,14,7,7 chr1 116385309 . C A 592.2 PASS AC=1;AF=0.724;AN=2;DP=1032;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant32-variant33-variant35-variant36-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,24:41:99:630,0,375:9,8,11,13 chr1 116385467 . A G 1535.48 PASS AC=1;AF=0.648;AN=2;DP=1073;MQ=60;set=variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant19-variant20-variant21-variant23-variant25-variant28-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,17:40:99:475,0,524:12,11,10,7 chr1 116386105 . G A 1839.83 PASS AC=1;AF=0.583;AN=2;DP=2101;MQ=60;set=variant4-variant5-variant6-variant9-variant10-variant12-variant14-variant15-variant19-variant20-variant28-variant30-variant34-variant35-variant37-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,46:113:99:1065,0,1871:29,38,19,27 chr1 116386139 . G A 3449.83 PASS AC=2;AF=1;AN=2;DP=4473;FS=0;MQRankSum=1.597;ReadPosRankSum=1.597;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,100:100:99:3365,299,0:0,0,41,59 chr1 116386243 . C T 2913.39 PASS AC=1;AF=0.583;AN=2;DP=3711;MQ=60;set=variant4-variant5-variant6-variant9-variant10-variant12-variant14-variant15-variant19-variant20-variant28-variant30-variant34-variant35-variant37-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:115,128:243:99:3086,0,4441:62,53,78,50 chr1 116386244 . C T 6155.89 PASS AC=1;AF=0.724;AN=2;DP=6363;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant32-variant33-variant35-variant36-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:130,117:247:99:2787,0,5089:80,50,63,54 chr1 116386542 . CGTGTGT C,CGT,CGTGT,CATGTGTGT 412.13 PASS AC=0,1,0,0;AF=0.184,0.237,0.263,0.079;AN=2;DP=454;set=variant2-variant5-variant9-variant10-variant11-variant15-variant17-variant19-variant20-variant21-variant25-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant40 GT:DP:GQ:SB 0/2:28:99:1,20,1,6 chr1 116386547 . G A 367.46 PASS AC=1;AF=0.667;AN=2;DP=128;set=variant5-variant30-variant31-variant35-variant36-variant40 GT:AD:DP:GQ:PL:SB 0/1:21,7:28:99:194,0,837:1,20,1,6 chr1 116519147 . C T 1986.62 PASS AC=2;AF=1;AN=2;DP=56;FS=0;FractionInformativeReads=1;MQ=60;QD=29.2;SOR=4.332;set=variant35 GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:2015,167,0:0,0,51,5 chr1 116534952 . G T 1099.32 PASS AC=2;AF=0.643;AN=2;DP=881;MQ=60;set=variant3-variant5-variant7-variant8-variant9-variant12-variant14-variant16-variant18-variant19-variant21-variant22-variant28-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,44:45:99:1950,109,0:1,0,16,28 chr1 116534953 . C T 1099.32 PASS AC=2;AF=0.643;AN=2;DP=866;MQ=60;set=variant3-variant5-variant7-variant8-variant9-variant12-variant14-variant16-variant18-variant19-variant21-variant22-variant28-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1950,109,0:0,0,16,28 chr1 116569530 . G C 1501.42 PASS AC=2;AF=0.955;AN=2;DP=2085;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:2054,186,0:0,0,41,21 chr1 116574306 . G A 1261.76 PASS AC=2;AF=0.869;AN=2;DP=2225;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1387,120,0:0,0,19,21 chr1 116577981 . G A 1664.38 PASS AC=2;AF=1;AN=2;DP=1864;FS=0;MQ=60;MQRankSum=-0.139;ReadPosRankSum=0.208;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1334,114,0:0,0,9,29 chr1 116607254 . G T 1111.4 PASS AC=2;AF=0.989;AN=2;DP=815;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.935;ReadPosRankSum=-1.203;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:854,66,0:0,0,4,18 chr1 116609126 . TC T 3546.49 PASS AC=2;AF=0.845;AN=2;DP=3970;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,100:100:99:3464,301,0:0,0,60,40 chr1 116610227 . G A 8648.57 PASS AC=2;AF=0.884;AN=2;DP=11065;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,190:190:99:6224,570,0:0,0,74,116 chr1 116610388 . A G 1927.79 PASS AC=2;AF=1;AN=2;DP=3210;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:2504,195,0:0,0,31,34 chr1 116611548 . A G 6852.16 PASS AC=2;AF=0.955;AN=2;DP=8775;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,222:222:99:6489,665,0:0,0,113,109 chr1 116611705 . T C 2860.36 PASS AC=2;AF=0.845;AN=2;DP=4181;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,111:111:99:3515,331,0:0,0,48,63 chr1 116611722 . A T 1225.52 PASS AC=1;AF=0.5;AN=2;DP=93;FS=1.676;FractionInformativeReads=1;MQ=60;MQRankSum=-0.566;QD=13.18;ReadPosRankSum=-0.981;SOR=0.527;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:49,44:93:99:1254,0,1282:20,29,20,24 chr1 116666569 . T A 991.04 PASS AC=1;AF=0.607;AN=2;DP=275;MQ=60;set=variant3-variant4-variant8-variant10-variant11-variant17-variant19-variant26-variant31-variant34-variant35-variant37-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:6,10:16:99:390,0,226:6,0,10,0 chr1 116667159 . G A 911.3 PASS AC=1;AF=0.6;AN=2;DP=119;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant8-variant26-variant35 GT:AD:DP:GQ:PL:SB 0/1:9,13:22:99:394,0,190:3,6,4,9 chr1 116670774 . A G 4217.49 PASS AC=1;AF=0.607;AN=2;DP=1579;MQ=60;set=variant3-variant4-variant8-variant10-variant11-variant17-variant19-variant26-variant31-variant34-variant35-variant37-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:60,55:115:99:1296,0,1406:28,32,32,23 chr1 116676035 . A C 3917.31 PASS AC=1;AF=0.607;AN=2;DP=1403;MQ=60;set=variant3-variant4-variant8-variant10-variant11-variant17-variant19-variant26-variant31-variant34-variant35-variant37-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:49,48:97:99:1193,0,1383:15,34,21,27 chr1 116676548 . A G 2479.5 PASS AC=1;AF=0.55;AN=2;DP=736;MQ=60;set=variant3-variant4-variant8-variant11-variant17-variant26-variant34-variant35-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:37,27:64:99:574,0,1020:18,19,13,14 chr1 116676668 . G C 1971.45 PASS AC=1;AF=0.607;AN=2;DP=760;MQ=60;set=variant3-variant4-variant8-variant10-variant11-variant17-variant19-variant26-variant31-variant34-variant35-variant37-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:33,22:55:99:504,0,891:13,20,11,11 chr1 116916056 . C T 1899.43 PASS AC=1;AF=0.5;AN=2;DP=1208;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant15-variant18-variant26-variant35-variant37-variant38-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:66,67:133:99:1787,0,1763:40,26,40,27 chr1 116932563 . T A 683.36 PASS AC=2;AF=0.863;AN=2;DP=624;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:665,48,0:0,0,1,15 chr1 116933158 . GT GTT,G 53.04 PASS AC=1,0;AF=0.375,0.125;AN=2;DP=124;set=variant-variant4-variant14-variant27-variant34-variant35-variant6-filterInvariant41 GT:DP:GQ:SB 0/1:13:81:2,6,1,4 chr1 116940481 . CT C,CTT 65.51 PASS AC=1,0;AF=0.409,0.091;AN=2;DP=3947;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant5-variant6-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant13-filterInvariant15-filterInvariant16-filterInvariant17-variant18-filterInvariant19-variant21-filterInvariant23-filterInvariant25-filterInvariant27-filterInvariant29-filterInvariant30-filterInvariant32-variant33-variant34-filterInvariant35-filterInvariant36-variant37-variant38-variant39-filterInvariant40-variant41-filterInvariant43-filterInvariant44 GT:DP:GQ:SB 0/1:135:99:62,48,14,11 chr1 116948712 . G A 2094.62 PASS AC=2;AF=0.829;AN=2;DP=2539;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,54:56:99:1769,119,0:1,1,21,33 chr1 117078729 . A G 1747.85 PASS AC=1;AF=0.5;AN=2;DP=207;FS=0;MQ=60;set=variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:48,72:120:99:1776,0,995:24,24,35,37 chr1 117102649 . C T 655.26 PASS AC=1;AF=0.5;AN=2;DP=341;FractionInformativeReads=1;MQ=60;set=variant13-variant16-variant19-variant22-variant29-variant34-variant35-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:24,15:39:99:394,0,567:9,15,4,11 chr1 117122285 . G GTCC 2244.53 PASS AC=1;AF=0.575;AN=2;DP=5241;set=variant-variant3-variant4-variant5-variant10-variant11-variant17-variant18-variant23-variant24-variant25-variant26-variant27-variant28-variant32-variant34-variant35-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:155,109:264:99:2412,0,8164:78,77,57,52 chr1 117122288 . G C 2812.53 PASS AC=1;AF=0.568;AN=2;DP=5712;set=variant-variant3-variant4-variant5-variant10-variant11-variant13-variant17-variant18-variant23-variant24-variant25-variant26-variant27-variant28-variant32-variant34-variant35-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:155,145:300:99:5363,0,3690:79,76,71,74 chr1 117142531 . G A 49.73 PASS AC=1;AF=0.605;AN=2;DP=1252;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,11:31:99:321,0,566:14,6,9,2 chr1 117142613 . C T 268.02 PASS AC=1;AF=0.5;AN=2;DP=4958;set=variant-variant2-filterInvariant3-variant4-variant5-variant6-filterInvariant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-filterInvariant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-filterInvariant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-filterInvariant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,40:108:99:766,0,1869:42,26,25,15 chr1 117142641 . G A 375.97 PASS AC=1;AF=0.5;AN=2;DP=6944;set=variant-variant2-variant3-variant4-variant5-variant6-filterInvariant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-filterInvariant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:93,56:149:99:1167,0,2704:58,35,37,19 chr1 117142700 . C A 572.75 PASS AC=1;AF=0.5;AN=2;DP=10247;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:209,58:267:99:974,0,6034:128,81,40,18 chr1 117142736 . A G 1359.71 PASS AC=1;AF=0.5;AN=2;DP=12259;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-filterInvariant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:230,96:326:99:2048,0,5520:128,102,63,33 chr1 117142855 . C T 1729.59 PASS AC=1;AF=0.5;AN=2;DP=12618;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:196,152:348:99:3488,0,5460:89,107,74,78 chr1 117142868 . C T 2622.4 PASS AC=1;AF=0.5;AN=2;DP=11869;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:201,145:346:99:5396,0,8920:91,110,69,76 chr1 117142869 . A G 2622.4 PASS AC=1;AF=0.5;AN=2;DP=11823;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:198,145:343:99:5396,0,8920:89,109,69,76 chr1 117142977 . A C,G 193.25 PASS AC=0,1;AF=0.047,0.453;AN=2;DP=6731;set=variant-variant2-variant3-variant4-variant5-filterInvariant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-filterInvariant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-filterInvariant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-filterInvariant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-filterInvariant42-variant43-variant44 GT:DP:GQ:SB 0/2:178:99:47,75,15,41 chr1 117146124 . T C 154.63 PASS AC=1;AF=0.575;AN=2;DP=426;FractionInformativeReads=1;set=variant3-variant4-variant5-variant10-variant11-variant17-variant18-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant34-variant35-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:12,10:22:99:291,0,273:7,5,8,2 chr1 117146504 . G A 495.41 PASS AC=1;AF=0.5;AN=2;DP=18380;set=filterInvariant-filterInvariant2-variant3-variant4-variant5-filterInvariant6-filterInvariant7-variant8-variant9-variant10-variant11-variant12-variant13-filterInvariant14-filterInvariant15-variant16-variant17-variant18-variant19-variant20-filterInvariant21-variant22-variant23-variant24-filterInvariant25-variant26-variant27-variant28-variant29-variant30-variant31-filterInvariant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:348,148:496:99:2156,0,9099:178,170,75,73 chr1 117146563 . G A 1169.47 PASS AC=1;AF=0.5;AN=2;DP=15374;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:302,124:426:99:3966,0,7948:127,175,58,66 chr1 117146571 . A G 1065.92 PASS AC=1;AF=0.5;AN=2;DP=14109;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:289,108:397:99:3143,0,11890:123,166,48,60 chr1 117146585 . G A 595.08 PASS AC=1;AF=0.5;AN=2;DP=7097;set=variant2-variant3-filterInvariant4-filterInvariant5-variant7-variant8-filterInvariant9-filterInvariant13-filterInvariant16-filterInvariant18-filterInvariant21-filterInvariant22-variant23-variant25-filterInvariant26-variant27-variant29-filterInvariant30-variant32-filterInvariant33-variant35-variant40-filterInvariant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:252,82:334:99:2752,0,10736:100,152,34,48 chr1 117146592 . C G 342.92 PASS AC=1;AF=0.5;AN=2;DP=10920;set=filterInvariant-filterInvariant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-filterInvariant14-filterInvariant15-variant16-variant17-variant18-variant19-variant20-filterInvariant21-variant22-variant23-variant24-variant25-variant26-variant27-filterInvariant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:231,71:302:99:2463,0,9889:89,142,28,43 chr1 117150617 . A G 68.37 PASS AC=1;AF=0.5;AN=2;DP=1303;set=filterInvariant4-variant8-filterInvariant17-filterInvariant27-filterInvariant32-filterInvariant35-filterInvariant40-filterInvariant42 GT:AD:DP:GQ:PL:SB 0/1:149,27:176:99:176,0,3885:87,62,15,12 chr1 117150628 . G C 215.34 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=1039;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:166,26:192:99:102,0,4368:93,73,14,12 chr1 117150928 . C T 515 PASS AC=1;AF=0.5;AN=2;DP=3765;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:71,39:110:99:1364,0,3313:23,48,13,26 chr1 117150933 . G A 543.75 PASS AC=1;AF=0.5;AN=2;DP=3567;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:69,38:107:99:1345,0,3295:21,48,12,26 chr1 117150966 . G T 192.93 PASS AC=1;AF=0.5;AN=2;DP=2180;set=variant-variant2-variant3-variant4-variant5-filterInvariant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,24:63:99:593,0,1088:12,27,6,18 chr1 117151062 . C T 37.69 PASS AC=1;AF=0.5;AN=2;DP=216;FractionInformativeReads=1;set=variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant16-variant17-variant23-variant25-variant26-variant27-variant29-variant31-variant35-variant37-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:7,4:11:99:144,0,389:2,5,0,4 chr1 117151066 . G A 37.69 PASS AC=1;AF=0.5;AN=2;DP=201;FractionInformativeReads=1;set=variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant16-variant17-variant23-variant25-variant26-variant27-variant29-variant31-variant35-variant37-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:6,4:10:99:144,0,389:2,4,0,4 chr1 117156459 . C T 608.98 PASS AC=1;AF=0.5;AN=2;DP=7812;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-filterInvariant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:122,70:192:99:1294,0,3298:66,56,43,27 chr1 117156490 . T C 497.11 PASS AC=1;AF=0.5;AN=2;DP=7424;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-filterInvariant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:134,65:199:99:1218,0,3513:72,62,35,30 chr1 117156584 . T C 424.83 PASS AC=1;AF=0.5;AN=2;DP=6974;set=variant-variant3-variant4-variant5-filterInvariant6-variant7-variant8-variant9-filterInvariant10-variant11-variant12-variant13-filterInvariant14-variant15-variant16-variant17-variant18-variant19-variant20-filterInvariant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:180,36:216:99:927,0,15166:94,86,7,29 chr1 117156585 . G A 424.83 PASS AC=1;AF=0.5;AN=2;DP=6965;set=variant-variant3-variant4-variant5-filterInvariant6-variant7-variant8-variant9-filterInvariant10-variant11-variant12-variant13-filterInvariant14-variant15-variant16-variant17-variant18-variant19-variant20-filterInvariant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:181,34:215:99:924,0,15190:95,86,6,28 chr1 117156600 . T C 60.03 PASS AC=1;AF=0.5;AN=2;DP=5551;set=filterInvariant-variant3-filterInvariant4-filterInvariant5-filterInvariant7-variant8-variant9-variant11-variant12-filterInvariant13-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant22-variant23-filterInvariant24-variant26-filterInvariant27-variant28-filterInvariant30-filterInvariant31-filterInvariant33-filterInvariant34-variant35-filterInvariant36-filterInvariant37-filterInvariant39-filterInvariant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:182,27:209:99:586,0,14814:94,88,5,22 chr1 117158934 . C T 127.47 PASS AC=1;AF=0.5;AN=2;DP=817;set=variant8-variant9-variant11-variant12-variant15-filterInvariant16-filterInvariant17-variant18-variant23-variant24-filterInvariant25-variant27-filterInvariant28-variant29-filterInvariant35-filterInvariant36-variant40-variant41-variant42-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:35,10:45:99:112,0,1044:12,23,5,5 chr1 117158972 . A G 34.92 PASS AC=1;AF=0.5;AN=2;DP=817;set=filterInvariant-variant8-variant9-filterInvariant10-variant11-variant12-filterInvariant15-filterInvariant16-variant17-filterInvariant18-filterInvariant19-filterInvariant23-variant25-variant26-variant27-variant28-filterInvariant29-variant32-variant35-variant36-variant37-filterInvariant39-variant40-variant41-filterInvariant42-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:17,12:29:99:210,0,492:7,10,6,6 chr1 117159024 . C T 32.96 PASS AC=1;AF=0.5;AN=2;DP=282;FractionInformativeReads=1;set=filterInvariant-variant8-variant9-variant11-filterInvariant18-variant23-variant24-filterInvariant25-variant26-variant27-variant28-filterInvariant29-variant35-variant36-variant37-filterInvariant41-filterInvariant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,6:19:91:91,0,334:4,9,3,3 chr1 117210149 . A C,ACTCCCCG 471.64 PASS AC=2,0;AF=0.828,0.047;AN=2;DP=279;MQ=60;set=variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant43-variant44 GT:DP:GQ:SB 1/1:4:12:0,0,1,3 chr1 117214318 . T TA 269.55 PASS AC=1;AF=0.5;AN=2;DP=75;MQ=60;set=variant10-variant11-variant24-variant35 GT:AD:DP:GQ:PL:SB 0/1:7,9:16:99:210,0,154:5,2,6,3 chr1 117236970 . G C 973.78 PASS AC=2;AF=0.671;AN=2;DP=2635;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:2269,194,0:0,0,16,49 chr1 117487165 . G A 120.13 PASS AC=2;AF=0.65;AN=2;DP=103;FS=0;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant13-variant20-variant21-variant35-variant36-variant37-variant40-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:410,39,0:0,0,9,4 chr1 117487710 . A G 5540.81 PASS AC=2;AF=0.909;AN=2;DP=6239;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,181:182:99:8094,542,0:1,0,76,105 chr1 117487711 . T A 5540.81 PASS AC=2;AF=0.909;AN=2;DP=6178;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,180:180:99:8094,542,0:0,0,76,104 chr1 117509981 . G A 5716.6 PASS AC=2;AF=0.579;AN=2;DP=1779;MQ=60;set=variant3-variant5-variant6-variant12-variant13-variant15-variant16-variant19-variant20-variant21-variant23-variant26-variant27-variant33-variant35-variant36-variant37-variant40-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,99:99:99:4262,298,0:0,0,35,64 chr1 117509987 . C T 5750.85 PASS AC=2;AF=0.579;AN=2;DP=1709;MQ=60;set=variant3-variant5-variant6-variant12-variant13-variant15-variant16-variant19-variant20-variant21-variant23-variant26-variant27-variant33-variant35-variant36-variant37-variant40-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,91:91:99:4141,286,0:0,0,29,62 chr1 117510061 . C T 2192.17 PASS AC=2;AF=0.579;AN=2;DP=738;MQ=60;set=variant3-variant5-variant6-variant12-variant13-variant15-variant16-variant19-variant20-variant21-variant23-variant26-variant27-variant33-variant35-variant36-variant37-variant40-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1192,99,0:0,0,6,27 chr1 117527645 . GTCT G 589.47 PASS AC=2;AF=0.609;AN=2;DP=1673;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant10-variant12-variant13-variant15-variant16-variant18-variant19-variant21-variant23-variant27-variant28-variant32-variant33-variant35-variant36-variant37-variant40-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:3356,229,0:0,0,26,50 chr1 117529458 . G A 535.38 PASS AC=2;AF=0.606;AN=2;DP=3825;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant37-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,116:116:99:3418,347,0:0,0,70,46 chr1 117530193 . CTTTTT CTTT,CTT,C,CT,CTTTT 213.95 PASS AC=1,1,0,0,0;AF=0.456,0.176,0.015,0.015,0.015;AN=2;DP=985;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-filterInvariant14-variant15-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant40-variant42-variant44 GT:DP:GQ:SB 2/1:17:99:0,0,5,12 chr1 117530273 . A G 184.13 PASS AC=2;AF=0.657;AN=2;DP=746;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant37-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:914,75,0:0,0,11,14 chr1 117530477 . G A 398.11 PASS AC=2;AF=0.657;AN=2;DP=1074;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant37-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1501,147,0:0,0,26,23 chr1 117530507 . C T 486.82 PASS AC=2;AF=0.657;AN=2;DP=1120;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant37-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1919,132,0:0,0,25,19 chr1 117530511 . C T 486.82 PASS AC=2;AF=0.657;AN=2;DP=1121;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant37-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1919,132,0:0,0,22,19 chr1 117531620 . G A 256.59 PASS AC=2;AF=0.606;AN=2;DP=1007;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant37-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,33:34:56:1018,56,0:1,0,15,18 chr1 117531813 . T C 356.95 PASS AC=2;AF=0.657;AN=2;DP=2015;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant37-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:1818,177,0:0,0,28,31 chr1 117531911 . A G 288.01 PASS AC=2;AF=0.643;AN=2;DP=1645;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant37-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1452,138,0:0,0,26,20 chr1 117532372 . G T 3028.76 PASS AC=2;AF=0.587;AN=2;DP=5389;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant10-variant12-variant13-variant15-variant16-variant18-variant19-variant21-variant23-variant27-variant28-variant32-variant33-variant35-variant36-variant37-variant40-variant42 GT:AD:DP:GQ:PL:SB 1/1:1,229:230:99:6474,678,0:1,0,104,125 chr1 117532790 . C T 5244.14 PASS AC=2;AF=0.578;AN=2;DP=8512;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant35-variant36-variant37-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,234:235:99:7167,693,0:1,0,137,97 chr1 117533010 . G GTTA 3097.22 PASS AC=2;AF=0.657;AN=2;DP=4590;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant37-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,99:99:99:4453,301,0:0,0,33,66 chr1 117555898 . G A 862.71 PASS AC=2;AF=1;AN=2;DP=1128;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1146,108,0:0,0,24,12 chr1 117559726 . A G 3791.22 PASS AC=2;AF=0.989;AN=2;DP=5403;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,140:140:99:4350,420,0:0,0,69,71 chr1 117602960 . C A 8260.14 PASS AC=2;AF=0.881;AN=2;DP=10195;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,236:236:99:7450,705,0:0,0,152,84 chr1 117618722 . T C 1140.06 PASS AC=2;AF=1;AN=2;DP=1148;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1439,138,0:0,0,30,16 chr1 117621947 . G C 203.05 PASS AC=2;AF=0.587;AN=2;DP=303;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant6-variant8-variant10-variant13-variant15-variant16-variant17-variant19-variant21-variant22-variant24-variant29-variant30-variant33-variant35-variant36-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:545,48,0:0,0,13,3 chr1 117628869 . ATG ATGTG,A,ATGTGTG 282.52 PASS AC=1,0,0;AF=0.35,0.15,0.025;AN=2;DP=238;set=variant-variant2-variant3-variant4-variant8-variant13-variant14-variant15-variant20-variant22-variant24-variant25-variant28-variant29-variant30-variant35-variant37-variant39-variant41-variant44 GT:DP:GQ:SB 0/1:17:18:2,0,14,1 chr1 117631391 . T C 2219.07 PASS AC=2;AF=0.907;AN=2;DP=2436;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1696,153,0:0,0,34,17 chr1 117633366 . T C 192.92 PASS AC=1;AF=0.577;AN=2;DP=117;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant8-variant13-variant15-variant16-variant19-variant29-variant30-variant35-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:7,6:13:99:179,0,218:3,4,1,5 chr1 117633918 . C T 1106.02 PASS AC=1;AF=0.5;AN=2;DP=485;FractionInformativeReads=1;MQ=60;set=variant3-variant13-variant15-variant24-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:39,27:66:99:577,0,868:20,19,16,11 chr1 117639828 . TA T 106.29 PASS AC=1;AF=0.583;AN=2;DP=369;MQ=60;set=variant2-variant3-variant11-variant12-variant13-variant15-variant16-variant17-variant20-variant28-variant29-variant30-variant34-variant35-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,5:18:87:87,0,312:10,3,3,2 chr1 117644937 . TCCCTGCAGCCA T 1487.4 PASS AC=1;AF=0.56;AN=2;DP=2522;MQ=60;set=variant2-variant3-variant6-variant7-variant8-variant9-variant11-variant13-variant15-variant16-variant17-variant20-variant27-variant28-variant29-variant30-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,53:102:99:2050,0,3135:28,21,26,27 chr1 117654777 . ATAAC A 106.67 PASS AC=1;AF=0.568;AN=2;DP=375;MQ=60;set=variant2-variant3-variant7-variant9-variant11-variant13-variant15-variant16-variant17-variant20-variant27-variant28-variant29-variant30-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,8:19:99:303,0,469:8,3,5,3 chr1 117655265 . C T 362.84 PASS AC=1;AF=0.5;AN=2;DP=48;FractionInformativeReads=1;MQ=60;set=variant21-variant35 GT:AD:DP:GQ:PL:SB 0/1:14,11:25:99:283,0,393:4,10,2,9 chr1 117656088 . A G 1404.54 PASS AC=1;AF=0.552;AN=2;DP=3702;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant20-variant24-variant25-variant27-variant28-variant29-variant30-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:79,74:153:99:1684,0,1928:44,35,37,37 chr1 117656276 . A G 285.79 PASS AC=1;AF=0.552;AN=2;DP=626;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant20-variant24-variant25-variant27-variant28-variant29-variant30-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,7:15:99:189,0,246:1,7,2,5 chr1 117660608 . C T 862.64 PASS AC=2;AF=0.905;AN=2;DP=1083;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:1004,84,0:0,0,23,5 chr1 117660754 . C T 1415.34 PASS AC=1;AF=0.563;AN=2;DP=2997;MQ=60;set=variant2-variant3-variant7-variant8-variant9-variant11-variant13-variant15-variant16-variant17-variant20-variant27-variant28-variant29-variant30-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:85,75:160:99:1710,0,2063:46,39,38,37 chr1 117663913 . C T 1508.46 PASS AC=1;AF=0.744;AN=2;DP=2669;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,29:60:99:763,0,779:14,17,16,13 chr1 117664046 . C T 2059.09 PASS AC=1;AF=0.744;AN=2;DP=4400;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,62:107:99:1428,0,946:21,24,29,33 chr1 117686492 . C A 155.91 PASS AC=1;AF=0.786;AN=2;DP=834;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,16:25:99:473,0,248:3,6,5,11 chr1 117686827 . C T 670.3 PASS AC=1;AF=0.786;AN=2;DP=3343;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,37:87:99:906,0,1180:27,23,22,15 chr1 117686914 . C T 894.97 PASS AC=1;AF=0.786;AN=2;DP=4459;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,71:129:99:1596,0,1387:31,27,41,30 chr1 117687125 . A T 1650.93 PASS AC=1;AF=0.786;AN=2;DP=6096;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:69,75:144:99:2152,0,1948:42,27,46,29 chr1 117690272 . G A 558.31 PASS AC=1;AF=0.864;AN=2;DP=3044;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:38,36:74:99:861,0,967:24,14,19,17 chr1 117696037 . G A 1091.81 PASS AC=1;AF=0.5;AN=2;DP=1183;MQ=60;set=variant-variant3-variant5-variant12-variant13-variant15-variant24-variant25-variant34-variant35-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:60,38:98:99:963,0,1612:26,34,17,21 chr1 117696083 . ATT A,AT 336.36 PASS AC=1,0;AF=0.097,0.403;AN=2;DP=2941;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-filterInvariant22-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant44 GT:DP:GQ:SB 0/1:45:99:13,13,10,9 chr1 117696148 . A G 514.69 PASS AC=1;AF=0.5;AN=2;DP=462;MQ=60;set=variant-variant3-variant5-variant12-variant13-variant15-variant24-variant25-variant34-variant35-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:19,17:36:99:524,0,607:3,16,4,13 chr1 117715026 . C T 1188.03 PASS AC=1;AF=0.684;AN=2;DP=3619;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:40,45:85:99:1092,0,948:24,16,25,20 chr1 117715817 . C A 251.29 PASS AC=1;AF=0.5;AN=2;DP=380;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant12-variant13-variant15-variant24-variant25-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:20,28:48:99:759,0,469:11,9,18,10 chr1 117715987 . AACAC AACACACAC,AACACAC,A,AACACACACAC,AACACACACACACAC 523.65 PASS AC=1,1,0,0,0;AF=0.171,0.524,0.012,0.012,0.012;AN=2;DP=1112;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 2/1:23:99:0,0,8,15 chr1 117910682 . G A 6198.16 PASS AC=2;AF=0.86;AN=2;DP=6810;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,159:159:99:4994,476,0:0,0,95,64 chr1 117957288 . A G 787.57 PASS AC=2;AF=0.86;AN=2;DP=721;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:513,39,0:0,0,12,1 chr1 117957505 . A G 664.95 PASS AC=1;AF=0.5;AN=2;DP=1326;MQ=60;set=variant-variant3-variant5-variant7-variant9-variant10-variant11-variant12-variant13-variant17-variant19-variant23-variant27-variant35-variant37-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:36,33:69:99:695,0,871:13,23,13,20 chr1 117984776 . A T 151.11 PASS AC=1;AF=0.525;AN=2;DP=355;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant13-variant14-variant17-variant18-variant19-variant21-variant22-variant23-variant28-variant30-variant33-variant35-variant36-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,16:25:99:473,0,249:7,2,12,4 chr1 117985030 . AT A 153.2 PASS AC=1;AF=0.5;AN=2;DP=275;MQ=60;set=variant-variant3-variant5-variant7-variant9-variant10-variant11-variant12-variant13-variant17-variant19-variant23-variant27-variant35-variant37-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:15,6:21:99:120,0,387:5,10,1,5 chr1 118003297 . A G 698.33 PASS AC=1;AF=0.5;AN=2;DP=57;FS=3.897;FractionInformativeReads=1;MQ=60;MQRankSum=0.359;QD=12.25;ReadPosRankSum=-0.295;SOR=1.345;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:29,28:57:99:727,0,713:12,17,8,20 chr1 118039722 . C T 42.17 PASS AC=1;AF=0.533;AN=2;DP=125;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant13-variant18-variant19-variant21-variant22-variant28-variant30-variant33-variant35-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:2,2:4:37:75,0,37:1,1,0,2 chr1 118053126 . T C 1010.95 PASS AC=1;AF=0.526;AN=2;DP=1940;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant13-variant17-variant18-variant19-variant21-variant22-variant23-variant28-variant30-variant33-variant35-variant36-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,43:89:99:963,0,1213:26,20,25,18 chr1 118057278 . C T 234.71 PASS AC=1;AF=0.5;AN=2;DP=248;MQ=60;set=variant-variant3-variant5-variant7-variant9-variant10-variant11-variant12-variant13-variant17-variant19-variant23-variant27-variant35-variant37-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:8,10:18:99:396,0,312:8,0,10,0 chr1 118057962 . A G 1104.62 PASS AC=1;AF=0.525;AN=2;DP=2879;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant13-variant14-variant17-variant18-variant19-variant21-variant22-variant23-variant28-variant30-variant33-variant35-variant36-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:84,74:158:99:1879,0,2127:43,41,33,41 chr1 118058319 . T C 1051.34 PASS AC=1;AF=0.5;AN=2;DP=1248;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant7-variant9-variant10-variant11-variant12-variant13-variant17-variant19-variant23-variant27-variant35-variant37-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:27,40:67:99:1104,0,689:13,14,17,23 chr1 118065284 . C G 90.63 PASS AC=1;AF=0.529;AN=2;DP=207;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant13-variant17-variant18-variant19-variant21-variant22-variant23-variant28-variant33-variant35-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,2:9:63:63,0,247:6,1,2,0 chr1 118067306 . T A 1777.51 PASS AC=1;AF=0.525;AN=2;DP=2295;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant13-variant14-variant17-variant18-variant19-variant21-variant22-variant23-variant28-variant30-variant33-variant35-variant36-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,52:113:99:1536,0,1608:31,30,21,31 chr1 118068034 . A G 1645.37 PASS AC=1;AF=0.525;AN=2;DP=2513;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant13-variant14-variant17-variant18-variant19-variant21-variant22-variant23-variant28-variant30-variant33-variant35-variant36-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:66,69:135:99:1851,0,1710:31,35,32,37 chr1 118068934 . G A 4634.41 PASS AC=1;AF=0.688;AN=2;DP=4891;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,55:113:99:1440,0,1735:12,46,16,39 chr1 118069063 . G A 192.99 PASS AC=2;AF=0.925;AN=2;DP=354;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:364,27,0:0,0,7,2 chr1 118069490 . CTCTCTCTCTCTCTATA C 52.98 PASS AC=2;AF=1;AN=2;DP=4;FS=0;FractionInformativeReads=0.5;MQ=60;QD=13.25;SOR=2.303;set=variant35 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:90,6,0:0,0,2,0 chr1 118069612 . CTT C 1150.72 PASS AC=1;AF=0.526;AN=2;DP=1733;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant13-variant17-variant18-variant19-variant21-variant22-variant23-variant28-variant30-variant33-variant35-variant36-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,44:90:99:1701,0,1862:39,7,35,9 chr1 118069830 . A G 6831.49 PASS AC=1;AF=0.5;AN=2;DP=8499;MQ=60;set=variant-variant3-variant5-variant7-variant9-variant10-variant11-variant12-variant13-variant17-variant19-variant23-variant27-variant35-variant37-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:210,218:428:99:5561,0,4789:96,114,84,134 chr1 118148830 . G T 271.65 PASS AC=2;AF=0.712;AN=2;DP=888;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1455,135,0:0,0,15,30 chr1 118165328 . T C 275.33 PASS AC=1;AF=0.595;AN=2;DP=856;MQ=60;set=variant2-variant4-variant7-variant9-variant10-variant11-variant16-variant21-variant23-variant24-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,21:36:99:717,0,566:15,0,18,3 chr1 118165691 . C T,G 1800.96 PASS AC=1,0;AF=0.391,0.152;AN=2;DP=3961;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant19-variant20-variant23-variant24-variant26-variant27-variant31-variant33-variant35-variant36-variant38-variant40-variant43-variant44 GT:DP:GQ:SB 0/1:200:99:50,63,38,49 chr1 118165973 . C T 1374.25 PASS AC=1;AF=0.619;AN=2;DP=3094;MQ=60;set=variant2-variant4-variant7-variant9-variant10-variant11-variant16-variant21-variant23-variant24-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:88,89:177:99:2231,0,2361:43,45,48,41 chr1 118166096 . C T 2339.18 PASS AC=1;AF=0.5;AN=2;DP=3743;MQ=60;set=variant2-variant4-variant7-variant9-variant10-variant16-variant21-variant23-variant27-variant29-variant32-variant33-variant34-variant35-variant37-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:113,140:253:99:3390,0,2857:63,50,74,66 chr1 118166750 . A G 244.48 PASS AC=1;AF=0.625;AN=2;DP=805;MQ=60;set=variant2-variant4-variant7-variant9-variant10-variant16-variant21-variant23-variant24-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,26:46:99:789,0,476:10,10,10,16 chr1 118166786 . CT C,CTT,CTTT,CTTTT 187.2 PASS AC=0,1,0,0;AF=0.12,0.28,0.08,0.02;AN=2;DP=954;set=variant2-filterInvariant3-variant4-variant6-variant7-filterInvariant8-variant11-variant12-variant14-variant18-variant19-variant20-variant23-variant26-filterInvariant27-variant31-variant33-variant35-variant36-filterInvariant38-filterInvariant39-variant40-variant41-variant42-variant43 GT:DP:GQ:SB 0/2:36:99:13,11,6,6 chr1 118166877 . C T 287.36 PASS AC=1;AF=0.556;AN=2;DP=636;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant19-variant20-variant23-variant26-variant35-variant36-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,16:39:99:494,0,728:10,13,7,9 chr1 118167199 . A G 2891 PASS AC=1;AF=0.579;AN=2;DP=4338;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant19-variant20-variant23-variant26-variant35-variant36-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:121,130:251:99:2999,0,2748:66,55,70,60 chr1 118168234 . C T 516.53 PASS AC=1;AF=0.559;AN=2;DP=765;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant11-variant12-variant14-variant19-variant20-variant23-variant26-variant35-variant36-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,21:46:99:659,0,704:14,11,8,13 chr1 118168804 . T TC 442.15 PASS AC=1;AF=0.559;AN=2;DP=627;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant11-variant12-variant14-variant19-variant20-variant23-variant26-variant35-variant36-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,17:49:99:487,0,1050:18,14,9,8 chr1 118168826 . C T 319.75 PASS AC=1;AF=0.5;AN=2;DP=700;MQ=60;set=variant2-variant4-variant7-variant9-variant10-variant16-variant21-variant23-variant27-variant29-variant32-variant33-variant34-variant35-variant37-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,31:52:99:864,0,565:13,8,17,14 chr1 118169463 . G A 193.31 PASS AC=1;AF=0.529;AN=2;DP=762;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant11-variant12-variant14-variant19-variant20-variant23-variant26-variant35-variant36-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,27:57:99:613,0,758:15,15,15,12 chr1 118170466 . CTGTG CTG,C 1212.25 PASS AC=1,0;AF=0.521,0.021;AN=2;DP=1739;set=variant-variant4-filterInvariant5-variant6-variant7-variant8-variant11-variant12-variant14-filterInvariant15-variant19-variant20-variant23-filterInvariant24-variant26-variant27-filterInvariant33-variant35-variant36-filterInvariant37-variant38-variant39-variant43-variant44 GT:DP:GQ:SB 0/1:53:99:15,9,22,7 chr1 118171000 . CATTT C 2034.61 PASS AC=1;AF=0.559;AN=2;DP=1685;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant11-variant12-variant14-variant19-variant20-variant23-variant26-variant35-variant36-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,62:100:99:2409,0,2150:13,25,21,41 chr1 118320859 . T A 611.96 PASS AC=2;AF=1;AN=2;DP=1028;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:785,69,0:0,0,15,8 chr1 118321119 . T C 2239.02 PASS AC=2;AF=0.919;AN=2;DP=2388;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:1759,177,0:0,0,31,28 chr1 118420019 . C CT 2625.87 PASS AC=1;AF=0.5;AN=2;DP=1330;MQ=60;set=variant7-variant9-variant19-variant23-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:111,89:200:99:1677,0,2444:54,57,46,43 chr1 118484265 . G A 2108.48 PASS AC=2;AF=1;AN=2;DP=3076;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,69:69:99:2098,206,0:0,0,34,35 chr1 118579224 . G GAC 67.13 PASS AC=1;AF=0.56;AN=2;DP=221;MQ=60;set=variant-variant5-variant7-variant9-variant11-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant37-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,10:11:1:288,0,1:1,0,9,1 chr1 118617372 . G A 763.82 PASS AC=1;AF=0.5;AN=2;DP=295;FractionInformativeReads=1;MQ=60;set=variant11-variant15-variant20-variant27-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:27,37:64:99:1123,0,731:7,20,8,29 chr1 118623681 . TACACAC T,TAC,TACACACAC 590.68 PASS AC=0,0,1;AF=0.525,0.088,0.075;AN=2;DP=762;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/3:18:99:7,1,7,3 chr1 118693217 . T C 872.95 PASS AC=1;AF=0.556;AN=2;DP=894;FractionInformativeReads=1;MQ=60;set=variant-variant7-variant10-variant11-variant18-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant35-variant38-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,26:42:99:663,0,426:7,9,14,12 chr1 119427228 . GAA GA,G,GAAA 508.6 PASS AC=1,0,0;AF=0.419,0.054,0.041;AN=2;DP=6389;set=variant-variant2-variant3-variant4-variant5-filterInvariant6-variant8-variant9-filterInvariant10-variant11-filterInvariant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-filterInvariant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant35-filterInvariant36-variant38-variant39-filterInvariant40-variant41-variant42-variant44 GT:DP:GQ:SB 0/1:127:99:38,40,26,23 chr1 119456589 . C T 219.05 PASS AC=1;AF=0.5;AN=2;DP=212;FractionInformativeReads=1;MQ=60;set=variant2-variant15-variant17-variant25-variant28-variant35-variant36-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:17,16:33:99:537,0,413:11,6,13,3 chr1 119466275 . A G 1502.29 PASS AC=2;AF=0.738;AN=2;DP=2016;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:1767,162,0:0,0,17,37 chr1 119573860 . T C 3046.69 PASS AC=1;AF=0.543;AN=2;DP=3250;MQ=60;set=variant3-variant6-variant7-variant8-variant10-variant11-variant16-variant20-variant21-variant22-variant23-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,68:115:99:1582,0,1231:32,15,41,27 chr1 119574074 . G C 2435.36 PASS AC=1;AF=0.726;AN=2;DP=6091;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,75:130:99:2023,0,1568:28,27,38,37 chr1 119574587 . C T 3279.49 PASS AC=1;AF=0.671;AN=2;DP=8861;set=variant-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:150,153:303:99:3808,0,3830:86,64,85,68 chr1 119575170 . C A 5352.24 PASS AC=1;AF=0.56;AN=2;DP=8344;MQ=60;set=variant3-variant6-variant7-variant8-variant10-variant11-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:205,142:347:99:3582,0,5727:98,107,66,76 chr1 119575232 . T C 4580.36 PASS AC=1;AF=0.56;AN=2;DP=7045;MQ=60;set=variant3-variant6-variant7-variant8-variant10-variant11-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:175,141:316:99:3471,0,4465:81,94,77,64 chr1 119683063 . G A 1394.45 PASS AC=1;AF=0.595;AN=2;DP=1629;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant7-variant8-variant11-variant17-variant20-variant21-variant22-variant23-variant24-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,34:74:99:900,0,1047:21,19,20,14 chr1 119683390 . G A 453.78 PASS AC=1;AF=0.6;AN=2;DP=455;MQ=60;set=variant3-variant6-variant7-variant8-variant11-variant20-variant21-variant22-variant23-variant24-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,10:25:99:276,0,448:4,11,2,8 chr1 119923531 . A C 750.39 PASS AC=2;AF=0.697;AN=2;DP=2620;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant21-variant23-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:2352,228,0:0,0,36,40 chr1 119923724 . T C,G 1068.53 PASS AC=2,0;AF=0.603,0.034;AN=2;DP=3979;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant21-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant40-variant41-variant42-variant43 GT:DP:GQ:SB 1/1:169:99:0,0,88,81 chr1 119925403 . C T 1042.41 PASS AC=2;AF=0.66;AN=2;DP=1886;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant13-variant14-variant16-variant17-variant19-variant21-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,86:86:99:2583,257,0:0,0,48,38 chr1 119925464 . G A 1151.42 PASS AC=2;AF=0.66;AN=2;DP=2814;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant13-variant14-variant16-variant17-variant19-variant21-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,122:123:99:3603,323,0:0,1,66,56 chr1 119927680 . A G 1360.93 PASS AC=2;AF=0.697;AN=2;DP=4340;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant21-variant23-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,132:133:99:4287,357,0:1,0,57,75 chr1 119927969 . T G 162.18 PASS AC=2;AF=0.654;AN=2;DP=290;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:272,24,0:0,0,2,6 chr1 119935507 . A T 292.42 PASS AC=2;AF=0.7;AN=2;DP=391;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant21-variant26-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:223,18,0:0,0,1,5 chr1 119936263 . G A 783.27 PASS AC=2;AF=0.638;AN=2;DP=1584;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant21-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:2527,216,0:0,0,54,18 chr1 120057158 . C T 3432.48 PASS AC=2;AF=0.635;AN=2;DP=7237;set=variant-variant4-variant5-variant6-variant7-variant8-variant12-variant13-variant14-variant18-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,342:342:99:10429,1023,0:0,0,127,215 chr1 120057246 . C A 2277.89 PASS AC=2;AF=0.714;AN=2;DP=2465;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,82:83:99:3064,238,0:0,1,6,76 chr1 120254506 . A G 470.4 PASS AC=2;AF=0.703;AN=2;DP=2345;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1703,159,0:0,0,34,19 chr1 120254545 . G C 720.98 PASS AC=2;AF=0.705;AN=2;DP=3154;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,73:73:99:2175,218,0:0,0,45,28 chr1 120262152 . C T 1497.96 PASS AC=2;AF=0.563;AN=2;DP=999;MQ=60;set=variant2-variant4-variant7-variant9-variant11-variant12-variant17-variant21-variant30-variant31-variant35-variant36-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,66:66:99:2423,198,0:0,0,52,14 chr1 120263018 . T C 2374.47 PASS AC=1;AF=0.5;AN=2;DP=1066;MQ=60;set=variant7-variant11-variant17-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:102,118:220:99:2832,0,2657:43,59,53,65 chr1 120263657 . A G 1631.92 PASS AC=1;AF=0.5;AN=2;DP=518;FractionInformativeReads=1;MQ=60;set=variant7-variant11-variant17-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:52,73:125:99:2050,0,1314:32,20,40,33 chr1 120267282 . AT ATT,ATTT,A 43.21 PASS AC=0,0,1;AF=0.15,0.2,0.175;AN=2;DP=257;set=variant3-variant4-variant5-variant10-variant11-variant13-variant14-variant17-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant33-filterInvariant35-variant41-variant43-variant44 GT:DP:GQ:SB 0/3:22:68:13,2,6,1 chr1 120267287 . T A 290.6 PASS AC=1;AF=0.5;AN=2;DP=51;FractionInformativeReads=1;MQ=60;set=variant12-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:14,10:24:99:273,0,374:11,3,9,1 chr1 120269549 . G A 1662.54 PASS AC=1;AF=0.5;AN=2;DP=462;FractionInformativeReads=1;MQ=60;set=variant12-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:89,91:180:99:2261,0,2152:55,34,57,34 chr1 120285546 . G A 2743.54 PASS AC=2;AF=0.845;AN=2;DP=4529;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,122:122:99:3769,365,0:0,0,68,54 chr1 120293367 . T C 3991.38 PASS AC=2;AF=0.833;AN=2;DP=5835;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,164:164:99:4965,448,0:0,0,97,67 chr1 120293748 . T G 295.68 PASS AC=2;AF=0.872;AN=2;DP=516;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:456,42,0:0,0,5,9 chr1 120296033 . AACAC A,AACACAC,AAC,AACACACAC 98.57 PASS AC=0,0,2,0;AF=0.107,0.196,0.482,0.018;AN=2;DP=380;FS=0;set=variant-variant2-variant3-variant5-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant24-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant41-variant42-variant44 GT:DP:GQ:SB 3/3:11:33:0,0,2,9 chr1 120307084 . C T 2904.15 PASS AC=1;AF=0.5;AN=2;DP=234;FS=0;FractionInformativeReads=0.991;MQ=60;MQRankSum=1.787;QD=12.41;ReadPosRankSum=0.126;SOR=0.693;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:116,116:232:99:2932,0,2927:55,61,55,61 chr1 120336857 . G C 1298.88 PASS AC=1;AF=0.5;AN=2;DP=351;FractionInformativeReads=1;MQ=60;set=variant18-variant23-variant35 GT:AD:DP:GQ:PL:SB 0/1:55,64:119:99:1704,0,1347:27,28,30,34 chr1 120336876 . T G 1494.09 PASS AC=2;AF=0.688;AN=2;DP=2483;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant35-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,108:108:99:4389,331,0:0,0,52,56 chr1 120337384 . T C 665.91 PASS AC=2;AF=0.688;AN=2;DP=714;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant35-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:953,96,0:0,0,12,20 chr1 120337403 . A G 440.92 PASS AC=2;AF=0.688;AN=2;DP=497;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant35-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:663,60,0:0,0,5,15 chr1 120341385 . C T 76.67 PASS AC=1;AF=0.5;AN=2;DP=42;FractionInformativeReads=1;MQ=60;set=variant18-variant23-variant35 GT:AD:DP:GQ:PL:SB 0/1:7,12:19:99:349,0,171:2,5,3,9 chr1 120344044 . G A 1105.29 PASS AC=2;AF=0.648;AN=2;DP=2783;MQ=60;set=variant2-variant3-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant27-variant29-variant30-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,117:117:99:3651,347,0:0,0,50,67 chr1 120344091 . C G 357.44 PASS AC=2;AF=0.654;AN=2;DP=2173;MQ=60;set=variant2-variant3-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant27-variant29-variant30-variant33-variant35-variant36-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,98:98:99:3223,294,0:0,0,47,51 chr1 120344105 . G A 963.22 PASS AC=2;AF=0.757;AN=2;DP=3027;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,94:94:99:3120,281,0:0,0,44,50 chr1 120344134 . T C 821.04 PASS AC=2;AF=0.757;AN=2;DP=2835;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,88:88:99:2927,264,0:0,0,39,49 chr1 120344146 . A G 684.73 PASS AC=2;AF=0.757;AN=2;DP=2750;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,88:88:99:2737,264,0:0,0,38,50 chr1 120344239 . T A 328.51 PASS AC=2;AF=0.654;AN=2;DP=1759;MQ=60;set=variant2-variant3-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant18-variant20-variant21-variant22-variant23-variant24-variant27-variant29-variant30-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:2317,213,0:0,0,34,37 chr1 120344398 . C T 430.57 PASS AC=2;AF=0.66;AN=2;DP=1221;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant7-variant9-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant27-variant29-variant30-variant33-variant35-variant36-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,63:63:99:1815,188,0:0,0,28,35 chr1 120344415 . C G 587.26 PASS AC=2;AF=0.667;AN=2;DP=1585;MQ=60;set=variant2-variant3-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:1814,174,0:0,0,25,33 chr1 120344900 . G A 832.99 PASS AC=2;AF=0.672;AN=2;DP=1275;MQ=60;set=variant2-variant3-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1274,126,0:0,0,22,20 chr1 120344936 . G C 228.83 PASS AC=2;AF=0.757;AN=2;DP=1627;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1240,117,0:0,0,21,18 chr1 120378678 . C T 3315.95 PASS AC=2;AF=0.784;AN=2;DP=5623;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,132:132:99:3849,395,0:0,0,72,60 chr1 120379730 . C CA,CAA 70.44 PASS AC=0,2;AF=0.647,0.147;AN=2;DP=114;set=variant-variant3-variant5-variant9-variant13-variant16-variant17-variant25-variant27-variant28-variant29-variant31-variant33-variant35-variant39-variant40-variant43 GT:DP:GQ:SB 2/2:1:6:0,0,1,0 chr1 120379737 . G A 107.14 PASS AC=2;AF=0.794;AN=2;DP=306;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:90,6,0:0,0,2,0 chr1 120380008 . T A 1340.87 PASS AC=2;AF=0.784;AN=2;DP=2229;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,52:52:99:1696,156,0:0,0,18,34 chr1 120384205 . A G 1874.33 PASS AC=2;AF=0.795;AN=2;DP=5089;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,119:119:99:3493,355,0:0,0,50,69 chr1 120387120 . G A 2242.92 PASS AC=2;AF=0.658;AN=2;DP=2724;set=variant-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,83:84:99:2888,241,0:1,0,18,65 chr1 120390071 . T C 717.87 PASS AC=2;AF=0.818;AN=2;DP=947;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:747,75,0:0,0,13,12 chr1 120462031 . A G 1125.65 PASS AC=1;AF=0.5;AN=2;DP=6615;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-filterInvariant35-variant36-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:125,12:137:99:158,0,6040:65,60,5,7 chr1 120462034 . C T 1119.64 PASS AC=1;AF=0.5;AN=2;DP=6660;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-filterInvariant35-variant36-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:127,14:141:99:261,0,6069:67,60,6,8 chr1 120462040 . A G 1117.09 PASS AC=1;AF=0.5;AN=2;DP=6700;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-filterInvariant35-variant36-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:126,15:141:99:226,0,5965:67,59,7,8 chr1 120462058 . G A 556.42 PASS AC=1;AF=0.5;AN=2;DP=6699;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-filterInvariant30-variant31-variant32-variant33-variant34-filterInvariant35-variant36-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:131,18:149:59:59,0,3602:68,63,8,10 chr1 120462093 . G T 1081.26 PASS AC=1;AF=0.5;AN=2;DP=6070;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-filterInvariant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:121,21:142:99:509,0,30047:59,62,7,14 chr1 120462094 . G A 1165.24 PASS AC=1;AF=0.5;AN=2;DP=6021;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-filterInvariant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:119,21:140:99:500,0,30737:57,62,7,14 chr1 120462103 . G T 1125.65 PASS AC=1;AF=0.5;AN=2;DP=5822;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:120,20:140:99:454,0,32705:58,62,7,13 chr1 120462109 . G A 1131.67 PASS AC=1;AF=0.5;AN=2;DP=5689;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-filterInvariant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:124,20:144:99:467,0,32645:62,62,7,13 chr1 120462118 . A G 972.74 PASS AC=1;AF=0.5;AN=2;DP=5471;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-filterInvariant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:122,18:140:99:383,0,32863:64,58,6,12 chr1 120462136 . T C 897.79 PASS AC=1;AF=0.5;AN=2;DP=5089;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-filterInvariant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-filterInvariant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-filterInvariant35-variant36-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:122,14:136:99:218,0,32899:60,62,4,10 chr1 120462148 . A G 639.83 PASS AC=1;AF=0.5;AN=2;DP=4611;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-filterInvariant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-filterInvariant35-variant36-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:123,13:136:99:170,0,32759:60,63,3,10 chr1 120462166 . A G 315.95 PASS AC=1;AF=0.5;AN=2;DP=4012;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-filterInvariant35-variant36-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:114,13:127:99:182,0,30625:54,60,3,10 chr1 120466547 . A G 411.68 PASS AC=1;AF=0.5;AN=2;DP=8042;MQ=60;set=variant-filterInvariant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-filterInvariant13-variant15-filterInvariant16-variant17-filterInvariant18-variant19-variant20-variant21-variant22-variant23-variant24-filterInvariant25-filterInvariant26-variant27-filterInvariant28-filterInvariant29-filterInvariant31-variant32-variant33-filterInvariant34-variant35-variant36-variant37-variant38-variant39-variant40-filterInvariant41 GT:AD:DP:GQ:PL:SB 0/1:156,19:175:99:413,0,6452:76,80,11,8 chr1 120466548 . C G 408.67 PASS AC=1;AF=0.5;AN=2;DP=8036;FractionInformativeReads=1;MQ=60;set=variant-filterInvariant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-filterInvariant13-variant15-filterInvariant16-variant17-filterInvariant18-variant19-variant20-variant21-variant22-variant23-variant24-filterInvariant25-filterInvariant26-variant27-filterInvariant28-filterInvariant29-filterInvariant31-variant32-variant33-filterInvariant34-variant35-variant36-variant37-variant38-variant39-variant40-filterInvariant41 GT:AD:DP:GQ:PL:SB 0/1:155,20:175:99:413,0,6452:76,79,11,9 chr1 120466556 . C T 406.14 PASS AC=1;AF=0.5;AN=2;DP=7768;FractionInformativeReads=1;MQ=60;set=variant-filterInvariant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-filterInvariant13-variant15-filterInvariant16-variant17-filterInvariant18-variant19-variant20-variant21-variant22-variant23-variant24-filterInvariant25-variant27-filterInvariant28-filterInvariant29-filterInvariant31-variant32-variant33-filterInvariant34-variant35-filterInvariant36-variant37-variant38-variant39-variant40-filterInvariant41 GT:AD:DP:GQ:PL:SB 0/1:156,21:177:99:410,0,6359:77,79,12,9 chr1 120466569 . T C 52.15 PASS AC=1;AF=0.5;AN=2;DP=5331;set=filterInvariant-filterInvariant2-variant3-variant4-variant5-filterInvariant6-variant7-filterInvariant8-filterInvariant9-variant10-variant11-variant12-filterInvariant16-filterInvariant19-filterInvariant20-variant21-variant23-variant24-variant25-filterInvariant33-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant38-filterInvariant39-filterInvariant40-filterInvariant41 GT:AD:DP:GQ:PL:SB 0/1:154,21:175:71:71,0,4304:75,79,13,8 chr1 120467933 . T G 280.05 PASS AC=1;AF=0.5;AN=2;DP=5045;set=filterInvariant-variant2-variant3-variant4-variant5-variant6-variant7-filterInvariant8-variant9-variant10-variant11-variant13-filterInvariant15-variant16-variant17-filterInvariant18-variant20-variant22-variant23-variant24-filterInvariant27-filterInvariant28-variant29-filterInvariant30-variant31-variant32-variant33-filterInvariant35-variant36-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:135,18:153:99:322,0,6429:80,55,11,7 chr1 120467942 . G A 252.97 PASS AC=1;AF=0.5;AN=2;DP=5411;set=filterInvariant-variant2-variant3-variant4-variant5-variant6-variant7-filterInvariant8-variant9-variant10-variant11-variant13-variant15-variant16-variant17-filterInvariant18-variant20-variant22-variant23-variant24-variant27-filterInvariant28-variant29-filterInvariant30-variant31-variant32-variant33-filterInvariant35-variant36-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:145,19:164:99:333,0,6804:85,60,12,7 chr1 120467947 . C T 205 PASS AC=1;AF=0.5;AN=2;DP=5583;set=filterInvariant-variant2-variant3-variant4-variant5-variant6-variant7-filterInvariant8-variant9-variant10-variant11-variant13-variant15-variant16-variant17-filterInvariant18-variant20-variant22-variant23-variant24-variant27-filterInvariant28-variant29-filterInvariant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:146,22:168:99:392,0,6717:84,62,14,8 chr1 120467978 . G T 360.25 PASS AC=1;AF=0.5;AN=2;DP=6863;set=filterInvariant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-filterInvariant14-filterInvariant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-filterInvariant26-variant27-variant28-variant29-filterInvariant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:175,24:199:99:466,0,8127:96,79,14,10 chr1 120467979 . A G 357.26 PASS AC=1;AF=0.5;AN=2;DP=6890;set=filterInvariant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-filterInvariant14-filterInvariant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-filterInvariant26-variant27-variant28-variant29-filterInvariant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:176,24:200:99:460,0,8170:97,79,14,10 chr1 120467981 . C A 338.89 PASS AC=1;AF=0.5;AN=2;DP=6933;FractionInformativeReads=1;set=filterInvariant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-filterInvariant14-filterInvariant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-filterInvariant26-variant27-variant28-variant29-filterInvariant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:181,24:205:99:460,0,8170:99,82,14,10 chr1 120468005 . G A 38.95 PASS AC=1;AF=0.5;AN=2;DP=6475;MQ=60;set=filterInvariant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-filterInvariant14-variant16-variant17-variant18-variant20-filterInvariant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-filterInvariant35-variant36-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:199,19:218:99:166,0,8222:102,97,7,12 chr1 120468014 . A G 1459.06 PASS AC=1;AF=0.5;AN=2;DP=5716;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant16-filterInvariant17-variant18-variant20-filterInvariant22-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:184,24:208:99:445,0,7780:89,95,14,10 chr1 120468034 . G A 1481.95 PASS AC=1;AF=0.5;AN=2;DP=5520;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant16-filterInvariant17-variant18-filterInvariant20-filterInvariant22-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:181,24:205:99:538,0,7648:84,97,13,11 chr1 120468038 . G A 1529.89 PASS AC=1;AF=0.5;AN=2;DP=5409;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant16-filterInvariant17-variant18-filterInvariant20-filterInvariant22-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:178,25:203:99:490,0,7918:82,96,13,12 chr1 120468040 . A T 1547.95 PASS AC=1;AF=0.5;AN=2;DP=5159;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant16-filterInvariant17-variant18-filterInvariant20-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:179,25:204:99:493,0,7964:83,96,13,12 chr1 120468061 . C T 2264.17 PASS AC=1;AF=0.5;AN=2;DP=4313;MQ=60;set=variant3-filterInvariant7-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant18-filterInvariant20-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-filterInvariant35-variant36-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:173,22:195:99:391,0,8263:79,94,12,10 chr1 120468065 . G A 2234.22 PASS AC=1;AF=0.5;AN=2;DP=4241;FractionInformativeReads=1;MQ=60;set=variant3-filterInvariant7-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant18-filterInvariant20-variant24-variant26-variant27-variant28-variant29-variant31-variant32-filterInvariant33-variant35-variant36-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:173,23:196:99:442,0,8144:81,92,12,11 chr1 120468071 . A G 2258.3 PASS AC=1;AF=0.5;AN=2;DP=4033;FractionInformativeReads=1;MQ=60;set=variant3-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant18-filterInvariant20-variant24-variant26-variant27-variant28-variant29-variant31-variant32-filterInvariant33-variant35-variant36-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:165,22:187:99:451,0,8077:81,84,10,12 chr1 120468083 . C T 2315.5 PASS AC=1;AF=0.5;AN=2;DP=3911;FractionInformativeReads=1;MQ=60;set=variant3-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant18-filterInvariant20-variant24-variant26-variant27-variant28-variant29-variant31-variant32-filterInvariant33-filterInvariant35-variant36-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:158,21:179:99:385,0,8073:77,81,7,14 chr1 120468086 . A G 2183.51 PASS AC=1;AF=0.5;AN=2;DP=3887;FractionInformativeReads=1;MQ=60;set=variant3-variant8-variant9-variant10-variant11-variant13-filterInvariant14-variant16-variant18-filterInvariant20-variant24-variant26-variant27-variant28-variant29-variant31-variant32-filterInvariant33-variant35-variant36-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:155,22:177:99:487,0,7815:75,80,7,15 chr1 120468101 . A G 1526.72 PASS AC=1;AF=0.5;AN=2;DP=3847;FractionInformativeReads=1;set=variant3-variant8-variant9-variant10-variant11-variant13-filterInvariant14-filterInvariant16-variant18-filterInvariant20-variant24-variant26-variant27-variant28-variant29-variant31-variant32-filterInvariant33-filterInvariant35-variant36-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:157,18:175:99:319,0,8319:74,83,5,13 chr1 120468104 . G A 1439.73 PASS AC=1;AF=0.5;AN=2;DP=3807;set=variant3-variant8-variant9-variant10-variant11-variant13-filterInvariant14-filterInvariant16-variant18-filterInvariant20-variant24-variant26-variant27-variant28-variant29-variant31-variant32-filterInvariant33-filterInvariant35-variant36-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:155,17:172:99:280,0,8397:71,84,5,12 chr1 120468127 . C T 360.04 PASS AC=1;AF=0.5;AN=2;DP=2656;FractionInformativeReads=1;set=variant8-variant10-variant11-variant13-filterInvariant16-filterInvariant24-filterInvariant26-variant27-variant28-filterInvariant29-variant31-filterInvariant33-filterInvariant35-filterInvariant36-filterInvariant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:150,17:167:99:232,0,9111:66,84,5,12 chr1 120468140 . T C 299.99 PASS AC=1;AF=0.5;AN=2;DP=2235;FractionInformativeReads=1;set=filterInvariant8-variant10-filterInvariant11-variant13-filterInvariant16-filterInvariant24-filterInvariant26-filterInvariant27-filterInvariant29-variant31-filterInvariant35-filterInvariant36-filterInvariant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:144,15:159:99:187,0,8826:64,80,4,11 chr1 120468146 . G A 323.92 PASS AC=1;AF=0.5;AN=2;DP=1741;FractionInformativeReads=1;set=filterInvariant8-variant10-filterInvariant11-variant13-filterInvariant26-filterInvariant27-variant31-filterInvariant35-filterInvariant36-filterInvariant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:140,14:154:99:148,0,8930:66,74,4,10 chr1 120468152 . A G 284.94 PASS AC=1;AF=0.5;AN=2;DP=1918;FractionInformativeReads=1;set=filterInvariant8-variant10-filterInvariant11-variant13-filterInvariant24-filterInvariant26-filterInvariant27-variant31-filterInvariant35-filterInvariant36-filterInvariant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:140,13:153:99:148,0,9160:66,74,4,9 chr1 120468158 . G A 264.02 PASS AC=1;AF=0.5;AN=2;DP=1927;FractionInformativeReads=1;set=filterInvariant8-variant10-filterInvariant11-variant13-filterInvariant24-filterInvariant26-filterInvariant27-variant31-filterInvariant35-filterInvariant36-filterInvariant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:140,12:152:76:76,0,9069:67,73,3,9 chr1 120469077 . T C 253.12 PASS AC=1;AF=0.5;AN=2;DP=275;FractionInformativeReads=1;MQ=60;set=variant2-variant11-variant12-variant17-variant22-variant24-variant25-variant30-variant31-variant32-variant35-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,14:23:99:496,0,292:7,2,12,2 chr1 120471424 . C T 330.65 PASS AC=2;AF=1;AN=2;DP=318;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:181,15,0:0,0,4,1 chr1 120478285 . T C 2133.06 PASS AC=2;AF=0.784;AN=2;DP=2680;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,66:66:99:1939,198,0:0,0,25,41 chr1 120480394 . T C 458.54 PASS AC=2;AF=0.989;AN=2;DP=552;MQ=60;MQRankSum=-1.109;ReadPosRankSum=0.471;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:499,39,0:0,0,11,2 chr1 120505996 . G C 1197.82 PASS AC=2;AF=0.795;AN=2;DP=1366;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1145,99,0:0,0,25,8 chr1 120512104 . T C 792.38 PASS AC=2;AF=0.989;AN=2;DP=1751;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1756,147,0:0,0,37,12 chr1 120539331 . C T 3355.88 PASS AC=1;AF=0.5;AN=2;DP=13284;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:181,179:360:99:4154,0,4312:94,87,95,84 chr1 120572547 . T C 100.77 PASS AC=1;AF=0.524;AN=2;DP=120;FractionInformativeReads=1;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant13-variant15-variant21-variant22-filterInvariant24-variant25-variant26-variant28-variant29-variant31-variant35-variant36-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,4:6:60:115,0,60:2,0,4,0 chr1 120572572 . C T 181.74 PASS AC=1;AF=0.543;AN=2;DP=159;FS=0;FractionInformativeReads=1;set=variant-variant4-variant5-variant7-variant8-variant9-variant13-filterInvariant14-variant15-variant21-filterInvariant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant34-variant35-variant36-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,6:8:54:189,0,54:2,0,6,0 chr1 120611496 . C A 223.68 PASS AC=1;AF=0.5;AN=2;DP=3895;set=filterInvariant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant18-filterInvariant21-filterInvariant22-variant25-variant26-filterInvariant27-variant28-variant29-variant31-filterInvariant32-filterInvariant33-variant34-variant35-variant36-filterInvariant39-variant42-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:182,26:208:99:526,0,8404:99,83,8,18 chr1 120611498 . G C 223.68 PASS AC=1;AF=0.5;AN=2;DP=3748;set=filterInvariant-filterInvariant2-variant4-variant5-filterInvariant6-filterInvariant7-variant8-variant11-filterInvariant12-variant14-variant15-filterInvariant18-filterInvariant21-filterInvariant22-filterInvariant25-variant26-filterInvariant27-variant28-filterInvariant29-filterInvariant32-filterInvariant33-variant34-variant35-variant36-filterInvariant39-variant42-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:180,24:204:99:526,0,8404:99,81,8,16 chr1 120611554 . T C 379.97 PASS AC=1;AF=0.5;AN=2;DP=10721;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-filterInvariant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:272,82:354:99:2616,0,11932:142,130,46,36 chr1 120611555 . T G 379.97 PASS AC=1;AF=0.5;AN=2;DP=10554;set=variant-variant2-filterInvariant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-filterInvariant20-variant21-variant22-filterInvariant24-variant25-filterInvariant26-variant27-variant28-filterInvariant29-variant30-variant31-filterInvariant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:273,83:356:99:2616,0,11932:143,130,46,37 chr1 120611715 . A G 2128.3 PASS AC=1;AF=0.5;AN=2;DP=11031;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:241,107:348:99:2053,0,6074:106,135,63,44 chr1 120611758 . G A 2404.29 PASS AC=1;AF=0.5;AN=2;DP=9977;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:163,142:305:99:3281,0,4198:70,93,77,65 chr1 120611830 . G A 2778.25 PASS AC=1;AF=0.5;AN=2;DP=9595;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:157,161:318:99:3856,0,4053:83,74,93,68 chr1 120611876 . C T 3138.46 PASS AC=1;AF=0.5;AN=2;DP=11649;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:205,198:403:99:4516,0,5007:114,91,112,86 chr1 120611964 . G C 4194.6 PASS AC=1;AF=0.5;AN=2;DP=17085;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-filterInvariant34-variant35-variant36-variant37-filterInvariant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:314,269:583:99:6132,0,7334:164,150,139,130 chr1 120612006 . G A,C 3792.33 PASS AC=1,0;AF=0.474,0.026;AN=2;DP=16229;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-filterInvariant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:524:99:141,123,121,139 chr1 120612040 . T TCCTCCGCCG,TCCGCCGCCGCCGCCGCCGCCGCCGCCGCCG,TCCTCCTCCG,TCCGCCGCCG,TCCGCCGCCGCCGCCGCCGCCGCCG,TCCTCCGCCGCCG,TCCGCCGCCGCCG 2304.84 PASS AC=1,0,0,0,0,0,0;AF=0.286,0.024,0.071,0.06,0.012,0.024,0.024;AN=2;DP=16558;set=variant-variant2-filterInvariant3-variant4-variant5-variant6-variant7-variant8-variant9-filterInvariant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-filterInvariant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:408:99:129,115,71,93 chr1 120612154 . C G 1568.54 PASS AC=1;AF=0.5;AN=2;DP=12396;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-filterInvariant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:278,72:350:99:2212,0,11224:111,167,35,37 chr1 120612163 . C A 1581.53 PASS AC=1;AF=0.5;AN=2;DP=12075;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-filterInvariant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:260,74:334:99:2260,0,10777:105,155,35,39 chr1 120612168 . C T 647.01 PASS AC=1;AF=0.5;AN=2;DP=9620;set=variant-filterInvariant2-variant4-variant5-variant6-filterInvariant7-variant8-variant9-variant11-filterInvariant12-variant13-variant14-variant15-variant16-variant18-variant19-filterInvariant20-variant21-filterInvariant22-variant23-variant24-variant25-variant26-variant27-variant28-filterInvariant29-variant32-variant33-variant35-variant36-filterInvariant37-variant40-variant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:231,95:326:99:1664,0,7309:104,127,33,62 chr1 120612265 . A G 278.36 PASS AC=1;AF=0.5;AN=2;DP=4799;set=variant-filterInvariant2-variant3-filterInvariant4-variant5-variant6-filterInvariant7-variant8-variant9-variant10-variant11-filterInvariant12-variant13-variant14-variant15-variant16-variant17-filterInvariant18-variant19-variant20-variant21-filterInvariant22-variant23-variant24-variant25-filterInvariant26-variant27-filterInvariant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-filterInvariant40-filterInvariant41-variant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:87,31:118:99:786,0,2257:32,55,1,30 chr1 120612269 . A G 71.02 PASS AC=1;AF=0.5;AN=2;DP=643;set=filterInvariant4-variant8-filterInvariant11-filterInvariant20-filterInvariant35-filterInvariant42 GT:AD:DP:GQ:PL:SB 0/1:103,14:117:99:130,0,4114:31,72,1,13 chr1 120904791 . A G 1586.55 PASS AC=2;AF=0.888;AN=2;DP=2557;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:2277,186,0:0,0,33,29 chr1 120925663 . C T 1850.42 PASS AC=2;AF=1;AN=2;DP=1944;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1222,123,0:0,0,14,27 chr1 120927081 . C T 64.76 PASS AC=2;AF=0.691;AN=2;DP=511;set=filterInvariant-variant2-variant5-variant6-filterInvariant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant19-filterInvariant20-variant21-filterInvariant22-filterInvariant23-variant24-variant25-variant27-variant28-variant29-filterInvariant31-variant32-variant33-variant34-filterInvariant35-variant36-filterInvariant40-variant41-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,18:19:25:509,25,0:1,0,15,3 chr1 121115761 . T G 147.58 PASS AC=1;AF=0.5;AN=2;DP=1749;set=variant-filterInvariant2-variant3-variant4-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant11-filterInvariant12-filterInvariant13-variant14-variant15-filterInvariant16-variant17-filterInvariant18-variant19-variant20-variant21-filterInvariant23-variant24-filterInvariant25-variant27-filterInvariant28-filterInvariant29-filterInvariant30-variant31-filterInvariant32-filterInvariant33-filterInvariant34-variant35-variant36-variant37-variant38-variant39-filterInvariant40-variant41-filterInvariant42-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:33,12:45:99:277,0,1156:32,1,12,0 chr1 121115786 . C A 294.44 PASS AC=1;AF=0.5;AN=2;DP=2916;set=variant-filterInvariant2-variant3-variant4-variant5-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-variant10-filterInvariant11-variant12-filterInvariant13-variant14-variant15-filterInvariant16-variant17-filterInvariant18-variant19-variant20-variant21-filterInvariant22-variant23-variant24-variant25-filterInvariant26-filterInvariant27-variant28-filterInvariant29-variant30-variant31-variant33-variant34-filterInvariant35-variant36-filterInvariant37-variant38-variant39-filterInvariant40-variant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:49,23:72:99:586,0,1413:39,10,23,0 chr1 121116647 . T A 505.67 PASS AC=1;AF=0.5;AN=2;DP=7628;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-filterInvariant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant27-variant28-variant29-variant32-variant33-variant35-filterInvariant36-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:161,100:261:99:1689,0,4092:99,62,53,47 chr1 121116678 . C T 2763.67 PASS AC=1;AF=0.531;AN=2;DP=8232;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:116,190:306:99:5066,0,4143:54,62,115,75 chr1 121116688 . A G 2955.37 PASS AC=1;AF=0.529;AN=2;DP=9195;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:120,200:320:99:7798,0,2044:50,70,118,82 chr1 121116733 . A G 80.24 PASS AC=1;AF=0.5;AN=2;DP=9826;set=filterInvariant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-filterInvariant12-variant13-variant14-variant15-filterInvariant16-variant17-variant18-filterInvariant19-variant20-filterInvariant23-variant24-variant25-variant27-filterInvariant28-variant32-variant33-variant35-variant38-variant39-filterInvariant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:251,90:341:99:1525,0,6581:137,114,32,58 chr1 121116933 . T C 1061.74 PASS AC=2;AF=0.676;AN=2;DP=1807;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,64:64:99:2262,192,0:0,0,12,52 chr1 121116953 . A G 984.23 PASS AC=2;AF=0.671;AN=2;DP=1222;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1551,126,0:0,0,6,36 chr1 121124501 . C A 95.97 PASS AC=1;AF=0.5;AN=2;DP=128;FractionInformativeReads=1;set=variant7-variant9-variant23-variant26-variant29-variant32-variant33-variant35-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:6,5:11:99:99,0,141:3,3,3,2 chr1 121124514 . G A 132.71 PASS AC=1;AF=0.5;AN=2;DP=83;FractionInformativeReads=1;set=variant7-variant26-variant29-variant33-variant35-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:6,4:10:69:69,0,148:3,3,2,2 chr1 142542708 . G T 62.36 PASS AC=1;AF=0.5;AN=2;DP=696;set=variant-variant2-variant3-variant6-variant7-variant8-filterInvariant9-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,8:25:99:285,0,669:14,3,7,1 chr1 142542709 . G T 62.36 PASS AC=1;AF=0.5;AN=2;DP=704;set=variant-variant2-variant3-variant6-variant7-variant8-filterInvariant9-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant26-filterInvariant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,8:25:99:282,0,711:14,3,7,1 chr1 142542710 . A C 62.36 PASS AC=1;AF=0.5;AN=2;DP=691;set=variant-variant2-variant3-variant6-variant7-variant8-filterInvariant9-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant26-filterInvariant28-variant29-variant30-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,8:25:99:282,0,711:14,3,7,1 chr1 142542768 . G C 145.05 PASS AC=1;AF=0.5;AN=2;DP=422;set=variant6-filterInvariant8-filterInvariant20-variant23-filterInvariant30-filterInvariant35-variant38-variant40-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:52,6:58:78:78,0,1741:34,18,5,1 chr1 142542830 . C T 854.23 PASS AC=1;AF=0.5;AN=2;DP=3521;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,35:78:99:847,0,1223:25,18,18,17 chr1 142542921 . A G 1087.04 PASS AC=1;AF=0.5;AN=2;DP=3564;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-filterInvariant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-filterInvariant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,31:81:99:1071,0,1987:24,26,15,16 chr1 142542922 . G A 1087.04 PASS AC=1;AF=0.5;AN=2;DP=3522;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-filterInvariant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-filterInvariant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,29:80:99:1071,0,1987:24,27,13,16 chr1 142542976 . T G 1356.05 PASS AC=2;AF=0.83;AN=2;DP=2290;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:1820,171,0:0,0,20,37 chr1 142667293 . C A 36.71 PASS AC=1;AF=0.5;AN=2;DP=172;set=filterInvariant2-filterInvariant10-filterInvariant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:50,11:61:99:150,0,1199:25,25,6,5 chr1 142667306 . C T 202.59 PASS AC=1;AF=0.5;AN=2;DP=1616;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-filterInvariant14-variant15-variant16-variant17-filterInvariant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-filterInvariant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,14:68:99:210,0,1355:27,27,8,6 chr1 142667399 . A G 212.86 PASS AC=1;AF=0.5;AN=2;DP=1369;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-filterInvariant11-variant12-variant14-variant15-variant16-variant17-filterInvariant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,12:42:99:208,0,839:11,19,5,7 chr1 142813098 . T C 49.04 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=1261;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:21,8:29:99:137,0,569:19,2,8,0 chr1 142813414 . T G 194.59 PASS AC=1;AF=0.5;AN=2;DP=470;FractionInformativeReads=1;set=variant3-variant8-filterInvariant9-filterInvariant12-filterInvariant14-variant19-variant21-variant24-filterInvariant25-variant26-variant27-variant31-variant35-variant37-filterInvariant38 GT:AD:DP:GQ:PL:SB 0/1:15,10:25:99:323,0,533:1,14,0,10 chr1 142824953 . T C 163.65 PASS AC=1;AF=0.5;AN=2;DP=1202;set=variant-variant3-variant4-filterInvariant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-filterInvariant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant35-filterInvariant36-filterInvariant37-variant38-variant39-variant40-filterInvariant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,11:37:99:240,0,740:19,7,8,3 chr1 142825124 . T C 597.79 PASS AC=1;AF=0.5;AN=2;DP=1127;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-filterInvariant21-variant22-filterInvariant24-variant25-variant26-variant30-variant31-variant32-variant33-variant35-variant36-filterInvariant37-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,5:27:99:118,0,553:8,14,0,5 chr1 142826166 . C T 61.62 PASS AC=1;AF=0.5;AN=2;DP=20;set=variant3-variant35 GT:AD:DP:GQ:PL:SB 0/1:1,2:3:36:81,0,36:1,0,2,0 chr1 142826178 . G A 165.08 PASS AC=1;AF=0.594;AN=2;DP=478;set=variant-variant3-variant4-variant5-variant6-variant7-filterInvariant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant22-variant24-variant25-variant26-variant29-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:1,2:3:36:81,0,36:1,0,2,0 chr1 142826248 . C T 144.38 PASS AC=1;AF=0.5;AN=2;DP=1153;set=variant4-variant5-variant6-filterInvariant8-filterInvariant11-filterInvariant13-variant14-variant15-variant16-filterInvariant17-variant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-variant26-filterInvariant27-filterInvariant30-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:21,6:27:93:93,0,632:19,2,6,0 chr1 142826355 . CA C 2560.03 PASS AC=1;AF=0.5;AN=2;DP=5351;set=variant3-filterInvariant4-variant6-filterInvariant7-variant8-filterInvariant10-filterInvariant12-variant14-variant15-variant19-variant21-filterInvariant23-filterInvariant24-variant25-filterInvariant26-filterInvariant27-filterInvariant28-variant31-filterInvariant32-filterInvariant33-variant34-variant35-variant37-variant39-filterInvariant40-filterInvariant42 GT:AD:DP:GQ:PL:SB 0/1:88,30:118:99:755,0,2992:54,34,15,15 chr1 142826369 . C A 2438.06 PASS AC=2;AF=0.614;AN=2;DP=8960;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,125:125:99:4009,375,0:0,0,68,57 chr1 142826454 . A G 519.15 PASS AC=1;AF=0.5;AN=2;DP=1435;set=variant3-variant8-filterInvariant19-variant21-filterInvariant25-filterInvariant27-variant31-variant35-filterInvariant37 GT:AD:DP:GQ:PL:SB 0/1:69,17:86:99:223,0,1866:20,49,7,10 chr1 142826519 . T A 1872.91 PASS AC=2;AF=1;AN=2;DP=1933;FS=0;MQRankSum=0.276;ReadPosRankSum=-0.377;set=variant-variant2-variant3-variant4-variant5-filterInvariant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-filterInvariant25-filterInvariant26-variant27-variant28-variant29-filterInvariant30-variant31-variant32-variant33-variant34-filterInvariant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:722,66,0:0,0,0,22 chr1 143163656 . G A 39.99 PASS AC=1;AF=0.5;AN=2;DP=583;set=variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant15-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-filterInvariant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,3:21:99:115,0,721:11,7,3,0 chr1 143163673 . C G 45.41 PASS AC=1;AF=0.5;AN=2;DP=565;set=filterInvariant3-variant4-variant5-variant8-variant9-variant15-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant27-variant29-filterInvariant30-variant31-variant32-variant34-variant35-variant36-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,5:25:99:106,0,829:13,7,4,1 chr1 143163706 . A T 166.36 PASS AC=1;AF=0.5;AN=2;DP=566;set=variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant15-variant17-variant18-variant19-variant22-variant24-variant25-filterInvariant27-variant34-variant35-filterInvariant37-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,4:26:99:123,0,898:13,9,3,1 chr1 143163708 . C T 166.36 PASS AC=1;AF=0.5;AN=2;DP=687;set=variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant15-variant17-variant18-variant19-variant22-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,5:27:99:123,0,898:13,9,3,2 chr1 143163731 . C A 44.77 PASS AC=1;AF=0.5;AN=2;DP=710;FractionInformativeReads=1;set=filterInvariant3-variant6-variant8-filterInvariant9-variant11-variant12-variant13-filterInvariant14-variant16-filterInvariant18-variant19-variant20-variant21-variant23-variant24-variant28-variant30-variant33-variant35-filterInvariant36-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:24,10:34:99:151,0,856:14,10,5,5 chr1 143163749 . A C 215.6 PASS AC=1;AF=0.512;AN=2;DP=1244;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,22:34:99:803,0,296:7,5,11,11 chr1 143163799 . G A 32.09 PASS AC=1;AF=0.5;AN=2;DP=685;FractionInformativeReads=1;set=filterInvariant4-variant6-variant8-filterInvariant9-variant11-variant12-variant13-variant14-variant16-variant19-variant23-variant24-variant27-variant28-filterInvariant29-variant33-variant35-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:34,10:44:99:138,0,1123:16,18,4,6 chr1 143163816 . G A 46.46 PASS AC=1;AF=0.5;AN=2;DP=726;FractionInformativeReads=1;set=variant-variant2-variant3-variant5-filterInvariant6-variant7-variant8-variant9-filterInvariant11-variant16-variant18-filterInvariant19-variant22-variant25-variant26-variant30-filterInvariant31-variant33-variant35-variant36-variant37-filterInvariant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,11:41:99:158,0,859:14,16,5,6 chr1 143210174 . C G 108.5 PASS AC=1;AF=0.5;AN=2;DP=2307;set=filterInvariant2-variant3-filterInvariant5-filterInvariant8-filterInvariant10-variant12-filterInvariant13-filterInvariant14-variant15-filterInvariant17-filterInvariant18-filterInvariant19-variant20-variant22-variant24-variant25-filterInvariant27-variant32-variant35-filterInvariant36-filterInvariant38-filterInvariant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:65,16:81:99:201,0,1710:31,34,7,9 chr1 143210193 . G GT,GTT 67.25 PASS AC=1,0;AF=0.455,0.045;AN=2;DP=1033;set=filterInvariant2-filterInvariant4-filterInvariant9-filterInvariant10-filterInvariant18-filterInvariant23-filterInvariant25-variant32-filterInvariant35-filterInvariant38-filterInvariant42 GT:DP:GQ:SB 0/1:84:83:35,38,4,7 chr1 143210233 . CT C 168.41 PASS AC=1;AF=0.5;AN=2;DP=2417;set=variant-variant3-filterInvariant4-filterInvariant6-variant7-variant9-variant10-variant11-variant12-filterInvariant14-variant16-variant17-filterInvariant18-variant19-filterInvariant20-filterInvariant21-filterInvariant26-variant29-filterInvariant31-filterInvariant33-filterInvariant35-filterInvariant37-variant38-variant39-filterInvariant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:70,8:78:99:122,0,2870:29,41,4,4 chr1 143210241 . A C 426.31 PASS AC=1;AF=0.5;AN=2;DP=930;set=variant3-filterInvariant4-variant11-filterInvariant14-filterInvariant16-variant17-filterInvariant18-filterInvariant19-filterInvariant26-filterInvariant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:70,8:78:99:119,0,2893:28,42,4,4 chr1 143210260 . T A 242.61 PASS AC=1;AF=0.5;AN=2;DP=2479;set=variant-variant3-filterInvariant4-variant6-filterInvariant7-variant9-variant10-variant11-variant12-variant14-filterInvariant15-variant16-variant17-filterInvariant18-variant19-variant20-filterInvariant22-filterInvariant24-filterInvariant26-variant29-variant31-filterInvariant33-filterInvariant35-filterInvariant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,8:73:99:134,0,1925:27,38,4,4 chr1 143210284 . C A 214.86 PASS AC=1;AF=0.5;AN=2;DP=1676;FractionInformativeReads=1;set=variant-filterInvariant3-filterInvariant4-variant6-filterInvariant8-variant9-variant10-variant11-variant12-filterInvariant15-variant16-filterInvariant18-filterInvariant20-filterInvariant24-variant29-variant31-filterInvariant33-filterInvariant35-variant37-variant38-filterInvariant39-filterInvariant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,6:58:96:96,0,1624:19,33,2,4 chr1 143210303 . T G 217.45 PASS AC=1;AF=0.5;AN=2;DP=1875;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-filterInvariant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-filterInvariant21-variant22-variant24-variant25-variant27-filterInvariant29-variant31-variant32-filterInvariant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,10:51:99:256,0,1100:17,24,2,8 chr1 143376703 . A T 61.77 PASS AC=2;AF=0.8;AN=2;DP=90;FS=0;FractionInformativeReads=1;SOR=0.693;set=filterInvariant2-variant8-filterInvariant11-filterInvariant13-filterInvariant15-filterInvariant17-filterInvariant23-filterInvariant26-filterInvariant29-filterInvariant31-filterInvariant34-filterInvariant35-filterInvariant37-filterInvariant38-filterInvariant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:180,12,0:0,0,2,2 chr1 143376705 . A C 61.77 PASS AC=2;AF=0.8;AN=2;DP=90;FS=0;FractionInformativeReads=1;SOR=0.693;set=filterInvariant2-variant8-filterInvariant11-filterInvariant13-filterInvariant15-filterInvariant17-filterInvariant23-filterInvariant26-filterInvariant29-filterInvariant31-filterInvariant34-filterInvariant35-filterInvariant37-filterInvariant38-filterInvariant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:180,12,0:0,0,2,2 chr1 143378110 . A G 352.44 PASS AC=1;AF=0.5;AN=2;DP=501;FractionInformativeReads=1;set=variant2-variant4-variant6-variant8-filterInvariant13-filterInvariant29-variant35 GT:AD:DP:GQ:PL:SB 0/1:36,17:53:99:331,0,901:24,12,11,6 chr1 143424027 . A C 41.5 PASS AC=2;AF=0.741;AN=2;DP=147;FS=0;FractionInformativeReads=1;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant20-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-filterInvariant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:119,9,0:0,0,3,0 chr1 143767312 . G T 242.84 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=1726;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:41,12:53:99:164,0,1036:36,5,12,0 chr1 143767513 . A T 5010.51 PASS AC=1;AF=0.5;AN=2;DP=27507;set=variant-filterInvariant2-variant3-variant4-variant5-filterInvariant6-variant7-filterInvariant8-variant9-variant10-variant11-variant12-filterInvariant13-variant14-variant15-filterInvariant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-filterInvariant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:466,204:670:99:6915,0,18508:214,252,90,114 chr1 143767522 . A G 4756.18 PASS AC=1;AF=0.5;AN=2;DP=26956;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:457,194:651:99:6829,0,18275:210,247,83,111 chr1 143767547 . G A 3632.87 PASS AC=1;AF=0.5;AN=2;DP=22221;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-filterInvariant17-variant18-variant19-filterInvariant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-filterInvariant37-variant38-variant39-variant40-variant41-filterInvariant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:413,156:569:99:2522,0,9987:195,218,62,94 chr1 143767628 . C T 352.58 PASS AC=1;AF=0.5;AN=2;DP=5273;set=filterInvariant2-variant6-filterInvariant7-filterInvariant8-filterInvariant11-filterInvariant15-filterInvariant16-filterInvariant19-filterInvariant22-filterInvariant23-filterInvariant28-variant30-variant34-filterInvariant35-filterInvariant36-filterInvariant38-filterInvariant39-variant40-filterInvariant41 GT:AD:DP:GQ:PL:SB 0/1:275,39:314:99:311,0,7710:125,150,6,33 chr1 143767643 . T C 749.77 PASS AC=1;AF=0.5;AN=2;DP=9706;set=variant-filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant5-variant6-variant7-filterInvariant8-filterInvariant10-filterInvariant11-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant28-filterInvariant29-filterInvariant30-filterInvariant32-filterInvariant33-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant38-filterInvariant39-filterInvariant40-variant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:248,51:299:99:563,0,6732:125,123,11,40 chr1 144013853 . T C 707.65 PASS AC=1;AF=0.5;AN=2;DP=8614;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-filterInvariant20-variant21-filterInvariant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-filterInvariant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:143,56:199:99:1285,0,3717:85,58,35,21 chr1 144013865 . T G 905.04 PASS AC=1;AF=0.5;AN=2;DP=9730;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:160,61:221:99:1261,0,4283:92,68,35,26 chr1 144014051 . G A 675.35 PASS AC=1;AF=0.5;AN=2;DP=5824;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-filterInvariant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:88,31:119:99:666,0,3534:32,56,9,22 chr1 144014068 . T C 972.73 PASS AC=1;AF=0.5;AN=2;DP=4700;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:37,58:95:99:1882,0,894:12,25,15,43 chr1 144052641 . CAAAAA CAAA,CAA,CA,C,CAAAAAA,CAAAA 221.22 PASS AC=0,1,0,0,0,0;AF=0.097,0.21,0.113,0.032,0.016,0.048;AN=2;DP=1647;set=variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-filterInvariant12-variant13-variant15-variant16-variant17-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant34-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:48:99:12,11,24,1 chr1 144615138 . T G 398.39 PASS AC=1;AF=0.529;AN=2;DP=1012;set=variant2-filterInvariant4-filterInvariant10-variant11-variant13-filterInvariant19-variant20-variant23-variant24-variant26-variant27-filterInvariant30-variant32-variant35-variant36-variant37-filterInvariant40 GT:AD:DP:GQ:PL:SB 0/1:79,35:114:99:593,0,1958:48,31,22,13 chr1 144615250 . G GAA 2343.51 PASS AC=1;AF=0.5;AN=2;DP=1982;set=variant2-variant4-variant11-variant13-variant19-variant20-variant23-variant24-variant26-variant27-variant30-variant32-variant35-variant36-variant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:91,58:149:99:2127,0,3750:44,47,26,32 chr1 144617119 . A C 562.37 PASS AC=1;AF=0.681;AN=2;DP=2158;set=variant-variant2-variant3-variant4-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-filterInvariant33-filterInvariant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-filterInvariant42 GT:AD:DP:GQ:PL:SB 0/1:71,14:85:99:327,0,1920:47,24,14,0 chr1 144617251 . A G 1353.8 PASS AC=1;AF=0.5;AN=2;DP=2052;set=variant2-variant4-variant10-variant11-variant13-variant19-variant20-variant23-variant24-variant26-variant27-variant30-variant32-variant35-variant36-variant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:66,66:132:99:1582,0,1607:24,42,30,36 chr1 144617992 . T A 113.81 PASS AC=1;AF=0.5;AN=2;DP=1683;set=variant2-variant4-variant6-variant10-variant11-variant12-variant13-variant14-filterInvariant15-filterInvariant16-variant20-variant21-variant22-filterInvariant23-variant25-variant26-variant27-variant28-variant29-filterInvariant34-variant35-variant40-filterInvariant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,15:71:99:523,0,2900:42,14,12,3 chr1 144617994 . A G 95.79 PASS AC=1;AF=0.5;AN=2;DP=1909;set=filterInvariant2-variant4-variant6-variant10-variant11-variant12-variant13-variant14-filterInvariant15-filterInvariant16-variant20-variant21-variant22-variant23-filterInvariant24-variant25-variant26-variant27-variant28-variant29-variant34-variant35-filterInvariant36-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,17:73:99:610,0,2888:41,15,14,3 chr1 144618000 . G A 107.14 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=596;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:76,13:89:99:100,0,3810:53,23,10,3 chr1 144618009 . A G 969.59 PASS AC=1;AF=0.5;AN=2;DP=4356;set=variant2-variant4-variant5-variant6-filterInvariant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-filterInvariant39-variant40-variant41-variant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:75,52:127:99:1345,0,1853:50,25,41,11 chr1 144618070 . G A 1779.77 PASS AC=1;AF=0.5;AN=2;DP=9246;set=variant-filterInvariant2-variant3-variant4-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant23-filterInvariant24-variant25-variant26-variant27-filterInvariant28-filterInvariant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:256,72:328:99:947,0,5621:142,114,42,30 chr1 144618123 . C T 491.59 PASS AC=1;AF=0.5;AN=2;DP=3352;set=filterInvariant2-filterInvariant5-filterInvariant6-filterInvariant11-filterInvariant22-filterInvariant24-filterInvariant28-filterInvariant29-filterInvariant35-variant40-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:316,65:381:99:455,0,7076:149,167,32,33 chr1 144618144 . A G 2855.35 PASS AC=2;AF=0.852;AN=2;DP=11016;set=variant-filterInvariant2-variant3-variant4-filterInvariant5-filterInvariant6-variant7-variant8-variant9-filterInvariant10-filterInvariant11-variant12-filterInvariant13-variant14-filterInvariant15-filterInvariant16-variant17-variant18-variant19-variant20-variant21-filterInvariant22-filterInvariant23-filterInvariant24-variant25-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant29-variant30-variant31-variant32-variant33-variant34-filterInvariant35-variant36-variant37-variant38-variant39-filterInvariant40-variant41-variant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 1/1:1,329:330:99:9849,986,0:1,0,146,183 chr1 144618201 . T C 448.97 PASS AC=1;AF=0.5;AN=2;DP=3238;set=filterInvariant2-filterInvariant3-filterInvariant4-variant5-filterInvariant6-filterInvariant8-variant9-variant10-filterInvariant11-variant12-filterInvariant13-filterInvariant15-variant16-filterInvariant18-filterInvariant19-variant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-variant25-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant29-filterInvariant30-filterInvariant31-variant32-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant38-variant40-variant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:88,26:114:99:327,0,2247:34,54,0,26 chr1 144619272 . T C 603.14 PASS AC=1;AF=0.5;AN=2;DP=1587;set=variant2-variant4-variant11-variant13-variant19-variant20-variant23-variant24-variant26-variant27-variant30-variant32-variant35-variant36-variant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:79,32:111:99:704,0,2124:49,30,27,5 chr1 144619318 . G A 3144.9 PASS AC=1;AF=0.676;AN=2;DP=6475;set=variant-variant2-variant3-variant4-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:113,77:190:99:1656,0,2988:69,44,48,29 chr1 144619346 . G A 4440.23 PASS AC=1;AF=0.635;AN=2;DP=8375;set=variant-variant2-variant3-variant4-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:149,93:242:99:3426,0,6223:84,65,56,37 chr1 144619354 . C T 3567.23 PASS AC=1;AF=0.5;AN=2;DP=3759;FractionInformativeReads=1;set=variant2-variant4-variant10-variant11-variant13-variant19-variant20-variant23-variant24-variant26-variant27-variant30-variant32-variant35-variant36-variant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:157,100:257:99:3632,0,6285:85,72,60,40 chr1 144619483 . A C 5031.2 PASS AC=1;AF=0.654;AN=2;DP=6841;set=variant-variant2-variant3-variant4-filterInvariant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-filterInvariant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:81,97:178:99:2534,0,1895:30,51,44,53 chr1 144621522 . A C 248.81 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=1461;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:207,24:231:99:357,0,10237:116,91,13,11 chr1 144621526 . G A 279.72 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=1509;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:207,27:234:99:419,0,10262:112,95,14,13 chr1 144621555 . A G 45.12 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=1326;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:209,36:245:99:174,0,5185:109,100,18,18 chr1 144676646 . T C 185.66 PASS AC=1;AF=0.6;AN=2;DP=2074;set=filterInvariant3-variant4-filterInvariant5-variant6-variant7-variant8-variant9-filterInvariant11-variant12-filterInvariant13-filterInvariant14-filterInvariant15-filterInvariant17-variant18-variant19-filterInvariant21-variant22-filterInvariant23-filterInvariant24-variant25-filterInvariant26-filterInvariant27-variant29-variant30-filterInvariant31-variant33-filterInvariant35-variant37-filterInvariant38-filterInvariant39-variant40-filterInvariant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:76,12:88:66:66,0,1921:41,35,4,8 chr1 144811810 . A G 169.34 PASS AC=1;AF=0.5;AN=2;DP=855;set=variant2-variant4-variant6-filterInvariant8-variant9-variant11-variant12-variant14-filterInvariant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-filterInvariant26-variant27-filterInvariant28-variant31-variant33-variant35-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,8:23:99:198,0,536:15,0,8,0 chr1 144811823 . A C 108.7 PASS AC=1;AF=0.5;AN=2;DP=1585;FractionInformativeReads=1;set=filterInvariant-variant2-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-filterInvariant29-variant30-variant31-variant33-filterInvariant34-variant35-filterInvariant36-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,9:32:99:329,0,1051:23,0,9,0 chr1 144811827 . G A 171.19 PASS AC=1;AF=0.5;AN=2;DP=1721;set=filterInvariant-variant2-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-filterInvariant29-variant30-variant31-variant33-filterInvariant34-variant35-filterInvariant36-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,11:37:99:360,0,1048:26,0,11,0 chr1 144811836 . G A 147.19 PASS AC=2;AF=0.881;AN=2;DP=2471;set=filterInvariant-variant2-variant3-variant4-variant5-variant6-variant7-filterInvariant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:2027,144,0:0,0,48,0 chr1 144811924 . T G 4451.43 PASS AC=2;AF=0.989;AN=2;DP=6738;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,155:155:99:4594,465,0:0,0,83,72 chr1 144811969 . A T 640.75 PASS AC=1;AF=0.5;AN=2;DP=6083;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant11-filterInvariant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-filterInvariant32-variant33-filterInvariant34-variant35-variant36-filterInvariant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:113,55:168:99:1037,0,2845:50,63,26,29 chr1 144811998 . C G 617.31 PASS AC=1;AF=0.5;AN=2;DP=4345;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:93,32:125:99:718,0,2699:28,65,9,23 chr1 144812018 . G A 520.22 PASS AC=1;AF=0.5;AN=2;DP=3063;FractionInformativeReads=1;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant11-filterInvariant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-filterInvariant32-variant33-variant34-variant35-variant36-filterInvariant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:77,18:95:99:510,0,3201:23,54,4,14 chr1 144812019 . A C 520.22 PASS AC=1;AF=0.5;AN=2;DP=2994;FractionInformativeReads=1;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant11-filterInvariant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-filterInvariant32-variant33-variant34-variant35-variant36-filterInvariant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:76,18:94:99:510,0,3201:23,53,4,14 chr1 144816086 . C G 640.14 PASS AC=2;AF=0.571;AN=2;DP=439;FractionInformativeReads=1;set=variant23-variant32-variant34-variant35-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,69:69:99:2076,207,0:0,0,20,49 chr1 144824666 . A C 96.55 PASS AC=2;AF=0.917;AN=2;DP=107;FractionInformativeReads=1;set=filterInvariant2-filterInvariant15-filterInvariant16-filterInvariant20-filterInvariant23-filterInvariant26-filterInvariant32-filterInvariant35-variant39-variant41-filterInvariant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:324,33,0:0,0,2,9 chr1 144828404 . T A 402.8 PASS AC=1;AF=0.5;AN=2;DP=1086;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-filterInvariant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-filterInvariant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,19:28:99:556,0,312:9,0,13,6 chr1 144828418 . C T 133.15 PASS AC=1;AF=0.5;AN=2;DP=1362;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-filterInvariant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,12:40:99:243,0,1068:20,8,10,2 chr1 144828454 . G C 87.25 PASS AC=1;AF=0.619;AN=2;DP=2266;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-filterInvariant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,13:60:99:151,0,1702:40,7,8,5 chr1 144828484 . G A 112.8 PASS AC=1;AF=0.5;AN=2;DP=3320;set=filterInvariant-variant2-variant3-variant4-variant5-filterInvariant6-variant7-filterInvariant8-filterInvariant9-variant10-variant11-variant12-variant13-filterInvariant14-filterInvariant15-filterInvariant16-filterInvariant17-variant19-filterInvariant20-variant21-filterInvariant22-variant23-filterInvariant25-filterInvariant26-variant27-filterInvariant28-variant29-variant30-variant31-variant32-filterInvariant33-variant34-variant35-filterInvariant36-variant37-variant39-filterInvariant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:82,13:95:99:266,0,3469:61,21,7,6 chr1 144828497 . C T 52.53 PASS AC=1;AF=0.5;AN=2;DP=3347;FractionInformativeReads=1;set=filterInvariant-variant2-variant3-filterInvariant4-variant5-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant11-variant12-filterInvariant13-filterInvariant15-filterInvariant17-filterInvariant19-variant21-filterInvariant22-variant23-filterInvariant25-variant27-filterInvariant28-variant29-variant30-variant31-variant32-variant34-filterInvariant35-filterInvariant36-filterInvariant37-variant39-variant41-filterInvariant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:108,14:122:99:221,0,4170:78,30,7,7 chr1 144828764 . G T 544.19 PASS AC=1;AF=0.5;AN=2;DP=9929;set=variant-variant2-filterInvariant3-variant4-variant5-variant6-filterInvariant7-filterInvariant9-variant10-variant11-variant12-filterInvariant13-filterInvariant14-filterInvariant15-variant16-variant17-variant18-filterInvariant19-variant20-variant21-variant22-filterInvariant23-variant24-variant25-filterInvariant26-filterInvariant27-variant28-variant29-variant30-variant31-filterInvariant32-filterInvariant33-variant34-variant35-variant36-variant37-variant38-variant39-filterInvariant40-variant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:194,26:220:99:508,0,9415:74,120,15,11 chr1 144828765 . A T 544.19 PASS AC=1;AF=0.5;AN=2;DP=9922;set=variant-variant2-filterInvariant3-variant4-variant5-variant6-filterInvariant7-filterInvariant9-variant10-variant11-variant12-filterInvariant13-filterInvariant14-filterInvariant15-variant16-variant17-variant18-filterInvariant19-variant20-variant21-variant22-filterInvariant23-variant24-variant25-filterInvariant26-filterInvariant27-variant28-variant29-variant30-variant31-filterInvariant32-filterInvariant33-variant34-variant35-variant36-variant37-variant38-variant39-filterInvariant40-variant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:194,26:220:99:508,0,9415:74,120,15,11 chr1 144828784 . A G 226.11 PASS AC=1;AF=0.5;AN=2;DP=8286;set=filterInvariant-filterInvariant2-filterInvariant3-variant4-variant5-variant6-filterInvariant7-filterInvariant9-variant10-filterInvariant11-variant12-filterInvariant13-variant15-variant16-filterInvariant17-variant18-variant19-variant20-filterInvariant21-filterInvariant22-variant24-filterInvariant25-filterInvariant26-variant27-filterInvariant28-filterInvariant29-filterInvariant30-variant31-filterInvariant32-variant34-filterInvariant35-filterInvariant36-variant37-variant38-variant39-filterInvariant40-variant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:180,28:208:99:122,0,4988:63,117,16,12 chr1 144828910 . A T 183.07 PASS AC=1;AF=0.5;AN=2;DP=1207;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:31,8:39:99:167,0,813:10,21,2,6 chr1 144852315 . C T 129.23 PASS AC=1;AF=0.5;AN=2;DP=215;FractionInformativeReads=1;set=variant23-variant32-variant35-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:29,32:61:99:721,0,1090:19,10,16,16 chr1 144852321 . C A 91.83 PASS AC=1;AF=0.5;AN=2;DP=2231;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-filterInvariant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-filterInvariant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,28:62:99:597,0,1347:17,17,19,9 chr1 144852390 . C T 146.07 PASS AC=1;AF=0.5;AN=2;DP=2786;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-filterInvariant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,46:86:99:914,0,859:18,22,25,21 chr1 144852476 . T C 275.96 PASS AC=1;AF=0.5;AN=2;DP=1842;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:22,35:57:99:1101,0,516:9,13,12,23 chr1 144852477 . G A 160.31 PASS AC=1;AF=0.5;AN=2;DP=374;set=variant3-variant9-filterInvariant21-filterInvariant25-filterInvariant35-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:46,11:57:99:103,0,1637:18,28,2,9 chr1 144852508 . AAACAT A 409.4 PASS AC=1;AF=0.5;AN=2;DP=668;set=variant3-variant6-variant8-variant9-variant11-variant12-variant13-filterInvariant14-filterInvariant17-variant21-filterInvariant25-variant26-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:30,11:41:99:335,0,1265:11,19,2,9 chr1 144852518 . C T 460.29 PASS AC=1;AF=0.5;AN=2;DP=628;FractionInformativeReads=1;set=variant3-variant6-variant8-variant9-variant11-variant12-variant13-filterInvariant14-variant17-variant21-filterInvariant23-variant25-variant26-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:25,13:38:99:418,0,1166:9,16,3,10 chr1 144852522 . C T 469.32 PASS AC=1;AF=0.5;AN=2;DP=638;FractionInformativeReads=1;set=variant3-filterInvariant4-variant6-variant8-variant9-variant11-variant12-variant13-filterInvariant14-variant17-variant21-filterInvariant23-variant25-variant26-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:24,12:36:99:418,0,1084:8,16,3,9 chr1 144852532 . G GCCC 394.36 PASS AC=1;AF=0.5;AN=2;DP=589;set=variant3-variant6-variant8-variant9-variant11-variant12-variant13-variant14-variant17-variant18-variant20-variant21-variant25-variant26-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:20,12:32:99:469,0,862:7,13,4,8 chr1 144852537 . T C 403.4 PASS AC=1;AF=0.5;AN=2;DP=557;FractionInformativeReads=1;set=variant3-filterInvariant4-variant6-variant8-variant9-variant11-variant12-variant13-variant14-filterInvariant17-variant18-variant20-variant21-variant25-variant26-variant29-variant30-variant31-filterInvariant32-variant35-variant36-variant37-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:17,11:28:99:447,0,832:6,11,4,7 chr1 144852545 . C T 331.4 PASS AC=1;AF=0.5;AN=2;DP=828;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,11:27:99:353,0,579:5,11,3,8 chr1 144852566 . G A 97.53 PASS AC=1;AF=0.5;AN=2;DP=294;FractionInformativeReads=1;set=variant3-variant6-variant8-variant9-variant11-variant12-variant13-variant14-variant20-variant21-variant26-variant35-variant36-variant37-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:14,11:25:99:304,0,394:4,10,3,8 chr1 144854180 . T C 2026.92 PASS AC=1;AF=0.5;AN=2;DP=7056;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:130,27:157:99:531,0,3739:89,41,23,4 chr1 144854245 . C T 2201.49 PASS AC=1;AF=0.5;AN=2;DP=16305;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-filterInvariant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-filterInvariant33-variant34-variant35-variant36-filterInvariant37-variant38-variant39-variant40-filterInvariant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:317,102:419:99:1791,0,8233:178,139,59,43 chr1 144854277 . A G 5887.67 PASS AC=2;AF=0.511;AN=2;DP=19169;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:2,495:497:99:19945,1453,0:2,0,246,249 chr1 144854351 . A C 5707 PASS AC=2;AF=0.784;AN=2;DP=13823;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,369:370:99:16988,1139,0:1,0,155,214 chr1 144854376 . C A 1412.48 PASS AC=1;AF=0.5;AN=2;DP=9024;set=variant-filterInvariant2-variant3-variant4-variant6-variant7-variant8-filterInvariant10-variant11-variant12-variant14-variant15-variant17-filterInvariant18-variant19-filterInvariant21-filterInvariant22-filterInvariant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-filterInvariant32-filterInvariant33-filterInvariant34-filterInvariant35-variant36-variant37-variant38-filterInvariant39-variant40-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:233,47:280:99:585,0,8598:83,150,19,28 chr1 144854380 . T C 4238.04 PASS AC=1;AF=0.5;AN=2;DP=10209;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:140,130:270:99:4030,0,3771:51,89,49,81 chr1 144854397 . T C 5409.55 PASS AC=2;AF=0.807;AN=2;DP=7614;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,188:188:99:8973,608,0:0,0,66,122 chr1 144854412 . A C 2069.17 PASS AC=1;AF=0.5;AN=2;DP=6201;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:88,67:155:99:1873,0,2629:30,58,29,38 chr1 144854454 . A C 82.8 PASS AC=1;AF=0.5;AN=2;DP=3623;set=filterInvariant-variant3-variant4-filterInvariant5-filterInvariant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-filterInvariant18-variant19-variant20-variant22-variant23-filterInvariant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant35-variant36-variant37-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:74,38:112:99:1116,0,2378:34,40,15,23 chr1 144854491 . T G 1770.3 PASS AC=1;AF=0.5;AN=2;DP=6105;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-filterInvariant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:86,61:147:99:2346,0,3474:43,43,33,28 chr1 144854497 . A G 1927.75 PASS AC=1;AF=0.5;AN=2;DP=6446;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-filterInvariant13-filterInvariant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:98,66:164:99:2411,0,3655:50,48,37,29 chr1 144854528 . A G 402.94 PASS AC=1;AF=0.5;AN=2;DP=7884;set=variant-variant2-variant3-variant4-variant5-filterInvariant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:169,33:202:99:931,0,7015:90,79,19,14 chr1 144854537 . T C 521.18 PASS AC=1;AF=0.5;AN=2;DP=8319;set=variant-variant2-variant3-variant4-variant5-filterInvariant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:176,33:209:99:878,0,7134:93,83,20,13 chr1 144854581 . T C 1244.95 PASS AC=1;AF=0.5;AN=2;DP=9251;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-filterInvariant15-variant16-variant17-filterInvariant18-variant19-variant20-variant21-variant22-variant23-filterInvariant24-variant25-variant26-variant27-variant28-filterInvariant29-filterInvariant30-variant31-variant32-variant33-variant34-variant35-variant36-filterInvariant37-variant38-variant39-variant40-variant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:186,43:229:99:1185,0,7431:88,98,20,23 chr1 144854594 . G T 1371.64 PASS AC=1;AF=0.5;AN=2;DP=8984;set=variant-variant2-variant3-variant4-variant5-filterInvariant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-filterInvariant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:173,40:213:99:1129,0,7418:80,93,17,23 chr1 144854597 . T C 4504.87 PASS AC=1;AF=0.5;AN=2;DP=8847;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:82,127:209:99:5052,0,2998:38,44,56,71 chr1 144854598 . C T 2548.15 PASS AC=1;AF=0.5;AN=2;DP=8801;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:121,86:207:99:3235,0,4760:55,66,37,49 chr1 144854730 . A G 312.12 PASS AC=1;AF=0.5;AN=2;DP=1113;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-filterInvariant27-filterInvariant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,4:27:93:93,0,815:2,21,0,4 chr1 144855812 . T C 234.82 PASS AC=1;AF=0.5;AN=2;DP=662;FractionInformativeReads=1;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-filterInvariant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:11,5:16:99:116,0,272:7,4,1,4 chr1 144855866 . A G 43.7 PASS AC=1;AF=0.5;AN=2;DP=370;set=variant-variant3-variant5-variant6-variant8-variant9-variant11-variant16-variant19-variant21-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant40-variant42-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:9,3:12:58:58,0,217:3,6,1,2 chr1 144855935 . A G 52.67 PASS AC=1;AF=0.5;AN=2;DP=255;FractionInformativeReads=1;set=variant-variant3-variant5-variant8-variant9-variant11-variant14-variant16-variant18-variant19-variant21-variant23-variant24-variant27-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,2:6:72:72,0,154:0,4,2,0 chr1 144857068 . A T 189.98 PASS AC=1;AF=0.5;AN=2;DP=667;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:9,14:23:99:416,0,251:2,7,4,10 chr1 144859720 . G C 91.72 PASS AC=2;AF=0.818;AN=2;DP=943;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:519,57,0:0,0,11,8 chr1 144860026 . G C 91.69 PASS AC=1;AF=0.5;AN=2;DP=1359;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:16,13:29:99:323,0,464:5,11,5,8 chr1 144863199 . G A 94.06 PASS AC=1;AF=0.5;AN=2;DP=243;FractionInformativeReads=1;set=variant23-variant32-variant35-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:25,10:35:99:334,0,1020:13,12,5,5 chr1 144863207 . C T,A 175.23 PASS AC=0,1;AF=0.453,0.047;AN=2;DP=1763;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-filterInvariant12-variant15-variant16-variant17-variant18-variant20-variant22-filterInvariant24-filterInvariant26-variant27-variant28-variant29-variant32-variant33-variant34-variant35-filterInvariant36-variant38-variant39-filterInvariant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:35:99:12,12,5,6 chr1 144863208 . A G 580.29 PASS AC=2;AF=0.511;AN=2;DP=2538;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1434,111,0:0,0,18,19 chr1 144863438 . G T 33.13 PASS AC=1;AF=0.5;AN=2;DP=258;set=filterInvariant32-variant35-filterInvariant39-filterInvariant42 GT:AD:DP:GQ:PL:SB 0/1:45,12:57:99:264,0,1308:24,21,11,1 chr1 144863505 . A G 538.74 PASS AC=1;AF=0.5;AN=2;DP=4074;set=variant2-variant3-variant4-variant5-variant6-filterInvariant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-filterInvariant28-filterInvariant29-variant30-variant31-filterInvariant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,35:83:99:709,0,1143:23,25,20,15 chr1 144863613 . C T 242.93 PASS AC=1;AF=0.5;AN=2;DP=1312;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:20,17:37:99:452,0,502:8,12,4,13 chr1 144864454 . G A 112.19 PASS AC=1;AF=0.5;AN=2;DP=1150;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:10,10:20:99:279,0,303:3,7,2,8 chr1 144865850 . G T 2165.41 PASS AC=1;AF=0.5;AN=2;DP=8448;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:110,96:206:99:2105,0,2468:51,59,50,46 chr1 144866509 . G A 184.38 PASS AC=1;AF=0.5;AN=2;DP=2643;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:32,31:63:99:813,0,836:19,13,22,9 chr1 144866643 . G A 134.98 PASS AC=1;AF=0.5;AN=2;DP=8379;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:100,87:187:99:1958,0,2325:48,52,42,45 chr1 144866662 . T C 94.6 PASS AC=1;AF=0.5;AN=2;DP=8117;set=filterInvariant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:97,83:180:99:1848,0,2293:48,49,37,46 chr1 144868170 . C T 401.66 PASS AC=1;AF=0.5;AN=2;DP=3593;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:43,47:90:99:1208,0,1231:11,32,14,33 chr1 144868204 . A C 231.51 PASS AC=1;AF=0.5;AN=2;DP=1849;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:26,18:44:99:564,0,822:5,21,1,17 chr1 144871738 . C A 451.41 PASS AC=1;AF=0.5;AN=2;DP=2588;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:35,38:73:99:1494,0,1948:26,9,25,13 chr1 144871755 . A T 611.68 PASS AC=1;AF=0.5;AN=2;DP=3227;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:41,43:84:99:1588,0,2091:29,12,26,17 chr1 144871782 . A G 659.76 PASS AC=1;AF=0.5;AN=2;DP=4281;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:55,60:115:99:1411,0,1222:34,21,31,29 chr1 144871889 . A C 1015.34 PASS AC=1;AF=0.5;AN=2;DP=5859;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:70,58:128:99:1475,0,1800:31,39,24,34 chr1 144873794 . C T 1498.53 PASS AC=1;AF=0.5;AN=2;DP=8324;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:124,76:200:99:2754,0,4963:76,48,47,29 chr1 144873818 . A G 2010.33 PASS AC=1;AF=0.5;AN=2;DP=10772;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:151,100:251:99:3754,0,6153:89,62,59,41 chr1 144873840 . A G 2374.63 PASS AC=1;AF=0.5;AN=2;DP=12461;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:169,118:287:99:4162,0,6512:100,69,64,54 chr1 144873887 . C T 2787.42 PASS AC=1;AF=0.5;AN=2;DP=15002;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:207,147:354:99:3441,0,5575:123,84,76,71 chr1 144873962 . CT C 1440.02 PASS AC=1;AF=0.5;AN=2;DP=12643;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:317,70:387:99:1546,0,11522:150,167,33,37 chr1 144874038 . T C 2554.08 PASS AC=1;AF=0.5;AN=2;DP=10333;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:157,91:248:99:2179,0,4071:51,106,30,61 chr1 144874070 . C T 1978.37 PASS AC=1;AF=0.5;AN=2;DP=6686;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:106,60:166:99:1345,0,3060:33,73,22,38 chr1 144874088 . G C 1643.95 PASS AC=1;AF=0.5;AN=2;DP=4965;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:77,44:121:99:1086,0,2264:21,56,14,30 chr1 144874641 . G C 355.59 PASS AC=1;AF=0.5;AN=2;DP=5382;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:85,64:149:99:1574,0,2294:56,29,39,25 chr1 144874760 . T C 1179.62 PASS AC=1;AF=0.5;AN=2;DP=10355;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:143,124:267:99:2843,0,3159:71,72,58,66 chr1 144874815 . T C 358.74 PASS AC=1;AF=0.5;AN=2;DP=5641;set=variant-variant2-filterInvariant3-variant4-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-filterInvariant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:147,30:177:99:463,0,3835:54,93,13,17 chr1 144875799 . G A 1527.03 PASS AC=1;AF=0.5;AN=2;DP=4598;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:76,56:132:99:1487,0,1964:53,23,41,15 chr1 144875979 . G C 678.4 PASS AC=1;AF=0.5;AN=2;DP=3151;set=variant2-variant4-variant11-variant13-variant19-variant20-variant23-variant24-filterInvariant26-variant27-variant30-variant32-variant35-variant36-variant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:179,60:239:99:1022,0,4907:70,109,24,36 chr1 144877176 . C T 1129.88 PASS AC=1;AF=0.5;AN=2;DP=4453;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:54,54:108:99:1348,0,1412:35,19,36,18 chr1 144877366 . A G 1309.05 PASS AC=1;AF=0.5;AN=2;DP=5105;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:75,57:132:99:1507,0,1877:25,50,15,42 chr1 144877390 . G A 945.15 PASS AC=1;AF=0.5;AN=2;DP=3645;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:52,40:92:99:1129,0,1451:14,38,9,31 chr1 144878928 . G T 2504.06 PASS AC=1;AF=0.5;AN=2;DP=10003;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:112,98:210:99:2575,0,3125:78,34,67,31 chr1 144879264 . A G 582.37 PASS AC=1;AF=0.602;AN=2;DP=1746;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:11,23:34:99:676,0,279:3,8,8,15 chr1 144879375 . T C 691.25 PASS AC=1;AF=0.5;AN=2;DP=4941;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:69,82:151:99:1996,0,1694:43,26,48,34 chr1 144881711 . T G 33.56 PASS AC=1;AF=0.5;AN=2;DP=1325;FractionInformativeReads=1;set=filterInvariant-variant2-variant3-variant5-variant6-variant7-variant11-variant12-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-filterInvariant33-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,19:52:99:563,0,992:8,25,2,17 chr1 144882581 . A G 1908.64 PASS AC=1;AF=0.5;AN=2;DP=4418;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:55,48:103:99:1597,0,1886:32,23,23,25 chr1 144882823 . C T 5139.25 PASS AC=1;AF=0.5;AN=2;DP=19290;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:238,246:484:99:6094,0,5934:95,143,94,152 chr1 144882912 . G T 994.54 PASS AC=1;AF=0.5;AN=2;DP=4557;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:103,31:134:99:596,0,3395:24,79,9,22 chr1 144886063 . T C 1145.18 PASS AC=1;AF=0.5;AN=2;DP=4135;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:57,44:101:99:1119,0,1387:34,23,31,13 chr1 144886092 . C T 1489.41 PASS AC=1;AF=0.5;AN=2;DP=5434;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:78,64:142:99:1551,0,1874:46,32,41,23 chr1 144886197 . A T 2470.65 PASS AC=1;AF=0.5;AN=2;DP=8208;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:113,124:237:99:3019,0,2562:59,54,66,58 chr1 144886350 . G T 301.25 PASS AC=1;AF=0.5;AN=2;DP=1440;MQ=60;set=variant2-variant4-variant11-variant13-variant19-variant20-variant23-variant24-variant26-variant27-variant30-variant32-variant35-variant36-variant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:76,39:115:99:920,0,2060:29,47,14,25 chr1 144886409 . A C 236.09 PASS AC=1;AF=0.5;AN=2;DP=1527;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:24,25:49:99:654,0,670:6,18,8,17 chr1 144890833 . T C 302.34 PASS AC=1;AF=0.5;AN=2;DP=1166;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:12,16:28:99:542,0,396:11,1,14,2 chr1 144891147 . T C 508.03 PASS AC=1;AF=0.5;AN=2;DP=710;set=variant2-variant4-variant11-variant13-variant19-variant20-variant23-variant24-variant26-variant27-variant30-variant32-variant35-variant36-variant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:33,7:40:99:182,0,1083:12,21,1,6 chr1 144892089 . G T 914.53 PASS AC=1;AF=0.5;AN=2;DP=3181;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:37,48:85:99:1266,0,1109:29,8,31,17 chr1 144892149 . G A 1865.57 PASS AC=1;AF=0.5;AN=2;DP=6725;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-filterInvariant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:80,84:164:99:1949,0,1973:45,35,45,39 chr1 144892368 . A T 437.21 PASS AC=1;AF=0.5;AN=2;DP=4454;MQ=60;set=variant-variant2-variant3-variant4-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-filterInvariant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:115,28:143:99:690,0,3431:54,61,14,14 chr1 144895460 . C T 394.17 PASS AC=1;AF=0.5;AN=2;DP=2691;MQ=60;set=variant-variant2-variant3-variant4-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-filterInvariant26-filterInvariant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-filterInvariant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:54,16:70:99:389,0,1588:13,41,3,13 chr1 144901139 . T C 7615.44 PASS AC=1;AF=0.5;AN=2;DP=21374;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-filterInvariant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:312,138:450:99:3805,0,7888:147,165,88,50 chr1 144901146 . T A 1464 PASS AC=1;AF=0.5;AN=2;DP=16229;set=variant-filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant8-filterInvariant9-variant10-filterInvariant11-variant12-variant13-variant14-filterInvariant17-filterInvariant18-variant19-filterInvariant20-variant21-filterInvariant23-variant24-filterInvariant25-filterInvariant26-filterInvariant27-variant28-variant30-variant31-variant32-filterInvariant33-filterInvariant34-filterInvariant35-variant36-variant37-filterInvariant38-variant40-filterInvariant42-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:382,59:441:99:403,0,17184:192,190,35,24 chr1 144910082 . A G 820.94 PASS AC=2;AF=0.727;AN=2;DP=3090;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:1931,186,0:0,0,25,37 chr1 144911702 . C A 415.59 PASS AC=1;AF=0.5;AN=2;DP=920;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:13,11:24:99:408,0,1015:10,3,6,5 chr1 144911704 . G C 415.59 PASS AC=1;AF=0.5;AN=2;DP=950;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:18,11:29:99:408,0,1015:13,5,6,5 chr1 144912153 . A G 161.01 PASS AC=2;AF=0.744;AN=2;DP=560;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:270,18,0:0,0,5,1 chr1 144912233 . C T 371.08 PASS AC=1;AF=0.5;AN=2;DP=1264;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-filterInvariant31-variant32-variant33-variant34-variant35-variant36-variant37-filterInvariant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,16:26:99:396,0,210:6,4,10,6 chr1 144915412 . T C 406.65 PASS AC=1;AF=0.5;AN=2;DP=4663;MQ=60;set=variant-variant2-variant3-variant4-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-filterInvariant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:109,27:136:99:473,0,3119:75,34,19,8 chr1 144915561 . G A 1600.31 PASS AC=1;AF=0.5;AN=2;DP=6400;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:88,81:169:99:1816,0,2236:30,58,31,50 chr1 144915623 . AG A 403 PASS AC=1;AF=0.5;AN=2;DP=909;set=variant2-filterInvariant4-variant11-variant13-variant19-variant20-variant23-variant24-variant26-variant27-variant30-variant32-variant35-variant36-variant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:37,13:50:99:336,0,1292:5,32,2,11 chr1 144915624 . G A 1014.16 PASS AC=1;AF=0.5;AN=2;DP=2529;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-filterInvariant27-variant28-variant29-filterInvariant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,15:50:99:360,0,1136:5,30,2,13 chr1 144916676 . C T 548.09 PASS AC=1;AF=0.5;AN=2;DP=5205;MQ=60;set=variant-variant2-filterInvariant3-variant5-variant6-variant7-variant8-variant9-variant11-filterInvariant12-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant27-filterInvariant28-variant29-filterInvariant32-variant33-variant34-variant35-variant36-filterInvariant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:137,31:168:99:464,0,3187:67,70,17,14 chr1 144916748 . C G 1631.42 PASS AC=1;AF=0.5;AN=2;DP=5632;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:71,55:126:99:1243,0,1785:31,40,24,31 chr1 144917546 . A G 1227.64 PASS AC=1;AF=0.5;AN=2;DP=5831;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:77,59:136:99:1410,0,1715:34,43,29,30 chr1 144917827 . CA C 82.25 PASS AC=1;AF=0.5;AN=2;DP=1055;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant15-variant16-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-filterInvariant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,7:35:99:157,0,915:16,12,5,2 chr1 144917841 . T C 590.47 PASS AC=1;AF=0.5;AN=2;DP=1594;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:30,13:43:99:328,0,696:17,13,8,5 chr1 144918034 . A G 61.66 PASS AC=1;AF=0.5;AN=2;DP=567;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-filterInvariant9-variant11-variant15-variant16-variant17-variant18-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant34-variant35-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,7:22:99:206,0,387:6,9,1,6 chr1 144918957 . T A 1270.16 PASS AC=1;AF=0.5;AN=2;DP=3877;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:42,40:82:99:948,0,972:24,18,20,20 chr1 144919094 . C T 469.18 PASS AC=1;AF=0.5;AN=2;DP=1116;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:14,7:21:99:236,0,445:2,12,1,6 chr1 144921924 . G A 969.02 PASS AC=1;AF=0.5;AN=2;DP=3620;MQ=60;set=variant2-variant4-variant11-variant13-variant19-variant20-variant23-variant24-variant26-variant27-filterInvariant30-variant32-variant35-variant36-variant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:183,74:257:99:1466,0,4893:103,80,41,33 chr1 144922109 . A G 1979.31 PASS AC=1;AF=0.5;AN=2;DP=9221;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:120,97:217:99:2410,0,3079:63,57,45,52 chr1 144922171 . C T 1873.19 PASS AC=1;AF=0.5;AN=2;DP=10009;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:129,119:248:99:2772,0,3193:60,69,66,53 chr1 144922294 . G A 150.82 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=100;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.799;QD=1.51;ReadPosRankSum=1.732;SOR=0.71;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:87,13:100:99:179,0,2573:29,58,4,9 chr1 144922523 . C T 644.47 PASS AC=1;AF=0.5;AN=2;DP=4763;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-filterInvariant9-variant11-variant12-variant15-variant16-variant17-filterInvariant18-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-filterInvariant32-filterInvariant33-filterInvariant34-variant35-filterInvariant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:105,24:129:99:310,0,2683:59,46,13,11 chr1 144922583 . G A 2290.83 PASS AC=1;AF=0.5;AN=2;DP=6341;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:96,57:153:99:1195,0,2133:48,48,29,28 chr1 144923728 . GT G 1284.28 PASS AC=1;AF=0.5;AN=2;DP=3455;MQ=60;set=variant2-variant4-variant11-variant13-variant19-variant20-variant23-variant24-variant26-variant27-variant30-variant32-variant35-variant36-variant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:158,58:216:99:1534,0,5265:78,80,28,30 chr1 144923823 . TAGGAAGAAACGGCA T 2299.16 PASS AC=2;AF=0.761;AN=2;DP=6057;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,102:102:99:4505,310,0:0,0,35,67 chr1 144923887 . T A 563.43 PASS AC=1;AF=0.5;AN=2;DP=1220;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant6-variant12-variant15-variant16-variant18-variant20-variant22-variant25-variant27-variant28-variant29-filterInvariant35-variant38-variant41-variant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,10:59:99:108,0,1347:17,32,2,8 chr1 144930571 . C A 842.96 PASS AC=1;AF=0.5;AN=2;DP=3282;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:29,31:60:99:746,0,699:19,10,19,12 chr1 144930596 . C A 1061.8 PASS AC=1;AF=0.5;AN=2;DP=4255;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:35,40:75:99:945,0,948:23,12,24,16 chr1 144930940 . T C 3408.15 PASS AC=1;AF=0.5;AN=2;DP=10589;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:134,134:268:99:3549,0,3351:65,69,68,66 chr1 144931330 . C T 1867.03 PASS AC=1;AF=0.5;AN=2;DP=13290;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:154,164:318:99:4268,0,4002:66,88,77,87 chr1 144931392 . G A 1785.93 PASS AC=1;AF=0.5;AN=2;DP=12111;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:135,131:266:99:2993,0,3319:67,68,61,70 chr1 144931727 . G A 1221.25 PASS AC=1;AF=0.5;AN=2;DP=8283;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-filterInvariant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:220,65:285:99:1351,0,6440:105,115,31,34 chr1 144932086 . G C 2510.74 PASS AC=1;AF=0.5;AN=2;DP=10396;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:115,133:248:99:3489,0,3036:56,59,62,71 chr1 144932151 . G T 637.43 PASS AC=1;AF=0.5;AN=2;DP=7247;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant15-variant16-variant17-variant18-variant20-variant22-filterInvariant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant36-filterInvariant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:184,48:232:99:775,0,5183:92,92,23,25 chr1 144932196 . TTCCGGCTCTGC T 5067.21 PASS AC=1;AF=0.5;AN=2;DP=5698;MQ=60;set=variant-variant4-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant17-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:112,114:226:99:4507,0,4407:55,57,69,45 chr1 144932208 . G A 5082 PASS AC=1;AF=0.5;AN=2;DP=5424;MQ=60;set=variant-variant4-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant17-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:110,116:226:99:4559,0,4294:54,56,69,47 chr1 144932220 . G T 4824.86 PASS AC=1;AF=0.5;AN=2;DP=5579;MQ=60;set=variant-variant4-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant17-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:111,120:231:99:4461,0,4243:56,55,66,54 chr1 144932342 . T G 2408.08 PASS AC=1;AF=0.5;AN=2;DP=14777;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:196,162:358:99:3925,0,5031:99,97,89,73 chr1 144932401 . G C 767.9 PASS AC=1;AF=0.5;AN=2;DP=11309;MQ=60;set=variant-variant2-variant3-variant4-variant8-variant9-variant10-variant11-variant12-variant13-variant14-filterInvariant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-filterInvariant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-filterInvariant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:281,76:357:99:1367,0,7462:139,142,37,39 chr1 144932414 . A C 2909.87 PASS AC=1;AF=0.5;AN=2;DP=13330;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:182,165:347:99:6339,0,8232:86,96,85,80 chr1 144932415 . C G 2909.87 PASS AC=1;AF=0.5;AN=2;DP=13271;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:182,164:346:99:6339,0,8232:86,96,85,79 chr1 144945941 . G A 789.81 PASS AC=2;AF=1;AN=2;DP=868;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.542;ReadPosRankSum=-1.735;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:622,48,0:0,0,15,1 chr1 144946183 . G A 3969.91 PASS AC=1;AF=0.5;AN=2;DP=17089;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:191,184:375:99:4235,0,4674:96,95,92,92 chr1 144946336 . C G 685.55 PASS AC=1;AF=0.5;AN=2;DP=264;FractionInformativeReads=1;MQ=60;set=variant23-variant35 GT:AD:DP:GQ:PL:SB 0/1:112,42:154:99:1086,0,3509:51,61,20,22 chr1 144946403 . T C 2271.18 PASS AC=1;AF=0.5;AN=2;DP=7138;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:83,70:153:99:1998,0,2229:45,38,37,33 chr1 144946510 . C T 7390.86 PASS AC=2;AF=0.943;AN=2;DP=8929;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,209:209:99:6555,626,0:0,0,101,108 chr1 144946768 . G A 1506.56 PASS AC=1;AF=0.5;AN=2;DP=4629;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:33,54:87:99:1343,0,866:10,23,24,30 chr1 144946876 . C T 400.79 PASS AC=1;AF=0.5;AN=2;DP=699;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,13:22:99:489,0,949:0,9,3,10 chr1 144951959 . T C 480.32 PASS AC=1;AF=0.5;AN=2;DP=3386;set=variant-variant4-filterInvariant7-filterInvariant10-variant11-filterInvariant13-filterInvariant14-filterInvariant17-filterInvariant19-variant22-filterInvariant23-variant24-filterInvariant25-variant29-variant32-variant34-variant35-variant36-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:124,41:165:99:736,0,4873:77,47,27,14 chr1 144951973 . T C 4189.54 PASS AC=1;AF=0.5;AN=2;DP=8820;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:78,98:176:99:3045,0,1781:44,34,61,37 chr1 144952078 . C A 2498.81 PASS AC=1;AF=0.5;AN=2;DP=11632;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:187,78:265:99:1514,0,4672:92,95,36,42 chr1 144952207 . C T 243.64 PASS AC=1;AF=0.5;AN=2;DP=4179;set=variant-filterInvariant4-variant5-variant7-variant8-variant9-filterInvariant11-filterInvariant12-filterInvariant14-filterInvariant15-variant17-variant18-filterInvariant21-variant22-filterInvariant23-filterInvariant24-variant25-variant26-variant28-variant31-variant33-filterInvariant34-filterInvariant35-variant36-variant37-variant39-filterInvariant41-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:111,17:128:89:89,0,2772:39,72,6,11 chr1 144952220 . C T 835.11 PASS AC=1;AF=0.5;AN=2;DP=5405;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-filterInvariant14-variant15-variant16-variant17-variant18-variant19-filterInvariant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-filterInvariant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:78,41:119:99:785,0,1863:25,53,14,27 chr1 144994658 . C A 4865.19 PASS AC=1;AF=0.5;AN=2;DP=20914;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:262,270:532:99:6626,0,6860:164,98,161,109 chr1 144994861 . C T 11380 PASS AC=2;AF=0.58;AN=2;DP=26573;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,752:752:99:23755,2249,0:0,0,343,409 chr1 144995219 . G A 42.67 PASS AC=1;AF=0.5;AN=2;DP=301;FractionInformativeReads=1;MQ=60;set=filterInvariant23-filterInvariant32-variant34-variant35-filterInvariant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:41,17:58:99:371,0,1288:12,29,5,12 chr1 145013802 . T G 1096.58 PASS AC=2;AF=1;AN=2;DP=1505;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,31:31:93:1032,93,0:0,0,22,9 chr1 145014053 . T C 197.04 PASS AC=1;AF=0.5;AN=2;DP=6835;MQ=60;set=filterInvariant2-variant3-filterInvariant4-filterInvariant5-variant6-filterInvariant7-variant9-filterInvariant10-variant11-variant12-variant14-variant18-variant19-variant20-filterInvariant21-variant23-variant24-variant25-filterInvariant26-filterInvariant27-filterInvariant31-variant32-variant33-filterInvariant34-variant35-filterInvariant36-variant37-variant38-variant39-filterInvariant40-filterInvariant41-variant42-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:139,112:251:99:2588,0,3433:65,74,51,61 chr1 145014103 . G C 1601.75 PASS AC=1;AF=0.5;AN=2;DP=6959;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:81,94:175:99:2547,0,2117:37,44,42,52 chr1 145014186 . GAA G,GA,GAAA 1305.56 PASS AC=1,0,0;AF=0.257,0.135,0.108;AN=2;DP=4502;MQ=60;set=variant-filterInvariant2-variant3-variant4-variant5-variant6-variant8-variant9-filterInvariant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:DP:GQ:SB 0/1:128:99:44,40,18,26 chr1 145014198 . A C 115.69 PASS AC=1;AF=0.5;AN=2;DP=605;MQ=60;set=filterInvariant3-filterInvariant23-variant35-filterInvariant39-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:107,29:136:99:763,0,4157:54,53,15,14 chr1 145014199 . C A 112.68 PASS AC=1;AF=0.5;AN=2;DP=607;MQ=60;set=filterInvariant3-filterInvariant23-variant35-filterInvariant39-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:109,29:138:99:763,0,4157:55,54,15,14 chr1 145014210 . G A 1593.67 PASS AC=1;AF=0.5;AN=2;DP=5262;MQ=60;set=variant-filterInvariant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-filterInvariant23-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-filterInvariant36-variant38-variant39-filterInvariant40-variant41-variant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:99,50:149:99:1778,0,3684:51,48,26,24 chr1 145014218 . G A 1686.75 PASS AC=1;AF=0.5;AN=2;DP=4032;MQ=60;set=variant-filterInvariant2-variant3-variant4-filterInvariant6-variant8-filterInvariant9-variant10-variant12-filterInvariant14-variant15-variant16-variant17-filterInvariant18-variant20-variant21-variant27-variant28-variant29-variant30-variant35-variant38-variant39-filterInvariant40-variant41-variant42-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:117,36:153:99:527,0,4595:61,56,18,18 chr1 145014263 . C T 2250.11 PASS AC=1;AF=0.5;AN=2;DP=7609;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:78,82:160:99:1957,0,1889:41,37,40,42 chr1 145014394 . C T 969.97 PASS AC=1;AF=0.5;AN=2;DP=2997;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:29,36:65:99:1404,0,1664:7,22,10,26 chr1 145014411 . T C 759.71 PASS AC=1;AF=0.5;AN=2;DP=2272;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:24,31:55:99:1229,0,1499:6,18,9,22 chr1 145015877 . G T 711.74 PASS AC=1;AF=0.5;AN=2;DP=4367;FractionInformativeReads=1;MQ=60;set=variant-filterInvariant2-variant3-filterInvariant6-variant8-variant9-filterInvariant10-variant12-filterInvariant15-variant16-variant17-filterInvariant18-filterInvariant20-filterInvariant21-filterInvariant27-variant28-variant29-filterInvariant30-filterInvariant33-variant35-variant38-filterInvariant39-filterInvariant41-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:143,42:185:99:759,0,3709:75,68,22,20 chr1 145016020 . T G 3447.14 PASS AC=2;AF=0.989;AN=2;DP=5351;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,132:132:99:3854,394,0:0,0,52,80 chr1 145016034 . A AC 121.35 PASS AC=1;AF=0.5;AN=2;DP=1054;MQ=60;set=filterInvariant5-variant7-filterInvariant12-filterInvariant15-variant19-variant22-variant25-filterInvariant32-filterInvariant35-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:86,16:102:99:113,0,2499:32,54,5,11 chr1 145016035 . A C 225.36 PASS AC=1;AF=0.5;AN=2;DP=1871;MQ=60;set=variant-variant3-filterInvariant4-variant8-filterInvariant12-filterInvariant14-variant16-variant17-filterInvariant18-filterInvariant20-variant28-variant29-filterInvariant30-variant35-variant38-filterInvariant40-filterInvariant41-filterInvariant42-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:72,29:101:99:461,0,1976:25,47,12,17 chr1 145017784 . CTT CT,C 159.27 PASS AC=2,0;AF=0.636,0.091;AN=2;DP=1028;set=Intersection GT:DP:GQ:SB 1/1:24:43:1,0,7,16 chr1 145017817 . C T 137.99 PASS AC=1;AF=0.5;AN=2;DP=111;set=variant7-variant9-variant14-variant18-variant21-variant22-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:11,6:17:99:164,0,352:2,9,1,5 chr1 145017831 . T TCCCTCCCCTCCCCTCCCTTCCCCCTCCCTCCCTCCCTC,TCCCTCCCCTCCCCTCCCTTCCCCCTCCCTCCCTC 537.27 PASS AC=0,1;AF=0.286,0.214;AN=2;DP=148;set=variant14-variant21-variant24-variant26-variant32-variant35-variant37 GT:DP:GQ:SB 0/2:24:99:7,4,1,12 chr1 145017851 . T TCCTC 477.58 PASS AC=1;AF=0.5;AN=2;DP=242;FractionInformativeReads=1;set=variant14-variant21-variant24-variant26-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:20,23:43:99:596,0,585:11,9,13,10 chr1 145018023 . G T 1059.8 PASS AC=1;AF=0.5;AN=2;DP=5442;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:72,58:130:99:1323,0,1720:31,41,24,34 chr1 145018102 . G GAGAA 380.43 PASS AC=1;AF=0.5;AN=2;DP=1489;MQ=60;set=variant2-variant5-variant6-variant7-filterInvariant8-variant9-variant10-variant11-variant15-variant16-variant19-filterInvariant20-variant21-variant22-variant23-variant24-variant25-variant26-filterInvariant27-variant28-filterInvariant29-variant31-variant32-variant33-variant34-filterInvariant35-filterInvariant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,5:40:99:103,0,1559:16,19,1,4 chr1 145021024 . G C 716.34 PASS AC=1;AF=0.5;AN=2;DP=3298;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-filterInvariant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-filterInvariant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:45,54:99:99:2320,0,1994:35,10,40,14 chr1 145021034 . C A 100.24 PASS AC=1;AF=0.5;AN=2;DP=2780;MQ=60;set=filterInvariant2-variant3-filterInvariant6-variant7-variant9-variant10-variant11-filterInvariant12-variant14-variant18-variant19-variant20-filterInvariant21-variant22-variant23-variant24-variant25-filterInvariant26-filterInvariant27-filterInvariant28-variant32-variant33-variant35-filterInvariant36-variant37-variant38-variant39-variant40-variant41-variant42-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:52,64:116:99:2399,0,2113:38,14,47,17 chr1 145021265 . A G 191.75 PASS AC=1;AF=0.5;AN=2;DP=5751;MQ=60;set=filterInvariant2-variant3-filterInvariant4-filterInvariant6-variant7-variant9-filterInvariant10-variant11-filterInvariant14-variant18-variant19-variant20-filterInvariant21-variant23-variant24-variant25-filterInvariant26-filterInvariant27-filterInvariant28-variant32-variant33-variant35-filterInvariant36-variant37-variant38-variant39-filterInvariant40-variant41-variant42-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:96,103:199:99:2645,0,2536:33,63,35,68 chr1 145038686 . AG A 174.45 PASS AC=1;AF=0.5;AN=2;DP=475;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant8-variant9-variant15-variant16-variant18-variant20-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,9:23:99:292,0,482:14,0,7,2 chr1 145038736 . C G 476.74 PASS AC=1;AF=0.5;AN=2;DP=1898;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:26,23:49:99:577,0,775:21,5,16,7 chr1 145038815 . A G 3081.99 PASS AC=2;AF=0.864;AN=2;DP=4927;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,147:147:99:4764,441,0:0,0,89,58 chr1 145038952 . C T 2089.6 PASS AC=1;AF=0.5;AN=2;DP=10232;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:151,116:267:99:2952,0,4234:69,82,56,60 chr1 145039026 . T C 540.29 PASS AC=1;AF=0.5;AN=2;DP=9933;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-filterInvariant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-filterInvariant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-filterInvariant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:197,94:291:99:1893,0,5113:84,113,46,48 chr1 145039562 . C T 833.96 PASS AC=1;AF=0.5;AN=2;DP=8007;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:112,116:228:99:2760,0,3036:72,40,68,48 chr1 145039594 . T C 231.42 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=2196;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:277,39:316:99:257,0,7753:175,102,24,15 chr1 145039633 . C T 476.87 PASS AC=1;AF=0.5;AN=2;DP=9102;MQ=60;set=variant-filterInvariant2-variant3-filterInvariant4-filterInvariant6-variant8-filterInvariant9-variant10-filterInvariant12-variant13-filterInvariant14-filterInvariant15-variant16-variant17-filterInvariant18-filterInvariant20-filterInvariant21-filterInvariant27-variant29-filterInvariant33-filterInvariant35-variant38-filterInvariant39-filterInvariant40-variant41-filterInvariant42-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:373,45:418:99:175,0,9942:212,161,29,16 chr1 145039744 . C A 394.42 PASS AC=1;AF=0.5;AN=2;DP=2515;MQ=60;set=filterInvariant34-filterInvariant35-filterInvariant39-variant41-filterInvariant42 GT:AD:DP:GQ:PL:SB 0/1:533,69:602:99:457,0,14558:281,252,34,35 chr1 145039821 . C A 2478.53 PASS AC=1;AF=0.5;AN=2;DP=18285;MQ=60;set=variant-variant2-variant4-variant5-variant6-filterInvariant7-variant8-variant9-variant11-filterInvariant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-filterInvariant37-filterInvariant39-variant40-variant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:455,148:603:99:2818,0,17858:224,231,76,72 chr1 145039831 . A G 2549.09 PASS AC=1;AF=0.5;AN=2;DP=19912;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-filterInvariant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-filterInvariant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-filterInvariant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:382,218:600:99:7139,0,10267:186,196,111,107 chr1 145039866 . A G 4713.77 PASS AC=1;AF=0.5;AN=2;DP=20613;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:297,284:581:99:7239,0,7165:137,160,135,149 chr1 145040039 . G C 2225.55 PASS AC=1;AF=0.5;AN=2;DP=9406;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:131,114:245:99:2748,0,3267:48,83,40,74 chr1 145040054 . A G 1520.53 PASS AC=1;AF=0.5;AN=2;DP=7552;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:114,86:200:99:2161,0,2914:39,75,31,55 chr1 145074882 . G T 94.66 PASS AC=1;AF=0.5;AN=2;DP=4324;MQ=60;set=filterInvariant-variant2-variant5-variant6-filterInvariant7-variant8-filterInvariant9-variant11-variant13-variant15-variant18-variant20-filterInvariant21-variant22-variant23-variant24-variant26-variant27-variant28-filterInvariant29-variant30-filterInvariant31-variant32-filterInvariant34-variant35-variant36-variant37-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:125,22:147:99:433,0,3889:91,34,18,4 chr1 145074919 . A G 677.17 PASS AC=1;AF=0.5;AN=2;DP=3278;MQ=60;set=variant5-variant6-filterInvariant8-filterInvariant20-filterInvariant21-filterInvariant24-filterInvariant27-filterInvariant30-variant31-filterInvariant34-filterInvariant35-filterInvariant40-variant41-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:200,37:237:99:423,0,5702:133,67,21,16 chr1 145074939 . T C 2060.97 PASS AC=1;AF=0.5;AN=2;DP=11990;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:155,143:298:99:3436,0,3970:95,60,88,55 chr1 145075519 . G C 181.35 PASS AC=1;AF=0.5;AN=2;DP=2150;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,51:75:99:1336,0,637:17,7,29,22 chr1 145075683 . C T 2480.3 PASS AC=1;AF=0.5;AN=2;DP=13825;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:193,205:398:99:4748,0,4736:118,75,120,85 chr1 145075854 . G C 6694.88 PASS AC=1;AF=0.5;AN=2;DP=26249;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:368,383:751:99:9062,0,8988:186,182,187,196 chr1 145075903 . C T 2896.28 PASS AC=1;AF=0.5;AN=2;DP=18036;MQ=60;set=variant-filterInvariant2-variant3-filterInvariant4-filterInvariant5-filterInvariant6-variant8-filterInvariant9-filterInvariant10-variant12-filterInvariant14-variant15-variant16-variant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant24-filterInvariant27-filterInvariant28-variant29-filterInvariant30-filterInvariant31-filterInvariant33-filterInvariant34-variant35-variant38-filterInvariant39-filterInvariant40-variant41-filterInvariant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:506,149:655:99:2678,0,13507:235,271,65,84 chr1 145076161 . C G 2249.43 PASS AC=1;AF=0.5;AN=2;DP=8527;MQ=60;set=variant2-filterInvariant4-variant5-variant6-filterInvariant7-filterInvariant8-variant11-filterInvariant13-variant15-variant16-filterInvariant19-variant20-filterInvariant21-variant22-variant23-variant24-variant26-variant27-variant28-filterInvariant29-variant30-variant31-variant32-filterInvariant33-filterInvariant34-filterInvariant35-variant36-variant37-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:299,39:338:99:115,0,8594:105,194,16,23 chr1 145076284 . C G 561.6 PASS AC=1;AF=0.625;AN=2;DP=1767;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:20,32:52:99:1029,0,640:3,17,7,25 chr1 145103844 . G A 617.51 PASS AC=1;AF=0.5;AN=2;DP=4769;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:77,38:115:99:912,0,2416:60,17,28,10 chr1 145103928 . G A 1379.64 PASS AC=1;AF=0.5;AN=2;DP=8223;MQ=60;set=variant-filterInvariant2-variant3-variant4-filterInvariant5-filterInvariant6-variant8-variant10-filterInvariant11-filterInvariant14-variant15-variant16-variant17-variant19-filterInvariant20-filterInvariant21-filterInvariant24-filterInvariant27-filterInvariant28-variant29-filterInvariant31-filterInvariant33-filterInvariant34-filterInvariant35-variant38-filterInvariant39-filterInvariant40-filterInvariant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:251,42:293:99:264,0,6321:133,118,22,20 chr1 145103947 . T C 1399.73 PASS AC=1;AF=0.5;AN=2;DP=13325;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:217,91:308:99:1737,0,5222:105,112,42,49 chr1 145104052 . AGT A 966.84 PASS AC=1;AF=0.5;AN=2;DP=5641;MQ=60;set=variant-filterInvariant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-filterInvariant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-filterInvariant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:78,46:124:99:1631,0,3024:19,59,15,31 chr1 145109430 . A T 260.49 PASS AC=1;AF=0.5;AN=2;DP=2502;MQ=60;set=variant-variant3-filterInvariant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant21-filterInvariant22-filterInvariant23-variant25-filterInvariant28-variant29-filterInvariant30-variant31-filterInvariant32-variant33-variant34-filterInvariant35-variant38-filterInvariant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,9:74:99:143,0,2073:49,16,6,3 chr1 145109456 . C T 863.17 PASS AC=1;AF=0.5;AN=2;DP=5344;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-filterInvariant23-variant24-filterInvariant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:76,35:111:99:680,0,2307:53,23,22,13 chr1 145109468 . A G 5854.28 PASS AC=1;AF=0.955;AN=2;DP=6598;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:13,109:122:99:3781,0,128:11,2,73,36 chr1 145109493 . C T 788.41 PASS AC=1;AF=0.5;AN=2;DP=6568;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant28-variant29-filterInvariant30-variant31-filterInvariant32-variant33-filterInvariant34-variant35-variant38-filterInvariant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:146,29:175:99:522,0,4217:92,54,22,7 chr1 145109549 . G T 1247.91 PASS AC=1;AF=0.5;AN=2;DP=14134;MQ=60;set=variant-variant2-variant3-filterInvariant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-filterInvariant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:230,59:289:99:1014,0,6329:125,105,40,19 chr1 145109583 . C A 4525.34 PASS AC=1;AF=0.5;AN=2;DP=15878;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:197,171:368:99:4167,0,5668:106,91,96,75 chr1 145109596 . C T 237.92 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=708;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:328,58:386:99:506,0,10852:181,147,29,29 chr1 145109661 . G A 1647.67 PASS AC=1;AF=0.5;AN=2;DP=14434;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-filterInvariant13-filterInvariant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-filterInvariant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:291,83:374:99:1319,0,7423:134,157,38,45 chr1 145109809 . T A 174.88 PASS AC=1;AF=0.5;AN=2;DP=1366;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-filterInvariant14-filterInvariant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,14:44:99:451,0,1101:3,27,1,13 chr1 145112284 . CCG C 232.12 PASS AC=1;AF=0.5;AN=2;DP=3146;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:60,17:77:99:530,0,3584:44,16,13,4 chr1 145112287 . T C 388.25 PASS AC=1;AF=0.5;AN=2;DP=3080;set=variant-variant2-variant3-filterInvariant4-filterInvariant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-filterInvariant27-variant28-variant29-variant30-filterInvariant31-variant32-variant33-variant34-variant35-variant36-variant37-filterInvariant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,19:78:99:530,0,1977:43,16,14,5 chr1 145112288 . G GCA 259.66 PASS AC=1;AF=0.5;AN=2;DP=3258;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-filterInvariant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,17:78:99:530,0,3584:44,17,13,4 chr1 145112313 . T C 678.15 PASS AC=1;AF=0.5;AN=2;DP=5034;set=variant-variant2-variant3-filterInvariant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-filterInvariant20-variant21-variant22-variant23-filterInvariant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:78,30:108:99:764,0,2662:62,16,22,8 chr1 145112414 . T C 2034.63 PASS AC=1;AF=0.5;AN=2;DP=16742;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:310,98:408:99:3145,0,13960:164,146,54,44 chr1 145112420 . C T 1691.25 PASS AC=1;AF=0.5;AN=2;DP=16981;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-filterInvariant8-variant9-variant10-variant11-variant12-variant13-filterInvariant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:305,114:419:99:1992,0,9292:166,139,60,54 chr1 145112428 . C T 2054.79 PASS AC=1;AF=0.5;AN=2;DP=17834;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:318,108:426:99:3287,0,14213:169,149,56,52 chr1 145112485 . C T 1028.37 PASS AC=1;AF=0.5;AN=2;DP=16240;MQ=60;set=variant-filterInvariant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-filterInvariant24-filterInvariant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-filterInvariant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:278,100:378:99:1927,0,7481:116,162,44,56 chr1 145115658 . TATTTTTAA T 1084.54 PASS AC=1;AF=0.5;AN=2;DP=3969;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:57,20:77:99:668,0,2650:47,10,16,4 chr1 145115810 . A G 3980.04 PASS AC=1;AF=0.5;AN=2;DP=14917;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:221,166:387:99:4794,0,5198:106,115,78,88 chr1 145115820 . T C 1185.79 PASS AC=1;AF=0.5;AN=2;DP=13880;MQ=60;set=variant-variant2-variant3-variant4-variant5-filterInvariant6-variant7-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-filterInvariant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-filterInvariant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:312,71:383:99:815,0,11794:147,165,32,39 chr1 145139088 . C CG 868.97 PASS AC=2;AF=1;AN=2;DP=973;FS=0;MQRankSum=-0.98;ReadPosRankSum=-1.281;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:1081,87,0:0,0,29,0 chr1 145209012 . G A 336.7 PASS AC=1;AF=0.5;AN=2;DP=2002;set=variant2-filterInvariant5-filterInvariant6-filterInvariant7-variant11-filterInvariant15-filterInvariant16-filterInvariant19-filterInvariant20-filterInvariant22-filterInvariant24-filterInvariant27-filterInvariant28-filterInvariant31-variant32-filterInvariant35-filterInvariant40-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:88,22:110:99:267,0,2160:60,28,15,7 chr1 145209116 . T C 620.93 PASS AC=1;AF=0.5;AN=2;DP=7392;set=variant2-filterInvariant4-variant5-filterInvariant6-filterInvariant7-filterInvariant8-variant9-filterInvariant11-filterInvariant13-filterInvariant14-filterInvariant15-filterInvariant16-variant18-filterInvariant19-filterInvariant21-filterInvariant22-variant23-filterInvariant24-variant25-variant26-filterInvariant27-variant28-filterInvariant32-variant33-variant35-filterInvariant36-filterInvariant39-filterInvariant40-filterInvariant42-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:189,48:237:99:549,0,4605:97,92,20,28 chr1 145209612 . GCCCCGCCAACCGCCGGGGTT G,GCCCCGCCAACCGCCGGGGTTCCCCGCCAACCGCCGGGGTT 6540.38 PASS AC=2,0;AF=0.648,0.023;AN=2;DP=14035;set=Intersection GT:DP:GQ:SB 1/1:218:99:1,0,134,83 chr1 145209819 . C T 63.81 PASS AC=1;AF=0.5;AN=2;DP=9681;set=filterInvariant-variant2-filterInvariant3-variant4-variant5-filterInvariant6-variant7-filterInvariant9-filterInvariant10-filterInvariant11-variant12-filterInvariant15-filterInvariant16-filterInvariant17-variant19-variant20-variant21-filterInvariant22-filterInvariant25-filterInvariant26-filterInvariant27-variant28-variant31-filterInvariant33-filterInvariant34-filterInvariant35-filterInvariant37-filterInvariant38-filterInvariant39-filterInvariant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:357,39:396:99:368,0,9298:167,190,6,33 chr1 145209869 . A C 883.92 PASS AC=1;AF=0.5;AN=2;DP=13508;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-filterInvariant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-filterInvariant23-filterInvariant24-variant25-filterInvariant26-variant27-variant28-filterInvariant29-filterInvariant30-variant31-filterInvariant32-variant33-variant34-variant35-filterInvariant36-variant37-variant38-variant39-variant40-variant41-variant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:273,71:344:99:2177,0,10942:120,153,48,23 chr1 145209870 . A G 883.92 PASS AC=1;AF=0.5;AN=2;DP=13585;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-filterInvariant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-filterInvariant23-variant24-variant25-variant26-variant27-variant28-filterInvariant29-filterInvariant30-variant31-filterInvariant32-variant33-variant34-variant35-filterInvariant36-variant37-variant38-variant39-variant40-variant41-variant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:272,72:344:99:2177,0,10942:121,151,49,23 chr1 145273302 . A G 1155.75 PASS AC=1;AF=0.5;AN=2;DP=31581;set=variant-variant2-variant4-variant5-variant6-filterInvariant7-variant8-variant9-variant11-filterInvariant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-filterInvariant29-filterInvariant31-variant32-variant33-filterInvariant34-variant35-variant36-filterInvariant37-filterInvariant39-variant40-variant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:733,191:924:99:2765,0,18268:434,299,109,82 chr1 145273345 . T C 1312.76 PASS AC=1;AF=0.5;AN=2;DP=41004;set=variant-filterInvariant2-variant4-variant5-variant6-filterInvariant7-variant8-variant9-variant11-filterInvariant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-filterInvariant29-filterInvariant30-filterInvariant31-variant32-variant33-filterInvariant34-variant35-variant36-filterInvariant37-filterInvariant39-variant40-variant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:930,241:1171:99:3144,0,22983:478,452,124,117 chr1 145273473 . T C 1114.92 PASS AC=1;AF=0.5;AN=2;DP=17561;set=variant-variant2-variant4-variant5-variant6-filterInvariant7-variant8-variant9-variant11-filterInvariant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-filterInvariant29-filterInvariant30-filterInvariant31-variant32-variant33-filterInvariant34-variant35-variant36-filterInvariant37-filterInvariant39-variant40-variant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:411,112:523:99:1845,0,11305:132,279,38,74 chr1 145273520 . G A 766.97 PASS AC=1;AF=0.5;AN=2;DP=7788;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-filterInvariant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:173,56:229:99:1433,0,5526:34,139,8,48 chr1 145281247 . T A 765.85 PASS AC=1;AF=0.5;AN=2;DP=4926;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-filterInvariant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-filterInvariant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:79,35:114:99:866,0,2305:76,3,34,1 chr1 145281361 . TC T 1193.5 PASS AC=1;AF=0.5;AN=2;DP=30445;set=filterInvariant-variant2-variant5-variant6-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant11-filterInvariant12-variant15-variant16-filterInvariant18-filterInvariant20-filterInvariant21-variant22-filterInvariant23-filterInvariant25-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant29-variant32-filterInvariant33-filterInvariant34-variant35-filterInvariant36-variant40-filterInvariant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:819,264:1083:99:6600,0,27201:494,325,171,93 chr1 145281408 . C T 3394.21 PASS AC=1;AF=0.5;AN=2;DP=53450;set=variant-variant2-filterInvariant4-variant5-variant6-filterInvariant7-variant8-variant9-variant11-filterInvariant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-filterInvariant29-filterInvariant30-filterInvariant31-variant32-variant33-filterInvariant34-variant35-variant36-filterInvariant37-filterInvariant39-variant40-variant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:1104,356:1460:99:5696,0,27994:619,485,210,146 chr1 145281543 . C T 3315.7 PASS AC=1;AF=0.5;AN=2;DP=39050;set=variant-variant2-filterInvariant3-variant5-variant6-variant7-variant8-filterInvariant9-variant10-variant11-filterInvariant12-variant13-variant14-variant15-filterInvariant16-variant17-variant18-variant19-filterInvariant20-variant21-variant22-variant23-filterInvariant24-variant25-filterInvariant26-variant27-variant28-variant29-variant30-filterInvariant31-filterInvariant32-variant33-variant34-variant35-variant36-variant37-variant38-filterInvariant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:787,268:1055:99:5027,0,21649:316,471,104,164 chr1 145281613 . C A 2178.96 PASS AC=1;AF=0.5;AN=2;DP=23891;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-filterInvariant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-filterInvariant29-variant30-variant31-variant32-variant33-filterInvariant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:511,165:676:99:4966,0,20846:188,323,62,103 chr1 145281633 . C A 2930.23 PASS AC=1;AF=0.5;AN=2;DP=20847;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-filterInvariant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-filterInvariant29-variant30-variant31-variant32-variant33-filterInvariant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:453,144:597:99:4610,0,19349:170,283,50,94 chr1 145281656 . A T 263.77 PASS AC=1;AF=0.5;AN=2;DP=14070;set=filterInvariant-variant2-variant5-variant6-variant7-filterInvariant8-filterInvariant9-variant11-filterInvariant12-variant15-variant16-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-variant22-variant23-variant24-filterInvariant25-filterInvariant26-variant28-variant29-variant31-variant32-filterInvariant33-filterInvariant34-variant35-variant40-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:373,114:487:99:3673,0,15232:144,229,41,73 chr1 145281780 . T A 314.56 PASS AC=1;AF=0.5;AN=2;DP=6927;set=variant-variant2-filterInvariant4-variant5-variant6-filterInvariant7-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant18-filterInvariant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-filterInvariant29-filterInvariant30-filterInvariant32-variant33-variant35-variant36-filterInvariant37-filterInvariant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:163,37:200:99:595,0,5110:87,76,17,20 chr1 145281818 . T A 285.02 PASS AC=1;AF=0.5;AN=2;DP=3407;set=filterInvariant-filterInvariant4-filterInvariant5-filterInvariant10-filterInvariant11-variant12-variant14-filterInvariant15-variant17-variant18-variant20-filterInvariant22-filterInvariant27-variant28-filterInvariant35-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:199,28:227:99:338,0,6584:112,87,20,8 chr1 145281824 . T G 259.85 PASS AC=1;AF=0.5;AN=2;DP=5033;set=filterInvariant2-variant5-filterInvariant7-variant8-variant10-variant11-filterInvariant13-variant14-variant16-filterInvariant18-variant22-variant23-variant26-filterInvariant28-variant29-filterInvariant30-variant31-variant32-filterInvariant33-variant35-variant36-variant38-filterInvariant39-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:171,72:243:99:1870,0,5002:100,71,43,29 chr1 145282093 . G A 1122.05 PASS AC=1;AF=0.5;AN=2;DP=7768;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-filterInvariant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:122,57:179:99:1540,0,3448:37,85,13,44 chr1 145290320 . C T 359.98 PASS AC=1;AF=0.5;AN=2;DP=981;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,10:27:99:309,0,541:11,6,7,3 chr1 145290346 . A G 746.92 PASS AC=1;AF=0.5;AN=2;DP=1597;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:17,23:40:99:787,0,526:13,4,15,8 chr1 145290351 . A G 40.15 PASS AC=1;AF=0.5;AN=2;DP=1149;set=filterInvariant2-variant4-variant5-variant7-variant9-variant10-variant11-variant15-variant17-variant20-variant21-variant22-filterInvariant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant37-filterInvariant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,14:47:99:354,0,1400:23,10,10,4 chr1 145290377 . T C 303.2 PASS AC=1;AF=0.5;AN=2;DP=2605;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-filterInvariant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,28:62:99:599,0,959:21,13,15,13 chr1 145290401 . T G 730.04 PASS AC=1;AF=0.5;AN=2;DP=3594;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-filterInvariant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-filterInvariant18-variant19-variant20-filterInvariant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,14:81:99:383,0,3042:38,29,8,6 chr1 145290409 . G A 733.04 PASS AC=1;AF=0.5;AN=2;DP=4040;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-filterInvariant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-filterInvariant18-variant19-variant20-filterInvariant21-variant22-variant23-filterInvariant24-variant25-variant26-filterInvariant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:71,16:87:99:418,0,3129:40,31,9,7 chr1 145290498 . T G 290.17 PASS AC=1;AF=0.5;AN=2;DP=4641;set=variant-variant2-variant3-filterInvariant4-variant5-variant6-variant7-variant9-filterInvariant10-variant11-variant12-variant13-variant14-filterInvariant15-variant16-variant17-variant19-variant20-filterInvariant21-variant22-variant23-filterInvariant25-filterInvariant26-filterInvariant27-filterInvariant28-variant29-variant30-filterInvariant31-filterInvariant32-variant33-variant35-variant36-filterInvariant37-filterInvariant38-filterInvariant40-variant41-variant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:89,20:109:99:263,0,2496:43,46,9,11 chr1 145290535 . C T 421.15 PASS AC=1;AF=0.5;AN=2;DP=3710;set=variant-variant2-variant3-filterInvariant4-variant5-variant6-variant7-filterInvariant8-variant9-filterInvariant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-filterInvariant21-variant22-filterInvariant23-filterInvariant25-filterInvariant26-filterInvariant27-filterInvariant28-variant29-filterInvariant30-filterInvariant31-variant32-variant33-filterInvariant35-variant36-filterInvariant37-filterInvariant38-filterInvariant39-variant40-variant41-variant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:79,14:93:99:160,0,2082:36,43,6,8 chr1 145290547 . C A 346.57 PASS AC=1;AF=0.5;AN=2;DP=3186;set=variant-variant2-variant3-filterInvariant4-variant5-variant6-variant7-filterInvariant8-variant9-filterInvariant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-filterInvariant21-variant22-variant23-variant25-variant26-filterInvariant27-filterInvariant28-variant29-filterInvariant30-filterInvariant31-filterInvariant32-variant33-filterInvariant35-variant36-filterInvariant37-filterInvariant38-filterInvariant39-variant40-variant41-variant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:69,12:81:99:159,0,1853:30,39,5,7 chr1 145290560 . T C 245.75 PASS AC=1;AF=0.5;AN=2;DP=2551;set=variant-variant2-variant3-filterInvariant4-variant5-variant6-variant7-filterInvariant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-filterInvariant27-variant29-filterInvariant30-variant31-filterInvariant32-variant33-filterInvariant35-variant36-filterInvariant37-variant39-variant40-variant41-variant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,9:74:99:99,0,1791:25,40,3,6 chr1 145290583 . G C 217 PASS AC=1;AF=0.5;AN=2;DP=1296;set=variant-filterInvariant2-variant3-variant4-variant5-variant6-filterInvariant8-variant9-variant10-variant11-filterInvariant12-variant13-variant14-variant16-variant17-filterInvariant20-variant22-filterInvariant25-variant26-filterInvariant29-variant31-variant33-filterInvariant35-variant36-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,6:53:99:102,0,1401:15,32,1,5 chr1 145293012 . G A 117.78 PASS AC=1;AF=0.5;AN=2;DP=3090;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-filterInvariant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-filterInvariant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,35:62:99:962,0,683:20,7,23,12 chr1 145293420 . C T 60.69 PASS AC=1;AF=0.5;AN=2;DP=1782;set=filterInvariant29-filterInvariant35-filterInvariant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:428,56:484:99:353,0,12441:240,188,35,21 chr1 145293425 . C A 891.1 PASS AC=1;AF=0.5;AN=2;DP=18718;set=variant-filterInvariant2-filterInvariant4-variant5-filterInvariant6-variant8-variant9-filterInvariant10-variant11-filterInvariant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-filterInvariant26-variant27-variant28-filterInvariant29-filterInvariant30-variant32-variant33-filterInvariant34-variant35-variant36-filterInvariant39-filterInvariant40-filterInvariant41-variant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:412,102:514:99:1363,0,11272:230,182,58,44 chr1 145293469 . G C 2753.93 PASS AC=1;AF=0.5;AN=2;DP=13268;set=variant2-variant5-filterInvariant6-filterInvariant7-filterInvariant8-variant11-filterInvariant12-variant15-variant16-filterInvariant20-variant22-filterInvariant23-variant24-filterInvariant29-variant32-filterInvariant34-variant35-variant40-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:518,125:643:99:3638,0,20853:268,250,67,58 chr1 145293490 . G C 2489.25 PASS AC=1;AF=0.5;AN=2;DP=27067;set=variant-variant2-variant4-variant5-variant6-filterInvariant7-variant8-variant9-variant11-filterInvariant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-filterInvariant29-variant30-filterInvariant31-variant32-variant33-filterInvariant34-variant35-variant36-filterInvariant37-variant39-variant40-variant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:545,132:677:99:3936,0,22819:265,280,67,65 chr1 145293498 . G C 2601.15 PASS AC=1;AF=0.5;AN=2;DP=28882;set=variant-variant2-variant4-variant5-variant6-filterInvariant7-variant8-variant9-filterInvariant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-filterInvariant29-variant30-filterInvariant31-variant32-variant33-filterInvariant34-variant35-variant36-filterInvariant37-filterInvariant38-variant39-variant40-filterInvariant41-variant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:540,129:669:99:3794,0,22650:257,283,62,67 chr1 145293510 . C G 1331.77 PASS AC=1;AF=0.5;AN=2;DP=26773;set=variant-variant2-variant4-variant5-filterInvariant6-variant7-variant8-variant9-filterInvariant10-variant11-filterInvariant12-filterInvariant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-filterInvariant22-variant23-variant24-variant25-variant26-variant27-variant28-filterInvariant29-filterInvariant30-variant32-variant33-filterInvariant34-variant35-variant36-filterInvariant39-variant40-filterInvariant41-variant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:549,125:674:99:3545,0,22486:252,297,59,66 chr1 145293515 . A G 274.11 PASS AC=1;AF=0.5;AN=2;DP=21345;set=filterInvariant-filterInvariant3-filterInvariant5-filterInvariant6-filterInvariant7-variant8-filterInvariant9-variant10-variant11-variant13-variant14-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant21-filterInvariant22-variant23-variant26-variant27-filterInvariant28-variant29-variant30-filterInvariant31-variant32-variant33-variant35-variant36-filterInvariant37-variant38-filterInvariant39-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:475,173:648:99:3513,0,13947:213,262,83,90 chr1 145293566 . G A 959.5 PASS AC=1;AF=0.5;AN=2;DP=19164;set=variant-variant2-filterInvariant3-filterInvariant4-variant5-variant6-variant7-variant8-filterInvariant9-variant10-variant11-filterInvariant12-filterInvariant13-variant14-variant15-variant17-variant18-variant19-variant21-filterInvariant22-variant23-variant25-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-filterInvariant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:414,90:504:99:1400,0,10414:188,226,36,54 chr1 145295309 . C G 55.01 PASS AC=2;AF=0.667;AN=2;DP=53;FractionInformativeReads=1;set=filterInvariant35-variant40-filterInvariant44 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:83,9,0:0,0,3,0 chr1 145295418 . T C 497.81 PASS AC=2;AF=0.75;AN=2;DP=105;FractionInformativeReads=1;MQRankSum=-0.405;ReadPosRankSum=-2.106;set=variant35-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:526,45,0:0,0,15,0 chr1 145295677 . G A 87.52 PASS AC=2;AF=0.75;AN=2;DP=18;FS=0;FractionInformativeReads=1;MQRankSum=-2.388;ReadPosRankSum=-1.614;set=variant35-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:116,12,0:0,0,0,4 chr1 145296207 . T C 265.43 PASS AC=1;AF=0.5;AN=2;DP=1495;FractionInformativeReads=1;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-filterInvariant12-variant13-variant16-variant17-variant18-filterInvariant19-variant20-variant21-variant22-variant24-variant26-variant28-variant29-variant30-filterInvariant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-filterInvariant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,11:27:99:305,0,545:14,2,8,3 chr1 145296268 . C T,G 1509.06 PASS AC=1,0;AF=0.389,0.125;AN=2;DP=3885;set=variant2-filterInvariant3-filterInvariant4-variant5-variant6-variant7-variant8-variant9-variant10-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-filterInvariant23-variant24-variant25-variant26-variant27-variant28-filterInvariant30-variant31-variant33-variant35-variant36-filterInvariant37-variant38-variant39-variant40-filterInvariant41-variant42-filterInvariant43-filterInvariant44 GT:DP:GQ:SB 0/1:59:99:19,7,21,12 chr1 145296372 . A G 2101.39 PASS AC=2;AF=0.558;AN=2;DP=10422;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-filterInvariant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,128:128:99:3837,384,0:0,0,65,63 chr1 145296478 . G T 1132.06 PASS AC=2;AF=0.557;AN=2;DP=6617;set=variant-variant2-filterInvariant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:4,85:89:99:2431,152,0:3,1,29,56 chr1 145297400 . G A 65.7 PASS AC=2;AF=0.575;AN=2;DP=246;FractionInformativeReads=1;set=variant-variant5-variant7-filterInvariant8-variant10-variant11-variant16-variant17-variant21-variant25-variant26-variant28-variant32-variant35-filterInvariant36-variant37-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:69,6,0:0,0,2,0 chr1 145297458 . G C 236.6 PASS AC=1;AF=0.5;AN=2;DP=2141;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-filterInvariant12-variant13-variant14-variant15-filterInvariant16-variant17-variant18-variant19-variant21-variant22-variant23-filterInvariant24-variant25-variant26-variant27-variant28-variant29-variant30-filterInvariant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-filterInvariant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,18:31:99:559,0,299:11,2,18,0 chr1 145297817 . G C 2392.12 PASS AC=2;AF=0.557;AN=2;DP=5067;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,93:93:99:3261,279,0:0,0,20,73 chr1 145298186 . C G 367.26 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=3454;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:30,35:65:99:755,0,563:13,17,18,17 chr1 145298416 . A G 114.49 PASS AC=1;AF=0.5;AN=2;DP=578;set=variant-filterInvariant2-variant4-variant5-variant6-variant8-variant9-variant11-variant13-variant15-variant16-variant18-variant19-filterInvariant20-variant21-variant23-variant24-variant25-filterInvariant26-variant27-variant28-variant29-variant32-variant33-variant35-variant36-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,7:21:99:173,0,440:13,1,7,0 chr1 145298473 . A G 147.76 PASS AC=1;AF=0.5;AN=2;DP=719;FractionInformativeReads=1;set=variant-variant2-filterInvariant4-variant5-variant8-variant9-variant11-variant13-filterInvariant15-variant16-variant18-variant19-filterInvariant20-variant21-variant23-variant24-variant25-variant27-variant29-variant32-variant33-variant35-variant36-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,10:29:99:189,0,478:7,12,6,4 chr1 145299758 . C T 90.01 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=260;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:78,14:92:71:71,0,1982:51,27,7,7 chr1 145299805 . A C 114.37 PASS AC=1;AF=0.5;AN=2;DP=3795;set=filterInvariant2-filterInvariant5-variant8-filterInvariant9-variant13-filterInvariant14-filterInvariant16-filterInvariant18-filterInvariant19-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant32-filterInvariant35-variant36-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:154,14:168:99:124,0,6769:91,63,7,7 chr1 145299809 . G A 99.35 PASS AC=1;AF=0.5;AN=2;DP=3766;set=filterInvariant2-filterInvariant5-variant8-filterInvariant9-variant13-filterInvariant16-filterInvariant18-filterInvariant19-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant32-filterInvariant35-variant36-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:155,14:169:99:121,0,6791:91,64,7,7 chr1 145301587 . G T 296.19 DRAGENHardSNP AC=1;AF=0.512;AN=2;DP=1811;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:29,23:52:99:505,0,697:29,0,23,0 chr1 145301604 . C T 118.1 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=174;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:73,11:84:63:63,0,1993:67,6,10,1 chr1 145301651 . T C 1076.91 PASS AC=1;AF=0.5;AN=2;DP=4289;set=variant2-variant5-variant6-filterInvariant8-filterInvariant9-variant11-filterInvariant12-variant16-filterInvariant19-filterInvariant21-variant24-filterInvariant25-filterInvariant27-filterInvariant28-filterInvariant29-filterInvariant32-filterInvariant33-variant35-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:190,65:255:99:1137,0,4895:125,65,46,19 chr1 145301697 . C T 1265.35 PASS AC=1;AF=0.5;AN=2;DP=14452;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-filterInvariant9-variant10-variant11-filterInvariant12-variant13-variant14-variant15-filterInvariant16-variant17-variant18-variant19-filterInvariant20-variant21-variant22-variant23-filterInvariant24-variant25-variant26-variant27-variant28-filterInvariant29-variant30-filterInvariant31-variant32-variant33-variant34-filterInvariant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:364,78:442:99:683,0,8203:197,167,37,41 chr1 145301793 . A G 1088.01 PASS AC=1;AF=0.5;AN=2;DP=9450;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-filterInvariant10-variant11-filterInvariant12-variant13-variant14-variant15-filterInvariant16-variant17-variant18-variant19-filterInvariant20-variant21-variant22-variant23-filterInvariant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:212,71:283:99:2085,0,8038:81,131,23,48 chr1 145301802 . C G 1096.32 PASS AC=1;AF=0.5;AN=2;DP=8235;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-filterInvariant9-variant10-variant11-variant12-variant13-variant14-variant15-filterInvariant16-variant17-variant18-variant19-filterInvariant20-variant21-variant22-variant23-filterInvariant24-variant25-variant26-variant27-variant28-variant29-variant30-filterInvariant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:182,57:239:99:1847,0,7462:69,113,14,43 chr1 145301831 . A G 85.46 PASS AC=1;AF=0.5;AN=2;DP=3369;set=filterInvariant-variant2-variant5-variant6-variant8-filterInvariant9-variant11-variant12-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-filterInvariant27-variant28-filterInvariant29-variant31-variant32-variant33-variant34-variant35-variant36-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,49:117:99:1738,0,2559:27,41,11,38 chr1 145301836 . A G 72.72 PASS AC=1;AF=0.5;AN=2;DP=2830;FractionInformativeReads=1;set=filterInvariant-variant2-variant5-variant6-variant8-filterInvariant9-variant11-variant12-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-filterInvariant27-filterInvariant29-variant32-variant33-variant34-variant35-variant36-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,43:103:99:1626,0,2491:22,38,9,34 chr1 145301853 . C G 574.01 PASS AC=2;AF=0.818;AN=2;DP=2530;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-filterInvariant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-filterInvariant27-filterInvariant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-filterInvariant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1611,126,0:0,0,13,24 chr1 145301887 . G A 319.61 PASS AC=1;AF=0.5;AN=2;DP=1609;set=variant2-variant4-variant5-variant6-variant7-variant8-filterInvariant9-variant10-variant11-variant12-variant13-variant14-variant15-filterInvariant16-variant17-variant18-variant19-variant21-filterInvariant22-variant23-filterInvariant24-variant25-variant26-filterInvariant27-variant28-variant29-filterInvariant30-variant32-variant33-variant34-variant35-variant36-filterInvariant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,12:30:99:429,0,670:8,10,6,6 chr1 145301907 . A C 313.59 PASS AC=1;AF=0.5;AN=2;DP=1577;FractionInformativeReads=1;set=variant2-variant4-variant5-variant6-variant7-variant8-filterInvariant9-variant10-variant11-variant12-variant13-variant14-variant15-filterInvariant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-filterInvariant27-variant28-variant29-filterInvariant30-filterInvariant31-variant32-variant33-variant34-variant35-variant36-filterInvariant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,14:29:99:465,0,575:6,9,5,9 chr1 145302505 . G C 732.77 PASS AC=2;AF=1;AN=2;DP=978;FS=0;MQRankSum=0.315;ReadPosRankSum=1.103;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:618,63,0:0,0,15,6 chr1 145302548 . C T 150.79 PASS AC=1;AF=0.5;AN=2;DP=296;FractionInformativeReads=1;set=variant5-filterInvariant16-filterInvariant19-filterInvariant25-variant28-variant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:32,7:39:99:192,0,1346:18,14,4,3 chr1 145302552 . G A 118.83 PASS AC=1;AF=0.5;AN=2;DP=304;FractionInformativeReads=1;set=variant5-filterInvariant16-filterInvariant19-filterInvariant25-variant28-variant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:34,7:41:99:192,0,1348:18,16,4,3 chr1 145302704 . A G 38.98 PASS AC=2;AF=0.833;AN=2;DP=70;FS=0;FractionInformativeReads=1;set=filterInvariant5-filterInvariant8-filterInvariant16-variant18-filterInvariant22-filterInvariant23-filterInvariant26-variant28-filterInvariant31-filterInvariant35-filterInvariant36-filterInvariant39-filterInvariant41-filterInvariant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:106,12,0:0,0,3,1 chr1 145303760 . G C 315.29 PASS AC=1;AF=0.5;AN=2;DP=1320;FractionInformativeReads=1;set=variant4-filterInvariant5-filterInvariant8-filterInvariant9-variant10-variant11-variant13-filterInvariant14-filterInvariant18-variant23-variant26-variant27-variant29-variant30-filterInvariant31-variant32-variant33-variant35-filterInvariant39 GT:AD:DP:GQ:PL:SB 0/1:56,16:72:99:276,0,1207:31,25,15,1 chr1 145304153 . A G 283 PASS AC=1;AF=0.5;AN=2;DP=1811;set=variant-variant2-variant3-filterInvariant4-variant5-variant6-variant8-variant11-variant13-variant14-variant15-filterInvariant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-filterInvariant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-filterInvariant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,12:54:99:200,0,1359:7,35,4,8 chr1 145304787 . G T 101.49 PASS AC=1;AF=0.5;AN=2;DP=1766;set=variant-variant2-filterInvariant3-variant4-variant6-variant7-filterInvariant9-filterInvariant11-filterInvariant13-variant15-variant16-filterInvariant17-variant18-variant20-filterInvariant21-variant22-variant24-variant28-variant31-filterInvariant32-filterInvariant34-filterInvariant35-variant38-filterInvariant40-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:49,10:59:99:139,0,1720:8,41,1,9 chr1 145310197 . C T 833.27 PASS AC=1;AF=0.5;AN=2;DP=3761;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:44,47:91:99:1023,0,1458:9,35,18,29 chr1 145310932 . C A 94.22 PASS AC=1;AF=0.523;AN=2;DP=850;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-filterInvariant9-variant10-variant11-filterInvariant12-variant13-variant14-filterInvariant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-filterInvariant25-variant26-variant27-variant28-variant29-variant31-variant32-filterInvariant33-filterInvariant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,10:29:99:238,0,563:17,2,10,0 chr1 145310983 . G C 1076.85 PASS AC=1;AF=0.591;AN=2;DP=3396;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:68,47:115:99:1407,0,1646:48,20,41,6 chr1 145311083 . A C 1674.9 PASS AC=1;AF=0.5;AN=2;DP=8358;set=variant2-variant5-filterInvariant6-variant7-variant8-variant10-variant11-filterInvariant12-variant13-variant14-variant15-variant16-variant18-filterInvariant19-filterInvariant20-variant22-variant23-variant25-variant26-filterInvariant28-filterInvariant29-variant31-variant32-filterInvariant33-filterInvariant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:196,119:315:99:2236,0,4669:113,83,64,55 chr1 145311380 . C A 110.15 PASS AC=1;AF=0.5;AN=2;DP=455;FractionInformativeReads=1;set=variant2-variant5-variant7-variant8-variant10-variant11-variant14-variant16-variant18-variant26-filterInvariant28-variant29-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,13:24:99:349,0,250:3,8,5,8 chr1 145311828 . C G 2543.6 PASS AC=2;AF=1;AN=2;DP=5991;FS=0;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-filterInvariant12-variant13-variant14-filterInvariant15-variant16-variant17-variant18-variant19-filterInvariant20-variant21-variant22-variant23-variant24-filterInvariant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-filterInvariant34-variant35-variant36-variant37-variant38-variant39-filterInvariant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,192:192:99:5722,575,0:0,0,117,75 chr1 145316432 . C T 32.94 PASS AC=2;AF=0.833;AN=2;DP=11;FS=0;FractionInformativeReads=1;MQRankSum=0.736;ReadPosRankSum=0.736;set=variant12-filterInvariant32-variant35 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:148,18,0:0,0,3,3 chr1 145316474 . C T 37.57 PASS AC=2;AF=1;AN=2;DP=4;FS=0;FractionInformativeReads=1;SOR=2.303;set=filterInvariant32-variant35 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:87,6,0:0,0,0,2 chr1 145316505 . T G 48.47 PASS AC=2;AF=1;AN=2;DP=2;FS=0;FractionInformativeReads=1;MQ=38.53;QD=24.24;SOR=2.303;set=variant35 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:77,6,0:0,0,0,2 chr1 145323539 . T G 297.12 PASS AC=1;AF=0.5;AN=2;DP=2005;FractionInformativeReads=1;set=filterInvariant-variant2-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-variant7-variant8-filterInvariant9-variant10-filterInvariant11-filterInvariant12-filterInvariant13-variant14-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant19-variant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant32-variant33-filterInvariant34-variant35-variant36-variant37-filterInvariant38-filterInvariant39-filterInvariant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:36,11:47:99:215,0,1124:35,1,11,0 chr1 145323614 . A G 158.29 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=1998;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:318,43:361:62:62,0,7747:193,125,23,20 chr1 145323757 . A T 3333.93 PASS AC=1;AF=0.773;AN=2;DP=7976;set=filterInvariant-variant2-filterInvariant3-filterInvariant4-variant5-filterInvariant6-variant7-variant8-filterInvariant9-variant10-filterInvariant11-filterInvariant12-variant13-variant14-filterInvariant15-variant16-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-variant23-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant27-variant28-filterInvariant29-filterInvariant30-variant31-variant32-variant33-filterInvariant34-variant35-variant36-variant37-variant38-variant39-filterInvariant40-variant41-filterInvariant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:82,139:221:99:3570,0,1739:33,49,38,101 chr1 145325891 . C G 55.7 PASS AC=2;AF=0.643;AN=2;DP=35;FractionInformativeReads=1;set=filterInvariant8-filterInvariant14-filterInvariant32-variant33-filterInvariant35-filterInvariant36-filterInvariant39 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:76,6,0:0,0,2,0 chr1 145327548 . A G 35.28 PASS AC=2;AF=1;AN=2;DP=2;FS=0;FractionInformativeReads=1;MQ=34.15;QD=17.64;SOR=2.303;set=variant35 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:64,6,0:0,0,0,2 chr1 145330728 . G A 114.84 PASS AC=1;AF=0.5;AN=2;DP=186;FractionInformativeReads=1;set=filterInvariant5-filterInvariant7-filterInvariant10-filterInvariant22-filterInvariant23-variant26-filterInvariant29-filterInvariant30-filterInvariant32-filterInvariant33-filterInvariant35-filterInvariant36-filterInvariant39-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:14,8:22:99:132,0,325:2,12,4,4 chr1 145358933 . T TA 37.4 PASS AC=2;AF=1;AN=2;DP=4;FS=0;FractionInformativeReads=1;SOR=0.693;set=variant33-variant35 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:75,6,0:0,0,1,1 chr1 145365506 . G T 679.23 DRAGENHardSNP AC=2;AF=1;AN=2;DP=2194;FS=0;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:1692,185,0:0,0,12,50 chr1 145367014 . G A 285.99 PASS AC=1;AF=0.595;AN=2;DP=766;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant30-variant31-variant34-variant35-filterInvariant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,4:18:99:117,0,408:10,4,4,0 chr1 145367083 . G C 468.33 PASS AC=1;AF=0.5;AN=2;DP=1627;set=variant3-variant4-variant5-filterInvariant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-filterInvariant28-variant29-variant30-variant31-variant32-variant33-variant34-filterInvariant35-variant36-variant37-variant38-filterInvariant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,6:30:76:76,0,641:10,14,4,2 chr1 145367094 . C T 36.22 PASS AC=1;AF=0.5;AN=2;DP=1921;set=filterInvariant2-variant3-filterInvariant4-variant5-variant6-variant7-variant8-variant9-variant11-filterInvariant12-variant13-variant14-variant15-variant16-filterInvariant17-filterInvariant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-filterInvariant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,6:32:78:78,0,660:11,15,4,2 chr1 145367178 . T G 68.77 PASS AC=1;AF=0.5;AN=2;DP=1569;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,6:22:99:163,0,526:5,11,1,5 chr1 145367229 . G C 199.14 PASS AC=1;AF=0.5;AN=2;DP=323;set=variant2-variant5-variant7-variant8-variant11-variant13-variant14-variant16-variant18-variant23-variant26-variant29-variant31-variant32-variant35-variant36-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:3,6:9:99:202,0,105:0,3,3,3 chr1 145367626 . A T 145.7 PASS AC=1;AF=0.5;AN=2;DP=20;FS=0;FractionInformativeReads=1;MQ=42.75;MQRankSum=1.967;QD=7.28;ReadPosRankSum=-1.273;SOR=0.527;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:12,8:20:99:174,0,266:8,4,5,3 chr1 145368461 . A C 1506.73 PASS AC=1;AF=0.5;AN=2;DP=14384;set=variant2-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant16-variant18-variant22-variant23-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:321,245:566:99:5927,0,8084:202,119,152,93 chr1 145368473 . G C 865.96 PASS AC=1;AF=0.5;AN=2;DP=26846;set=filterInvariant-filterInvariant2-variant3-filterInvariant4-variant5-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant13-filterInvariant14-filterInvariant15-filterInvariant16-filterInvariant17-variant18-filterInvariant19-variant20-variant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant27-filterInvariant28-variant30-filterInvariant31-filterInvariant32-filterInvariant33-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant38-filterInvariant39-filterInvariant41-filterInvariant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:537,110:647:99:1102,0,15016:319,218,66,44 chr1 145368518 . C T 1449.22 PASS AC=1;AF=0.5;AN=2;DP=37792;set=filterInvariant-variant2-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-variant10-filterInvariant11-filterInvariant12-filterInvariant13-variant14-variant15-variant16-filterInvariant17-variant18-filterInvariant19-variant20-variant21-filterInvariant22-variant23-variant24-variant25-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant29-variant30-variant31-variant32-filterInvariant33-filterInvariant34-variant35-filterInvariant36-filterInvariant37-variant38-filterInvariant39-filterInvariant40-variant41-variant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:697,185:882:99:1979,0,18312:390,307,96,89 chr1 145438578 . C A 811.53 PASS AC=2;AF=1;AN=2;DP=917;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.545;ReadPosRankSum=-1.139;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:555,48,0:0,0,9,7 chr1 145440086 . C T 1096.04 PASS AC=1;AF=0.5;AN=2;DP=264;FractionInformativeReads=1;MQ=60;set=variant8-variant23-variant35 GT:AD:DP:GQ:PL:SB 0/1:39,46:85:99:1235,0,935:17,22,20,26 chr1 145441620 . T C 9188.9 PASS AC=2;AF=0.943;AN=2;DP=10161;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,252:253:99:7336,710,0:1,0,133,119 chr1 145441840 . TA T 6736.82 PASS AC=2;AF=0.943;AN=2;DP=6432;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,170:170:99:6308,511,0:0,0,95,75 chr1 145442254 . G C 6977.94 PASS AC=2;AF=0.955;AN=2;DP=5774;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,148:148:99:6359,445,0:0,0,48,100 chr1 145442264 . T A 6549.05 PASS AC=2;AF=0.955;AN=2;DP=5145;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,133:133:99:5921,409,0:0,0,45,88 chr1 145458154 . CTTTT CTT,CTTT,C 81 PASS AC=0,1,0;AF=0.125,0.313,0.063;AN=2;DP=154;set=variant3-variant12-variant21-variant22-variant23-variant34-filterInvariant35-filterInvariant36 GT:DP:GQ:SB 0/2:11:68:2,3,1,5 chr1 145471549 . A C 190.46 PASS AC=2;AF=1;AN=2;DP=546;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.552;ReadPosRankSum=-0.822;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:412,36,0:0,0,9,3 chr1 145472558 . GCCC G,GCC,GC 1437.38 PASS AC=0,0,2;AF=0.136,0.17,0.614;AN=2;DP=3308;set=variant-variant2-variant3-filterInvariant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 3/3:76:99:0,1,43,32 chr1 145474626 . A C 610.64 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=6169;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:169,60:229:99:670,0,3433:39,130,58,2 chr1 145474630 . T C 159.58 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=5906;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:171,62:233:99:687,0,3463:37,134,62,0 chr1 145475728 . T G 37.72 PASS AC=2;AF=0.596;AN=2;DP=279;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant12-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant31-variant34-variant35-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:234,21,0:0,0,2,5 chr1 145500921 . C CTA 15988.8 PASS AC=2;AF=0.955;AN=2;DP=11302;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,249:249:99:11331,779,0:0,0,159,90 chr1 145507826 . A T 1380.61 PASS AC=1;AF=0.577;AN=2;DP=2665;MQ=60;set=variant2-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant16-variant18-variant21-variant22-variant23-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,44:91:99:1076,0,1115:20,27,19,25 chr1 145510376 . A G 546.92 DRAGENHardSNP AC=2;AF=0.955;AN=2;DP=1132;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:659,75,0:0,0,11,14 chr1 145517063 . G A 787.99 PASS AC=2;AF=0.953;AN=2;DP=994;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:918,75,0:0,0,20,5 chr1 145530254 . C T 2265.37 PASS AC=1;AF=0.528;AN=2;DP=3344;MQ=60;set=variant-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant13-variant17-variant23-variant24-variant27-variant29-variant30-variant33-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:96,76:172:99:1718,0,2344:47,49,37,39 chr1 145531980 . T C 2251.69 PASS AC=2;AF=1;AN=2;DP=2850;FS=0;MQ=60;MQRankSum=-0.675;ReadPosRankSum=-0.147;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,89:89:99:3117,267,0:0,0,53,36 chr1 145532010 . CTGTG CTGTGTG,CTGTGTGTG,CTGTGTGTGTG,C,CTG 227.92 PASS AC=1,0,0,0,0;AF=0.21,0.194,0.065,0.048,0.065;AN=2;DP=2080;set=variant-filterInvariant3-variant4-variant6-variant7-filterInvariant8-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant18-filterInvariant22-variant24-variant27-variant28-variant29-variant30-variant31-filterInvariant33-variant34-filterInvariant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:DP:GQ:SB 0/1:44:99:19,13,5,7 chr1 145532549 . T C 6078.82 PASS AC=2;AF=1;AN=2;DP=7570;FS=0;MQ=60;MQRankSum=1.492;ReadPosRankSum=0.409;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,184:184:99:5470,551,0:0,0,92,92 chr1 145532994 . GT G 2287.88 PASS AC=1;AF=0.593;AN=2;DP=2267;MQ=60;set=variant2-variant3-variant6-variant7-variant8-variant9-variant12-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant31-variant34-variant35-variant36-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,45:91:99:1741,0,2546:27,19,23,22 chr1 145533001 . T C 2296.9 PASS AC=1;AF=0.593;AN=2;DP=2361;MQ=60;set=variant2-variant3-variant6-variant7-variant8-variant9-variant12-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant31-variant34-variant35-variant36-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,46:94:99:1760,0,2565:27,21,23,23 chr1 145533175 . T C 1124.36 PASS AC=1;AF=0.593;AN=2;DP=2332;MQ=60;set=variant2-variant3-variant6-variant7-variant8-variant9-variant12-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant31-variant34-variant35-variant36-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,55:114:99:1492,0,1572:26,33,28,27 chr1 145533314 . T C 2866.24 PASS AC=1;AF=0.656;AN=2;DP=5775;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant31-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:98,106:204:99:2673,0,2408:61,37,59,47 chr1 145535611 . T G 1574.28 PASS AC=1;AF=0.75;AN=2;DP=1558;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,22:41:99:566,0,449:11,8,14,8 chr1 145535921 . T C 6516.04 PASS AC=1;AF=0.75;AN=2;DP=9532;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:123,135:258:99:3682,0,2996:67,56,83,52 chr1 145538664 . A G 5392.48 PASS AC=1;AF=0.75;AN=2;DP=6852;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:96,82:178:99:1969,0,2346:51,45,40,42 chr1 145558565 . C G 2765.2 PASS AC=2;AF=0.989;AN=2;DP=3886;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,128:128:99:4217,383,0:0,0,39,89 chr1 145561594 . C T 624.13 PASS AC=2;AF=0.63;AN=2;DP=3317;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant21-variant26-variant29-variant33-variant34-variant35-variant37-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,190:190:99:5538,566,0:0,0,97,93 chr1 145562881 . T C 1241.49 PASS AC=2;AF=0.655;AN=2;DP=3330;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant21-variant24-variant25-variant26-variant28-variant29-variant33-variant34-variant35-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,123:124:99:3607,326,0:1,0,66,57 chr1 145566535 . C T 326.2 PASS AC=2;AF=0.655;AN=2;DP=1037;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant21-variant24-variant25-variant26-variant28-variant29-variant33-variant34-variant35-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1193,114,0:0,0,26,12 chr1 145568537 . AT A 213.29 PASS AC=2;AF=0.977;AN=2;DP=775;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:251,27,0:0,0,1,8 chr1 145581644 . C CT 62.49 PASS AC=1;AF=0.5;AN=2;DP=34;MQ=60;set=variant14-variant35 GT:AD:DP:GQ:PL:SB 0/1:4,5:9:74:102,0,74:1,3,0,5 chr1 145585317 . A G 2749.25 PASS AC=2;AF=0.989;AN=2;DP=5231;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,147:147:99:4493,440,0:0,0,89,58 chr1 145586309 . C T 1454.01 PASS AC=2;AF=1;AN=2;DP=1764;FS=0;MQ=60;MQRankSum=-0.657;ReadPosRankSum=0.179;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:845,81,0:0,0,15,12 chr1 145586403 . G T 1535.56 PASS AC=2;AF=0.977;AN=2;DP=1744;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1121,114,0:0,0,20,18 chr1 145586671 . CTTTTA C 4506.5 PASS AC=1;AF=0.5;AN=2;DP=455;MQ=60;set=variant14-variant35 GT:AD:DP:GQ:PL:SB 0/1:121,116:237:99:4506,0,8528:72,49,67,49 chr1 145586678 . AC A 4509.59 PASS AC=1;AF=0.5;AN=2;DP=456;FractionInformativeReads=1;MQ=60;set=variant14-variant35 GT:AD:DP:GQ:PL:SB 0/1:125,116:241:99:4503,0,8560:74,51,67,49 chr1 145586780 . T C 3069.65 PASS AC=2;AF=0.595;AN=2;DP=6150;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant9-variant11-variant12-variant14-variant15-variant17-variant21-variant23-variant25-variant27-variant33-variant35-variant37-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,323:323:99:9643,966,0:0,0,160,163 chr1 145588536 . C T 1714.2 PASS AC=2;AF=0.757;AN=2;DP=4500;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,158:158:99:4680,470,0:0,0,85,73 chr1 145589491 . A T 1992.3 PASS AC=2;AF=0.989;AN=2;DP=4276;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,102:102:99:3002,302,0:0,0,44,58 chr1 145589516 . G C 545.13 PASS AC=2;AF=0.633;AN=2;DP=2711;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant33-variant34-variant35-variant37-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,89:89:99:2919,266,0:0,0,37,52 chr1 145589666 . C A 400.31 PASS AC=2;AF=0.989;AN=2;DP=683;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:872,78,0:0,0,6,20 chr1 145594799 . C T 481.36 PASS AC=2;AF=0.743;AN=2;DP=484;FractionInformativeReads=1;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:673,60,0:0,0,15,5 chr1 145597116 . C T 2751.98 PASS AC=2;AF=0.989;AN=2;DP=4498;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,103:103:99:3200,308,0:0,0,45,58 chr1 145597256 . C G 337.44 PASS AC=1;AF=0.5;AN=2;DP=58;FractionInformativeReads=1;MQ=60;MQRankSum=1.68;set=variant14-variant35 GT:AD:DP:GQ:PL:SB 0/1:15,14:29:99:462,0,449:5,10,4,10 chr1 145598459 . T C 2378.69 PASS AC=2;AF=0.989;AN=2;DP=3720;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:2560,225,0:0,0,33,42 chr1 145601861 . G A 2798 PASS AC=2;AF=0.989;AN=2;DP=3739;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,85:85:99:2815,255,0:0,0,29,56 chr1 145688667 . TA T 3834.15 PASS AC=2;AF=0.909;AN=2;DP=6814;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:20,159:179:79:3526,79,0:11,9,79,80 chr1 145695923 . T G 593.94 PASS AC=2;AF=0.989;AN=2;DP=871;MQ=60;MQRankSum=-1.169;ReadPosRankSum=0.734;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:354,30,0:0,0,8,2 chr1 145697315 . ATTT AT,A,ATT,ATTTT,ATTTTT 1326.8 PASS AC=0,0,1,1,0;AF=0.211,0.224,0.25,0.039,0.013;AN=2;DP=7034;set=variant-variant3-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 3/4:132:99:11,22,41,58 chr1 145697799 . A G 7194.57 PASS AC=2;AF=0.989;AN=2;DP=7829;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,154:154:99:4984,461,0:0,0,58,96 chr1 145697814 . CT C 345.97 PASS AC=1;AF=0.5;AN=2;DP=6040;set=filterInvariant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-filterInvariant17-variant18-variant19-variant20-filterInvariant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,41:88:99:572,0,774:20,27,14,27 chr1 145706564 . CAA CA,CAAA,CAAAA,C 168.86 PASS AC=1,0,0,0;AF=0.227,0.25,0.045,0.023;AN=2;DP=579;set=variant3-filterInvariant4-filterInvariant5-variant6-variant9-variant11-variant15-variant16-variant17-variant20-variant21-variant22-variant25-variant26-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant41 GT:DP:GQ:SB 0/1:31:99:8,9,12,2 chr1 145826770 . G A 4554.81 PASS AC=2;AF=0.757;AN=2;DP=5120;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,122:122:99:4154,364,0:0,0,73,49 chr1 146013577 . A C 352.31 PASS AC=1;AF=0.534;AN=2;DP=2690;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:24,44:68:99:1121,0,480:11,13,16,28 chr1 146055321 . T C 133.51 DRAGENHardSNP AC=1;AF=0.848;AN=2;DP=113;FS=0;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:0,3:3:34:61,0,34:0,0,2,1 chr1 146055329 . T C 230.93 DRAGENHardSNP AC=1;AF=0.542;AN=2;DP=336;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:5,7:12:99:139,0,156:4,1,4,3 chr1 146057292 . T C 727.18 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=547;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:23,17:40:99:308,0,457:11,12,8,9 chr1 146215022 . T C 386.62 DRAGENHardSNP AC=2;AF=0.693;AN=2;DP=1403;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:689,69,0:0,0,23,0 chr1 146215111 . G A 5334.07 DRAGENHardSNP AC=2;AF=0.761;AN=2;DP=8761;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,174:174:99:7848,533,0:0,0,118,56 chr1 146215113 . G A 5334.07 DRAGENHardSNP AC=2;AF=0.761;AN=2;DP=8939;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,177:177:99:7848,533,0:0,0,119,58 chr1 146215138 . A G 3652.35 PASS AC=2;AF=0.795;AN=2;DP=10834;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant11-variant12-filterInvariant13-filterInvariant14-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant29-filterInvariant30-variant31-filterInvariant32-filterInvariant33-variant34-filterInvariant35-filterInvariant36-filterInvariant37-variant38-filterInvariant39-variant40-filterInvariant41-filterInvariant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 1/1:0,215:215:99:5884,644,0:0,0,137,78 chr1 146215189 . G C 1472.67 PASS AC=1;AF=0.548;AN=2;DP=7521;set=filterInvariant-filterInvariant2-filterInvariant5-filterInvariant6-variant7-filterInvariant8-variant9-filterInvariant11-variant12-variant15-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant20-filterInvariant22-filterInvariant23-filterInvariant24-variant25-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant29-filterInvariant32-filterInvariant33-variant34-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:100,108:208:99:2305,0,2151:44,56,57,51 chr1 146215223 . G C 5189.29 PASS AC=2;AF=0.727;AN=2;DP=10113;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-variant7-filterInvariant8-variant9-filterInvariant10-filterInvariant11-variant12-variant13-filterInvariant14-variant15-filterInvariant16-filterInvariant17-filterInvariant18-variant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-variant24-variant25-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant29-variant30-variant31-filterInvariant32-filterInvariant33-variant34-filterInvariant35-filterInvariant36-filterInvariant37-variant38-filterInvariant39-variant40-filterInvariant41-filterInvariant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 1/1:1,181:182:99:7871,505,0:1,0,75,106 chr1 146215232 . A C 4924.69 PASS AC=2;AF=0.727;AN=2;DP=9730;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-variant7-filterInvariant8-variant9-filterInvariant10-filterInvariant11-variant12-variant13-filterInvariant14-variant15-filterInvariant16-filterInvariant17-filterInvariant18-variant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-variant25-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant29-variant30-variant31-filterInvariant32-filterInvariant33-variant34-filterInvariant35-filterInvariant36-filterInvariant37-variant38-filterInvariant39-variant40-filterInvariant41-filterInvariant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 1/1:1,180:181:99:7869,505,0:1,0,68,112 chr1 146215276 . C T 1759.76 PASS AC=2;AF=0.75;AN=2;DP=6557;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-variant7-filterInvariant8-variant9-filterInvariant10-filterInvariant11-variant12-variant13-filterInvariant14-variant15-filterInvariant16-filterInvariant17-filterInvariant18-variant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-variant25-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant29-variant30-variant31-filterInvariant32-filterInvariant33-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant37-variant38-filterInvariant39-variant40-filterInvariant41-filterInvariant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 1/1:3,105:108:99:2976,228,0:3,0,28,77 chr1 146215376 . T C 359.41 PASS AC=2;AF=0.727;AN=2;DP=1993;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-variant13-filterInvariant14-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant38-filterInvariant39-filterInvariant40-filterInvariant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 1/1:1,28:29:51:716,51,0:1,0,6,22 chr1 146244609 . C T 515.77 PASS AC=2;AF=0.857;AN=2;DP=241;FractionInformativeReads=1;set=filterInvariant3-filterInvariant4-filterInvariant19-filterInvariant34-filterInvariant35-filterInvariant36-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:282,36,0:0,0,6,6 chr1 146250855 . C T 213.34 DRAGENHardSNP AC=2;AF=0.641;AN=2;DP=1946;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,21:21:62:489,62,0:0,0,10,11 chr1 146250905 . G C 248.36 DRAGENHardSNP AC=2;AF=0.621;AN=2;DP=2024;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:2,19:21:13:405,13,0:1,1,9,10 chr1 146317771 . C A 565.91 PASS AC=2;AF=0.589;AN=2;DP=595;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:724,57,0:0,0,4,15 chr1 146320949 . C T 286.36 PASS AC=1;AF=0.5;AN=2;DP=78;FractionInformativeReads=1;set=variant5-variant35-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:11,7:18:99:112,0,256:5,6,4,3 chr1 146395447 . A G 395.24 PASS AC=1;AF=0.5;AN=2;DP=3865;set=variant-variant2-variant3-variant4-variant5-variant6-filterInvariant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-filterInvariant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,19:75:99:257,0,1464:36,20,11,8 chr1 146395537 . A G 299.67 PASS AC=1;AF=0.5;AN=2;DP=3964;set=variant-variant2-variant3-variant4-variant5-filterInvariant6-filterInvariant7-variant8-filterInvariant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-filterInvariant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-filterInvariant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,17:84:99:220,0,1645:27,40,6,11 chr1 146398203 . A G,T 1041.54 DRAGENHardSNP AC=1,0;AF=0.489,0.011;AN=2;DP=3558;FractionInformativeReads=1;set=FilteredInAll GT:DP:GQ:SB 0/1:75:99:25,14,22,14 chr1 146398208 . A G 1155.19 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=3921;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:40,41:81:99:1487,0,1902:26,14,24,17 chr1 146398387 . G C 46.93 PASS AC=1;AF=0.5;AN=2;DP=1311;set=filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant6-filterInvariant7-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant14-filterInvariant15-filterInvariant17-filterInvariant18-filterInvariant19-variant20-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant27-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-filterInvariant34-filterInvariant35-filterInvariant37-filterInvariant38-filterInvariant39-filterInvariant40-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:38,16:54:99:289,0,965:22,16,2,14 chr1 146399411 . G A 510.32 PASS AC=2;AF=0.927;AN=2;DP=1080;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:699,69,0:0,0,16,7 chr1 146409969 . A C 213.43 DRAGENHardSNP AC=2;AF=0.789;AN=2;DP=370;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:664,72,0:0,0,18,6 chr1 146410018 . C T 434.41 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=52;FS=1.09;FractionInformativeReads=1;MQ=26.31;MQRankSum=0.531;QD=8.35;ReadPosRankSum=0.22;SOR=0.46;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:27,25:52:99:463,0,542:17,10,14,11 chr1 146418342 . G T 145.87 DRAGENHardSNP AC=1;AF=0.75;AN=2;DP=150;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:7,12:19:99:243,0,119:4,3,7,5 chr1 146418491 . T C 156.95 DRAGENHardSNP AC=1;AF=0.688;AN=2;DP=52;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:3,5:8:53:107,0,53:1,2,1,4 chr1 146466146 . G T 1634.11 PASS AC=2;AF=0.789;AN=2;DP=1323;set=variant3-variant5-variant7-variant9-variant15-variant18-variant19-variant21-variant23-variant24-variant26-variant28-variant29-variant32-variant35-variant37-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,85:85:99:2838,255,0:0,0,17,68 chr1 146491003 . T C 67.72 PASS AC=2;AF=0.625;AN=2;DP=100;FractionInformativeReads=1;set=variant3-variant9-variant15-variant19-variant24-variant26-variant28-variant35-filterInvariant37-variant39-variant40-filterInvariant42 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:159,18,0:0,0,4,2 chr1 146491156 . A C 32.29 DRAGENHardSNP AC=2;AF=1;AN=2;DP=2;FS=0;FractionInformativeReads=1;MQ=25.5;QD=16.14;SOR=2.303;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:61,6,0:0,0,0,2 chr1 146493279 . C T 691.77 PASS AC=2;AF=0.947;AN=2;DP=517;FractionInformativeReads=1;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-filterInvariant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:45:653,45,0:0,0,13,1 chr1 146493280 . A G 691.77 PASS AC=2;AF=0.947;AN=2;DP=522;FractionInformativeReads=1;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-filterInvariant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:653,45,0:0,0,14,1 chr1 146494510 . T C 373.62 PASS AC=2;AF=0.765;AN=2;DP=117;FractionInformativeReads=1;set=variant4-variant5-variant7-variant13-variant15-variant20-variant21-variant23-variant25-variant26-filterInvariant28-variant29-variant35-variant37-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:306,21,0:0,0,5,2 chr1 146494511 . G A 106.77 PASS AC=2;AF=0.75;AN=2;DP=70;FS=0;FractionInformativeReads=1;set=variant5-variant7-variant15-variant23-variant26-filterInvariant28-variant29-variant35-variant37-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:306,21,0:0,0,5,2 chr1 146495506 . T G 360.3 PASS AC=2;AF=1;AN=2;DP=334;FS=0;FractionInformativeReads=1;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:311,24,0:0,0,6,2 chr1 146495752 . C T 78.16 PASS AC=2;AF=0.727;AN=2;DP=163;FractionInformativeReads=1;set=variant3-variant5-variant9-variant23-variant26-variant28-variant29-variant35-variant37-variant39-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:239,21,0:0,0,4,3 chr1 146514576 . T C 1536.43 PASS AC=1;AF=0.543;AN=2;DP=3812;set=variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant15-variant16-variant18-variant19-variant23-variant24-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:85,79:164:99:1812,0,2000:52,33,48,31 chr1 146584316 . T A 289.04 PASS AC=1;AF=0.525;AN=2;DP=1673;set=variant-variant7-variant8-variant13-variant14-variant15-variant17-variant19-variant21-variant22-variant25-variant27-variant31-variant32-variant33-variant35-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:54,43:97:99:880,0,1284:23,31,20,23 chr1 146584337 . G A 200.93 PASS AC=1;AF=0.524;AN=2;DP=1481;set=variant-variant7-variant8-variant13-variant14-variant15-variant17-variant19-variant21-variant22-variant25-variant27-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:47,38:85:99:845,0,1122:20,27,17,21 chr1 146586670 . T G 151.77 PASS AC=1;AF=0.682;AN=2;DP=136;FractionInformativeReads=1;set=variant-variant2-variant3-variant7-variant8-variant9-variant10-variant14-variant16-variant17-variant18-variant21-variant25-variant29-variant31-variant35-variant36-variant37-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,3:7:99:114,0,296:4,0,3,0 chr1 146586676 . T C 196.77 PASS AC=1;AF=0.696;AN=2;DP=150;FractionInformativeReads=1;set=variant-variant2-variant6-variant7-variant8-variant9-variant10-variant14-variant16-variant17-variant18-variant21-variant25-variant26-variant29-variant31-variant35-variant36-variant37-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,3:8:99:111,0,344:5,0,3,0 chr1 146586677 . G A 196.77 PASS AC=1;AF=0.696;AN=2;DP=155;FractionInformativeReads=1;set=variant-variant2-variant6-variant7-variant8-variant9-variant10-variant14-variant16-variant17-variant18-variant21-variant25-variant26-variant29-variant31-variant35-variant36-variant37-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,3:8:99:111,0,344:5,0,3,0 chr1 146586688 . G A 222.3 PASS AC=1;AF=0.673;AN=2;DP=220;FractionInformativeReads=1;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant16-variant17-variant18-variant21-variant25-variant26-variant29-variant31-variant33-variant35-variant36-variant37-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,3:9:99:100,0,228:5,1,3,0 chr1 146586703 . G T 286.77 PASS AC=1;AF=0.679;AN=2;DP=300;FractionInformativeReads=1;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant16-variant17-variant18-variant21-variant25-variant26-variant27-variant29-variant31-variant33-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,3:14:99:136,0,581:8,3,3,0 chr1 146586705 . A C 286.77 PASS AC=1;AF=0.679;AN=2;DP=315;FractionInformativeReads=1;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant16-variant17-variant18-variant21-variant25-variant26-variant27-variant29-variant31-variant33-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,5:16:99:136,0,581:8,3,4,1 chr1 146627405 . C G 7227.02 PASS AC=1;AF=0.632;AN=2;DP=7848;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:109,107:216:99:2881,0,3044:50,59,55,52 chr1 146628407 . T C 7439.25 PASS AC=1;AF=0.632;AN=2;DP=7286;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:118,102:220:99:2558,0,3025:70,48,59,43 chr1 146628479 . C G 2919.02 PASS AC=1;AF=0.524;AN=2;DP=5822;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant15-variant16-variant18-variant19-variant20-variant23-variant24-variant28-variant31-variant33-variant34-variant35-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:139,151:290:99:3698,0,3138:74,65,79,72 chr1 146628635 . A G 3813.21 PASS AC=1;AF=0.632;AN=2;DP=3440;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,55:104:99:1421,0,1313:14,35,16,39 chr1 146628742 . T G 959.91 PASS AC=1;AF=0.636;AN=2;DP=885;FractionInformativeReads=1;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,7:23:99:212,0,470:4,12,0,7 chr1 146629400 . GC G 1043.07 PASS AC=1;AF=0.563;AN=2;DP=2661;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant10-variant12-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,41:77:99:1297,0,1111:14,22,12,29 chr1 146629916 . C T 6294.69 PASS AC=1;AF=0.563;AN=2;DP=14251;set=variant-variant2-variant3-variant6-variant7-variant8-variant10-variant12-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:246,210:456:99:5363,0,6165:124,122,115,95 chr1 146633933 . G A 799.8 PASS AC=1;AF=0.632;AN=2;DP=1856;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,44:66:99:1074,0,565:15,7,26,18 chr1 146643555 . A G 1597.83 PASS AC=1;AF=0.632;AN=2;DP=2819;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,37:74:99:930,0,873:21,16,23,14 chr1 146644199 . C A 224.34 PASS AC=1;AF=0.553;AN=2;DP=480;MQ=60;set=variant-variant7-variant8-variant14-variant17-variant19-variant21-variant22-variant25-variant27-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:18,17:35:99:348,0,410:8,10,9,8 chr1 146656292 . A G 775.48 PASS AC=2;AF=0.898;AN=2;DP=2864;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:2145,195,0:0,0,17,48 chr1 146658041 . G GA 2317.99 PASS AC=1;AF=0.528;AN=2;DP=4691;MQ=60;set=variant-variant7-variant8-variant14-variant17-variant19-variant21-variant22-variant25-variant27-variant31-variant32-variant33-variant35-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:142,100:242:99:2224,0,3541:81,61,57,43 chr1 146672906 . C T 1368.77 PASS AC=2;AF=0.898;AN=2;DP=5087;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,118:118:99:3636,352,0:0,0,63,55 chr1 146673178 . A G 1137.52 PASS AC=2;AF=0.966;AN=2;DP=1259;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:1093,90,0:0,0,5,25 chr1 146680262 . A G 713.25 PASS AC=2;AF=0.898;AN=2;DP=1798;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-filterInvariant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1239,102,0:0,0,29,5 chr1 146685121 . G A 670.24 PASS AC=2;AF=0.898;AN=2;DP=2058;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:1703,173,0:0,0,25,33 chr1 146687250 . A T 510.49 PASS AC=2;AF=0.966;AN=2;DP=523;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:530,36,0:0,0,10,2 chr1 146696955 . G C 629.27 PASS AC=1;AF=0.643;AN=2;DP=2034;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant13-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,23:71:99:503,0,1223:26,22,11,12 chr1 146714255 . A G 1383.97 PASS AC=1;AF=0.8;AN=2;DP=3845;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,50:109:99:1170,0,1534:29,30,28,22 chr1 146714281 . C G 1160.21 PASS AC=1;AF=0.636;AN=2;DP=3173;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant13-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,51:103:99:1313,0,1355:26,26,29,22 chr1 146714392 . G T,C 2135.73 PASS AC=1,1;AF=0.233,0.628;AN=2;DP=7339;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 2/1:181:99:0,0,102,79 chr1 146714588 . C T 678.67 PASS AC=1;AF=0.73;AN=2;DP=2034;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,24:56:99:666,0,888:8,24,6,18 chr1 146724093 . A G 2340.16 PASS AC=2;AF=0.966;AN=2;DP=2990;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,73:73:99:2612,219,0:0,0,32,41 chr1 146727363 . G A 116.11 PASS AC=1;AF=0.5;AN=2;DP=29;FractionInformativeReads=1;MQ=60;set=variant32-variant35 GT:AD:DP:GQ:PL:SB 0/1:9,8:17:99:222,0,347:9,0,6,2 chr1 146727388 . G T 330.39 PASS AC=1;AF=0.556;AN=2;DP=268;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant7-variant8-variant14-variant17-variant19-variant21-variant22-variant27-variant31-variant32-variant33-variant35-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,7:19:99:176,0,417:11,1,6,1 chr1 146728162 . T TA 3319.4 PASS AC=2;AF=0.966;AN=2;DP=3714;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:2653,214,0:0,0,47,24 chr1 146736092 . C T 554.15 PASS AC=1;AF=0.556;AN=2;DP=987;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant7-variant8-variant14-variant17-variant19-variant21-variant22-variant27-variant31-variant32-variant33-variant35-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:41,30:71:99:732,0,1166:25,16,20,10 chr1 146739277 . T C 351.8 PASS AC=1;AF=0.73;AN=2;DP=1873;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,24:53:99:698,0,826:7,22,6,18 chr1 146740502 . C G 2462.65 PASS AC=1;AF=0.556;AN=2;DP=3746;MQ=60;set=variant-variant3-variant7-variant8-variant14-variant17-variant19-variant21-variant22-variant27-variant31-variant32-variant33-variant35-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:107,101:208:99:2540,0,2616:52,55,48,53 chr1 146740576 . G A 2579.68 PASS AC=2;AF=0.872;AN=2;DP=9138;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,216:216:99:6633,647,0:0,0,96,120 chr1 146747153 . T C 1546.45 PASS AC=2;AF=0.86;AN=2;DP=4300;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,130:130:99:3971,389,0:0,0,49,81 chr1 146747232 . C T 265.78 PASS AC=1;AF=0.63;AN=2;DP=660;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant14-variant15-variant16-variant18-variant20-variant23-variant24-variant25-variant26-variant28-variant31-variant33-variant34-variant35-variant36-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:18,17:35:99:616,0,579:2,16,1,16 chr1 146748008 . CAGCCA C 310.54 PASS AC=1;AF=0.63;AN=2;DP=626;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant14-variant15-variant16-variant18-variant20-variant23-variant24-variant25-variant26-variant28-variant31-variant33-variant34-variant35-variant36-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:16,7:23:99:246,0,651:5,11,1,6 chr1 146748072 . A G 238.54 PASS AC=2;AF=0.989;AN=2;DP=353;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:540,36,0:0,0,0,12 chr1 146751782 . A C 3652.31 PASS AC=2;AF=0.966;AN=2;DP=5896;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,140:141:99:4119,410,0:0,1,72,68 chr1 146756222 . AAAAC A 227.78 PASS AC=1;AF=0.63;AN=2;DP=1029;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant14-variant15-variant16-variant18-variant20-variant23-variant24-variant25-variant26-variant28-variant31-variant33-variant34-variant35-variant36-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:24,10:34:99:348,0,1172:10,14,3,7 chr1 146759306 . T C 330.04 PASS AC=1;AF=0.556;AN=2;DP=670;MQ=60;set=variant-variant3-variant7-variant8-variant14-variant17-variant19-variant21-variant22-variant27-variant31-variant32-variant33-variant35-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:19,13:32:99:327,0,439:12,7,9,4 chr1 146759528 . A G 249.11 PASS AC=1;AF=0.63;AN=2;DP=570;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant14-variant15-variant16-variant18-variant20-variant23-variant24-variant25-variant26-variant28-variant31-variant33-variant34-variant35-variant36-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,15:23:99:484,0,289:0,8,3,12 chr1 146762865 . A G 103.54 PASS AC=1;AF=0.864;AN=2;DP=154;FS=0;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,4:5:31:145,0,31:1,0,4,0 chr1 146763089 . G A 1432.49 PASS AC=1;AF=0.793;AN=2;DP=4346;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,42:87:99:1022,0,1156:27,18,21,21 chr1 146763415 . T C 399.59 PASS AC=1;AF=0.793;AN=2;DP=926;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,8:22:99:283,0,498:1,13,0,8 chr1 146763438 . A G 393.12 PASS AC=2;AF=0.955;AN=2;DP=634;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:580,45,0:0,0,1,14 chr1 146766069 . C CAT 5400.27 PASS AC=2;AF=0.966;AN=2;DP=5892;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,118:118:99:5377,361,0:0,0,76,42 chr1 146767149 . G T 2481.48 PASS AC=2;AF=0.966;AN=2;DP=3446;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,82:82:99:2599,244,0:0,0,52,30 chr1 146767320 . A G 4136.4 PASS AC=1;AF=0.793;AN=2;DP=11073;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:125,153:278:99:3755,0,2863:70,55,82,71 chr1 146767486 . T C 2745.48 PASS AC=1;AF=0.793;AN=2;DP=5067;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,63:131:99:2358,0,2568:19,49,17,46 chr1 146767490 . G A 5694.46 PASS AC=2;AF=0.966;AN=2;DP=5072;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,122:122:99:4812,375,0:0,0,32,90 chr1 146767494 . C G 2562.17 PASS AC=1;AF=0.793;AN=2;DP=4399;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,52:112:99:2156,0,2390:16,44,14,38 chr1 147013362 . A G 184.62 PASS AC=2;AF=0.763;AN=2;DP=1476;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1322,123,0:0,0,14,27 chr1 147087721 . T A 1523.96 PASS AC=2;AF=0.683;AN=2;DP=1646;MQ=60;set=variant-variant2-variant4-variant7-variant8-variant11-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:1800,162,0:0,0,17,37 chr1 147091972 . C T 877.86 PASS AC=2;AF=0.648;AN=2;DP=3120;MQ=60;set=variant-variant2-variant4-variant8-variant11-variant14-variant15-variant16-variant17-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,138:138:99:4660,410,0:0,0,60,78 chr1 147096718 . A T 1129.52 PASS AC=1;AF=0.5;AN=2;DP=106;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.609;QD=10.66;ReadPosRankSum=-2.485;SOR=0.638;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:58,48:106:99:1158,0,1530:21,37,18,30 chr1 147096794 . A G 1474.61 PASS AC=2;AF=0.932;AN=2;DP=2618;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1775,167,0:0,0,22,34 chr1 147096828 . C G 1375.41 PASS AC=2;AF=0.989;AN=2;DP=2021;MQ=60;MQRankSum=0.796;ReadPosRankSum=-0.726;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1456,129,0:0,0,19,24 chr1 147097635 . C T 639.04 PASS AC=2;AF=0.92;AN=2;DP=2920;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,86:86:99:2801,257,0:0,0,38,48 chr1 147119273 . G A 2984.52 PASS AC=2;AF=0.811;AN=2;DP=3533;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,104:104:99:2917,310,0:0,0,52,52 chr1 147121977 . C T 2546.5 PASS AC=2;AF=1;AN=2;DP=4059;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,126:126:99:3658,378,0:0,0,71,55 chr1 147124310 . T G 1895.41 PASS AC=2;AF=0.817;AN=2;DP=2912;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,99:99:99:2905,296,0:0,0,58,41 chr1 147131465 . T C 2437.89 PASS AC=2;AF=0.805;AN=2;DP=3084;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,80:80:99:2415,239,0:0,0,49,31 chr1 147131501 . A T 940.89 PASS AC=2;AF=0.638;AN=2;DP=3002;MQ=60;set=variant-variant2-variant4-variant6-variant8-variant10-variant11-variant14-variant15-variant16-variant17-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,105:106:99:3133,275,0:1,0,58,47 chr1 147131945 . T C 337.42 PASS AC=2;AF=0.808;AN=2;DP=522;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:496,36,0:0,0,3,9 chr1 147228874 . C T 407.26 PASS AC=2;AF=0.63;AN=2;DP=1309;MQ=60;set=variant-variant4-variant5-variant7-variant8-variant11-variant13-variant16-variant18-variant19-variant25-variant26-variant27-variant30-variant31-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:1982,193,0:0,0,29,36 chr1 147229299 . G A 925.32 PASS AC=2;AF=0.866;AN=2;DP=1658;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:837,75,0:0,0,15,10 chr1 147229382 . G A 1202.9 PASS AC=2;AF=1;AN=2;DP=2286;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:1817,180,0:0,0,29,31 chr1 147229563 . G A 503.89 PASS AC=2;AF=0.632;AN=2;DP=1156;MQ=60;set=variant-variant4-variant5-variant7-variant8-variant11-variant16-variant19-variant25-variant26-variant27-variant30-variant31-variant35-variant36-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1689,159,0:0,0,27,26 chr1 147230217 . T C 1930.55 PASS AC=2;AF=0.866;AN=2;DP=3869;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,123:123:99:3892,369,0:0,0,76,47 chr1 147230625 . G A 1022.42 PASS AC=1;AF=0.5;AN=2;DP=100;FS=3.753;FractionInformativeReads=1;MQ=60;MQRankSum=-1.633;QD=10.22;ReadPosRankSum=2.166;SOR=1.072;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:59,41:100:99:1051,0,1650:28,31,16,25 chr1 147231531 . T C 458.04 PASS AC=2;AF=1;AN=2;DP=592;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:522,42,0:0,0,4,10 chr1 147232488 . A G 73.72 PASS AC=1;AF=0.5;AN=2;DP=47;MQ=60;set=variant4-variant19-variant35 GT:AD:DP:GQ:PL:SB 0/1:8,6:14:99:143,0,253:5,3,4,2 chr1 147232555 . T C 719.01 PASS AC=2;AF=1;AN=2;DP=1129;FS=0;MQ=60;MQRankSum=1.083;ReadPosRankSum=-0.758;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,31:31:93:1184,93,0:0,0,21,10 chr1 147245324 . T C 980.89 PASS AC=2;AF=1;AN=2;DP=1492;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1211,114,0:0,0,24,14 chr1 147245383 . T C 988.29 PASS AC=1;AF=0.611;AN=2;DP=998;MQ=60;set=variant5-variant6-variant11-variant14-variant15-variant17-variant22-variant25-variant27-variant28-variant31-variant33-variant35-variant36-variant37-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:27,26:53:99:591,0,673:15,12,14,12 chr1 147245474 . G C 2084.55 PASS AC=2;AF=1;AN=2;DP=2769;FS=0;MQ=60;MQRankSum=1.354;ReadPosRankSum=0.409;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:1571,141,0:0,0,20,27 chr1 147245497 . C T 748.37 PASS AC=1;AF=0.611;AN=2;DP=977;MQ=60;set=variant5-variant6-variant11-variant14-variant15-variant17-variant22-variant25-variant27-variant28-variant31-variant33-variant35-variant36-variant37-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:17,25:42:99:593,0,474:6,11,12,13 chr1 147381397 . GA G,GAA 126.29 PASS AC=0,2;AF=0.17,0.477;AN=2;DP=1927;MQ=60;set=variant-variant2-variant3-filterInvariant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 2/2:40:74:1,2,18,19 chr1 147381444 . A C 116.07 PASS AC=1;AF=0.756;AN=2;DP=930;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-filterInvariant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,10:24:99:216,0,386:4,10,4,6 chr1 147561737 . T C 39.97 PASS AC=2;AF=0.906;AN=2;DP=67;FractionInformativeReads=1;set=variant2-filterInvariant4-filterInvariant11-variant13-filterInvariant14-filterInvariant17-filterInvariant19-filterInvariant21-filterInvariant24-filterInvariant25-filterInvariant27-filterInvariant28-filterInvariant29-filterInvariant34-filterInvariant35-filterInvariant40 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:208,24,0:0,0,3,5 chr1 147581468 . C T 1157.4 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=598;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:34,21:55:99:358,0,701:20,14,11,10 chr1 147595042 . T G 382.34 PASS AC=1;AF=0.55;AN=2;DP=162;FS=0;FractionInformativeReads=1;set=variant3-variant4-variant19-variant25-variant31-variant34-variant35-variant36-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:7,7:14:99:241,0,251:7,0,7,0 chr1 147595200 . C G 843.87 PASS AC=1;AF=0.55;AN=2;DP=602;set=variant3-variant4-variant19-variant25-variant31-variant34-variant35-variant36-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:40,22:62:99:478,0,1012:17,23,9,13 chr1 147806559 . C T 1131.66 PASS AC=2;AF=0.872;AN=2;DP=3970;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,91:91:99:3190,273,0:0,0,58,33 chr1 147806874 . G C 593.73 PASS AC=2;AF=0.895;AN=2;DP=1423;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1774,120,0:0,0,4,36 chr1 147806880 . T C 1170.3 PASS AC=2;AF=1;AN=2;DP=1241;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1620,108,0:0,0,4,31 chr1 148009349 . A G 697.94 PASS AC=1;AF=0.5;AN=2;DP=16657;set=filterInvariant2-variant5-variant6-filterInvariant7-filterInvariant8-variant9-variant11-filterInvariant12-filterInvariant16-filterInvariant18-variant19-variant21-filterInvariant22-variant24-filterInvariant25-filterInvariant28-variant29-filterInvariant32-filterInvariant33-variant34-variant35-variant40-filterInvariant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:810,149:959:99:1994,0,23519:484,326,88,61 chr1 148009715 . G GGA 44.31 PASS AC=1;AF=0.5;AN=2;DP=2810;set=filterInvariant-variant2-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant15-variant16-variant18-variant19-variant20-filterInvariant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,44:101:99:1318,0,1828:30,27,21,23 chr1 148009846 . CA C 35.66 PASS AC=1;AF=0.5;AN=2;DP=1661;set=filterInvariant-variant2-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,30:62:99:935,0,963:20,12,18,12 chr1 148010217 . A G 143.25 PASS AC=1;AF=0.5;AN=2;DP=106;FS=0;FractionInformativeReads=1;set=variant5-variant15-filterInvariant16-variant20-variant23-variant28-filterInvariant35-filterInvariant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:10,4:14:85:85,0,230:0,10,0,4 chr1 148010726 . T G 72.41 DRAGENHardSNP AC=1;AF=0.561;AN=2;DP=375;FS=0;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:5,9:14:93:188,0,93:5,0,9,0 chr1 148010911 . G A 3363.42 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=20112;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:222,259:481:99:4854,0,4318:116,106,128,131 chr1 148015667 . C T 35.26 DRAGENHardSNP AC=1;AF=0.75;AN=2;DP=20;FractionInformativeReads=1;MQRankSum=0.053;ReadPosRankSum=-1.221;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:14,4:18:83:83,0,352:6,8,4,0 chr1 148015713 . A G 113.41 PASS AC=1;AF=0.5;AN=2;DP=373;FractionInformativeReads=1;set=filterInvariant4-filterInvariant11-filterInvariant20-filterInvariant23-filterInvariant24-filterInvariant26-filterInvariant30-filterInvariant32-filterInvariant35-filterInvariant37-filterInvariant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,8:31:99:113,0,593:11,12,5,3 chr1 148017256 . G A 46.71 DRAGENHardSNP AC=1;AF=0.6;AN=2;DP=58;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:4,4:8:66:66,0,83:4,0,2,2 chr1 148017292 . C G 69.39 DRAGENHardSNP AC=1;AF=0.55;AN=2;DP=64;FS=0;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:3,5:8:56:104,0,56:2,1,2,3 chr1 148017629 . C T 141.1 PASS AC=1;AF=0.5;AN=2;DP=5895;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant13-filterInvariant14-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant38-filterInvariant39-filterInvariant40-filterInvariant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:150,34:184:99:310,0,3513:69,81,11,23 chr1 148021700 . G A 346.74 PASS AC=1;AF=0.557;AN=2;DP=2295;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant13-filterInvariant14-variant15-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant38-filterInvariant39-filterInvariant40-filterInvariant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:42,21:63:99:309,0,898:22,20,11,10 chr1 148021837 . T C 64.64 PASS AC=1;AF=0.56;AN=2;DP=359;FractionInformativeReads=1;set=variant2-filterInvariant3-variant4-variant5-variant7-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant31-variant34-variant35-filterInvariant38-variant39-filterInvariant41 GT:AD:DP:GQ:PL:SB 0/1:14,3:17:84:84,0,846:2,12,0,3 chr1 148021838 . G A 64.64 PASS AC=1;AF=0.56;AN=2;DP=348;FractionInformativeReads=1;set=variant2-filterInvariant3-variant4-variant5-variant7-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant31-variant34-variant35-filterInvariant38-variant39-filterInvariant41 GT:AD:DP:GQ:PL:SB 0/1:14,3:17:84:84,0,846:2,12,0,3 chr1 148023403 . G A 297.95 PASS AC=1;AF=0.547;AN=2;DP=1302;set=filterInvariant-filterInvariant2-filterInvariant3-variant4-filterInvariant5-variant6-variant7-filterInvariant8-filterInvariant10-filterInvariant11-filterInvariant12-variant13-filterInvariant14-variant15-variant16-variant17-variant18-filterInvariant19-variant20-filterInvariant21-variant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant27-variant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant32-variant33-filterInvariant34-variant35-filterInvariant36-filterInvariant37-filterInvariant38-filterInvariant39-filterInvariant40-filterInvariant41-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,11:34:99:218,0,563:18,5,9,2 chr1 148023489 . C T 187.46 PASS AC=1;AF=0.543;AN=2;DP=1859;set=filterInvariant-filterInvariant2-filterInvariant3-variant4-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant13-filterInvariant14-filterInvariant17-variant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant23-filterInvariant24-filterInvariant25-variant26-filterInvariant27-variant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant32-variant33-variant34-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant38-filterInvariant39-filterInvariant40-filterInvariant41-filterInvariant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:50,10:60:99:100,0,1161:30,20,5,5 chr1 148023509 . G A 457.93 PASS AC=1;AF=0.534;AN=2;DP=2323;set=filterInvariant-filterInvariant2-filterInvariant3-variant4-filterInvariant5-variant6-variant7-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant13-filterInvariant14-variant15-variant16-filterInvariant17-variant18-filterInvariant19-variant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-variant26-filterInvariant27-variant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant32-variant33-variant34-variant35-filterInvariant36-filterInvariant37-filterInvariant38-filterInvariant39-filterInvariant40-filterInvariant41-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,22:60:99:413,0,798:19,19,11,11 chr1 148025663 . C T 196.61 PASS AC=1;AF=0.5;AN=2;DP=395;FractionInformativeReads=1;set=filterInvariant3-filterInvariant14-filterInvariant18-filterInvariant22-variant24-variant26-variant35-variant36-filterInvariant41 GT:AD:DP:GQ:PL:SB 0/1:32,7:39:99:189,0,1368:23,9,5,2 chr1 148025668 . G A 200.58 PASS AC=1;AF=0.5;AN=2;DP=435;FractionInformativeReads=1;set=filterInvariant3-filterInvariant14-filterInvariant18-filterInvariant22-variant24-variant26-variant35-variant36-filterInvariant41 GT:AD:DP:GQ:PL:SB 0/1:37,8:45:99:207,0,1402:27,10,6,2 chr1 148025702 . G A 258.74 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=632;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:59,14:73:99:129,0,1455:38,21,7,7 chr1 148252049 . A C 569.2 PASS AC=1;AF=0.5;AN=2;DP=10230;set=filterInvariant2-variant4-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant10-filterInvariant11-filterInvariant12-variant13-filterInvariant16-filterInvariant17-filterInvariant18-variant19-filterInvariant20-filterInvariant21-filterInvariant22-variant24-filterInvariant25-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-variant34-variant35-filterInvariant36-filterInvariant37-filterInvariant39-filterInvariant40-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:282,74:356:99:787,0,7143:134,148,41,33 chr1 148252111 . C T 276.17 PASS AC=1;AF=0.5;AN=2;DP=10470;set=filterInvariant-variant2-variant3-variant4-variant5-variant6-variant7-filterInvariant9-variant10-variant11-variant12-variant13-filterInvariant14-variant16-filterInvariant17-variant18-variant19-variant20-variant21-variant22-filterInvariant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-filterInvariant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:200,70:270:99:931,0,5027:74,126,36,34 chr1 148252164 . A C 294.59 PASS AC=1;AF=0.5;AN=2;DP=4092;set=variant2-variant3-variant4-variant5-variant6-variant7-filterInvariant9-filterInvariant10-variant11-filterInvariant12-variant13-filterInvariant14-filterInvariant15-variant16-filterInvariant17-variant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-variant24-filterInvariant25-variant26-filterInvariant27-variant28-variant29-filterInvariant31-variant32-filterInvariant33-variant34-filterInvariant35-variant36-variant37-variant38-variant39-variant40-filterInvariant41-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:81,13:94:72:72,0,2532:19,62,2,11 chr1 148341688 . T C 43.29 PASS AC=1;AF=0.577;AN=2;DP=83;FractionInformativeReads=1;set=variant-filterInvariant5-filterInvariant11-filterInvariant15-filterInvariant16-filterInvariant19-variant21-filterInvariant23-filterInvariant28-filterInvariant32-filterInvariant33-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:1,3:4:25:97,0,25:0,1,1,2 chr1 148341812 . G A 150.43 PASS AC=1;AF=0.5;AN=2;DP=152;FractionInformativeReads=1;set=filterInvariant5-filterInvariant11-variant12-variant15-filterInvariant16-filterInvariant19-variant24-filterInvariant28-filterInvariant29-filterInvariant32-filterInvariant35-variant40-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:76:76,0,85:1,2,0,3 chr1 148341981 . T C 34.95 PASS AC=1;AF=0.5;AN=2;DP=3349;FractionInformativeReads=1;set=filterInvariant-filterInvariant2-filterInvariant5-variant6-filterInvariant8-filterInvariant9-filterInvariant12-filterInvariant15-filterInvariant16-filterInvariant18-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant28-variant29-filterInvariant32-filterInvariant33-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant40-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:108,76:184:99:1314,0,2192:54,54,38,38 chr1 148342344 . G A,C 478.05 PASS AC=1,0;AF=0.447,0.053;AN=2;DP=1841;FractionInformativeReads=1;set=variant-variant2-variant3-variant5-variant6-filterInvariant8-variant11-variant16-variant20-filterInvariant21-variant24-variant28-filterInvariant31-filterInvariant32-variant34-variant35-variant39-variant40-variant44 GT:DP:GQ:SB 0/1:109:99:71,23,11,4 chr1 148342345 . A T 478.05 PASS AC=1;AF=0.5;AN=2;DP=1702;FractionInformativeReads=1;set=variant-variant2-variant5-variant6-filterInvariant8-variant11-variant16-variant20-filterInvariant21-variant24-variant28-filterInvariant31-filterInvariant32-variant34-variant35-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:94,15:109:99:344,0,3901:71,23,11,4 chr1 148342369 . A G 1481.27 PASS AC=1;AF=0.5;AN=2;DP=4917;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-filterInvariant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-filterInvariant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:124,50:174:99:1768,0,5080:85,39,35,15 chr1 148342373 . C T 1595.58 PASS AC=1;AF=0.5;AN=2;DP=5234;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant11-filterInvariant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-filterInvariant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-filterInvariant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:128,53:181:99:1787,0,5099:87,41,37,16 chr1 148342446 . A T 1131.83 PASS AC=1;AF=0.5;AN=2;DP=8043;set=variant-variant2-variant5-variant6-filterInvariant8-variant9-variant11-filterInvariant12-filterInvariant15-variant16-variant19-variant20-variant21-filterInvariant22-variant24-filterInvariant27-variant28-filterInvariant29-filterInvariant31-variant32-variant33-variant34-variant35-filterInvariant36-variant40-variant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:247,73:320:99:1142,0,6519:139,108,42,31 chr1 148342488 . T C 1064.88 PASS AC=1;AF=0.5;AN=2;DP=10305;set=variant-variant2-variant5-variant6-filterInvariant8-variant9-variant11-variant12-filterInvariant15-variant16-filterInvariant19-variant20-filterInvariant21-filterInvariant22-variant24-filterInvariant25-variant27-variant28-filterInvariant29-filterInvariant31-variant32-variant33-variant34-variant35-filterInvariant36-variant40-filterInvariant41-variant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:289,126:415:99:1997,0,7816:145,144,65,61 chr1 148342562 . A G 1068.51 PASS AC=1;AF=0.5;AN=2;DP=4075;set=variant2-filterInvariant6-variant11-filterInvariant12-filterInvariant16-filterInvariant27-filterInvariant28-filterInvariant33-variant35-filterInvariant40-filterInvariant42-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:303,76:379:99:981,0,7805:139,164,30,46 chr1 148342639 . T C 177.99 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=192;FS=12.025;FractionInformativeReads=0.99;MQ=45.95;MQRankSum=-1.941;QD=0.93;ReadPosRankSum=-0.128;SOR=0.202;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:160,30:190:99:206,0,4419:51,109,15,15 chr1 148344491 . T A 38.95 PASS AC=1;AF=0.5;AN=2;DP=2375;set=variant-variant2-variant3-variant4-variant5-filterInvariant6-variant7-variant8-filterInvariant9-variant10-filterInvariant11-variant12-variant13-filterInvariant14-variant15-variant16-variant17-filterInvariant18-variant19-variant20-filterInvariant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-filterInvariant29-filterInvariant30-filterInvariant31-variant32-filterInvariant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,15:56:99:417,0,1280:34,7,14,1 chr1 148344521 . C T 364.79 PASS AC=1;AF=0.5;AN=2;DP=3512;set=variant2-filterInvariant3-variant4-variant5-variant7-variant9-variant10-filterInvariant11-variant12-variant13-variant15-variant16-variant17-filterInvariant18-filterInvariant19-filterInvariant21-variant22-filterInvariant23-variant24-variant26-variant27-variant28-variant29-filterInvariant30-variant31-variant32-filterInvariant33-variant35-filterInvariant36-variant37-variant40-variant41-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:76,30:106:99:634,0,2002:56,20,25,5 chr1 148344564 . T C 323.21 PASS AC=1;AF=0.5;AN=2;DP=7849;set=variant-variant2-variant3-filterInvariant4-filterInvariant5-variant6-variant7-variant8-variant9-variant10-filterInvariant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-filterInvariant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:162,55:217:99:991,0,4524:99,63,41,14 chr1 148344615 . G GC 409.77 PASS AC=1;AF=0.5;AN=2;DP=7286;set=filterInvariant2-filterInvariant3-variant4-filterInvariant5-filterInvariant13-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant19-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant27-variant28-filterInvariant31-filterInvariant32-filterInvariant35-filterInvariant36-filterInvariant37-variant40-filterInvariant41-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:338,48:386:99:524,0,13722:177,161,20,28 chr1 148344624 . T C,A 1879.8 PASS AC=1,0;AF=0.386,0.114;AN=2;DP=13312;set=Intersection GT:DP:GQ:SB 0/1:250:99:87,57,44,62 chr1 148344627 . G A 757.93 PASS AC=1;AF=0.5;AN=2;DP=6939;FractionInformativeReads=1;set=variant2-filterInvariant4-variant5-variant6-variant8-variant9-variant10-variant12-filterInvariant13-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-filterInvariant25-variant31-filterInvariant35-variant40-filterInvariant42-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:341,58:399:99:509,0,12593:170,171,35,23 chr1 148344660 . G C 153.13 PASS AC=1;AF=0.5;AN=2;DP=10939;set=filterInvariant-filterInvariant2-variant4-variant5-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant11-variant13-filterInvariant14-filterInvariant15-variant16-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant21-filterInvariant24-variant25-filterInvariant26-variant27-variant28-filterInvariant29-filterInvariant30-filterInvariant32-filterInvariant33-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant38-variant40-filterInvariant41-variant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:327,53:380:99:540,0,7532:176,151,12,41 chr1 148344741 . G C 389.8 PASS AC=1;AF=0.5;AN=2;DP=4428;set=variant-filterInvariant3-filterInvariant7-filterInvariant8-filterInvariant10-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant18-variant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant25-filterInvariant26-variant27-filterInvariant28-filterInvariant29-variant30-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant38-variant39-filterInvariant41-variant42-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:184,29:213:99:231,0,4735:82,102,5,24 chr1 148756363 . A G 376.77 DRAGENHardSNP AC=2;AF=0.932;AN=2;DP=569;FS=0;FractionInformativeReads=1;MQRankSum=-3.418;ReadPosRankSum=-1.275;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,19:19:60:900,60,0:0,0,14,5 chr1 148756384 . G A 401.49 PASS AC=2;AF=0.682;AN=2;DP=931;FractionInformativeReads=1;set=filterInvariant-filterInvariant2-filterInvariant3-variant4-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant13-filterInvariant14-variant15-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant38-filterInvariant39-filterInvariant40-filterInvariant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:1125,75,0:0,0,16,9 chr1 148756397 . C T 475.68 PASS AC=2;AF=0.693;AN=2;DP=1080;FractionInformativeReads=1;set=filterInvariant-filterInvariant2-filterInvariant3-variant4-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant13-filterInvariant14-variant15-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant38-filterInvariant39-filterInvariant40-filterInvariant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:1150,78,0:0,0,16,10 chr1 148756432 . C A 628.5 PASS AC=2;AF=0.705;AN=2;DP=1484;set=filterInvariant-filterInvariant2-filterInvariant3-variant4-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant13-filterInvariant14-variant15-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant38-filterInvariant39-filterInvariant40-filterInvariant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 1/1:0,33:33:98:801,98,0:0,0,16,17 chr1 148756515 . A C 446.32 DRAGENHardSNP AC=2;AF=0.92;AN=2;DP=862;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:495,33,0:0,0,1,10 chr1 148756518 . C T 421.77 DRAGENHardSNP AC=2;AF=0.738;AN=2;DP=678;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:495,33,0:0,0,1,10 chr1 148756648 . C T 694.51 PASS AC=2;AF=1;AN=2;DP=67;FS=0;FractionInformativeReads=1;set=variant4-filterInvariant9-variant15-filterInvariant22-filterInvariant25-filterInvariant28-filterInvariant35-filterInvariant43 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:60,6,0:0,0,0,2 chr1 148756664 . G T 601.77 PASS AC=2;AF=1;AN=2;DP=49;FS=0;FractionInformativeReads=1;set=variant4-filterInvariant9-variant15-filterInvariant22-filterInvariant25-filterInvariant28-filterInvariant31-filterInvariant33-filterInvariant35-filterInvariant39-filterInvariant40-filterInvariant43 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:90,6,0:0,0,0,2 chr1 148756665 . G T 601.77 PASS AC=2;AF=1;AN=2;DP=49;FS=0;FractionInformativeReads=1;set=variant4-filterInvariant9-variant15-filterInvariant22-filterInvariant25-filterInvariant28-filterInvariant31-filterInvariant33-filterInvariant35-filterInvariant39-filterInvariant40-filterInvariant43 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:90,6,0:0,0,0,2 chr1 148873398 . C A 228.79 PASS AC=1;AF=0.5;AN=2;DP=146;set=variant32-filterInvariant35-filterInvariant42 GT:AD:DP:GQ:PL:SB 0/1:39,9:48:90:90,0,1051:31,8,6,3 chr1 148873515 . T C 169.2 PASS AC=1;AF=0.5;AN=2;DP=1793;FractionInformativeReads=1;set=filterInvariant5-variant8-variant18-filterInvariant20-filterInvariant26-filterInvariant29-filterInvariant34-filterInvariant35-variant39-filterInvariant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:174,14:188:64:64,0,7463:77,97,8,6 chr1 148873516 . C A 169.2 PASS AC=1;AF=0.5;AN=2;DP=1793;FractionInformativeReads=1;set=filterInvariant5-variant8-variant18-filterInvariant20-filterInvariant26-filterInvariant29-filterInvariant34-filterInvariant35-variant39-filterInvariant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:174,14:188:64:64,0,7463:77,97,8,6 chr1 148873574 . G T 818.7 PASS AC=1;AF=0.5;AN=2;DP=4281;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:72,37:109:99:718,0,1634:29,43,13,24 chr1 148882326 . C A 257.24 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=2097;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:16,20:36:99:428,0,365:7,9,8,12 chr1 148889551 . TAA T,AAA 1553.41 PASS AC=1,1;AF=0.5,0.05;AN=2;DP=3572;set=variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant2-variant22-variant24-variant25-variant26-variant27-variant28-variant-variant29-variant30-variant31-variant32-variant33-variant34-variant4-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:DP:GQ:SB 1/2:97:99:10,2,51,34 chr1 148889689 . T C 258.96 PASS AC=1;AF=0.5;AN=2;DP=106;FS=2.199;FractionInformativeReads=1;MQ=43.72;MQRankSum=-0.166;QD=2.44;ReadPosRankSum=1.159;SOR=0.408;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:86,20:106:99:287,0,3230:28,58,8,12 chr1 148889699 . A G 703.23 PASS AC=1;AF=0.5;AN=2;DP=3655;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:47,48:95:99:1477,0,1133:16,31,18,30 chr1 148889778 . T C 209.12 PASS AC=1;AF=0.5;AN=2;DP=837;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,14:27:99:405,0,348:1,12,2,12 chr1 148903047 . G A 391.27 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=18554;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:366,154:520:99:2305,0,8028:204,162,69,85 chr1 148903118 . C T 289.77 PASS AC=1;AF=0.5;AN=2;DP=12082;set=filterInvariant2-filterInvariant4-filterInvariant5-filterInvariant6-variant7-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant11-variant12-filterInvariant14-filterInvariant15-filterInvariant16-variant17-filterInvariant18-variant19-variant20-filterInvariant21-filterInvariant22-filterInvariant23-variant24-filterInvariant25-variant26-filterInvariant27-filterInvariant28-variant29-variant30-filterInvariant31-filterInvariant32-variant33-filterInvariant34-filterInvariant35-filterInvariant36-variant37-filterInvariant38-filterInvariant39-variant40-filterInvariant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:301,49:350:99:830,0,13627:178,123,10,39 chr1 148903133 . C T 179.5 PASS AC=1;AF=0.5;AN=2;DP=6737;set=filterInvariant6-filterInvariant7-filterInvariant10-filterInvariant12-filterInvariant14-filterInvariant16-filterInvariant17-variant18-variant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant26-variant30-variant33-filterInvariant35-filterInvariant37-filterInvariant39-filterInvariant40-filterInvariant41-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:341,31:372:99:302,0,14606:210,131,7,24 chr1 149279677 . G A 641.34 PASS AC=1;AF=0.5;AN=2;DP=2144;set=variant-variant2-variant6-variant7-variant12-variant15-variant16-variant25-variant35-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:168,45:213:99:649,0,4305:65,103,19,26 chr1 149279739 . C T 2695.91 PASS AC=2;AF=0.784;AN=2;DP=4104;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-filterInvariant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-filterInvariant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,80:80:99:2866,240,0:0,0,12,68 chr1 149290370 . G A 175.91 PASS AC=1;AF=0.5;AN=2;DP=1409;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-filterInvariant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-filterInvariant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,19:40:99:393,0,552:13,8,10,9 chr1 149290383 . G T 140.38 PASS AC=1;AF=0.5;AN=2;DP=1422;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-filterInvariant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-filterInvariant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-filterInvariant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,18:38:99:413,0,430:12,8,9,9 chr1 149290881 . C T 293.82 PASS AC=1;AF=0.5;AN=2;DP=3206;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-filterInvariant23-variant24-variant25-variant28-variant29-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,78:129:99:2017,0,852:24,27,34,44 chr1 149376972 . C T 389.72 PASS AC=2;AF=0.741;AN=2;DP=428;FractionInformativeReads=1;set=variant-variant4-variant6-filterInvariant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-filterInvariant17-variant18-variant21-variant23-filterInvariant24-variant25-variant28-filterInvariant29-filterInvariant32-variant34-variant35-variant36-variant37-filterInvariant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:620,54,0:0,0,0,18 chr1 149379237 . A G 135.76 PASS AC=2;AF=1;AN=2;DP=700;FS=0;set=filterInvariant-variant2-variant3-filterInvariant4-filterInvariant5-filterInvariant6-variant8-filterInvariant11-variant12-filterInvariant14-variant15-variant17-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-filterInvariant34-filterInvariant35-variant36-variant37-variant38-filterInvariant39-filterInvariant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:66,6,0:0,0,2,0 chr1 149665167 . A G 5595.19 PASS AC=2;AF=0.977;AN=2;DP=9015;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,228:228:99:6850,683,0:0,0,128,100 chr1 149665214 . T G 2091.06 PASS AC=1;AF=0.5;AN=2;DP=10796;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:173,155:328:99:3398,0,3912:93,80,76,79 chr1 149665383 . A G 1556.55 PASS AC=1;AF=0.523;AN=2;DP=6707;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:71,68:139:99:1633,0,1646:25,46,24,44 chr1 149675876 . A G 89.23 PASS AC=2;AF=1;AN=2;DP=206;FS=0;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-filterInvariant6-variant7-variant8-filterInvariant9-variant10-variant11-variant12-filterInvariant13-variant14-variant15-variant16-filterInvariant17-variant19-variant20-variant21-variant22-variant24-filterInvariant25-filterInvariant26-filterInvariant28-filterInvariant30-variant31-variant33-filterInvariant34-filterInvariant35-variant36-variant38-filterInvariant39-filterInvariant40-variant41-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:142,18,0:0,0,3,3 chr1 149676075 . G A 71.06 PASS AC=2;AF=0.987;AN=2;DP=174;FractionInformativeReads=1;MQRankSum=0.533;ReadPosRankSum=-1.381;set=filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant5-variant6-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant11-filterInvariant12-filterInvariant13-filterInvariant15-variant16-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-variant23-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant32-variant33-filterInvariant34-filterInvariant35-filterInvariant38-filterInvariant39-filterInvariant40-variant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:95,9,0:0,0,3,0 chr1 149676261 . A T 972.37 PASS AC=1;AF=0.5;AN=2;DP=1156;set=variant27-variant32-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:243,68:311:99:1009,0,7215:148,95,39,29 chr1 149676264 . T C 205.45 PASS AC=1;AF=0.5;AN=2;DP=5330;set=filterInvariant3-variant5-filterInvariant7-variant9-filterInvariant12-filterInvariant17-filterInvariant18-filterInvariant22-filterInvariant24-filterInvariant26-filterInvariant28-filterInvariant31-variant35-filterInvariant36-filterInvariant37-filterInvariant41-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:251,66:317:99:817,0,7253:150,101,40,26 chr1 149676293 . C A 403.86 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=748;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:312,61:373:99:615,0,7566:167,145,30,31 chr1 149676401 . A G 429.07 PASS AC=1;AF=0.5;AN=2;DP=8607;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:104,80:184:99:1901,0,2574:43,61,23,57 chr1 149785120 . C A 33.65 PASS AC=1;AF=0.5;AN=2;DP=4616;FractionInformativeReads=1;set=filterInvariant-variant4-variant5-variant8-variant9-variant13-variant15-variant16-variant18-variant19-variant22-variant23-variant24-variant25-variant29-variant30-filterInvariant32-variant34-variant35-variant36-filterInvariant38-filterInvariant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:170,23:193:99:437,0,41805:94,76,12,11 chr1 149785132 . C G 848.55 PASS AC=1;AF=0.5;AN=2;DP=4648;FractionInformativeReads=1;set=variant4-variant5-variant8-variant9-variant13-variant15-variant16-variant18-variant19-variant22-variant23-variant24-variant25-variant29-variant30-filterInvariant32-variant34-filterInvariant35-variant36-filterInvariant38-filterInvariant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:180,22:202:99:370,0,49241:99,81,11,11 chr1 149785138 . C G 811.67 PASS AC=1;AF=0.5;AN=2;DP=4703;FractionInformativeReads=1;set=variant4-variant5-variant8-variant9-variant13-filterInvariant15-variant16-variant18-variant19-variant22-variant23-variant24-variant25-variant29-variant30-filterInvariant32-filterInvariant34-filterInvariant35-variant36-filterInvariant38-filterInvariant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:176,22:198:99:358,0,53914:98,78,11,11 chr1 149785147 . C G 703.46 PASS AC=1;AF=0.5;AN=2;DP=4717;FractionInformativeReads=1;set=variant4-variant5-filterInvariant8-variant9-variant13-filterInvariant15-filterInvariant16-variant18-variant19-variant22-variant23-variant24-variant25-variant29-filterInvariant30-filterInvariant32-filterInvariant34-filterInvariant35-variant36-filterInvariant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:186,22:208:99:349,0,58826:102,84,11,11 chr1 149785162 . C A 538.51 PASS AC=1;AF=0.5;AN=2;DP=4441;FractionInformativeReads=1;set=filterInvariant4-variant5-filterInvariant8-filterInvariant9-variant13-filterInvariant15-filterInvariant16-filterInvariant18-variant19-variant22-variant23-variant24-variant25-variant30-filterInvariant32-filterInvariant34-filterInvariant35-variant36-filterInvariant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:197,20:217:99:223,0,64641:106,91,10,10 chr1 149785165 . T C 508.56 PASS AC=1;AF=0.5;AN=2;DP=4428;FractionInformativeReads=1;set=filterInvariant4-variant5-filterInvariant8-filterInvariant9-variant13-filterInvariant15-filterInvariant16-filterInvariant18-filterInvariant19-variant22-variant23-variant24-filterInvariant25-variant30-filterInvariant32-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:198,19:217:99:184,0,65063:108,90,9,10 chr1 149876370 . A T 210.79 PASS AC=1;AF=0.5;AN=2;DP=403;MQ=60;set=variant-variant6-variant11-variant12-variant21-variant22-variant23-variant27-variant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:15,27:42:99:773,0,373:7,8,12,15 chr1 149880650 . C T 126.8 PASS AC=1;AF=0.5;AN=2;DP=183;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant12-variant22-variant23-variant25-variant27-variant35 GT:AD:DP:GQ:PL:SB 0/1:12,16:28:99:532,0,391:11,1,14,2 chr1 149885583 . A G 1455.83 PASS AC=2;AF=0.919;AN=2;DP=2151;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,42:43:85:1491,85,0:1,0,27,15 chr1 149906413 . T C 1850.51 PASS AC=1;AF=0.589;AN=2;DP=3398;MQ=60;set=variant-variant2-variant4-variant6-variant8-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant38-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,79:140:99:2022,0,1641:20,41,32,47 chr1 149907259 . G A 1563.01 PASS AC=1;AF=0.5;AN=2;DP=284;FractionInformativeReads=1;MQ=60;set=variant27-variant35 GT:AD:DP:GQ:PL:SB 0/1:85,67:152:99:1740,0,2308:46,39,33,34 chr1 149912782 . A G 1632.21 PASS AC=2;AF=1;AN=2;DP=2685;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1684,158,0:0,0,24,29 chr1 149914683 . G A 3473.92 PASS AC=2;AF=1;AN=2;DP=6439;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,163:163:99:4548,486,0:0,0,88,75 chr1 149915418 . A C 91.26 PASS AC=1;AF=0.5;AN=2;DP=668;set=filterInvariant2-filterInvariant3-filterInvariant4-variant6-filterInvariant8-filterInvariant11-filterInvariant35-variant39-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:64,17:81:99:200,0,2395:12,52,17,0 chr1 149915424 . A C 37.95 PASS AC=1;AF=0.5;AN=2;DP=443;set=filterInvariant2-filterInvariant4-variant6-filterInvariant23-filterInvariant31-filterInvariant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:64,16:80:99:194,0,2463:11,53,16,0 chr1 149922148 . G A 1712.13 PASS AC=1;AF=0.5;AN=2;DP=262;FractionInformativeReads=1;MQ=60;set=variant27-variant35 GT:AD:DP:GQ:PL:SB 0/1:48,72:120:99:1642,0,1054:21,27,34,38 chr1 150039678 . G A 2164.58 PASS AC=2;AF=0.821;AN=2;DP=3541;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,107:107:99:3223,320,0:0,0,55,52 chr1 150117533 . G A 5261.83 PASS AC=2;AF=1;AN=2;DP=6264;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,155:155:99:5142,462,0:0,0,38,117 chr1 150122493 . T C 1498.86 PASS AC=2;AF=1;AN=2;DP=2214;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,80:80:99:2356,239,0:0,0,34,46 chr1 150128425 . C T 832.5 PASS AC=2;AF=0.821;AN=2;DP=1261;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1069,108,0:0,0,12,24 chr1 150129267 . G A 926.53 PASS AC=2;AF=1;AN=2;DP=2060;FS=0;MQ=60;MQRankSum=1.54;ReadPosRankSum=0.385;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1820,167,0:0,0,20,36 chr1 150206772 . TAA TA,TAAA,T,TAAAA 66.52 PASS AC=1,0,0,0;AF=0.435,0.022,0.022,0.022;AN=2;DP=346;MQ=60;set=variant2-variant3-variant6-variant7-variant10-variant11-variant15-variant17-variant18-variant19-variant24-variant25-filterInvariant26-variant27-variant29-variant30-variant31-variant34-variant35-variant38-variant39-variant40-variant43 GT:DP:GQ:SB 0/1:17:99:8,0,6,3 chr1 150234657 . G T 934.87 PASS AC=2;AF=0.556;AN=2;DP=847;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant12-variant14-variant21-variant28-variant31-variant35 GT:AD:DP:GQ:PL:SB 1/1:2,104:106:99:3056,268,0:1,1,48,56 chr1 150236314 . CT C,CTT 125.59 PASS AC=1,0;AF=0.438,0.063;AN=2;DP=839;set=variant3-filterInvariant4-filterInvariant7-filterInvariant8-variant9-filterInvariant10-filterInvariant11-filterInvariant12-variant13-variant15-variant17-variant20-variant24-filterInvariant25-variant26-variant28-filterInvariant29-variant31-filterInvariant32-variant35-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:26:99:4,10,1,11 chr1 150297334 . CT C,CTT 132.08 PASS AC=1,0;AF=0.483,0.017;AN=2;DP=1036;set=variant-variant4-variant5-variant8-variant10-variant12-variant13-variant14-filterInvariant15-variant16-filterInvariant17-variant18-filterInvariant19-variant21-variant22-filterInvariant24-variant25-variant27-variant28-filterInvariant29-variant30-variant31-variant33-variant35-filterInvariant36-variant37-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:41:97:5,4,20,12 chr1 150300727 . T C 673.68 PASS AC=2;AF=0.676;AN=2;DP=1936;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:1703,171,0:0,0,36,21 chr1 150301006 . ATTTT ATT,ATTTTT,A,AT,ATTTTTTTTT,ATTT,ATTTTTTTTTT 295.04 PASS AC=1,0,0,0,0,0,0;AF=0.188,0.021,0.042,0.125,0.042,0.083,0.021;AN=2;DP=1105;set=variant4-filterInvariant7-variant8-variant10-variant12-variant14-variant15-variant19-variant21-variant24-variant28-variant29-variant31-variant32-variant33-variant34-variant35-filterInvariant36-variant37-filterInvariant38-variant39-variant41-variant42-variant44 GT:DP:GQ:SB 0/1:25:34:1,3,4,17 chr1 150307270 . T G 164.58 PASS AC=2;AF=0.681;AN=2;DP=531;set=variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:960,78,0:0,0,21,5 chr1 150316087 . G A 468.5 PASS AC=1;AF=0.5;AN=2;DP=51;FractionInformativeReads=1;MQ=60;set=variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:11,18:29:99:497,0,371:1,10,3,15 chr1 150317239 . CT C 66.34 PASS AC=2;AF=0.75;AN=2;DP=315;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant9-variant10-variant11-variant16-variant18-variant21-variant24-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:282,30,0:0,0,2,8 chr1 150321486 . G A 270.08 PASS AC=2;AF=0.595;AN=2;DP=503;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant6-variant12-variant14-variant16-variant18-variant19-variant21-variant24-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:842,78,0:0,0,17,9 chr1 150321568 . C G 676.05 PASS AC=1;AF=0.5;AN=2;DP=338;FractionInformativeReads=1;MQ=60;set=variant2-variant24-variant29-variant31-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:24,30:54:99:704,0,634:13,11,15,15 chr1 150389964 . GA G 367.31 PASS AC=2;AF=0.676;AN=2;DP=1250;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1174,123,0:0,0,33,8 chr1 150413940 . G T 2537.28 PASS AC=2;AF=0.676;AN=2;DP=6123;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,153:153:99:5153,458,0:0,0,85,68 chr1 150432802 . G A 770.72 PASS AC=1;AF=0.538;AN=2;DP=439;MQ=60;set=variant2-variant6-variant16-variant18-variant19-variant24-variant27-variant29-variant31-variant33-variant35-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:23,21:44:99:560,0,643:9,14,7,14 chr1 150432870 . GGTT G,GGTTGTT 143.38 PASS AC=2,0;AF=0.464,0.232;AN=2;DP=319;MQ=60;set=variant2-variant4-variant5-variant6-variant8-variant11-variant12-variant14-variant15-variant16-variant18-variant20-variant21-variant24-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant41-variant42-variant43 GT:DP:GQ:SB 1/1:11:33:0,0,4,7 chr1 150445819 . A G 1553.67 PASS AC=2;AF=0.595;AN=2;DP=3022;MQ=60;set=variant2-variant4-variant5-variant6-variant12-variant14-variant16-variant18-variant19-variant21-variant24-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,125:126:99:4059,339,0:1,0,67,58 chr1 150446032 . TAA TAAA,TA,TAAAAAAAAAAA,TAAAAAAAAAA,T,TAAAAAA,TAAAAAAAAAAAA 166.75 PASS AC=0,1,0,0,0,0,0;AF=0.043,0.329,0.086,0.043,0.014,0.014,0.014;AN=2;DP=4708;set=filterInvariant-variant2-variant3-variant6-variant8-filterInvariant9-filterInvariant10-variant11-filterInvariant12-filterInvariant13-variant14-filterInvariant15-variant16-filterInvariant17-variant18-variant19-variant22-filterInvariant23-variant24-variant26-variant27-filterInvariant28-variant29-variant31-variant32-variant35-variant36-variant37-filterInvariant38-variant39-variant40-variant41-filterInvariant42-variant43-variant44 GT:DP:GQ:SB 0/2:101:99:14,28,24,35 chr1 150446067 . C T 2038.7 PASS AC=2;AF=0.619;AN=2;DP=2557;set=variant2-variant4-variant5-variant6-variant12-variant14-variant16-variant18-variant19-variant21-variant24-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,133:133:99:4157,389,0:0,0,55,78 chr1 150447269 . G A 3482.62 PASS AC=2;AF=0.676;AN=2;DP=8292;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,254:254:99:7716,761,0:0,0,118,136 chr1 150447398 . A G 1119 PASS AC=2;AF=0.595;AN=2;DP=2408;set=variant2-variant4-variant5-variant6-variant12-variant14-variant16-variant18-variant19-variant21-variant24-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,101:101:99:3325,303,0:0,0,42,59 chr1 150447462 . C T 1560.75 PASS AC=2;AF=0.591;AN=2;DP=1664;MQ=60;set=variant2-variant4-variant5-variant6-variant8-variant12-variant14-variant16-variant18-variant19-variant21-variant24-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:2550,225,0:0,0,35,40 chr1 150447772 . G GT 1970.1 PASS AC=1;AF=0.5;AN=2;DP=494;MQ=60;set=variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:125,107:232:99:2007,0,2787:61,64,51,56 chr1 150448019 . G A 9513.43 PASS AC=2;AF=1;AN=2;DP=11034;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,239:239:99:7062,715,0:0,0,123,116 chr1 150460168 . A G 225.69 PASS AC=2;AF=0.662;AN=2;DP=533;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:581,54,0:0,0,12,6 chr1 150470322 . C A 272.38 PASS AC=2;AF=0.619;AN=2;DP=687;FractionInformativeReads=1;set=variant2-variant4-variant5-variant6-variant12-variant14-variant16-variant18-variant19-variant21-variant24-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1140,101,0:0,0,9,25 chr1 150471848 . A AT 45.77 PASS AC=2;AF=0.667;AN=2;DP=650;MQ=60;set=variant-filterInvariant4-variant6-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:348,39,0:0,0,3,10 chr1 150476797 . T C 2124.25 PASS AC=1;AF=0.5;AN=2;DP=139;FS=3.159;FractionInformativeReads=1;MQ=60;MQRankSum=-0.418;QD=15.28;ReadPosRankSum=0.396;SOR=0.469;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:57,82:139:99:2152,0,1346:37,20,48,34 chr1 150477061 . C T 2113.57 PASS AC=2;AF=0.595;AN=2;DP=3390;MQ=60;set=variant2-variant4-variant5-variant6-variant12-variant14-variant16-variant18-variant19-variant21-variant24-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,178:178:99:5078,530,0:0,0,84,94 chr1 150482738 . G A 146.24 PASS AC=1;AF=0.594;AN=2;DP=827;MQ=60;set=variant-variant2-variant6-variant16-variant18-variant19-variant24-variant27-variant29-variant31-variant33-variant34-variant35-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:37,16:53:99:366,0,940:13,24,4,12 chr1 150483236 . A C 72.36 PASS AC=2;AF=0.676;AN=2;DP=797;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:1035,81,0:0,0,21,6 chr1 150483355 . C T 990.78 PASS AC=2;AF=0.595;AN=2;DP=2288;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant6-variant12-variant14-variant16-variant18-variant19-variant21-variant24-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,118:118:99:3820,354,0:0,0,72,46 chr1 150483840 . C T 440.81 PASS AC=2;AF=0.667;AN=2;DP=2009;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:1865,161,0:0,0,26,28 chr1 150484395 . ACC A 1319.24 PASS AC=2;AF=0.681;AN=2;DP=2665;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,73:73:99:3065,220,0:0,0,33,40 chr1 150484555 . C G 105.45 PASS AC=2;AF=0.671;AN=2;DP=721;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:59:593,59,0:0,0,9,11 chr1 150484844 . A T 1470.82 PASS AC=1;AF=0.5;AN=2;DP=298;FractionInformativeReads=1;MQ=60;set=variant12-variant28-variant35 GT:AD:DP:GQ:PL:SB 0/1:60,53:113:99:1233,0,1747:39,21,32,21 chr1 150484987 . G A 1703.24 PASS AC=2;AF=0.636;AN=2;DP=4169;MQ=60;set=variant2-variant4-variant5-variant6-variant12-variant14-variant16-variant18-variant19-variant21-variant24-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,207:207:99:6416,618,0:0,0,101,106 chr1 150485566 . T G 141.61 PASS AC=2;AF=0.676;AN=2;DP=805;FractionInformativeReads=1;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:990,66,0:0,0,17,5 chr1 150485571 . T C 536.62 PASS AC=2;AF=1;AN=2;DP=1036;FS=0;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:990,66,0:0,0,17,5 chr1 150486381 . G C 422 PASS AC=1;AF=0.5;AN=2;DP=216;MQ=60;set=variant4-variant5-variant6-variant12-filterInvariant14-variant18-variant21-variant28-variant31-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:7,7:14:99:243,0,218:1,6,0,7 chr1 150522242 . T C 288.82 PASS AC=2;AF=0.735;AN=2;DP=818;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:695,66,0:0,0,12,10 chr1 150522471 . C CTG 682.4 PASS AC=2;AF=0.735;AN=2;DP=1839;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:2257,153,0:0,0,29,21 chr1 150526044 . G C 467.63 PASS AC=1;AF=0.6;AN=2;DP=4311;MQ=60;set=variant-variant4-variant5-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant27-variant28-variant30-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:89,101:190:99:2276,0,2113:46,43,51,50 chr1 150526406 . C T 2325.74 PASS AC=1;AF=0.595;AN=2;DP=3515;MQ=60;set=variant-variant4-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant20-variant21-variant22-variant28-variant30-variant32-variant34-variant35-variant37-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:93,75:168:99:1687,0,2476:45,48,38,37 chr1 150528090 . G GACAC 694.07 PASS AC=1;AF=0.645;AN=2;DP=3087;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,38:83:99:1439,0,1794:22,23,14,24 chr1 150528118 . T TACAC,TACACAC 633.13 PASS AC=1,0;AF=0.632,0.013;AN=2;DP=2424;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:69:99:21,21,12,15 chr1 150528175 . GCA G 248.46 PASS AC=1;AF=0.645;AN=2;DP=1118;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,14:51:99:477,0,1470:14,23,3,11 chr1 150528207 . A G 207.12 PASS AC=1;AF=0.5;AN=2;DP=65;MQ=60;set=variant12-variant28-variant35 GT:AD:DP:GQ:PL:SB 0/1:13,19:32:99:524,0,431:3,10,6,13 chr1 150528208 . C T 159.39 PASS AC=1;AF=0.607;AN=2;DP=504;FractionInformativeReads=1;set=variant-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant28-variant30-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,11:31:99:291,0,762:6,14,2,9 chr1 150529322 . T TAA 1986.04 PASS AC=2;AF=0.92;AN=2;DP=2499;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:3427,235,0:0,0,35,42 chr1 150531008 . T C 2370.84 PASS AC=2;AF=0.92;AN=2;DP=8443;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,228:228:99:7170,683,0:0,0,139,89 chr1 150531050 . G A 3150.1 PASS AC=2;AF=0.86;AN=2;DP=9670;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,255:255:99:7501,758,0:0,0,141,114 chr1 150531170 . C T 6137.71 PASS AC=2;AF=1;AN=2;DP=9825;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,229:229:99:6978,685,0:0,0,95,134 chr1 150531380 . T C 723.51 PASS AC=1;AF=0.643;AN=2;DP=1929;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,33:67:99:845,0,924:20,14,18,15 chr1 150547747 . G A 780.26 PASS AC=1;AF=0.677;AN=2;DP=1265;MQ=60;set=variant-variant4-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,25:39:99:790,0,412:3,11,10,15 chr1 150548887 . C CCTAT 9352.87 PASS AC=2;AF=1;AN=2;DP=7788;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,165:165:99:7599,511,0:0,0,90,75 chr1 150550019 . T TA 1632.1 PASS AC=2;AF=1;AN=2;DP=2253;FS=0;MQ=60;MQRankSum=1.555;ReadPosRankSum=1.466;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:1743,141,0:0,0,11,36 chr1 150552042 . G A 2869.56 PASS AC=1;AF=0.5;AN=2;DP=2065;MQ=60;set=variant5-variant12-variant14-variant16-variant24-variant27-variant28-variant31-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:110,118:228:99:2876,0,2678:40,70,45,73 chr1 150552263 . GGCCGGGGCCGGGGCCTGA G 521.99 PASS AC=1;AF=0.75;AN=2;DP=420;set=variant4-variant5-variant6-variant8-variant9-variant11-variant13-variant15-variant16-variant17-variant18-variant21-variant22-variant25-variant27-variant29-variant30-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,8:19:99:128,0,484:5,6,4,4 chr1 150599849 . C T 349.2 PASS AC=1;AF=0.5;AN=2;DP=376;FractionInformativeReads=1;MQ=60;set=variant5-variant12-variant28-variant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:39,31:70:99:762,0,908:24,15,13,18 chr1 150600150 . C A 121.4 PASS AC=1;AF=0.5;AN=2;DP=27;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.802;QD=4.5;ReadPosRankSum=1.577;SOR=0.559;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:20,7:27:99:150,0,474:8,12,3,4 chr1 150600181 . C T 645.9 PASS AC=1;AF=0.73;AN=2;DP=611;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,6:18:99:127,0,285:5,7,3,3 chr1 150618961 . T G 7420.88 PASS AC=1;AF=0.662;AN=2;DP=7361;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:106,107:213:99:2965,0,2736:60,46,58,49 chr1 150619602 . T C 9747.98 PASS AC=2;AF=1;AN=2;DP=11021;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,237:237:99:7473,710,0:0,0,118,119 chr1 150620569 . C G 1623.04 PASS AC=2;AF=0.69;AN=2;DP=4642;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant10-variant11-variant12-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,149:149:99:4477,445,0:0,0,60,89 chr1 150666797 . G A 41.5 PASS AC=2;AF=0.679;AN=2;DP=241;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant10-variant11-variant12-variant14-variant16-variant17-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:536,42,0:0,0,2,12 chr1 150669414 . T G 353.06 PASS AC=2;AF=0.672;AN=2;DP=575;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant10-variant11-variant12-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:784,75,0:0,0,17,8 chr1 150670484 . T G 1226 PASS AC=2;AF=0.672;AN=2;DP=1701;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant10-variant11-variant12-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,74:75:99:2186,179,0:1,0,47,27 chr1 150671243 . AC A 1141.43 PASS AC=2;AF=0.69;AN=2;DP=1278;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant10-variant11-variant12-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1378,105,0:0,0,14,21 chr1 150678910 . T C 265.32 PASS AC=2;AF=0.672;AN=2;DP=650;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant10-variant11-variant12-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:651,45,0:0,0,15,0 chr1 150679033 . G A 1413.75 PASS AC=2;AF=0.679;AN=2;DP=4062;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant10-variant11-variant12-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,150:150:99:4264,448,0:0,0,84,66 chr1 150679358 . C T 646.57 PASS AC=2;AF=0.69;AN=2;DP=1031;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant10-variant11-variant12-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1118,105,0:0,0,21,14 chr1 150680988 . A T 80.01 PASS AC=2;AF=0.685;AN=2;DP=168;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant10-variant11-variant12-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant35-variant36-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:356,27,0:0,0,1,8 chr1 150689984 . A AT 115.75 PASS AC=1;AF=0.773;AN=2;DP=135;set=variant3-variant17-variant20-variant24-variant25-variant26-variant29-variant35-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:1,4:5:12:91,0,12:0,1,1,3 chr1 150702663 . A C 1374.79 PASS AC=2;AF=0.69;AN=2;DP=2136;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant10-variant11-variant12-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:2766,225,0:0,0,60,15 chr1 150702717 . G C 1966.5 PASS AC=2;AF=0.69;AN=2;DP=5062;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant10-variant11-variant12-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,192:192:99:5566,573,0:0,0,117,75 chr1 150703034 . CAGA C 614.49 PASS AC=2;AF=0.672;AN=2;DP=1332;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant10-variant11-variant12-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:2025,136,0:0,0,23,22 chr1 150703366 . TAACA T 605.49 PASS AC=2;AF=0.661;AN=2;DP=1206;set=variant2-variant3-variant5-variant6-variant7-variant10-variant11-variant12-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1616,109,0:0,0,16,20 chr1 150705755 . G A 207.15 PASS AC=2;AF=0.69;AN=2;DP=357;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant10-variant11-variant12-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:317,27,0:0,0,2,7 chr1 150727539 . G A 1624.45 PASS AC=2;AF=0.672;AN=2;DP=5007;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant10-variant11-variant12-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:2,173:175:99:5150,474,0:1,1,90,83 chr1 150730184 . C A 276.05 PASS AC=2;AF=0.69;AN=2;DP=746;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant10-variant11-variant12-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:1092,87,0:0,0,24,5 chr1 150730279 . A G 1512.13 PASS AC=2;AF=0.672;AN=2;DP=3507;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant10-variant11-variant12-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,126:126:99:3880,376,0:0,0,81,45 chr1 150738200 . A G 488.2 PASS AC=2;AF=0.672;AN=2;DP=1201;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant10-variant11-variant12-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1074,99,0:0,0,24,9 chr1 150738483 . CGGGA C 174.95 PASS AC=2;AF=0.672;AN=2;DP=745;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant10-variant11-variant12-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:1080,72,0:0,0,6,18 chr1 150771703 . T C 3074.51 PASS AC=2;AF=0.977;AN=2;DP=4453;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,108:108:99:3270,324,0:0,0,60,48 chr1 150779481 . TTC TCTCTCTCTCTCTCTC,TTCTCTCTCTCTCTCTCTCTC,TTCTCTCTCTCTCTCTCTCTCTCTCTC,TTCTCTCTCTCTCTCTCTCTCTCTC,TTCTCTCTCTCTCTCTCTCTCTC,T,TCTCTCTCTCTCTCTCTC,TTCTCTCTCTCTCTCTC 394.19 PASS AC=0,2,0,0,0,0,0,0;AF=0.083,0.389,0.028,0.028,0.083,0.056,0.028,0.028;AN=2;DP=291;set=variant2-variant3-variant5-variant7-variant10-variant12-variant19-variant24-variant25-variant26-variant30-variant31-variant32-variant35-variant36-variant41-variant43-variant44 GT:DP:GQ:SB 2/2:11:33:0,0,4,7 chr1 150779755 . C T 3709.04 PASS AC=2;AF=0.977;AN=2;DP=5264;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,116:116:99:3229,347,0:0,0,57,59 chr1 150782110 . CAAAAAAAAAAAAAA C,CAAAAAAAAAAAA,CAAAAAA,CAAAA,CAAAAAAAAAAAAA,CAAAAAAAAAAA,CAAAAAAAA,CAAAAAAAAAA 164.33 PASS AC=0,0,1,1,0,0,0,0;AF=0.074,0.044,0.103,0.324,0.029,0.044,0.059,0.015;AN=2;DP=384;set=variant2-variant3-variant5-variant6-variant7-variant8-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 4/3:12:99:0,1,9,2 chr1 150782120 . A C 421.09 PASS AC=1;AF=0.688;AN=2;DP=102;set=variant3-variant17-variant22-variant24-variant31-variant32-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:7,3:10:99:105,0,271:5,2,3,0 chr1 150782122 . A C 421.09 PASS AC=1;AF=0.667;AN=2;DP=260;set=variant3-variant5-variant7-variant11-variant14-variant16-variant17-variant19-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant35-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:7,3:10:99:102,0,310:5,2,3,0 chr1 150782124 . A C 420.92 PASS AC=1;AF=0.706;AN=2;DP=216;set=variant3-variant7-variant11-variant14-variant17-variant19-variant22-variant23-variant24-variant25-variant26-variant27-variant31-variant32-variant35-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,3:11:99:102,0,311:6,2,3,0 chr1 150783108 . TA T 614.35 PASS AC=1;AF=0.5;AN=2;DP=5596;set=variant-variant2-variant3-filterInvariant4-filterInvariant5-variant6-variant7-filterInvariant8-variant9-variant10-variant11-filterInvariant12-variant13-variant14-filterInvariant15-variant16-filterInvariant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:108,41:149:99:442,0,1771:56,52,19,22 chr1 150783934 . GCACA GCACACACA,GCACACACACA,G,GCGCACACACA,GCACACACACACACACA,GCACACA,GCACACACACACA,GCACACACACACACA 1292.78 PASS AC=2,0,0,0,0,0,0,0;AF=0.42,0.409,0.011,0.011,0.023,0.011,0.034,0.011;AN=2;DP=1941;set=Intersection GT:DP:GQ:SB 1/1:25:81:0,0,7,18 chr1 150783985 . T C 493.84 PASS AC=2;AF=0.672;AN=2;DP=1154;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant10-variant11-variant12-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1353,111,0:0,0,18,19 chr1 150789961 . A T 380.17 PASS AC=2;AF=0.741;AN=2;DP=438;set=variant3-variant5-variant6-variant7-variant10-variant11-variant12-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:233,27,0:0,0,3,6 chr1 150790289 . CAA CA,CAAA,C,CAAAA 62.91 PASS AC=0,1,0,0;AF=0.129,0.355,0.016,0.032;AN=2;DP=664;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant39-variant40-variant42-variant44 GT:DP:GQ:SB 0/2:17:58:5,1,9,2 chr1 150801466 . T C 1317.92 PASS AC=2;AF=0.953;AN=2;DP=1515;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1068,108,0:0,0,23,13 chr1 150802272 . AT A 523.8 PASS AC=1;AF=0.5;AN=2;DP=258;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant19-variant20-variant35-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:21,9:30:99:274,0,756:14,7,4,5 chr1 150804401 . GA G,GAA 408.76 PASS AC=0,1;AF=0.211,0.329;AN=2;DP=1531;set=variant2-variant3-filterInvariant4-filterInvariant5-variant6-variant7-variant8-filterInvariant10-filterInvariant11-variant12-variant13-filterInvariant14-variant15-variant16-variant17-variant19-variant20-variant21-filterInvariant22-filterInvariant23-variant24-variant25-variant26-variant27-filterInvariant28-filterInvariant29-variant31-filterInvariant33-filterInvariant34-variant35-variant36-variant38-filterInvariant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:22:63:3,3,5,11 chr1 150804429 . A C 273.78 PASS AC=2;AF=0.672;AN=2;DP=785;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant10-variant11-variant12-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:685,54,0:0,0,5,13 chr1 150808889 . C G 754.71 PASS AC=2;AF=0.7;AN=2;DP=2378;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant10-variant11-variant12-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant37-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:2104,216,0:0,0,33,39 chr1 150811712 . T C 46.72 PASS AC=2;AF=0.739;AN=2;DP=133;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant12-variant14-variant16-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant35-variant36-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:213,15,0:0,0,5,0 chr1 150811794 . T C 453.61 PASS AC=2;AF=0.7;AN=2;DP=1042;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant10-variant11-variant12-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant37-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1307,114,0:0,0,29,9 chr1 150825511 . C T 447.01 PASS AC=2;AF=0.704;AN=2;DP=301;FractionInformativeReads=1;set=variant3-variant5-variant6-variant7-variant10-variant11-variant12-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:482,42,0:0,0,2,12 chr1 150849071 . ACC A,AC,ACCC 540.37 PASS AC=0,2,0;AF=0.239,0.67,0.045;AN=2;DP=1530;MQ=60;set=Intersection GT:DP:GQ:SB 2/2:35:99:0,0,18,17 chr1 150914922 . CA C,CAA,CAAA 54.99 PASS AC=0,1,0;AF=0.114,0.409,0.023;AN=2;DP=443;MQ=60;set=variant-variant3-filterInvariant4-variant5-variant7-variant10-variant12-variant15-variant16-variant17-variant19-variant20-variant24-variant26-variant28-variant31-variant32-variant34-variant35-variant40-filterInvariant42-variant43 GT:DP:GQ:SB 0/2:11:8:1,2,7,1 chr1 150923774 . T A 810.08 PASS AC=2;AF=0.685;AN=2;DP=1787;MQ=60;set=variant2-variant3-variant7-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,91:91:99:2761,272,0:0,0,52,39 chr1 150932953 . GAA GA,G 48.38 PASS AC=1,0;AF=0.458,0.042;AN=2;DP=171;MQ=60;set=variant3-variant7-variant9-variant10-variant16-variant17-variant25-variant31-variant33-variant35-variant41-variant42 GT:DP:GQ:SB 0/1:19:99:7,2,7,3 chr1 150935872 . A G 823.81 PASS AC=2;AF=0.714;AN=2;DP=2173;MQ=60;set=variant2-variant3-variant7-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant37-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:2371,216,0:0,0,45,27 chr1 150937594 . T C 1176.88 PASS AC=2;AF=0.714;AN=2;DP=1912;set=variant2-variant3-variant7-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant37-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,85:85:99:2380,254,0:0,0,51,34 chr1 150937661 . A G 1917.43 PASS AC=2;AF=0.685;AN=2;DP=3742;FractionInformativeReads=1;set=variant2-variant3-variant7-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:2,157:159:99:4324,426,0:1,1,74,83 chr1 150937771 . T A 2127.11 PASS AC=2;AF=0.977;AN=2;DP=2981;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,67:67:99:2044,201,0:0,0,27,40 chr1 150937964 . AAGG A 1769.46 PASS AC=2;AF=0.692;AN=2;DP=1785;MQ=60;set=variant2-variant3-variant7-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,73:73:99:3259,220,0:0,0,34,39 chr1 150938571 . G A 450.09 PASS AC=2;AF=0.685;AN=2;DP=1643;MQ=60;set=variant2-variant3-variant7-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,74:74:99:2440,222,0:0,0,44,30 chr1 150938616 . G A 1902.61 PASS AC=2;AF=1;AN=2;DP=3369;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,104:104:99:3237,311,0:0,0,56,48 chr1 150939744 . C A 970.37 PASS AC=2;AF=0.692;AN=2;DP=2267;MQ=60;set=variant2-variant3-variant7-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,101:101:99:3157,301,0:0,0,44,57 chr1 150940357 . G T 970.21 PASS AC=2;AF=0.692;AN=2;DP=1665;MQ=60;set=variant2-variant3-variant7-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:3434,232,0:0,0,26,51 chr1 150940358 . C T 970.2 PASS AC=2;AF=0.692;AN=2;DP=1639;MQ=60;set=variant2-variant3-variant7-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:3434,232,0:0,0,26,50 chr1 150941381 . C T 322.55 PASS AC=2;AF=0.714;AN=2;DP=874;MQ=60;set=variant2-variant3-variant7-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant37-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1092,99,0:0,0,23,10 chr1 150944541 . A G 277.7 PASS AC=2;AF=1;AN=2;DP=605;FS=0;MQ=60;MQRankSum=1.542;ReadPosRankSum=1.349;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:860,72,0:0,0,5,19 chr1 150947256 . C G 580.88 PASS AC=2;AF=0.685;AN=2;DP=670;set=variant2-variant3-variant7-variant10-variant11-variant12-variant13-filterInvariant14-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:941,84,0:0,0,13,15 chr1 150958977 . T C 590.51 PASS AC=2;AF=0.742;AN=2;DP=2138;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant7-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,74:74:99:2468,221,0:0,0,37,37 chr1 150960350 . A C 511.02 PASS AC=1;AF=0.65;AN=2;DP=2002;MQ=60;set=variant2-variant3-variant5-variant7-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant37-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:50,30:80:99:773,0,1324:35,15,23,7 chr1 150968188 . A G 57.97 PASS AC=2;AF=0.989;AN=2;DP=274;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.731;ReadPosRankSum=-0.731;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:369,30,0:0,0,2,8 chr1 150969567 . A G 2281.78 PASS AC=2;AF=0.989;AN=2;DP=4069;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,119:119:99:3520,357,0:0,0,61,58 chr1 150969992 . T C 4514.47 PASS AC=2;AF=0.932;AN=2;DP=8272;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,198:198:99:5743,592,0:0,0,98,100 chr1 150970577 . G T 1536.64 PASS AC=2;AF=0.989;AN=2;DP=3344;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,98:98:99:3314,292,0:0,0,65,33 chr1 150970836 . T A 1233.91 PASS AC=1;AF=0.677;AN=2;DP=1453;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant27-variant29-variant30-variant33-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,23:43:99:752,0,590:4,16,8,15 chr1 150972538 . G A 2595.09 PASS AC=2;AF=1;AN=2;DP=2495;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1681,150,0:0,0,16,34 chr1 150973514 . G A 1199.25 PASS AC=2;AF=0.845;AN=2;DP=1175;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:923,90,0:0,0,18,12 chr1 150974162 . G A 3291.53 PASS AC=2;AF=0.814;AN=2;DP=5241;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,126:126:99:3521,376,0:0,0,64,62 chr1 150975108 . T C 3128.44 PASS AC=2;AF=0.932;AN=2;DP=4944;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,117:117:99:3787,350,0:0,0,64,53 chr1 150981267 . G C 1429.24 PASS AC=1;AF=0.5;AN=2;DP=496;MQ=60;set=variant3-variant7-variant19-variant20-variant35-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:21,53:74:99:1486,0,512:13,8,25,28 chr1 150981620 . C T 328.45 PASS AC=2;AF=1;AN=2;DP=455;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:566,45,0:0,0,2,13 chr1 150990466 . C CAT 1247.11 PASS AC=1;AF=0.706;AN=2;DP=2291;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:40,38:78:99:1474,0,1595:16,24,15,23 chr1 150990825 . A G 506.5 PASS AC=1;AF=0.791;AN=2;DP=613;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,6:11:99:196,0,154:3,2,5,1 chr1 150991285 . A G 849.09 PASS AC=1;AF=0.849;AN=2;DP=945;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,12:23:99:343,0,341:2,9,3,9 chr1 150997940 . T C 530.44 PASS AC=1;AF=0.718;AN=2;DP=1731;MQ=60;set=variant-filterInvariant2-variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:33,17:50:99:415,0,921:21,12,11,6 chr1 150998221 . ATT AT,A 459.65 PASS AC=1,0;AF=0.731,0.013;AN=2;DP=1769;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43 GT:DP:GQ:SB 0/1:49:99:8,16,9,16 chr1 150999863 . A G 2772.08 PASS AC=2;AF=0.652;AN=2;DP=5678;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,183:183:99:5972,549,0:0,0,68,115 chr1 151001583 . G A 861.29 PASS AC=1;AF=0.825;AN=2;DP=880;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:15,5:20:99:143,0,491:2,13,0,5 chr1 151006539 . C A 2175.29 PASS AC=1;AF=0.884;AN=2;DP=5113;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:66,52:118:99:1173,0,1620:27,39,25,27 chr1 151006691 . C T 467.38 PASS AC=1;AF=0.5;AN=2;DP=47;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.53;QD=9.94;ReadPosRankSum=-0.31;SOR=0.784;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:26,21:47:99:496,0,578:13,13,10,11 chr1 151007574 . G C 2978.79 PASS AC=1;AF=0.5;AN=2;DP=484;FractionInformativeReads=1;MQ=60;set=variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:154,130:284:99:3007,0,3630:83,71,67,63 chr1 151008914 . T A 107.99 PASS AC=2;AF=1;AN=2;DP=4;FS=0;FractionInformativeReads=1;MQ=60;QD=27;SOR=1.609;set=variant35 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:136,12,0:0,0,3,1 chr1 151008928 . G A 196.77 PASS AC=2;AF=0.929;AN=2;DP=191;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:176,15,0:0,0,4,1 chr1 151015299 . G GA 187.98 PASS AC=2;AF=0.882;AN=2;DP=506;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:315,36,0:0,0,8,4 chr1 151017254 . GT GTT,G 141.53 PASS AC=1,0;AF=0.4,0.1;AN=2;DP=112;MQ=60;set=variant12-filterInvariant16-variant34-variant35-variant39 GT:DP:GQ:SB 0/1:27:99:8,5,10,4 chr1 151017408 . C T 724.04 PASS AC=1;AF=0.5;AN=2;DP=173;FractionInformativeReads=1;MQ=60;set=variant12-variant35 GT:AD:DP:GQ:PL:SB 0/1:56,31:87:99:652,0,1453:28,28,13,18 chr1 151018837 . GA G,GAA 132.8 PASS AC=1,0;AF=0.417,0.083;AN=2;DP=111;MQ=60;set=variant12-variant25-variant34-variant35-variant39-variant44 GT:DP:GQ:SB 0/1:16:99:5,3,3,5 chr1 151018861 . A G 936.83 PASS AC=1;AF=0.833;AN=2;DP=755;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,11:17:99:387,0,219:2,4,7,4 chr1 151019180 . A G 3279.75 PASS AC=2;AF=0.875;AN=2;DP=4026;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,99:99:99:3290,296,0:0,0,45,54 chr1 151019329 . G C 493.89 PASS AC=1;AF=0.5;AN=2;DP=201;FractionInformativeReads=1;MQ=60;set=variant12-variant34-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:42,34:76:99:803,0,1084:17,25,14,20 chr1 151024688 . T G 1138.08 PASS AC=2;AF=1;AN=2;DP=1383;FS=0;MQ=60;MQRankSum=0.612;ReadPosRankSum=1.019;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:1020,84,0:0,0,15,13 chr1 151025777 . A G 328.28 PASS AC=1;AF=0.5;AN=2;DP=46;FractionInformativeReads=1;MQ=60;set=variant12-variant35 GT:AD:DP:GQ:PL:SB 0/1:15,6:21:99:126,0,398:7,8,3,3 chr1 151026815 . C T 3590.79 PASS AC=2;AF=0.875;AN=2;DP=4144;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,100:100:99:3046,299,0:0,0,48,52 chr1 151028135 . G C 2131 PASS AC=1;AF=0.5;AN=2;DP=435;MQ=60;set=variant12-variant35 GT:AD:DP:GQ:PL:SB 0/1:130,121:251:99:2853,0,3074:65,65,57,64 chr1 151028234 . G T 3039.34 PASS AC=2;AF=1;AN=2;DP=5315;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,139:140:99:4485,374,0:1,0,55,84 chr1 151030122 . C T 206.71 PASS AC=1;AF=0.5;AN=2;DP=15;FS=0;FractionInformativeReads=1;MQ=60;set=variant12-variant35 GT:AD:DP:GQ:PL:SB 0/1:1,3:4:34:101,0,34:1,0,0,3 chr1 151030172 . AACACACACACACACACACACACACAC AACACACACACACAC,AACACACACACACACACACAC,AACACACACACACACAC,AACACACACACACACACACACAC,AACACACACACAC,A,AACACACACACACACACACACACAC 35.31 PASS AC=0,0,1,0,0,1,0;AF=0.324,0.108,0.27,0.054,0.054,0.027,0.081;AN=2;DP=282;FS=0;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 6/3:10:97:1,1,6,2 chr1 151031476 . T A 1281.1 PASS AC=2;AF=0.875;AN=2;DP=2316;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:1826,177,0:0,0,25,34 chr1 151031667 . T C 2701.97 PASS AC=2;AF=0.888;AN=2;DP=4135;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,118:118:99:3634,353,0:0,0,62,56 chr1 151032150 . C G 5817.84 PASS AC=2;AF=1;AN=2;DP=7917;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,206:206:99:6182,617,0:0,0,101,105 chr1 151039609 . A G 1288.83 PASS AC=2;AF=0.888;AN=2;DP=1038;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:582,54,0:0,0,13,5 chr1 151040435 . G A 9887.61 PASS AC=1;AF=0.833;AN=2;DP=9949;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:123,114:237:99:2852,0,3107:59,64,59,55 chr1 151070252 . CA C 744.23 PASS AC=2;AF=0.833;AN=2;DP=1907;set=variant-variant4-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:4,69:73:99:1608,133,0:1,3,49,20 chr1 151089885 . G C 1856.35 PASS AC=1;AF=0.5;AN=2;DP=379;FractionInformativeReads=1;MQ=60;set=variant10-variant12-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:52,54:106:99:2118,0,2795:30,22,33,21 chr1 151089888 . A C 1853.34 PASS AC=1;AF=0.5;AN=2;DP=561;FractionInformativeReads=1;MQ=60;set=variant10-variant12-variant34-variant35-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:52,54:106:99:2080,0,2798:30,22,32,22 chr1 151091181 . A G 5443.06 PASS AC=2;AF=0.875;AN=2;DP=7292;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,167:167:99:4631,498,0:0,0,76,91 chr1 151091233 . G A 896.88 PASS AC=1;AF=0.5;AN=2;DP=194;FractionInformativeReads=1;MQ=60;set=variant12-variant35 GT:AD:DP:GQ:PL:SB 0/1:45,46:91:99:1124,0,1153:16,29,21,25 chr1 151091279 . CTT CTTT,CT,C 73.55 PASS AC=0,1,0;AF=0.065,0.457,0.022;AN=2;DP=1207;MQ=60;set=filterInvariant-variant5-filterInvariant6-filterInvariant9-filterInvariant10-variant11-filterInvariant14-variant15-filterInvariant16-variant21-filterInvariant23-filterInvariant24-variant27-variant28-filterInvariant29-variant30-filterInvariant33-variant34-filterInvariant35-filterInvariant37-variant38-variant39-filterInvariant44 GT:DP:GQ:SB 0/2:23:88:1,15,1,6 chr1 151093309 . C T 205.36 PASS AC=1;AF=0.5;AN=2;DP=45;FractionInformativeReads=1;MQ=60;set=variant12-variant34-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:5,5:10:99:175,0,193:1,4,0,5 chr1 151093945 . A G 304.78 PASS AC=2;AF=0.956;AN=2;DP=262;FS=0;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:458,36,0:0,0,5,7 chr1 151093983 . T C 182.97 PASS AC=2;AF=0.955;AN=2;DP=176;FS=0;FractionInformativeReads=1;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant15-variant17-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:324,27,0:0,0,4,5 chr1 151096924 . CT C,CTT 321.47 PASS AC=1,0;AF=0.487,0.013;AN=2;DP=3326;set=variant-filterInvariant2-variant3-filterInvariant4-filterInvariant5-variant6-variant7-variant8-variant10-filterInvariant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-filterInvariant19-variant20-variant21-variant22-variant23-filterInvariant24-variant25-filterInvariant26-filterInvariant27-filterInvariant28-variant31-filterInvariant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-filterInvariant42-variant43-variant44 GT:DP:GQ:SB 0/1:90:99:44,20,17,9 chr1 151097499 . TTTAG T 1702.86 PASS AC=1;AF=0.611;AN=2;DP=1953;MQ=60;set=variant-variant4-variant6-variant8-variant12-variant14-variant17-variant19-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant35-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:50,62:112:99:2404,0,2750:22,28,24,38 chr1 151097716 . G C 3735.56 PASS AC=2;AF=1;AN=2;DP=4830;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,121:121:99:3908,363,0:0,0,63,58 chr1 151104055 . C T 76.41 PASS AC=2;AF=0.924;AN=2;DP=228;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant17-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:515,51,0:0,0,10,7 chr1 151104078 . C T 79.61 PASS AC=1;AF=0.708;AN=2;DP=221;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant12-variant13-variant17-variant19-variant20-variant22-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant35-variant36-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,11:17:99:260,0,138:4,2,6,5 chr1 151104598 . A G 1977.6 PASS AC=2;AF=0.875;AN=2;DP=3189;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,104:104:99:3226,312,0:0,0,50,54 chr1 151104950 . G A 4188.73 PASS AC=2;AF=0.784;AN=2;DP=4759;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,141:141:99:4579,420,0:0,0,89,52 chr1 151105824 . C G 2767.25 PASS AC=2;AF=0.85;AN=2;DP=4151;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,97:97:99:3190,290,0:0,0,41,56 chr1 151108137 . T G 1891.68 PASS AC=2;AF=0.863;AN=2;DP=4992;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,149:149:99:4509,446,0:0,0,91,58 chr1 151110832 . G A 1755.76 PASS AC=1;AF=0.556;AN=2;DP=1060;MQ=60;set=variant6-variant8-variant25-variant27-variant28-variant29-variant33-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:71,53:124:99:1074,0,1840:39,32,28,25 chr1 151114882 . C CT 1867.97 PASS AC=2;AF=0.85;AN=2;DP=3251;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,72:73:99:2688,218,0:1,0,47,25 chr1 151115186 . C T 1361.1 PASS AC=2;AF=0.784;AN=2;DP=2364;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,66:66:99:1882,197,0:0,0,30,36 chr1 151117392 . A C 105.72 PASS AC=1;AF=0.5;AN=2;DP=13;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.696;QD=8.13;ReadPosRankSum=-1.67;SOR=0.765;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:8,5:13:99:134,0,243:6,2,4,1 chr1 151144057 . C T 2540.64 PASS AC=1;AF=0.545;AN=2;DP=2197;MQ=60;set=variant-variant9-variant10-variant11-variant22-variant30-variant33-variant35-variant36-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:105,99:204:99:2447,0,2759:61,44,49,50 chr1 151146186 . C G 965.03 PASS AC=2;AF=0.977;AN=2;DP=2791;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:1991,209,0:0,0,25,45 chr1 151146276 . T C 157.38 PASS AC=2;AF=0.977;AN=2;DP=785;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:693,57,0:0,0,5,14 chr1 151149601 . A G 449.11 PASS AC=2;AF=1;AN=2;DP=875;FS=0;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:861,81,0:0,0,8,19 chr1 151205303 . A G 409.28 PASS AC=2;AF=0.813;AN=2;DP=1357;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1512,111,0:0,0,4,33 chr1 151209063 . C T 1061.19 PASS AC=2;AF=0.813;AN=2;DP=4645;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,126:126:99:3973,378,0:0,0,78,48 chr1 151209297 . CTT CTTTT,C,CTTT,CTTTTT,CT 296.7 PASS AC=1,0,0,0,0;AF=0.286,0.036,0.143,0.036,0.036;AN=2;DP=932;set=variant2-variant4-variant6-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant21-variant23-variant24-variant25-filterInvariant26-variant27-filterInvariant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant40-variant41-variant44 GT:DP:GQ:SB 0/1:16:51:0,5,3,8 chr1 151210789 . C T 1395.16 PASS AC=2;AF=0.775;AN=2;DP=4451;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,130:130:99:3903,390,0:0,0,66,64 chr1 151212399 . C CCTT 1003.35 PASS AC=2;AF=0.909;AN=2;DP=3247;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,78:78:99:3539,240,0:0,0,58,20 chr1 151215011 . A G 1351.23 PASS AC=1;AF=0.5;AN=2;DP=520;MQ=60;set=variant7-variant8-variant17-variant24-variant35 GT:AD:DP:GQ:PL:SB 0/1:59,68:127:99:1683,0,1341:34,25,40,28 chr1 151220596 . T C 1645.83 PASS AC=2;AF=1;AN=2;DP=2032;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.87;ReadPosRankSum=-0.606;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1636,159,0:0,0,27,26 chr1 151220893 . AAG A 3236.01 PASS AC=2;AF=0.775;AN=2;DP=7435;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,187:187:99:8335,563,0:0,0,104,83 chr1 151227371 . A G 464.36 PASS AC=2;AF=0.898;AN=2;DP=1241;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:1028,84,0:0,0,7,21 chr1 151237589 . TC T 1292.91 PASS AC=2;AF=0.813;AN=2;DP=4905;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,120:120:99:3698,360,0:0,0,53,67 chr1 151238222 . G A 450.93 PASS AC=2;AF=0.775;AN=2;DP=1710;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1429,122,0:0,0,7,34 chr1 151239051 . T C 1295.24 PASS AC=2;AF=0.813;AN=2;DP=4163;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,127:127:99:4021,380,0:0,0,56,71 chr1 151239570 . C T 1081.12 PASS AC=2;AF=0.775;AN=2;DP=4561;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,132:132:99:4260,395,0:0,0,67,65 chr1 151240008 . A G 318.24 PASS AC=2;AF=0.8;AN=2;DP=1462;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1053,101,0:0,0,10,24 chr1 151254041 . T C 1289.44 PASS AC=2;AF=0.852;AN=2;DP=4436;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,130:130:99:4255,390,0:0,0,88,42 chr1 151263782 . A G 731.36 PASS AC=2;AF=0.732;AN=2;DP=2579;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,72:74:99:2311,172,0:1,1,37,35 chr1 151264513 . A G 1051.48 PASS AC=2;AF=1;AN=2;DP=2269;FS=0;MQ=60;MQRankSum=0.075;ReadPosRankSum=-0.377;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,52:52:99:1669,156,0:0,0,24,28 chr1 151271782 . A C 228.19 PASS AC=2;AF=0.75;AN=2;DP=856;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:774,66,0:0,0,6,16 chr1 151278505 . A G 978.54 PASS AC=2;AF=0.852;AN=2;DP=3195;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,98:98:99:3014,293,0:0,0,60,38 chr1 151280400 . C G 283.32 PASS AC=2;AF=0.852;AN=2;DP=1565;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:976,90,0:0,0,13,17 chr1 151283019 . T C 299.37 PASS AC=2;AF=0.776;AN=2;DP=482;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:814,69,0:0,0,5,18 chr1 151288172 . G A 1500.51 PASS AC=2;AF=0.707;AN=2;DP=5081;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,154:154:99:4848,462,0:0,0,76,78 chr1 151288391 . A G 5169.08 PASS AC=2;AF=1;AN=2;DP=9250;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,221:221:99:6818,662,0:0,0,99,122 chr1 151297464 . CTT CT,C 53.53 PASS AC=0,1;AF=0.417,0.25;AN=2;DP=55;FS=0;set=variant2-variant7-variant10-variant20-variant30-variant35 GT:DP:GQ:SB 0/2:5:40:0,2,1,2 chr1 151299692 . A AC,ACCCCC,ACC 52.41 PASS AC=1,0,0;AF=0.5,0.05,0.05;AN=2;DP=120;MQ=60;set=variant8-variant15-variant16-variant21-variant22-variant25-variant30-variant35-variant37-variant41 GT:DP:GQ:SB 0/1:15:30:3,2,3,7 chr1 151313774 . A G 146.4 PASS AC=2;AF=0.732;AN=2;DP=1539;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:802,81,0:0,0,16,11 chr1 151314379 . T C 1289.24 PASS AC=2;AF=0.852;AN=2;DP=4819;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,107:107:99:3409,321,0:0,0,52,55 chr1 151315287 . G C 933.25 PASS AC=1;AF=0.563;AN=2;DP=881;FractionInformativeReads=1;set=variant-variant9-variant11-variant30-variant33-variant35-variant36-variant38 GT:AD:DP:GQ:PL:SB 0/1:79,65:144:99:1635,0,1832:35,44,30,35 chr1 151316161 . G A 770.43 PASS AC=2;AF=1;AN=2;DP=1712;FS=0;MQ=60;MQRankSum=1.209;ReadPosRankSum=1.209;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1282,123,0:0,0,21,20 chr1 151337788 . A G 354.27 PASS AC=2;AF=0.683;AN=2;DP=1784;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1456,138,0:0,0,20,26 chr1 151341728 . G GC 171.47 PASS AC=1;AF=0.677;AN=2;DP=450;MQ=60;set=variant2-variant4-variant5-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant22-variant24-variant25-variant26-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,14:18:84:416,0,84:0,4,6,8 chr1 151372138 . G A 1874.54 PASS AC=2;AF=0.826;AN=2;DP=3131;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,86:86:99:2740,258,0:0,0,44,42 chr1 151372770 . A G 1489.83 PASS AC=2;AF=1;AN=2;DP=2478;FS=0;MQRankSum=0;ReadPosRankSum=1.496;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:2099,162,0:0,0,19,35 chr1 151373200 . T C 4617.25 PASS AC=2;AF=1;AN=2;DP=4879;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,123:123:99:3849,369,0:0,0,63,60 chr1 151374545 . C T 723.83 PASS AC=2;AF=0.86;AN=2;DP=707;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:435,30,0:0,0,0,10 chr1 151377248 . T C 2271.92 PASS AC=2;AF=1;AN=2;DP=1801;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:2051,159,0:0,0,21,32 chr1 151379250 . G A 1072.65 PASS AC=2;AF=0.826;AN=2;DP=1189;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1483,129,0:0,0,33,10 chr1 151380503 . AAAAAG A 59.54 PASS AC=1;AF=0.553;AN=2;DP=512;MQ=60;set=variant4-filterInvariant5-variant8-filterInvariant9-filterInvariant12-variant14-variant15-variant16-variant19-filterInvariant22-variant24-filterInvariant25-variant26-filterInvariant28-variant31-filterInvariant35-variant38-filterInvariant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:10,5:15:71:71,0,217:7,3,4,1 chr1 151381320 . GA G 1558.6 PASS AC=2;AF=0.826;AN=2;DP=1974;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:1000,96,0:0,0,11,21 chr1 151384711 . A G 2097.57 PASS AC=2;AF=0.864;AN=2;DP=2486;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:1583,144,0:0,0,34,14 chr1 151384733 . G A 2435.69 PASS AC=2;AF=0.864;AN=2;DP=3233;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,63:63:99:1862,189,0:0,0,40,23 chr1 151395782 . T C 1116.28 PASS AC=2;AF=0.837;AN=2;DP=1014;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:909,72,0:0,0,21,3 chr1 151396037 . A C 2748.68 PASS AC=2;AF=0.826;AN=2;DP=3383;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:2326,231,0:0,0,30,47 chr1 151400942 . A C 237.97 PASS AC=2;AF=0.826;AN=2;DP=1265;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,31:32:55:925,55,0:1,0,10,21 chr1 151402045 . A G 2033.1 PASS AC=2;AF=0.864;AN=2;DP=2843;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1530,146,0:0,0,34,15 chr1 151431632 . T C 61.77 PASS AC=2;AF=0.978;AN=2;DP=111;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.026;ReadPosRankSum=0;set=variant3-variant4-variant6-variant7-variant11-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant29-variant32-variant33-variant35-variant37-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:145,12,0:0,0,1,3 chr1 151483854 . A G 983.26 PASS AC=2;AF=1;AN=2;DP=1324;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,21:21:66:944,66,0:0,0,17,4 chr1 151483892 . G A 1676.79 PASS AC=2;AF=1;AN=2;DP=2190;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1737,129,0:0,0,34,8 chr1 151483911 . T TGCCCGA,TGCCCGAGCCCGA 2255.88 PASS AC=2,0;AF=0.909,0.057;AN=2;DP=2750;set=Intersection GT:DP:GQ:SB 1/1:50:95:1,1,36,12 chr1 151499635 . C T 1232.05 PASS AC=2;AF=0.881;AN=2;DP=1903;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:1720,171,0:0,0,22,35 chr1 151501698 . A G 2688.1 PASS AC=2;AF=0.966;AN=2;DP=2857;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:1774,170,0:0,0,36,21 chr1 151501737 . T C 3392.08 PASS AC=2;AF=0.966;AN=2;DP=3816;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,83:83:99:2445,249,0:0,0,46,37 chr1 151501952 . C T 906.94 PASS AC=1;AF=0.5;AN=2;DP=91;FS=4.06;FractionInformativeReads=1;MQ=60;MQRankSum=1.576;QD=9.97;ReadPosRankSum=0.662;SOR=1.173;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:52,39:91:99:935,0,1399:24,28,14,25 chr1 151504689 . T C 46.72 PASS AC=1;AF=0.5;AN=2;DP=62;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant12-variant17-variant28-variant31-variant32-variant35 GT:AD:DP:GQ:PL:SB 0/1:3,2:5:75:75,0,120:2,1,2,0 chr1 151504690 . G A 51.2 PASS AC=1;AF=0.609;AN=2;DP=152;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant9-variant11-variant13-variant17-variant19-variant20-variant24-variant25-variant27-variant29-variant30-variant32-variant33-variant35-variant36-variant37-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:2,3:5:75:79,0,75:2,0,2,1 chr1 151508061 . A C 58.5 PASS AC=1;AF=0.604;AN=2;DP=492;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant6-variant7-variant9-variant11-variant13-variant17-variant19-variant20-variant23-variant24-variant25-variant27-variant29-variant30-variant32-variant33-variant35-variant36-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,16:33:99:413,0,371:10,7,8,8 chr1 151509966 . T TA 494.89 PASS AC=2;AF=0.909;AN=2;DP=1833;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:3,30:33:21:725,21,0:1,2,13,17 chr1 151510026 . A G 993.56 PASS AC=2;AF=0.932;AN=2;DP=2054;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,31:31:93:1033,93,0:0,0,16,15 chr1 151512802 . G T 1369.11 PASS AC=1;AF=0.5;AN=2;DP=2172;MQ=60;set=variant-variant3-variant12-variant14-variant17-variant19-variant22-variant28-variant31-variant32-variant35-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:86,74:160:99:1789,0,2287:50,36,40,34 chr1 151518479 . CT C 80.5 PASS AC=1;AF=0.571;AN=2;DP=250;MQ=60;set=variant-filterInvariant3-variant12-variant14-variant17-variant19-filterInvariant21-variant22-variant23-variant31-variant32-variant35-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:10,8:18:99:155,0,349:2,8,0,8 chr1 151518484 . T TTC 196.53 PASS AC=1;AF=0.609;AN=2;DP=358;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant9-variant11-variant13-variant17-variant19-variant20-variant23-variant24-variant27-variant29-variant30-variant32-variant33-variant35-variant36-variant37-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,9:19:99:313,0,384:0,10,2,7 chr1 151535020 . ATC ATCTC,A 192.71 PASS AC=1,0;AF=0.543,0.022;AN=2;DP=337;set=variant-variant5-variant6-variant9-variant11-variant13-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant30-variant32-variant33-variant35-variant37-variant38-variant41-variant43-variant44 GT:DP:GQ:SB 0/1:8:71:5,1,1,1 chr1 151536685 . C T 539.97 PASS AC=1;AF=0.5;AN=2;DP=630;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant12-variant14-variant17-variant19-variant22-variant28-variant31-variant32-variant35-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:43,21:64:99:511,0,1336:23,20,12,9 chr1 151538507 . T TC 216.58 PASS AC=2;AF=0.977;AN=2;DP=548;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:445,42,0:0,0,2,12 chr1 151538784 . TTC T,TTCTC 252.64 PASS AC=1,0;AF=0.265,0.265;AN=2;DP=794;MQ=60;set=variant-variant5-variant7-variant11-variant12-variant18-variant20-variant21-variant22-variant23-variant26-variant28-variant31-variant35-variant39-variant40-variant42 GT:DP:GQ:SB 0/1:34:99:9,10,5,10 chr1 151542099 . G T 4470.42 PASS AC=1;AF=0.795;AN=2;DP=5876;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:93,85:178:99:2240,0,2483:49,44,47,38 chr1 151546931 . A G 545.3 PASS AC=2;AF=0.932;AN=2;DP=945;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:712,57,0:0,0,3,16 chr1 151547253 . C T 401.57 PASS AC=1;AF=0.5;AN=2;DP=181;FractionInformativeReads=1;MQ=60;set=variant-variant16-variant23-variant30-variant32-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:17,16:33:99:526,0,446:10,7,14,2 chr1 151551078 . A G 69.72 PASS AC=2;AF=0.866;AN=2;DP=324;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:316,24,0:0,0,6,2 chr1 151551320 . G A 2448.68 PASS AC=1;AF=0.78;AN=2;DP=4435;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,52:113:99:1252,0,1431:31,30,29,23 chr1 151552301 . TG T 482.2 PASS AC=1;AF=0.788;AN=2;DP=519;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,9:16:99:316,0,234:2,5,1,8 chr1 151553918 . C T 151.77 PASS AC=1;AF=0.78;AN=2;DP=451;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,7:15:99:226,0,279:7,1,6,1 chr1 151554503 . T C 4904.63 PASS AC=1;AF=0.78;AN=2;DP=6279;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:71,88:159:99:2333,0,1759:43,28,54,34 chr1 151555701 . C T 325.66 PASS AC=1;AF=0.811;AN=2;DP=466;FractionInformativeReads=1;set=variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,7:18:99:136,0,277:6,5,4,3 chr1 151555741 . A G 186.72 PASS AC=1;AF=0.852;AN=2;DP=826;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:17,6:23:99:120,0,413:10,7,2,4 chr1 151634512 . A AT 348.48 PASS AC=2;AF=0.744;AN=2;DP=1299;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:95:932,95,0:0,0,22,8 chr1 151634803 . G A 445.65 PASS AC=1;AF=0.667;AN=2;DP=1266;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,26:51:99:861,0,757:5,20,3,23 chr1 151664882 . CTT CTTT,CTTTT,C,CT,CTTTTT 183.1 PASS AC=1,0,0,0,0;AF=0.235,0.206,0.044,0.044,0.044;AN=2;DP=1670;set=variant-variant3-variant6-variant7-variant8-variant9-variant10-filterInvariant11-variant12-variant14-filterInvariant15-filterInvariant16-variant17-variant19-variant20-variant21-variant22-filterInvariant23-variant24-variant25-variant26-variant27-variant29-variant32-variant33-filterInvariant34-variant35-variant36-variant37-variant39-variant40-filterInvariant41-variant43-variant44 GT:DP:GQ:SB 0/1:42:99:8,11,13,10 chr1 151668978 . TTTCG T 40.69 PASS AC=1;AF=0.5;AN=2;DP=4;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.026;QD=10.17;ReadPosRankSum=1.026;SOR=2.303;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:2,2:4:78:78,0,78:1,1,0,2 chr1 151675414 . A G 2209.85 PASS AC=2;AF=1;AN=2;DP=2908;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,78:78:99:2393,234,0:0,0,31,47 chr1 151675486 . A G 380.46 PASS AC=1;AF=0.571;AN=2;DP=389;MQ=60;set=variant-variant16-variant23-variant30-variant32-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:27,40:67:99:934,0,673:13,14,21,19 chr1 151675618 . T C 1128.54 PASS AC=2;AF=1;AN=2;DP=2711;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,83:83:99:2649,248,0:0,0,47,36 chr1 151681567 . G A 2027.01 PASS AC=1;AF=0.571;AN=2;DP=1241;MQ=60;set=variant-variant16-variant23-variant30-variant32-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:100,107:207:99:2488,0,2548:61,39,61,46 chr1 151686081 . C T 115.39 PASS AC=1;AF=0.662;AN=2;DP=488;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,7:9:22:199,0,22:1,1,3,4 chr1 151686983 . T A 1491.26 PASS AC=1;AF=0.621;AN=2;DP=5636;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:87,97:184:99:2253,0,1961:45,42,49,48 chr1 151694298 . A G 683.57 PASS AC=2;AF=0.625;AN=2;DP=192;FractionInformativeReads=1;MQ=60;set=variant22-variant28-variant35-variant38 GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1405,135,0:0,0,17,28 chr1 151700189 . C CCTG 639.95 PASS AC=2;AF=0.92;AN=2;DP=1593;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1620,108,0:0,0,9,27 chr1 151733379 . CAAA CAAAAAAA,CAAAAA,CA,CAAAA,C,CAAAAAA,CAA,CAAAAAAAAAAAAAAAAAA 927.24 PASS AC=0,0,0,0,0,0,1,0;AF=0.017,0.138,0.052,0.086,0.052,0.069,0.138,0.017;AN=2;DP=1735;set=variant3-variant4-variant5-filterInvariant6-filterInvariant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-filterInvariant22-variant23-variant24-filterInvariant25-variant26-variant27-variant31-variant32-filterInvariant35-variant36-filterInvariant37-variant38-filterInvariant39-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/7:28:99:6,8,8,6 chr1 151736876 . C T 7966.75 PASS AC=2;AF=0.671;AN=2;DP=7727;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,200:200:99:6123,599,0:0,0,94,106 chr1 151737349 . T A 564.76 PASS AC=2;AF=0.886;AN=2;DP=2038;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:1647,162,0:0,0,33,21 chr1 151738184 . ATT A,AT 1978.82 PASS AC=0,2;AF=0.125,0.852;AN=2;DP=4873;MQ=60;set=Intersection GT:DP:GQ:SB 2/2:54:63:1,3,11,39 chr1 151740479 . C A 2247.15 PASS AC=2;AF=1;AN=2;DP=2423;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:1752,173,0:0,0,35,23 chr1 151740666 . T C 4591.75 PASS AC=2;AF=1;AN=2;DP=6604;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,186:186:99:5696,556,0:0,0,93,93 chr1 151742550 . GGAGAGA G 815.28 PASS AC=2;AF=0.609;AN=2;DP=1743;set=variant2-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:2639,181,0:0,0,42,17 chr1 151742565 . GGGAGACCATGGGGAGACGGAGAC G 911.47 PASS AC=2;AF=0.609;AN=2;DP=2438;set=variant2-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:3126,230,0:0,0,49,26 chr1 151743870 . TA T 252.62 PASS AC=2;AF=0.606;AN=2;DP=890;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:974,78,0:0,0,8,18 chr1 151746235 . C T 351.4 PASS AC=2;AF=0.606;AN=2;DP=844;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1326,111,0:0,0,15,22 chr1 151746524 . C A 549.72 PASS AC=2;AF=0.606;AN=2;DP=1814;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:2311,213,0:0,0,35,36 chr1 151747043 . C T 1133.01 PASS AC=2;AF=0.606;AN=2;DP=2596;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2261,210,0:0,0,31,39 chr1 151747733 . C T 693.15 PASS AC=2;AF=0.606;AN=2;DP=1804;set=variant2-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1720,153,0:0,0,25,26 chr1 151747799 . G A 675.6 PASS AC=2;AF=0.676;AN=2;DP=1844;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1686,147,0:0,0,30,19 chr1 151748425 . C A 307.11 PASS AC=2;AF=0.662;AN=2;DP=884;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:749,63,0:0,0,8,13 chr1 151751081 . G A 602.54 PASS AC=2;AF=0.606;AN=2;DP=1501;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:2081,185,0:0,0,39,23 chr1 151752733 . ATACTATCTATACAACCAGTCCTCAATTACTTTATATACAACCTCAGT A 304.74 PASS AC=2;AF=0.606;AN=2;DP=999;set=variant2-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant38-variant39-variant40-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:89:1195,89,0:0,0,6,21 chr1 151754112 . T C 1070.35 PASS AC=2;AF=0.606;AN=2;DP=2976;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,92:92:99:2957,275,0:0,0,36,56 chr1 151763246 . G A 119.26 PASS AC=2;AF=0.905;AN=2;DP=486;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:626,57,0:0,0,12,7 chr1 151763815 . C T 140.78 PASS AC=2;AF=0.895;AN=2;DP=1434;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1321,118,0:0,0,23,17 chr1 151773152 . A G 1467.68 PASS AC=2;AF=1;AN=2;DP=2473;FS=0;MQ=60;MQRankSum=0.037;ReadPosRankSum=1.585;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,64:64:99:2080,191,0:0,0,34,30 chr1 151778683 . C T 334.55 PASS AC=2;AF=0.662;AN=2;DP=1523;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:3,44:47:99:1531,109,0:3,0,14,30 chr1 151780177 . C T 432.91 PASS AC=2;AF=0.638;AN=2;DP=1854;MQ=60;set=variant4-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1832,168,0:0,0,22,34 chr1 151783688 . A C 634.6 PASS AC=2;AF=0.65;AN=2;DP=1091;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1410,114,0:0,0,30,8 chr1 151786281 . G A 107.99 PASS AC=1;AF=0.575;AN=2;DP=214;FractionInformativeReads=1;MQ=60;set=variant4-variant8-variant11-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:10,6:16:99:134,0,325:2,8,2,4 chr1 151789588 . C CTGTGTG,CTGTGTGTG,CTG,CTGTGTGTGTG,CTGTG 1526.57 PASS AC=0,1,0,1,0;AF=0.318,0.602,0.023,0.034,0.011;AN=2;DP=1535;set=Intersection GT:DP:GQ:SB 2/4:34:99:0,0,27,7 chr1 151789609 . C T 1378.64 PASS AC=2;AF=0.989;AN=2;DP=2400;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1757,120,0:0,0,32,9 chr1 151789611 . C T 408.38 PASS AC=2;AF=0.909;AN=2;DP=2396;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1755,119,0:0,0,32,9 chr1 151789647 . T G 1354.99 PASS AC=2;AF=0.694;AN=2;DP=3625;set=variant2-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant35-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,142:142:99:4344,424,0:0,0,89,53 chr1 151803764 . G C 250.39 PASS AC=2;AF=0.943;AN=2;DP=692;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:897,69,0:0,0,8,15 chr1 151811226 . G A 1821.37 PASS AC=2;AF=0.989;AN=2;DP=2314;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:1907,179,0:0,0,36,24 chr1 151812578 . A C 510.1 PASS AC=2;AF=1;AN=2;DP=676;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:705,57,0:0,0,16,3 chr1 151819031 . T G 2382.08 PASS AC=2;AF=1;AN=2;DP=3746;FS=0;MQ=60;MQRankSum=1.254;ReadPosRankSum=-0.378;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,100:100:99:3219,298,0:0,0,48,52 chr1 151819691 . AGGAGGCAGGAGGCAGGCAGGGGAGGCAGGAGGCAGGAGGCAGGCAGG A 710.26 PASS AC=2;AF=0.966;AN=2;DP=4764;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,28:28:99:1356,141,0:0,0,15,13 chr1 151820298 . G C 4739.7 PASS AC=2;AF=1;AN=2;DP=7779;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,201:201:99:5800,602,0:0,0,110,91 chr1 151820324 . T C 4726.58 PASS AC=2;AF=0.854;AN=2;DP=7153;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,196:196:99:5677,587,0:0,0,105,91 chr1 151825713 . G C 30.23 PASS AC=2;AF=0.736;AN=2;DP=676;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:405,36,0:0,0,9,3 chr1 151825991 . G T 246.29 PASS AC=2;AF=0.797;AN=2;DP=2932;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,81:81:99:2417,242,0:0,0,39,42 chr1 151846059 . C T 246.9 PASS AC=2;AF=0.94;AN=2;DP=249;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:387,30,0:0,0,8,2 chr1 151846517 . C T 538.5 PASS AC=1;AF=0.717;AN=2;DP=408;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant35-variant36-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:2,7:9:65:207,0,65:0,2,2,5 chr1 151861477 . A G 93.57 PASS AC=2;AF=1;AN=2;DP=43;FS=0;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant7-variant9-variant14-variant20-variant23-variant25-variant26-variant27-variant28-variant32-variant34-variant35-variant36-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:135,9,0:0,0,3,0 chr1 151862661 . G A 1781.53 PASS AC=1;AF=0.712;AN=2;DP=2237;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant35-variant36-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:48,35:83:99:796,0,1235:31,17,20,15 chr1 151867560 . G A 665.01 PASS AC=2;AF=0.898;AN=2;DP=2346;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1858,149,0:0,0,26,24 chr1 151881885 . A C 621.79 PASS AC=2;AF=0.898;AN=2;DP=3030;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,86:86:99:2882,258,0:0,0,44,42 chr1 151955279 . G GAGAAAAGCTCTGCTGTGTA 987.43 PASS AC=1;AF=0.545;AN=2;DP=706;MQ=60;set=variant-variant4-variant5-variant6-variant9-variant10-variant12-variant13-variant16-variant18-variant19-variant20-variant21-variant24-variant27-variant31-variant33-variant34-variant35-variant37-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:28,12:40:99:586,0,4444:23,5,12,0 chr1 151964879 . T C 93.19 PASS AC=1;AF=0.6;AN=2;DP=233;MQ=60;set=variant-variant4-variant5-variant6-variant9-variant10-variant12-variant16-variant18-variant19-variant20-variant21-variant24-variant27-variant31-variant33-variant35-variant37-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:9,4:13:99:141,0,273:7,2,4,0 chr1 151964935 . C G 655.91 PASS AC=1;AF=0.529;AN=2;DP=553;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant14-variant15-variant16-variant17-variant21-variant23-variant28-variant29-variant30-variant35-variant36-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,19:30:99:572,0,312:9,2,14,5 chr1 151966348 . C T 1708.48 PASS AC=1;AF=0.712;AN=2;DP=2017;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant35-variant36-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,42:78:99:931,0,925:17,19,20,22 chr1 152005327 . TA T 1580.63 PASS AC=1;AF=0.543;AN=2;DP=2371;MQ=60;set=variant2-variant7-variant11-variant13-variant15-variant16-variant17-variant21-variant23-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:75,51:126:99:1626,0,2574:35,40,23,28 chr1 152005482 . C G 454.35 PASS AC=1;AF=0.552;AN=2;DP=378;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant7-variant10-variant11-variant13-variant15-variant16-variant20-variant21-variant22-variant23-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,4:12:99:144,0,321:0,8,0,4 chr1 152009530 . T C 1324.19 PASS AC=2;AF=0.898;AN=2;DP=4135;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,118:118:99:3754,353,0:0,0,44,74 chr1 152057002 . A G 1234.5 PASS AC=1;AF=0.5;AN=2;DP=552;MQ=60;set=variant12-variant15-variant19-variant21-variant35 GT:AD:DP:GQ:PL:SB 0/1:50,57:107:99:1718,0,1536:12,38,15,42 chr1 152058907 . C T 1611.64 PASS AC=1;AF=0.5;AN=2;DP=123;FS=2.305;FractionInformativeReads=1;MQ=60;MQRankSum=-1.056;QD=13.1;ReadPosRankSum=-0.939;SOR=0.513;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:64,59:123:99:1640,0,1599:25,39,26,33 chr1 152060796 . A T 415.47 PASS AC=2;AF=1;AN=2;DP=718;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:411,39,0:0,0,4,9 chr1 152079823 . C G 5109.07 PASS AC=1;AF=0.607;AN=2;DP=9514;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant24-variant26-variant27-variant28-variant29-variant31-variant33-variant35-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:165,171:336:99:4426,0,4132:71,94,66,105 chr1 152079989 . T G 6590.65 PASS AC=1;AF=0.7;AN=2;DP=5995;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:121,98:219:99:2547,0,3347:68,53,52,46 chr1 152081921 . G C 7990.71 PASS AC=1;AF=0.707;AN=2;DP=7184;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant31-variant33-variant35-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:130,126:256:99:3158,0,3209:71,59,64,62 chr1 152084039 . G T 2183.93 PASS AC=1;AF=0.5;AN=2;DP=207;FS=1.727;FractionInformativeReads=0.995;MQ=59.82;MQRankSum=-1.721;QD=10.55;ReadPosRankSum=2.747;SOR=0.558;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:112,94:206:99:2212,0,2749:46,66,42,52 chr1 152085505 . A C 4664.24 PASS AC=2;AF=1;AN=2;DP=5541;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,131:131:99:4037,393,0:0,0,54,77 chr1 152126467 . T C 4440.48 PASS AC=1;AF=0.694;AN=2;DP=3412;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant37-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:71,58:129:99:1919,0,2242:49,22,51,7 chr1 152128121 . G A 6061.98 PASS AC=1;AF=0.5;AN=2;DP=4276;set=variant12-variant15-variant16-variant19-variant21-variant35 GT:AD:DP:GQ:PL:SB 0/1:366,349:715:99:8192,0,8989:184,182,181,168 chr1 152184487 . T G 2354.45 PASS AC=2;AF=0.989;AN=2;DP=1804;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:1235,87,0:0,0,28,1 chr1 152184534 . C G 4572.31 PASS AC=1;AF=0.779;AN=2;DP=4395;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,41:88:99:1155,0,1395:34,13,31,10 chr1 152184623 . A G 4509.58 PASS AC=1;AF=0.5;AN=2;DP=1702;MQ=60;set=variant7-variant11-variant34-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:158,151:309:99:3804,0,3869:100,58,89,62 chr1 152184704 . C T 17302.2 PASS AC=1;AF=0.779;AN=2;DP=20707;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:216,249:465:99:5942,0,5021:111,105,119,130 chr1 152184950 . T G 11110.9 PASS AC=1;AF=0.779;AN=2;DP=15103;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:192,171:363:99:4285,0,4677:87,105,78,93 chr1 152185095 . T A 5658.15 PASS AC=1;AF=0.779;AN=2;DP=6282;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,80:137:99:2068,0,1622:26,31,37,43 chr1 152185184 . C T 7437.06 PASS AC=1;AF=0.779;AN=2;DP=9548;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:103,115:218:99:2980,0,2555:56,47,62,53 chr1 152185500 . C G 3490.54 PASS AC=1;AF=0.5;AN=2;DP=4377;MQ=60;set=variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant18-variant27-variant29-variant30-variant31-variant34-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:120,102:222:99:2537,0,3396:43,77,47,55 chr1 152185750 . G A 6016.15 PASS AC=1;AF=0.525;AN=2;DP=5374;set=variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant18-variant27-variant29-variant30-variant31-variant34-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:97,201:298:99:5172,0,3196:43,54,111,90 chr1 152185762 . C G 3981.12 PASS AC=1;AF=0.763;AN=2;DP=7158;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant22-variant23-variant25-variant26-variant27-variant28-variant29-filterInvariant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:202,81:283:99:2705,0,8387:107,95,34,47 chr1 152185768 . T G 3760.3 PASS AC=1;AF=0.757;AN=2;DP=6816;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant22-variant25-variant26-variant27-variant28-variant29-filterInvariant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:202,75:277:99:2702,0,8490:107,95,31,44 chr1 152185774 . A G 3289.18 PASS AC=1;AF=0.75;AN=2;DP=6232;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant22-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:219,71:290:99:2319,0,9024:115,104,31,40 chr1 152185780 . G A 3105.31 PASS AC=1;AF=0.75;AN=2;DP=5955;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant22-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:229,65:294:99:2064,0,9669:120,109,28,37 chr1 152185790 . T C 2311.77 PASS AC=1;AF=0.727;AN=2;DP=5272;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant22-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:231,49:280:99:1689,0,9654:125,106,21,28 chr1 152185792 . G A 1996.77 PASS AC=1;AF=0.727;AN=2;DP=5071;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant22-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-filterInvariant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:228,44:272:99:1353,0,9678:122,106,16,28 chr1 152185796 . A G 1771.77 PASS AC=1;AF=0.727;AN=2;DP=4804;set=variant-variant2-variant3-variant4-variant5-variant6-filterInvariant7-variant8-variant9-variant10-variant11-variant12-filterInvariant13-variant14-variant16-filterInvariant18-variant19-variant22-variant25-variant27-variant28-filterInvariant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-filterInvariant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:229,39:268:99:981,0,9621:119,110,14,25 chr1 152185812 . C CAG 817.73 PASS AC=1;AF=0.761;AN=2;DP=2090;FractionInformativeReads=1;set=variant-variant2-filterInvariant3-variant4-filterInvariant5-variant6-filterInvariant9-filterInvariant11-variant12-variant14-filterInvariant16-variant19-variant22-variant25-filterInvariant27-variant28-variant32-variant33-filterInvariant35-variant36-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:213,15:228:99:241,0,8881:103,110,4,11 chr1 152186099 . C T 1348.77 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=462;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:26,105:131:99:2253,0,352:21,5,39,66 chr1 152186141 . C T 496.69 DRAGENHardSNP AC=1;AF=0.84;AN=2;DP=1599;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:67,52:119:99:1061,0,1294:35,32,11,41 chr1 152186699 . T A 309.08 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=14229;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:336,77:413:99:889,0,7667:204,132,60,17 chr1 152186766 . G A 921.84 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=20029;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:408,215:623:99:3405,0,8490:187,221,109,106 chr1 152187183 . C A 666.01 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=12510;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:351,129:480:99:2267,0,8407:76,275,27,102 chr1 152187451 . C T 119.61 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=447;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:65,24:89:99:342,0,1416:40,25,16,8 chr1 152187554 . C T 303.13 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=5685;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:93,62:155:99:1207,0,1999:54,39,35,27 chr1 152187562 . A C 1782.51 DRAGENHardSNP AC=2;AF=1;AN=2;DP=6216;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,131:131:99:4474,396,0:0,0,78,53 chr1 152187935 . C T 1703.23 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=7765;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:110,115:225:99:4626,0,4947:66,44,90,25 chr1 152187945 . C T 1980.14 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=9686;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:126,168:294:99:5694,0,5013:80,46,120,48 chr1 152188062 . T C 1610.47 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=2494;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:450,102:552:99:886,0,9521:218,232,46,56 chr1 152188109 . T A 1592.2 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=22758;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:295,235:530:99:4480,0,6970:199,96,87,148 chr1 152188463 . G A 2538.03 PASS AC=1;AF=0.5;AN=2;DP=53267;set=variant-filterInvariant4-variant6-variant7-filterInvariant8-variant10-variant11-variant13-variant15-filterInvariant16-variant20-variant21-variant23-variant24-variant25-filterInvariant26-filterInvariant28-variant29-filterInvariant30-variant32-variant33-filterInvariant35-variant36-filterInvariant38-filterInvariant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:1133,225:1358:99:2054,0,26929:492,641,93,132 chr1 152188920 . C T 462.01 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=7432;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:186,45:231:99:353,0,4194:82,104,20,25 chr1 152188998 . C T 319.16 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=4857;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:118,29:147:99:332,0,2756:33,85,8,21 chr1 152189038 . A G 39.31 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=146;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:76,15:91:99:124,0,1795:17,59,5,10 chr1 152190720 . C T 166.79 PASS AC=1;AF=0.789;AN=2;DP=329;FS=0;FractionInformativeReads=1;set=variant-filterInvariant2-filterInvariant3-filterInvariant4-variant5-variant6-filterInvariant7-filterInvariant8-variant10-filterInvariant11-filterInvariant12-variant13-filterInvariant15-filterInvariant16-filterInvariant18-variant19-filterInvariant20-variant21-variant22-filterInvariant23-variant24-variant25-variant26-filterInvariant27-filterInvariant28-variant29-filterInvariant30-variant31-filterInvariant32-variant33-filterInvariant35-filterInvariant36-filterInvariant38-variant39-filterInvariant40-variant41-variant42-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:5,5:10:99:135,0,133:5,0,5,0 chr1 152191687 . A G 6794.62 PASS AC=1;AF=0.5;AN=2;DP=1762;MQ=60;set=variant7-variant11-variant34-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:191,184:375:99:7128,0,7414:89,102,94,90 chr1 152191696 . G C 6800.86 PASS AC=1;AF=0.5;AN=2;DP=1779;MQ=60;set=variant7-variant11-variant34-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:190,191:381:99:7181,0,7771:93,97,96,95 chr1 152191709 . C G 6813.51 PASS AC=1;AF=0.786;AN=2;DP=16282;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:187,207:394:99:5475,0,7099:94,93,108,99 chr1 152191879 . G A 6919.62 PASS AC=1;AF=0.779;AN=2;DP=19019;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:228,234:462:99:5805,0,5643:121,107,114,120 chr1 152192097 . C CGG 235.1 DRAGENHardINDEL AC=1;AF=0.5;AN=2;DP=2360;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:330,25:355:99:231,0,14055:166,164,25,0 chr1 152192100 . A C 67.19 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=4812;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:337,31:368:99:323,0,14480:170,167,30,1 chr1 152192101 . ATC A 49.14 DRAGENHardINDEL AC=1;AF=0.5;AN=2;DP=3745;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:350,34:384:99:297,0,14724:174,176,32,2 chr1 152192114 . C T 4760.26 PASS AC=1;AF=0.581;AN=2;DP=17057;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:230,182:412:99:4434,0,6523:125,105,93,89 chr1 152192163 . G T 104.55 PASS AC=1;AF=0.5;AN=2;DP=13218;set=filterInvariant-variant6-filterInvariant7-filterInvariant9-variant10-variant11-filterInvariant12-variant13-variant15-filterInvariant16-variant19-variant20-variant21-variant23-variant24-variant25-filterInvariant26-variant28-variant29-filterInvariant30-filterInvariant32-filterInvariant33-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:331,104:435:99:1371,0,9083:165,166,48,56 chr1 152192219 . G C 44.07 PASS AC=1;AF=0.5;AN=2;DP=13257;set=filterInvariant-variant6-filterInvariant7-filterInvariant9-variant10-variant11-filterInvariant12-variant13-variant15-filterInvariant16-variant19-variant20-variant21-variant23-variant24-variant25-filterInvariant26-variant28-variant29-filterInvariant30-filterInvariant32-filterInvariant33-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:324,104:428:99:1390,0,9085:159,165,48,56 chr1 152192259 . T C 516.65 PASS AC=1;AF=0.5;AN=2;DP=7604;set=filterInvariant6-filterInvariant10-filterInvariant12-filterInvariant13-variant15-filterInvariant19-filterInvariant20-variant21-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant29-filterInvariant35-filterInvariant36-filterInvariant38-filterInvariant39-filterInvariant40-filterInvariant41-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:327,36:363:99:168,0,9439:157,170,2,34 chr1 152192293 . C T 6323.97 PASS AC=1;AF=0.779;AN=2;DP=15241;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:177,179:356:99:4441,0,4497:92,85,84,95 chr1 152192631 . C T 7465.84 PASS AC=1;AF=0.779;AN=2;DP=19684;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:242,249:491:99:5953,0,6261:113,129,122,127 chr1 152192687 . T C 6293.09 PASS AC=2;AF=0.989;AN=2;DP=17135;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,432:432:99:13633,1293,0:0,0,199,233 chr1 152192825 . C T 1897.27 PASS AC=1;AF=0.609;AN=2;DP=7192;set=variant-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:118,128:246:99:3231,0,3290:52,66,63,65 chr1 152192978 . T C 6164.6 PASS AC=2;AF=0.989;AN=2;DP=17094;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,444:444:99:13789,1331,0:0,0,249,195 chr1 152193052 . A G 7120.94 PASS AC=2;AF=0.989;AN=2;DP=18428;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,474:475:99:15197,1418,0:1,0,239,235 chr1 152193121 . G T 8362.16 PASS AC=1;AF=0.779;AN=2;DP=20036;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:292,260:552:99:6168,0,7711:146,146,129,131 chr1 152193162 . C T 7267.42 PASS AC=1;AF=0.5;AN=2;DP=2591;set=variant7-variant11-variant34-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:285,317:602:99:8139,0,7197:148,137,166,151 chr1 152193286 . G T 3020.87 PASS AC=1;AF=0.609;AN=2;DP=17593;set=variant-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:343,326:669:99:12266,0,19229:166,177,166,160 chr1 152193291 . G T 9286.85 PASS AC=1;AF=0.779;AN=2;DP=24408;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:339,320:659:99:12151,0,19211:163,176,163,157 chr1 152193544 . A G 4795.25 PASS AC=1;AF=0.786;AN=2;DP=7906;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:78,103:181:99:2676,0,1993:28,50,42,61 chr1 152193547 . G A 4819.95 PASS AC=2;AF=0.989;AN=2;DP=8076;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,177:177:99:6993,535,0:0,0,67,110 chr1 152193605 . C T 1596.7 PASS AC=1;AF=0.5;AN=2;DP=592;set=variant7-variant11-variant34-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:69,49:118:99:1196,0,1740:29,40,25,24 chr1 152193851 . C T 3908.52 PASS AC=1;AF=0.786;AN=2;DP=5087;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,52:119:99:1206,0,1553:33,34,25,27 chr1 152193990 . A G 1179.44 PASS AC=1;AF=0.786;AN=2;DP=1245;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,13:26:99:379,0,354:4,9,4,9 chr1 152195579 . G A 2005.74 PASS AC=1;AF=0.5;AN=2;DP=2836;MQ=60;set=variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant18-variant27-variant29-variant30-variant31-variant34-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:86,69:155:99:1705,0,2331:52,34,46,23 chr1 152195728 . AT A 6864.44 PASS AC=2;AF=0.989;AN=2;DP=12115;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,278:278:99:7552,829,0:0,0,122,156 chr1 152195851 . TAGTC T 2241.7 PASS AC=1;AF=0.779;AN=2;DP=2878;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,34:63:99:1341,0,1585:7,22,9,25 chr1 152196717 . C A 156.22 PASS AC=2;AF=0.989;AN=2;DP=602;FractionInformativeReads=1;MQ=60;MQRankSum=-1.936;ReadPosRankSum=0.421;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:400,36,0:0,0,4,8 chr1 152196814 . C T 111.22 PASS AC=2;AF=1;AN=2;DP=160;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:123,9,0:0,0,0,3 chr1 152274685 . T A 4722.79 PASS AC=2;AF=1;AN=2;DP=5961;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,112:112:99:3340,334,0:0,0,72,40 chr1 152276377 . C G 245.67 PASS AC=1;AF=0.5;AN=2;DP=2184;set=filterInvariant3-filterInvariant5-variant7-variant8-variant9-variant10-filterInvariant11-variant14-variant18-variant27-variant29-variant30-filterInvariant31-variant35-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:117,33:150:99:440,0,3614:59,58,21,12 chr1 152276459 . C T 1194.24 PASS AC=1;AF=0.5;AN=2;DP=6745;set=variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant14-variant16-variant18-variant27-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant34-variant35-filterInvariant37-filterInvariant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:262,86:348:99:1085,0,6410:147,115,43,43 chr1 152276583 . C G 130.76 PASS AC=1;AF=0.55;AN=2;DP=2046;set=filterInvariant5-filterInvariant11-variant13-filterInvariant14-filterInvariant29-variant34-filterInvariant35-variant37-filterInvariant41-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:212,21:233:99:122,0,9020:100,112,12,9 chr1 152276699 . A G 175.75 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=687;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:187,19:206:58:58,0,5184:104,83,2,17 chr1 152277396 . T C 6458.96 PASS AC=1;AF=0.5;AN=2;DP=9984;set=variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant14-variant16-variant18-variant27-variant29-variant30-variant31-variant34-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:306,257:563:99:6379,0,7683:138,168,111,146 chr1 152277554 . G A 4213.66 PASS AC=1;AF=0.5;AN=2;DP=1643;set=variant7-variant11-variant34-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:154,152:306:99:3778,0,3865:68,86,74,78 chr1 152277717 . C A 2562.66 PASS AC=1;AF=0.553;AN=2;DP=4768;set=variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant14-variant16-variant18-variant27-variant29-variant30-variant31-variant34-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:154,115:269:99:2734,0,4201:87,67,44,71 chr1 152277822 . T C 311.22 PASS AC=1;AF=0.5;AN=2;DP=2394;set=filterInvariant5-filterInvariant7-filterInvariant8-filterInvariant10-filterInvariant11-filterInvariant16-variant29-filterInvariant31-filterInvariant35-filterInvariant37-filterInvariant41-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:221,18:239:69:69,0,12626:102,119,0,18 chr1 152278484 . C T 444.47 PASS AC=1;AF=0.5;AN=2;DP=279;FS=0;FractionInformativeReads=1;set=variant7-variant11-variant34-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,20:57:99:578,0,1363:37,0,20,0 chr1 152278555 . T C 1583.6 PASS AC=1;AF=0.5;AN=2;DP=3736;set=variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant14-variant16-variant18-variant27-variant29-variant30-variant31-variant34-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:100,49:149:99:1362,0,2973:72,28,39,10 chr1 152278689 . C A 17128.6 PASS AC=1;AF=0.553;AN=2;DP=15493;set=variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant14-variant16-variant18-variant27-variant29-variant30-variant31-variant34-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:221,502:723:99:13373,0,4920:127,94,286,216 chr1 152278814 . C T 862.17 PASS AC=1;AF=0.5;AN=2;DP=18948;set=filterInvariant3-filterInvariant5-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant14-filterInvariant16-filterInvariant18-filterInvariant27-filterInvariant29-filterInvariant30-variant34-filterInvariant35-variant37-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:786,148:934:99:1239,0,22028:342,444,70,78 chr1 152279406 . T G 151.22 PASS AC=1;AF=0.563;AN=2;DP=240;FS=0;FractionInformativeReads=1;set=variant4-variant7-variant8-variant9-variant15-variant17-variant21-variant24-variant25-variant26-variant28-variant30-variant35-variant36-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,7:12:99:224,0,154:5,0,7,0 chr1 152279729 . C T 9589.15 PASS AC=1;AF=0.553;AN=2;DP=12072;set=variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant14-variant16-variant18-variant27-variant29-variant30-variant31-variant34-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:334,342:676:99:8102,0,8081:160,174,171,171 chr1 152279841 . G C 6045.84 PASS AC=1;AF=0.553;AN=2;DP=7311;set=variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant14-variant16-variant18-variant27-variant29-variant30-variant31-variant34-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:181,199:380:99:5022,0,4702:76,105,84,115 chr1 152279920 . A G 3613.43 PASS AC=1;AF=0.5;AN=2;DP=4015;set=variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant14-variant16-variant18-variant27-variant29-variant30-variant31-variant34-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:116,110:226:99:3264,0,3195:55,61,49,61 chr1 152279964 . C T 2756.61 PASS AC=1;AF=0.5;AN=2;DP=1024;set=variant7-variant11-variant34-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:124,107:231:99:3056,0,3566:72,52,60,47 chr1 152280032 . T C 5021.65 PASS AC=1;AF=0.5;AN=2;DP=6155;set=variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant14-variant16-variant18-variant27-variant29-variant30-variant31-variant34-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:173,166:339:99:4228,0,4398:99,74,97,69 chr1 152280170 . C G 2853.77 PASS AC=1;AF=0.5;AN=2;DP=4184;set=variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant14-variant16-variant18-variant27-variant29-variant30-variant31-variant34-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:131,131:262:99:3472,0,3409:50,81,44,87 chr1 152280265 . C G 284.48 PASS AC=1;AF=0.5;AN=2;DP=1557;set=variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant14-variant16-variant18-variant27-variant29-variant30-variant31-variant34-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:73,17:90:99:444,0,2296:40,33,2,15 chr1 152280347 . C T 308.63 PASS AC=1;AF=0.5;AN=2;DP=1856;set=variant7-variant8-filterInvariant10-filterInvariant14-filterInvariant16-filterInvariant27-filterInvariant29-variant31-variant34-filterInvariant35-variant37-variant41-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:126,15:141:99:260,0,5708:77,49,12,3 chr1 152280372 . G A 478.96 PASS AC=1;AF=0.553;AN=2;DP=3898;set=filterInvariant3-filterInvariant5-variant7-variant8-filterInvariant9-variant10-filterInvariant11-filterInvariant14-variant16-filterInvariant18-variant27-variant29-variant30-variant31-variant34-variant35-variant37-filterInvariant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:146,41:187:99:1015,0,6103:86,60,38,3 chr1 152280471 . C G 586.75 PASS AC=1;AF=0.5;AN=2;DP=7077;set=filterInvariant3-filterInvariant5-filterInvariant7-filterInvariant8-variant9-filterInvariant10-filterInvariant11-variant14-filterInvariant16-variant18-variant27-filterInvariant29-variant30-variant31-filterInvariant34-variant35-filterInvariant37-filterInvariant41-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:291,97:388:99:1277,0,7353:148,143,49,48 chr1 152280559 . T C 49.18 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=583;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:280,29:309:81:81,0,13295:134,146,10,19 chr1 152280685 . C A 1168.93 PASS AC=1;AF=0.5;AN=2;DP=6042;set=variant7-filterInvariant9-variant11-variant16-filterInvariant18-filterInvariant29-filterInvariant31-variant34-filterInvariant35-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:507,58:565:99:990,0,21735:266,241,43,15 chr1 152280687 . C T 1243.93 PASS AC=1;AF=0.5;AN=2;DP=6119;set=variant7-filterInvariant9-variant11-variant16-filterInvariant18-filterInvariant29-filterInvariant31-variant34-filterInvariant35-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:512,61:573:99:1132,0,21493:268,244,46,15 chr1 152280688 . A G 1250.68 PASS AC=1;AF=0.5;AN=2;DP=6156;set=variant7-filterInvariant9-variant11-variant16-filterInvariant18-filterInvariant29-filterInvariant31-variant34-filterInvariant35-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:509,63:572:99:1165,0,21429:267,242,46,17 chr1 152280691 . A T 1262.75 PASS AC=1;AF=0.5;AN=2;DP=6283;set=variant7-filterInvariant9-variant11-variant16-filterInvariant18-filterInvariant29-filterInvariant31-variant34-variant35-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:512,67:579:99:1199,0,21251:266,246,48,19 chr1 152280736 . T C 5293.26 PASS AC=1;AF=0.5;AN=2;DP=11580;set=variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant14-variant16-variant18-variant27-variant29-variant30-variant31-variant34-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:488,123:611:99:3658,0,18699:228,260,59,64 chr1 152280759 . A G 5900.55 PASS AC=1;AF=0.5;AN=2;DP=11214;set=variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant14-variant16-variant18-variant27-variant29-variant30-variant31-variant34-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:429,137:566:99:4115,0,17657:191,238,62,75 chr1 152280782 . A G 13508 PASS AC=1;AF=0.55;AN=2;DP=10441;set=variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant18-variant27-variant29-variant30-variant31-variant34-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:165,342:507:99:13796,0,5665:74,91,147,195 chr1 152280788 . T G 4216.49 PASS AC=1;AF=0.5;AN=2;DP=9811;set=variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant14-variant16-variant18-variant27-variant29-variant30-variant31-variant34-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:151,333:484:99:13576,0,5421:68,83,140,193 chr1 152280864 . A G 6915.21 PASS AC=1;AF=0.553;AN=2;DP=5961;set=variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant14-variant16-variant18-variant27-variant29-variant30-variant31-variant34-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:115,173:288:99:4760,0,2611:51,64,72,101 chr1 152280900 . T G 2592.89 PASS AC=1;AF=0.5;AN=2;DP=5399;set=variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant14-variant16-variant18-variant27-variant29-variant30-variant31-variant34-filterInvariant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:231,43:274:99:520,0,6698:110,121,15,28 chr1 152281317 . G T 4720.81 PASS AC=1;AF=0.5;AN=2;DP=2262;set=variant7-variant11-variant34-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:235,244:479:99:6284,0,5980:118,117,115,129 chr1 152281479 . G T 10767.5 PASS AC=1;AF=0.55;AN=2;DP=9703;set=variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant18-variant27-variant29-variant30-variant31-variant34-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:204,178:382:99:4611,0,5692:96,108,84,94 chr1 152281691 . G A 8071.82 PASS AC=1;AF=0.5;AN=2;DP=3155;set=variant7-variant11-variant34-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:389,292:681:99:6785,0,9589:180,209,139,153 chr1 152281745 . G T 6785.58 PASS AC=1;AF=0.5;AN=2;DP=2590;set=variant7-variant11-variant34-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:324,255:579:99:6001,0,8266:139,185,113,142 chr1 152281907 . A G 800.94 PASS AC=1;AF=0.5;AN=2;DP=256;FS=13.847;FractionInformativeReads=1;MQ=59.57;MQRankSum=-2.555;QD=3.13;ReadPosRankSum=-4.961;SOR=1.753;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:221,35:256:99:829,0,11162:130,91,27,8 chr1 152281911 . T C 3506.39 PASS AC=1;AF=0.5;AN=2;DP=528;FractionInformativeReads=1;set=variant24-variant35 GT:AD:DP:GQ:PL:SB 0/1:223,38:261:99:860,0,11175:129,94,29,9 chr1 152282092 . T C 924.11 PASS AC=1;AF=0.5;AN=2;DP=2221;set=variant7-variant11-variant34-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:425,65:490:99:1236,0,23910:215,210,22,43 chr1 152282101 . T C 704.15 PASS AC=1;AF=0.5;AN=2;DP=2241;FractionInformativeReads=1;set=filterInvariant7-filterInvariant11-filterInvariant34-filterInvariant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:456,56:512:99:1028,0,25416:237,219,16,40 chr1 152282104 . C T 456.22 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=2236;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:462,53:515:99:928,0,25534:236,226,14,39 chr1 152282111 . T C 87.88 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=2223;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:470,42:512:99:430,0,25320:239,231,11,31 chr1 152282794 . G A 2571.77 PASS AC=1;AF=0.5;AN=2;DP=1123;set=variant7-variant11-variant34-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:127,142:269:99:3777,0,3497:57,70,48,94 chr1 152282910 . G C 2931.06 PASS AC=1;AF=0.5;AN=2;DP=1137;set=variant7-variant11-variant34-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:182,120:302:99:2794,0,4786:92,90,63,57 chr1 152282952 . A G 3053.4 PASS AC=1;AF=0.5;AN=2;DP=1226;set=variant7-variant11-variant34-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:162,136:298:99:2954,0,4113:80,82,71,65 chr1 152283236 . T C 5637.68 PASS AC=1;AF=0.5;AN=2;DP=7120;set=variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant14-variant16-variant18-variant27-variant29-variant30-variant31-variant34-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:192,234:426:99:6309,0,4747:98,94,120,114 chr1 152283862 . G C 2394.07 PASS AC=1;AF=0.55;AN=2;DP=4011;set=variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant18-variant27-variant29-variant30-variant31-variant34-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:112,111:223:99:2804,0,2973:58,54,56,55 chr1 152283975 . A G 4355.61 PASS AC=1;AF=0.553;AN=2;DP=6411;set=variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant14-variant16-variant18-variant27-variant29-variant30-variant31-variant34-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:184,166:350:99:4354,0,4717:100,84,95,71 chr1 152284424 . G C 4464.88 PASS AC=1;AF=0.5;AN=2;DP=1853;set=variant7-variant11-variant34-variant35-filterInvariant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:166,149:315:99:4255,0,4574:85,81,85,64 chr1 152284478 . A G 30.14 PASS AC=1;AF=0.5;AN=2;DP=3356;set=filterInvariant5-variant7-variant11-filterInvariant16-variant34-variant35-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:368,56:424:99:1196,0,15226:210,158,48,8 chr1 152284497 . A G 2497.7 PASS AC=1;AF=0.5;AN=2;DP=2934;FractionInformativeReads=1;set=variant7-variant11-variant34-variant35-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:411,55:466:99:1066,0,17346:230,181,47,8 chr1 152284505 . C G 2420.4 PASS AC=1;AF=0.5;AN=2;DP=3100;FractionInformativeReads=1;set=variant7-variant11-variant34-filterInvariant35-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:428,53:481:99:929,0,17443:241,187,45,8 chr1 152284854 . A G 3508.98 PASS AC=1;AF=0.553;AN=2;DP=4811;set=variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant14-variant16-variant18-variant27-variant29-variant30-variant31-variant34-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:121,157:278:99:4381,0,2934:64,57,84,73 chr1 152284996 . C T 4832.99 PASS AC=1;AF=0.5;AN=2;DP=353;FS=4.058;FractionInformativeReads=1;MQ=59.99;MQRankSum=1.003;QD=13.69;ReadPosRankSum=1.433;SOR=0.868;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:164,189:353:99:4861,0,4194:83,81,86,103 chr1 152285099 . C T 5392.54 PASS AC=1;AF=0.5;AN=2;DP=7604;set=variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant14-variant16-variant18-variant27-variant29-variant30-variant31-variant34-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:180,167:347:99:4422,0,4671:93,87,88,79 chr1 152285181 . G T 4519.07 PASS AC=1;AF=0.5;AN=2;DP=1788;set=variant7-variant11-variant34-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:191,180:371:99:4541,0,4785:96,95,94,86 chr1 152285930 . G A 4315.27 PASS AC=1;AF=0.5;AN=2;DP=5890;set=variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant14-variant16-variant18-variant27-variant29-variant30-variant31-variant34-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:155,169:324:99:4350,0,3839:80,75,92,77 chr1 152286002 . T C 4769.13 PASS AC=1;AF=0.553;AN=2;DP=6275;set=variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant14-variant16-variant18-variant27-variant29-variant30-variant31-variant34-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:145,198:343:99:5144,0,3392:77,68,107,91 chr1 152286204 . G T 3021.54 PASS AC=1;AF=0.5;AN=2;DP=888;MQ=60;set=variant34-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:155,169:324:99:4334,0,3977:76,79,77,92 chr1 152286367 . C A 3570.45 PASS AC=1;AF=0.5;AN=2;DP=4841;set=variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant14-variant16-variant18-variant27-variant29-variant30-variant31-variant34-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:134,125:259:99:3160,0,3523:60,74,60,65 chr1 152287341 . CT C 127.74 PASS AC=1;AF=0.5;AN=2;DP=198;MQ=60;set=variant3-variant8-variant9-variant10-variant11-variant13-variant16-variant27-variant29-variant31-variant32-variant34-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,8:17:99:166,0,189:0,9,2,6 chr1 152297517 . A G 602.21 PASS AC=1;AF=0.5;AN=2;DP=292;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant14-variant16-variant27-variant29-variant30-variant31-variant34-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,8:13:99:267,0,157:3,2,7,1 chr1 152328095 . C T 12471.3 PASS AC=1;AF=0.5;AN=2;DP=3382;set=variant7-variant11-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:395,424:819:99:10562,0,10023:180,215,192,232 chr1 152328411 . A G 8617.41 PASS AC=1;AF=0.522;AN=2;DP=17618;set=filterInvariant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-filterInvariant14-variant16-variant18-variant27-variant29-variant30-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:533,275:808:99:7184,0,13765:277,256,151,124 chr1 152329852 . C T 1966.77 PASS AC=1;AF=0.5;AN=2;DP=813;FractionInformativeReads=1;MQ=60;set=variant7-variant11-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:130,89:219:99:2245,0,3457:59,71,45,44 chr1 152384833 . T C 1592 PASS AC=1;AF=0.884;AN=2;DP=2388;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,32:67:99:830,0,889:11,24,10,22 chr1 152484129 . G A 3053.34 PASS AC=1;AF=0.713;AN=2;DP=8366;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:152,125:277:99:2949,0,3893:66,86,59,66 chr1 152487979 . C T 2256.82 PASS AC=1;AF=0.713;AN=2;DP=2973;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,44:78:99:1011,0,875:16,18,22,22 chr1 152488063 . C T 2822.4 PASS AC=1;AF=0.725;AN=2;DP=4280;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,56:107:99:1345,0,1211:28,23,29,27 chr1 152488428 . T C 1482.57 PASS AC=1;AF=0.732;AN=2;DP=2007;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,23:37:99:734,0,438:4,10,5,18 chr1 152538358 . G C 1409.29 PASS AC=1;AF=0.577;AN=2;DP=1741;MQ=60;set=variant10-variant15-variant17-variant19-variant21-variant25-variant26-variant27-variant35-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:74,79:153:99:2016,0,2021:46,28,47,32 chr1 152539393 . G A 51.23 PASS AC=1;AF=0.542;AN=2;DP=67;FractionInformativeReads=1;MQ=60;set=variant4-variant12-variant15-variant20-variant28-variant30-variant33-variant34-variant35-variant36-variant37-variant42 GT:AD:DP:GQ:PL:SB 0/1:3,7:10:97:163,0,97:0,3,3,4 chr1 152551801 . C A 138.96 PASS AC=1;AF=0.524;AN=2;DP=294;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant9-variant13-variant15-variant17-variant20-variant23-variant24-variant25-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant42 GT:AD:DP:GQ:PL:SB 0/1:7,6:13:99:172,0,188:5,2,4,2 chr1 152552285 . C A 2830.61 PASS AC=1;AF=0.558;AN=2;DP=9114;set=variant-variant2-variant5-variant6-variant9-variant11-variant12-variant13-variant15-variant17-variant20-variant21-variant23-variant24-variant25-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:201,225:426:99:5292,0,4976:109,92,122,103 chr1 152552461 . C A 3769.74 PASS AC=1;AF=0.571;AN=2;DP=3418;MQ=60;set=variant4-variant8-variant10-variant15-variant19-variant21-variant25-variant26-variant27-variant35-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:114,106:220:99:2795,0,2819:44,70,37,69 chr1 152595194 . G A 150.99 PASS AC=1;AF=0.571;AN=2;DP=778;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant20-variant21-variant23-variant24-variant25-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:15,11:26:99:214,0,401:9,6,6,5 chr1 152636843 . A T 845.26 PASS AC=1;AF=0.543;AN=2;DP=3083;set=variant-variant2-variant5-variant6-variant9-variant12-variant13-variant15-variant17-variant20-variant23-variant24-variant25-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:79,82:161:99:2339,0,2116:45,34,39,43 chr1 152637150 . A T 2215.84 PASS AC=1;AF=0.607;AN=2;DP=4493;MQ=60;set=variant-variant2-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant20-variant21-variant23-variant24-variant25-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:99,78:177:99:1837,0,2648:32,67,27,51 chr1 152649114 . T A 357.84 PASS AC=1;AF=0.625;AN=2;DP=418;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant20-variant21-variant23-variant24-variant25-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:14,14:28:99:441,0,401:3,11,3,11 chr1 152659805 . G A 1345.36 PASS AC=1;AF=0.587;AN=2;DP=2493;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant9-variant12-variant13-variant15-variant17-variant20-variant23-variant24-variant25-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:78,54:132:99:1405,0,2042:28,50,17,37 chr1 152659848 . A G 869.67 PASS AC=1;AF=0.587;AN=2;DP=1453;MQ=60;set=variant-variant2-variant5-variant6-variant9-variant12-variant13-variant15-variant17-variant20-variant23-variant24-variant25-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:49,33:82:99:899,0,1381:15,34,9,24 chr1 152670737 . G A 225.83 PASS AC=1;AF=0.587;AN=2;DP=1095;MQ=60;set=variant-variant2-variant5-variant6-variant9-variant12-variant13-variant15-variant17-variant20-variant23-variant24-variant25-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:33,25:58:99:644,0,862:19,14,16,9 chr1 152672005 . T C 30.16 PASS AC=1;AF=0.587;AN=2;DP=393;MQ=60;set=variant-variant2-variant5-variant6-variant9-variant12-variant13-variant15-variant17-variant20-variant23-variant24-variant25-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:7,5:12:99:145,0,224:1,6,1,4 chr1 152681543 . T C 3551.41 PASS AC=2;AF=1;AN=2;DP=13896;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,309:309:99:9193,926,0:0,0,166,143 chr1 152681680 . C CAGCTCTGGGGGCTGCTGT 526.66 PASS AC=2;AF=0.75;AN=2;DP=7196;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,122:122:99:5526,378,0:0,0,40,82 chr1 152682058 . TTTTCTGA T 499.41 PASS AC=1;AF=0.6;AN=2;DP=725;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant9-variant12-variant13-variant15-variant17-variant20-variant23-variant24-variant25-variant26-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:19,16:35:99:606,0,1546:5,14,3,13 chr1 152691078 . A G 398.46 PASS AC=1;AF=0.611;AN=2;DP=1318;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant15-variant17-variant20-variant23-variant24-variant25-variant26-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:35,20:55:99:504,0,831:19,16,12,8 chr1 152691272 . G T 94.73 PASS AC=1;AF=0.615;AN=2;DP=302;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant9-variant10-variant12-variant15-variant17-variant20-variant23-variant24-variant25-variant26-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,7:15:99:181,0,181:3,5,2,5 chr1 152691943 . G A 959.31 PASS AC=1;AF=0.611;AN=2;DP=2739;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant15-variant17-variant20-variant23-variant24-variant25-variant26-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:67,54:121:99:1243,0,1753:44,23,35,19 chr1 152692074 . G C 2947.8 PASS AC=1;AF=0.611;AN=2;DP=7074;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant15-variant17-variant20-variant23-variant24-variant25-variant26-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:154,160:314:99:4023,0,3788:81,73,93,67 chr1 152692472 . A C 590.39 PASS AC=1;AF=0.611;AN=2;DP=4019;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant15-variant17-variant20-variant23-variant24-variant25-variant26-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:84,80:164:99:2194,0,2030:42,42,42,38 chr1 152692588 . A G 1125.67 PASS AC=1;AF=0.611;AN=2;DP=4682;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant15-variant17-variant20-variant23-variant24-variant25-variant26-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:117,109:226:99:2942,0,2665:55,62,55,54 chr1 152692781 . G T 1487.35 PASS AC=1;AF=0.611;AN=2;DP=3756;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant15-variant17-variant20-variant23-variant24-variant25-variant26-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:81,87:168:99:2143,0,1983:40,41,40,47 chr1 152692862 . G C 1342.26 PASS AC=1;AF=0.611;AN=2;DP=3180;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant15-variant17-variant20-variant23-variant24-variant25-variant26-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:72,68:140:99:1579,0,1808:32,40,28,40 chr1 152692948 . T A 1376.04 PASS AC=1;AF=0.611;AN=2;DP=1858;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant15-variant17-variant20-variant23-variant24-variant25-variant26-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:41,35:76:99:1291,0,1584:16,25,13,22 chr1 152692952 . G A 1348.1 PASS AC=1;AF=0.611;AN=2;DP=1771;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant15-variant17-variant20-variant23-variant24-variant25-variant26-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:40,33:73:99:1269,0,1587:15,25,12,21 chr1 152730656 . A G 41.67 PASS AC=1;AF=0.672;AN=2;DP=495;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant27-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:17,11:28:99:286,0,514:5,12,4,7 chr1 152732106 . A T 1961.86 PASS AC=1;AF=0.536;AN=2;DP=1878;MQ=60;set=variant4-variant10-variant15-variant19-variant21-variant26-variant27-variant31-variant35-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:77,69:146:99:1849,0,2026:50,27,46,23 chr1 152732436 . G C 1323.71 PASS AC=1;AF=0.657;AN=2;DP=4669;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:78,58:136:99:1632,0,2367:34,44,20,38 chr1 152733301 . T A 2001.06 PASS AC=1;AF=0.657;AN=2;DP=10979;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:206,177:383:99:4367,0,4922:101,105,95,82 chr1 152734187 . G A 1445.16 PASS AC=1;AF=0.667;AN=2;DP=2948;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:65,64:129:99:1387,0,1532:33,32,32,32 chr1 152734633 . T A 42.2 PASS AC=1;AF=0.71;AN=2;DP=327;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,2:8:63:63,0,200:1,5,0,2 chr1 152749091 . C T 3253.32 PASS AC=1;AF=0.538;AN=2;DP=2906;MQ=60;set=variant10-variant15-variant19-variant21-variant26-variant27-variant31-variant35-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:132,118:250:99:3249,0,3560:67,65,66,52 chr1 152758766 . G C 399.77 PASS AC=1;AF=0.617;AN=2;DP=1111;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,13:26:99:296,0,349:8,5,7,6 chr1 152758915 . G T 205.92 PASS AC=1;AF=0.533;AN=2;DP=262;FractionInformativeReads=1;MQ=60;set=variant4-variant10-variant15-variant16-variant19-variant21-variant26-variant27-variant31-variant35-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,7:15:99:229,0,173:3,5,1,6 chr1 152759678 . C T 1320.38 PASS AC=1;AF=0.667;AN=2;DP=5620;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:95,92:187:99:2355,0,2546:65,30,61,31 chr1 152759950 . A G 1489.44 PASS AC=1;AF=0.667;AN=2;DP=5936;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:98,102:200:99:2942,0,2641:52,46,48,54 chr1 152771293 . A G 768.97 PASS AC=1;AF=0.632;AN=2;DP=2595;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:27,42:69:99:988,0,747:7,20,14,28 chr1 152777465 . A G 429.26 PASS AC=1;AF=0.633;AN=2;DP=1978;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:35,30:65:99:986,0,1087:23,12,20,10 chr1 152777868 . A G 1344.66 PASS AC=1;AF=0.633;AN=2;DP=4879;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:97,85:182:99:2659,0,3041:74,23,62,23 chr1 152777964 . G A 1738.21 PASS AC=1;AF=0.617;AN=2;DP=9703;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:202,145:347:99:3107,0,4656:97,105,72,73 chr1 152882982 . C G,CAGCAGCAGGAGGGGCAGCTGGAGCTCTCTG 773.67 PASS AC=0,2;AF=0.103,0.868;AN=2;DP=1807;set=variant5-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant3-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant4-variant32-variant33-variant6-variant34-variant35-variant8-variant36-variant38-variant39-variant40-variant9-variant41-variant42-variant43 GT:DP:GQ:SB 2/2:25:99:0,0,21,4 chr1 152944156 . C T 106.77 PASS AC=1;AF=0.765;AN=2;DP=94;FS=0;FractionInformativeReads=1;set=variant2-variant10-variant12-variant14-variant18-variant23-variant24-variant26-variant28-variant29-variant31-variant33-variant34-variant35-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:1,4:5:22:157,0,22:1,0,4,0 chr1 152944594 . C T 1406.3 PASS AC=2;AF=0.737;AN=2;DP=6722;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,202:203:99:6124,593,0:0,1,97,105 chr1 152957573 . T C 300.5 PASS AC=1;AF=0.629;AN=2;DP=719;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,8:16:99:193,0,231:7,1,6,2 chr1 152957832 . C A 493.88 PASS AC=1;AF=0.636;AN=2;DP=2409;set=variant-variant2-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,42:80:99:1176,0,1162:18,20,20,22 chr1 152957887 . G A 473.52 PASS AC=1;AF=0.632;AN=2;DP=2982;set=variant-variant2-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,47:95:99:1078,0,1333:29,19,25,22 chr1 152974119 . C T 32.98 PASS AC=1;AF=0.667;AN=2;DP=204;MQ=60;set=variant-variant2-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant28-variant29-variant32-variant34-variant35-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:68:76,0,68:2,1,2,1 chr1 152974247 . C G 326.41 PASS AC=1;AF=0.625;AN=2;DP=639;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,9:25:99:330,0,718:8,8,4,5 chr1 152974254 . C T 326.41 PASS AC=1;AF=0.613;AN=2;DP=605;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,9:25:99:330,0,718:8,8,4,5 chr1 152974285 . A G 197.45 PASS AC=1;AF=0.661;AN=2;DP=523;MQ=60;set=variant-variant2-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,6:19:99:124,0,286:6,7,2,4 chr1 152975277 . G A 1139.59 PASS AC=1;AF=0.636;AN=2;DP=1553;MQ=60;set=variant-variant2-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,32:67:99:963,0,948:23,12,19,13 chr1 152975495 . G A 2039.17 PASS AC=1;AF=0.636;AN=2;DP=8178;MQ=60;set=variant-variant2-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:131,102:233:99:2284,0,3420:71,60,56,46 chr1 152975763 . C A 977.61 PASS AC=1;AF=0.636;AN=2;DP=3104;set=variant-variant2-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,46:88:99:1591,0,1530:27,15,28,18 chr1 152975829 . A G 1704 PASS AC=1;AF=0.636;AN=2;DP=5411;set=variant-variant2-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:90,85:175:99:2481,0,2684:56,34,49,36 chr1 152975941 . C G 1657.28 PASS AC=1;AF=0.629;AN=2;DP=6647;MQ=60;set=variant-variant2-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:116,84:200:99:2096,0,3076:53,63,39,45 chr1 152976108 . C T 4631.35 PASS AC=1;AF=0.636;AN=2;DP=6552;MQ=60;set=variant-variant2-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:102,91:193:99:3571,0,5916:64,38,54,37 chr1 152976114 . G C 4801.4 PASS AC=1;AF=0.636;AN=2;DP=6857;MQ=60;set=variant-variant2-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:105,93:198:99:3563,0,5981:65,40,58,35 chr1 152976306 . T G 3571.28 PASS AC=1;AF=0.636;AN=2;DP=8881;MQ=60;set=variant-variant2-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:127,130:257:99:3314,0,3085:49,78,52,78 chr1 153003803 . AT A 312.26 PASS AC=1;AF=0.613;AN=2;DP=516;MQ=60;set=variant-variant2-variant6-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant34-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,4:12:89:89,0,211:3,5,0,4 chr1 153004652 . G A 199.33 PASS AC=1;AF=0.606;AN=2;DP=750;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,12:27:99:326,0,563:15,0,9,3 chr1 153004721 . A T 614.64 PASS AC=1;AF=0.606;AN=2;DP=2324;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,41:92:99:1040,0,1171:29,22,25,16 chr1 153004778 . C T 734.75 PASS AC=1;AF=0.606;AN=2;DP=3818;MQ=60;set=variant-variant2-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:82,69:151:99:1675,0,2087:42,40,38,31 chr1 153004809 . T C 813.73 PASS AC=1;AF=0.606;AN=2;DP=4327;MQ=60;set=variant-variant2-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:88,76:164:99:1837,0,2102:47,41,41,35 chr1 153004848 . T C 1236.8 PASS AC=1;AF=0.606;AN=2;DP=4223;set=variant-variant2-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:83,69:152:99:2539,0,3174:44,39,33,36 chr1 153004853 . C T 1239.81 PASS AC=1;AF=0.606;AN=2;DP=4169;FractionInformativeReads=1;set=variant-variant2-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:79,66:145:99:2455,0,3217:42,37,31,35 chr1 153004983 . C T 509.23 PASS AC=1;AF=0.606;AN=2;DP=2901;set=variant-variant2-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant20-filterInvariant21-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,46:91:99:1308,0,1294:23,22,30,16 chr1 153005156 . C T 1325.87 PASS AC=1;AF=0.606;AN=2;DP=5994;MQ=60;set=variant-variant2-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:100,101:201:99:2626,0,2598:48,52,45,56 chr1 153012354 . T G 463.45 PASS AC=1;AF=0.6;AN=2;DP=1573;FractionInformativeReads=1;set=variant-variant2-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,27:48:99:1071,0,1011:10,11,16,11 chr1 153012356 . C T 463.45 PASS AC=1;AF=0.6;AN=2;DP=1560;FractionInformativeReads=1;set=variant-variant2-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,27:48:99:1071,0,1011:10,11,16,11 chr1 153013630 . G C,A 454.22 PASS AC=1,0;AF=0.6,0.014;AN=2;DP=2135;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:68:99:17,17,16,18 chr1 153013742 . G T 127.69 PASS AC=1;AF=0.609;AN=2;DP=399;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,13:19:99:434,0,179:0,6,2,11 chr1 153014082 . T A 254.87 PASS AC=1;AF=0.615;AN=2;DP=304;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant32-variant35-variant36-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,3:11:61:61,0,230:6,2,2,1 chr1 153029137 . C T 557.87 PASS AC=1;AF=0.597;AN=2;DP=1249;set=variant-variant2-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,18:36:99:550,0,667:6,12,5,13 chr1 153044009 . G A 215.07 PASS AC=1;AF=0.594;AN=2;DP=1047;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,10:24:99:181,0,305:8,6,6,4 chr1 153044071 . C A 628.07 PASS AC=1;AF=0.594;AN=2;DP=2335;MQ=60;set=variant-variant2-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,27:62:99:624,0,888:20,15,13,14 chr1 153066262 . T C 661.97 PASS AC=1;AF=0.515;AN=2;DP=3787;set=variant-variant2-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,33:100:99:610,0,1753:29,38,16,17 chr1 153113913 . A G 702.39 PASS AC=2;AF=0.764;AN=2;DP=2820;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:2145,204,0:0,0,41,27 chr1 153114077 . G T 436.36 PASS AC=2;AF=0.7;AN=2;DP=402;MQ=60;set=variant2-variant5-variant8-variant10-variant12-variant13-variant17-variant18-variant20-variant30-variant32-variant35-variant37-variant40-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:939,78,0:0,0,5,21 chr1 153122171 . G A 788.1 PASS AC=2;AF=0.736;AN=2;DP=1817;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1560,146,0:0,0,32,17 chr1 153122310 . G A 1294.69 PASS AC=2;AF=0.729;AN=2;DP=3787;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,143:143:99:4298,427,0:0,0,85,58 chr1 153122620 . T C 1120.78 PASS AC=2;AF=0.736;AN=2;DP=4626;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,154:154:99:4917,462,0:0,0,69,85 chr1 153189978 . A G 270.03 PASS AC=1;AF=0.617;AN=2;DP=790;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-filterInvariant12-variant14-variant15-variant16-variant19-variant22-variant23-variant26-variant27-variant29-variant32-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,15:37:99:361,0,564:13,9,8,7 chr1 153233510 . A G 439.29 PASS AC=1;AF=0.696;AN=2;DP=1362;set=variant-variant3-variant4-variant6-variant7-variant9-variant11-variant12-variant15-variant17-variant19-variant22-variant23-variant25-variant27-variant30-variant31-variant32-variant33-variant35-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,29:62:99:816,0,814:14,19,12,17 chr1 153233991 . A ACTCTGGCGGCGG 862.95 PASS AC=1;AF=0.762;AN=2;DP=2681;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,38:65:99:1647,0,3156:11,16,17,21 chr1 153234602 . T C 315.51 PASS AC=1;AF=0.762;AN=2;DP=1316;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,21:37:99:582,0,435:5,11,7,14 chr1 153270362 . C G 244.3 PASS AC=1;AF=0.615;AN=2;DP=1256;MQ=60;set=variant2-variant3-variant4-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant35-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,24:39:99:706,0,409:11,4,16,8 chr1 153270857 . T C 222.45 PASS AC=1;AF=0.632;AN=2;DP=792;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant35-variant36-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,11:28:99:364,0,476:5,12,1,10 chr1 153271524 . C T 349.25 PASS AC=1;AF=0.618;AN=2;DP=1908;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant35-variant36-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,28:60:99:694,0,976:23,9,19,9 chr1 153277423 . C T 1568.7 PASS AC=1;AF=0.615;AN=2;DP=3024;MQ=60;set=variant2-variant3-variant4-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant35-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,52:101:99:1276,0,1250:22,27,27,25 chr1 153277660 . A T 546.44 PASS AC=1;AF=0.635;AN=2;DP=1074;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant35-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,17:39:99:442,0,595:9,13,5,12 chr1 153279462 . TAAG T 2844.21 PASS AC=2;AF=0.808;AN=2;DP=2793;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,59:61:99:2606,135,0:1,1,38,21 chr1 153282892 . C T 279.29 PASS AC=1;AF=0.596;AN=2;DP=667;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant7-variant8-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant35-variant37-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,11:18:99:336,0,203:5,2,9,2 chr1 153283004 . C T 3566.18 PASS AC=2;AF=0.833;AN=2;DP=4691;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,127:127:99:3829,380,0:0,0,78,49 chr1 153283179 . A G 1295.35 PASS AC=1;AF=0.615;AN=2;DP=3212;MQ=60;set=variant2-variant5-variant6-variant9-variant11-variant12-variant14-variant16-variant17-variant18-variant23-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:69,43:112:99:1070,0,1722:30,39,14,29 chr1 153302827 . T G 3980.05 PASS AC=2;AF=0.825;AN=2;DP=4380;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,98:98:99:3418,294,0:0,0,26,72 chr1 153302887 . G A 640.75 PASS AC=1;AF=0.607;AN=2;DP=1423;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant6-variant8-variant9-variant11-variant12-variant14-variant16-variant17-variant18-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:29,23:52:99:598,0,881:10,19,10,13 chr1 153303638 . A G 291.54 PASS AC=1;AF=0.6;AN=2;DP=955;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:19,19:38:99:484,0,548:4,15,6,13 chr1 153309981 . G A 295.33 PASS AC=1;AF=0.615;AN=2;DP=873;MQ=60;set=variant2-variant5-variant6-variant9-variant11-variant12-variant14-variant16-variant17-variant18-variant23-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:17,22:39:99:662,0,362:7,10,7,15 chr1 153312644 . A G 719.91 PASS AC=2;AF=0.929;AN=2;DP=2090;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,61:61:99:1898,183,0:0,0,41,20 chr1 153313912 . A G 255.13 PASS AC=2;AF=0.824;AN=2;DP=390;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:311,24,0:0,0,7,1 chr1 153314153 . C A 1547.96 PASS AC=2;AF=0.8;AN=2;DP=2713;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,78:78:99:2333,233,0:0,0,38,40 chr1 153314347 . C T 465.43 PASS AC=2;AF=0.808;AN=2;DP=583;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:532,45,0:0,0,3,12 chr1 153315467 . T TAAG 359.93 PASS AC=2;AF=0.929;AN=2;DP=1118;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:1302,87,0:0,0,19,10 chr1 153315579 . A G 594.95 PASS AC=2;AF=0.929;AN=2;DP=3980;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:2371,216,0:0,0,41,31 chr1 153315784 . T C 469.53 PASS AC=2;AF=0.929;AN=2;DP=1605;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1309,114,0:0,0,9,29 chr1 153320159 . G C 102.99 PASS AC=2;AF=0.853;AN=2;DP=303;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:205,15,0:0,0,4,1 chr1 153320334 . T C 1524.15 PASS AC=2;AF=0.8;AN=2;DP=2452;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:1669,173,0:0,0,32,26 chr1 153320372 . T G 1879.53 PASS AC=2;AF=0.8;AN=2;DP=3191;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,67:67:99:1970,199,0:0,0,34,33 chr1 153320581 . T C 363.46 PASS AC=2;AF=0.8;AN=2;DP=773;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:723,54,0:0,0,2,16 chr1 153321010 . C A 706.98 PASS AC=2;AF=0.8;AN=2;DP=1217;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:900,72,0:0,0,20,4 chr1 153321197 . T G 1957.08 PASS AC=2;AF=0.8;AN=2;DP=1966;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1725,146,0:0,0,18,31 chr1 153321217 . G GAGA 2205.09 PASS AC=2;AF=0.8;AN=2;DP=1617;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1667,114,0:0,0,13,25 chr1 153321348 . G T 142.99 PASS AC=2;AF=0.829;AN=2;DP=437;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:377,27,0:0,0,1,8 chr1 153321368 . CCAGGTAGCT C 142.73 PASS AC=2;AF=0.833;AN=2;DP=338;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:225,15,0:0,0,0,5 chr1 153362788 . T C 1297.65 PASS AC=1;AF=0.553;AN=2;DP=1650;MQ=60;set=variant3-variant5-variant8-variant14-variant15-variant17-variant21-variant25-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:59,57:116:99:1554,0,1460:27,32,27,30 chr1 153390411 . T TA 570.61 PASS AC=2;AF=0.875;AN=2;DP=1058;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:81:815,81,0:0,0,16,10 chr1 153390542 . G C 608.2 PASS AC=1;AF=0.5;AN=2;DP=673;set=variant10-variant11-variant13-variant27-variant32-variant35-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:41,23:64:99:534,0,1200:23,18,14,9 chr1 153391729 . G A 1769.29 PASS AC=1;AF=0.5;AN=2;DP=2243;FractionInformativeReads=1;set=variant10-variant11-variant12-variant13-variant23-variant27-variant32-variant33-variant35-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:90,85:175:99:2050,0,2106:50,40,46,39 chr1 153391786 . T C 1822.4 PASS AC=1;AF=0.5;AN=2;DP=2459;set=variant10-variant11-variant12-variant13-variant23-variant27-variant32-variant33-variant35-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:101,97:198:99:2239,0,2250:52,49,50,47 chr1 153392042 . A C 1346.5 PASS AC=1;AF=0.5;AN=2;DP=761;set=variant10-variant11-variant12-variant13-variant23-variant27-variant32-variant33-variant35-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:29,27:56:99:1032,0,1505:13,16,14,13 chr1 153392044 . C G 1346.5 PASS AC=1;AF=0.5;AN=2;DP=758;set=variant10-variant11-variant12-variant13-variant23-variant27-variant32-variant33-variant35-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:30,26:56:99:1032,0,1505:14,16,14,12 chr1 153392302 . G T 932.85 PASS AC=1;AF=0.5;AN=2;DP=1192;MQ=60;set=variant10-variant11-variant12-variant13-variant23-variant27-variant32-variant33-variant35-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:69,40:109:99:921,0,1637:38,31,23,17 chr1 153392993 . T C 1070.47 PASS AC=1;AF=0.5;AN=2;DP=1094;MQ=60;set=variant10-variant11-variant12-variant13-variant23-variant27-variant32-variant33-variant35-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:53,51:104:99:1339,0,1335:23,30,27,24 chr1 153393048 . C T 915.94 PASS AC=1;AF=0.5;AN=2;DP=1053;set=variant10-variant11-variant12-variant13-variant23-variant27-variant32-variant33-variant35-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:40,51:91:99:1399,0,1067:22,18,26,25 chr1 153393318 . T C 858.95 PASS AC=1;AF=0.5;AN=2;DP=1043;set=variant10-variant11-variant12-variant13-variant23-variant27-variant32-variant33-variant35-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:53,38:91:99:1103,0,1517:27,26,16,22 chr1 153393554 . T C 2350.51 PASS AC=1;AF=0.5;AN=2;DP=1815;FractionInformativeReads=1;MQ=60;set=variant10-variant11-variant12-variant13-variant23-variant27-variant32-variant33-variant35-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:73,77:150:99:2152,0,1959:40,33,47,30 chr1 153410798 . A G 2046.43 PASS AC=1;AF=0.5;AN=2;DP=278;FractionInformativeReads=1;MQ=60;set=variant32-variant35 GT:AD:DP:GQ:PL:SB 0/1:63,56:119:99:1446,0,1651:31,32,20,36 chr1 153410822 . C A 4761.48 PASS AC=1;AF=0.813;AN=2;DP=5344;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,64:112:99:1743,0,1189:21,27,32,32 chr1 153411720 . T C 625.95 PASS AC=1;AF=0.5;AN=2;DP=462;FractionInformativeReads=1;MQ=60;set=variant9-variant12-variant19-variant23-variant28-variant32-variant33-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:38,35:73:99:805,0,933:24,14,17,18 chr1 153411752 . C T 669.68 PASS AC=1;AF=0.5;AN=2;DP=427;FractionInformativeReads=1;MQ=60;set=variant9-variant12-variant19-variant23-variant28-variant32-variant33-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:40,27:67:99:615,0,1012:22,18,12,15 chr1 153411867 . G A 223.58 PASS AC=1;AF=0.813;AN=2;DP=492;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,16:20:99:545,0,123:0,4,2,14 chr1 153412392 . T G 2025.58 PASS AC=2;AF=0.884;AN=2;DP=4993;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,108:108:99:3192,323,0:0,0,57,51 chr1 153431200 . T C 1980.81 PASS AC=2;AF=0.884;AN=2;DP=2956;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:2722,225,0:0,0,60,15 chr1 153431406 . C G 5055.4 PASS AC=2;AF=0.977;AN=2;DP=7962;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,180:180:99:5805,540,0:0,0,73,107 chr1 153432265 . C G 1870.3 PASS AC=2;AF=0.884;AN=2;DP=2593;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1764,168,0:0,0,29,27 chr1 153535848 . CA C 148.54 PASS AC=1;AF=0.5;AN=2;DP=85;FS=0;MQ=60;set=variant18-filterInvariant35 GT:AD:DP:GQ:PL:SB 0/1:35,12:47:99:137,0,747:20,15,7,5 chr1 153538449 . C T 214.45 PASS AC=2;AF=0.826;AN=2;DP=628;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:434,39,0:0,0,4,9 chr1 153585584 . G A 715.34 PASS AC=2;AF=0.652;AN=2;DP=1320;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:1730,173,0:0,0,24,34 chr1 153587256 . A T 1945.69 PASS AC=2;AF=0.657;AN=2;DP=2926;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:2447,227,0:0,0,42,34 chr1 153587308 . C T 1543.77 PASS AC=2;AF=0.697;AN=2;DP=2748;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:2262,224,0:0,0,38,37 chr1 153588208 . G A 271.52 PASS AC=2;AF=0.657;AN=2;DP=844;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:887,75,0:0,0,19,6 chr1 153588279 . G A 1331.4 PASS AC=2;AF=0.657;AN=2;DP=2574;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,63:63:99:2068,189,0:0,0,42,21 chr1 153588843 . G A 841.59 PASS AC=2;AF=0.657;AN=2;DP=1659;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1290,129,0:0,0,15,28 chr1 153589205 . G GTCTC,GTC 94.2 PASS AC=2,0;AF=0.866,0.11;AN=2;DP=354;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:8:24:0,0,4,4 chr1 153600778 . G A 1193.19 PASS AC=2;AF=0.662;AN=2;DP=1642;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1763,134,0:0,0,36,9 chr1 153602861 . G C 1468.17 PASS AC=2;AF=0.681;AN=2;DP=2335;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1922,168,0:0,0,37,19 chr1 153604029 . C T 4554.55 PASS AC=2;AF=0.841;AN=2;DP=5734;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,142:143:99:4302,419,0:0,1,79,63 chr1 153604112 . G A 3818.35 PASS AC=2;AF=0.714;AN=2;DP=4969;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,159:159:99:4777,472,0:0,0,83,76 chr1 153604422 . T C 238.52 PASS AC=1;AF=0.696;AN=2;DP=291;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant12-variant15-variant17-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,7:8:21:242,0,21:1,0,0,7 chr1 153604519 . G A 832.03 PASS AC=2;AF=0.7;AN=2;DP=1128;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:83:780,83,0:0,0,16,12 chr1 153606387 . G A 373.66 PASS AC=2;AF=0.7;AN=2;DP=781;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,31:31:92:1031,92,0:0,0,25,6 chr1 153606851 . A G 902.31 PASS AC=2;AF=0.722;AN=2;DP=1628;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1671,126,0:0,0,8,34 chr1 153609039 . T C 1858.34 PASS AC=2;AF=0.7;AN=2;DP=1947;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1298,137,0:0,0,25,21 chr1 153616857 . T C 1857.24 PASS AC=2;AF=0.7;AN=2;DP=1373;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1454,114,0:0,0,3,35 chr1 153618766 . C T 9786.38 PASS AC=2;AF=0.7;AN=2;DP=8640;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,258:258:99:8164,771,0:0,0,89,169 chr1 153618837 . GT G,GTT 1165.19 PASS AC=2,0;AF=0.588,0.038;AN=2;DP=3421;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-filterInvariant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-filterInvariant21-variant22-filterInvariant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-filterInvariant32-variant33-variant34-variant35-filterInvariant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:DP:GQ:SB 1/1:50:99:1,0,11,38 chr1 153631071 . G A 1978.91 PASS AC=2;AF=0.654;AN=2;DP=3315;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant35-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,125:125:99:4035,374,0:0,0,84,41 chr1 153634058 . G T 723.56 PASS AC=2;AF=0.7;AN=2;DP=781;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:1033,90,0:0,0,15,15 chr1 153635425 . G A 1617.53 PASS AC=2;AF=0.686;AN=2;DP=1683;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1811,149,0:0,0,25,25 chr1 153636468 . CTA C 1023.02 PASS AC=2;AF=0.625;AN=2;DP=561;set=variant-variant4-variant7-variant8-variant10-variant12-variant14-variant15-variant17-variant18-variant19-variant22-variant24-variant25-variant26-variant28-variant29-variant31-variant33-variant34-variant35-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:880,63,0:0,0,17,4 chr1 153636471 . CT C 1023.12 PASS AC=2;AF=0.625;AN=2;DP=581;set=variant-variant4-variant7-variant8-variant10-variant12-variant14-variant15-variant17-variant18-variant19-variant22-variant24-variant25-variant26-variant28-variant29-variant31-variant33-variant34-variant35-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:880,63,0:0,0,17,4 chr1 153636860 . A G 6602.13 PASS AC=2;AF=0.686;AN=2;DP=7041;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,194:194:99:5978,580,0:0,0,103,91 chr1 153637617 . G A 1201.77 PASS AC=2;AF=0.65;AN=2;DP=1156;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1231,123,0:0,0,25,16 chr1 153640665 . G A 918.68 PASS AC=2;AF=0.65;AN=2;DP=445;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:594,42,0:0,0,10,4 chr1 153642835 . G C 4100.52 PASS AC=2;AF=0.977;AN=2;DP=5174;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,150:151:99:4644,443,0:1,0,63,87 chr1 153642909 . A G 2497.78 PASS AC=2;AF=0.65;AN=2;DP=1981;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,93:93:99:2811,278,0:0,0,39,54 chr1 153651269 . TTCTCTCTCTC TTCTCTCTC,T,TTCTCTCTCTCTC,TTCTCTC 3503.19 PASS AC=2,0,0,0;AF=0.569,0.014,0.028,0.028;AN=2;DP=4267;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-filterInvariant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant40-filterInvariant41-variant42-variant44 GT:DP:GQ:SB 1/1:129:99:0,0,71,58 chr1 153656352 . T G 1744.83 PASS AC=2;AF=0.661;AN=2;DP=1219;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1682,138,0:0,0,13,33 chr1 153660514 . AC A 647.02 PASS AC=2;AF=0.65;AN=2;DP=675;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:756,75,0:0,0,19,6 chr1 153661374 . CG C 3143.26 PASS AC=2;AF=0.65;AN=2;DP=3144;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,108:108:99:4046,325,0:0,0,73,35 chr1 153662584 . GTCTCTCTC GTCTCTC,GTCTC,G,GTCTCTCTCTC 77.04 PASS AC=2,0,0,0;AF=0.615,0.077,0.077,0.077;AN=2;DP=101;FS=0;set=variant7-variant12-variant13-variant15-variant20-variant22-variant27-variant29-variant34-variant35-variant37-variant41-variant44 GT:DP:GQ:SB 1/1:6:8:1,0,4,1 chr1 153662617 . T A 100.1 PASS AC=2;AF=0.833;AN=2;DP=86;FS=0;set=variant7-variant12-variant15-variant22-variant34-variant35-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:276,30,0:0,0,7,3 chr1 153665919 . T TC 2794.35 PASS AC=2;AF=0.662;AN=2;DP=3757;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,141:141:99:4789,430,0:0,0,70,71 chr1 153700841 . A G 2598.18 PASS AC=2;AF=0.977;AN=2;DP=4645;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,129:129:99:4013,387,0:0,0,62,67 chr1 153701376 . G C 424.22 PASS AC=2;AF=1;AN=2;DP=530;FS=0;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:329,27,0:0,0,6,3 chr1 153731750 . GAAA GAA,GA,GAAAA,G 256.6 PASS AC=1,0,0,0;AF=0.556,0.019,0.056,0.019;AN=2;DP=474;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant13-variant14-filterInvariant15-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant30-variant32-variant33-variant35-variant36-variant41-variant42-variant43 GT:DP:GQ:SB 0/1:17:99:9,1,5,2 chr1 153732708 . CAAAAAAA CAAAAAAAA,CAAAAAA,C,CAA,CAAAAA,CAAAA 80.81 PASS AC=0,0,0,0,1,0;AF=0.077,0.077,0.115,0.038,0.115,0.077;AN=2;DP=366;set=variant3-filterInvariant4-variant10-variant14-variant18-variant21-variant29-variant35-variant37-variant39-variant41-filterInvariant43-variant44 GT:DP:GQ:SB 0/5:16:99:5,3,7,1 chr1 153743317 . G A 1789.09 PASS AC=2;AF=0.641;AN=2;DP=2198;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:1918,195,0:0,0,28,37 chr1 153750207 . C CCTT 871.3 PASS AC=1;AF=0.593;AN=2;DP=2488;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant25-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,46:105:99:1785,0,4922:36,23,29,17 chr1 153750214 . TC T 893.95 PASS AC=1;AF=0.571;AN=2;DP=2853;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,49:116:99:1802,0,5090:40,27,31,18 chr1 153777669 . G T 1178.08 PASS AC=1;AF=0.645;AN=2;DP=1337;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,31:47:99:674,0,402:8,8,15,16 chr1 153777848 . C T 1121.74 PASS AC=1;AF=0.645;AN=2;DP=1299;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,12:37:99:247,0,655:13,12,5,7 chr1 153779089 . GT G,GTT 3599.31 PASS AC=1,0;AF=0.672,0.016;AN=2;DP=3988;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:115:99:29,30,33,23 chr1 153779412 . A G 9268.77 PASS AC=1;AF=0.645;AN=2;DP=9721;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:123,155:278:99:3670,0,3064:61,62,74,81 chr1 153780298 . C T 1928.3 PASS AC=1;AF=0.645;AN=2;DP=2375;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,46:85:99:1174,0,879:20,19,25,21 chr1 153781888 . G A 1780.99 PASS AC=1;AF=0.645;AN=2;DP=1989;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,34:65:99:852,0,818:15,16,19,15 chr1 153782188 . CA C,CAA,CAAA,CAAAAA 161.02 PASS AC=1,0,0,0;AF=0.288,0.154,0.038,0.019;AN=2;DP=2369;set=filterInvariant-filterInvariant2-filterInvariant4-filterInvariant6-variant9-filterInvariant10-variant14-filterInvariant15-filterInvariant16-variant17-variant18-filterInvariant19-variant20-filterInvariant21-filterInvariant25-variant27-filterInvariant31-variant32-filterInvariant33-variant34-filterInvariant35-filterInvariant36-filterInvariant38-variant39-variant40-filterInvariant41 GT:DP:GQ:SB 0/1:62:96:30,17,9,6 chr1 153784666 . CTT CTTT,CT,C,CTTTT 280.89 PASS AC=1,1,0,0;AF=0.182,0.466,0.023,0.011;AN=2;DP=1866;set=Intersection GT:DP:GQ:SB 2/1:36:99:0,1,12,23 chr1 153790501 . C T 2615.14 PASS AC=1;AF=0.652;AN=2;DP=2418;MQ=60;set=variant-variant3-variant7-variant9-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:79,42:121:99:829,0,1926:43,36,22,20 chr1 153790790 . CTTT CTT,C,CT,CTTTT 142.98 PASS AC=0,0,0,1;AF=0.5,0.019,0.148,0.019;AN=2;DP=436;set=variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant23-variant24-variant25-variant29-variant30-variant31-variant32-variant35-variant40-variant41-variant42-variant44 GT:DP:GQ:SB 0/4:7:11:0,3,0,4 chr1 153800931 . TACACACACAC TACAC,TAC,TACACACACACAC,TACACACACACACAC,T 206.46 PASS AC=0,1,0,0,0;AF=0.016,0.484,0.194,0.113,0.032;AN=2;DP=292;FS=0;set=variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:6:72:0,2,0,4 chr1 153903390 . A C 45.58 PASS AC=1;AF=0.5;AN=2;DP=242;MQ=60;set=filterInvariant13-filterInvariant22-filterInvariant32-variant35 GT:AD:DP:GQ:PL:SB 0/1:48,17:65:99:173,0,957:18,30,17,0 chr1 153903399 . A C 86.77 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=317;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:55,17:72:99:141,0,2426:21,34,17,0 chr1 153904574 . T C 606.44 PASS AC=1;AF=0.635;AN=2;DP=1176;set=variant-variant3-variant7-variant9-variant10-variant11-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,14:39:99:340,0,607:14,11,9,5 chr1 153906397 . A G 1149.2 PASS AC=1;AF=0.676;AN=2;DP=2049;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,43:75:99:1122,0,790:13,19,17,26 chr1 153907278 . CCTGCTGCTG C,CCTGCTGCTGCTG 4841.32 PASS AC=1,0;AF=0.615,0.019;AN=2;DP=3986;set=variant-variant3-variant7-variant9-variant10-variant11-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant43-variant44 GT:DP:GQ:SB 0/1:164:99:59,36,46,23 chr1 153909069 . G C 1837.75 PASS AC=1;AF=0.64;AN=2;DP=2430;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant7-variant9-variant10-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,59:115:99:1469,0,1466:28,28,30,29 chr1 153913699 . T G 1401.27 PASS AC=1;AF=0.64;AN=2;DP=1705;MQ=60;set=variant-variant3-variant7-variant9-variant10-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,28:76:99:638,0,1226:29,19,15,13 chr1 153913770 . A G 1492.64 PASS AC=1;AF=0.676;AN=2;DP=3012;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,37:104:99:803,0,1698:35,32,17,20 chr1 153917369 . C T 710.81 PASS AC=1;AF=0.64;AN=2;DP=523;MQ=60;set=variant-variant3-variant7-variant9-variant10-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,5:18:99:130,0,397:10,3,4,1 chr1 153920286 . G A 682.99 PASS AC=1;AF=0.64;AN=2;DP=693;MQ=60;set=variant-variant3-variant7-variant9-variant10-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,13:19:99:302,0,130:4,2,7,6 chr1 153920564 . A G 1674.6 PASS AC=1;AF=0.64;AN=2;DP=2108;MQ=60;set=variant-variant3-variant7-variant9-variant10-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,48:100:99:1392,0,1422:25,27,25,23 chr1 153921483 . AC A 1130.78 PASS AC=1;AF=0.652;AN=2;DP=1242;MQ=60;set=variant-variant3-variant7-variant9-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,35:59:99:967,0,665:18,6,24,11 chr1 153926078 . T C 1798.63 PASS AC=1;AF=0.64;AN=2;DP=1850;MQ=60;set=variant-variant3-variant7-variant9-variant10-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,43:73:99:1135,0,774:12,18,17,26 chr1 153927052 . C G 277.42 PASS AC=1;AF=0.615;AN=2;DP=474;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant7-variant9-variant10-variant11-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,2:8:63:63,0,153:2,4,0,2 chr1 153927270 . T C 635.42 PASS AC=1;AF=0.652;AN=2;DP=691;MQ=60;set=variant-variant3-variant7-variant9-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,18:44:99:394,0,700:18,8,9,9 chr1 153932270 . C T 750.05 PASS AC=1;AF=0.556;AN=2;DP=817;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant8-variant17-variant24-variant29-variant31-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:43,50:93:99:1208,0,967:25,18,27,23 chr1 153954778 . AACACAC AACAC,AAC,AACACACAC,A 34.33 PASS AC=1,0,1,0;AF=0.339,0.089,0.089,0.036;AN=2;DP=909;set=variant2-variant4-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-filterInvariant17-filterInvariant18-filterInvariant26-filterInvariant27-variant28-variant29-variant30-variant31-variant33-filterInvariant34-variant35-variant38-variant39-variant41-variant42-variant44 GT:DP:GQ:SB 1/3:31:99:1,2,17,11 chr1 153955069 . C T 2473.56 PASS AC=1;AF=0.5;AN=2;DP=192;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.69;QD=12.88;ReadPosRankSum=1.022;SOR=0.7;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:98,94:192:99:2502,0,2554:45,53,43,51 chr1 153964542 . A T 1868.4 PASS AC=1;AF=0.5;AN=2;DP=131;FS=1.397;FractionInformativeReads=1;MQ=60;MQRankSum=-0.294;QD=14.26;ReadPosRankSum=-1.39;SOR=0.532;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:59,72:131:99:1897,0,1726:33,26,37,35 chr1 153964837 . G GT 177.4 PASS AC=1;AF=0.531;AN=2;DP=319;set=variant-variant2-variant3-variant9-variant19-variant20-variant21-filterInvariant22-variant26-variant27-variant33-variant34-variant35-variant36-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,7:14:87:87,0,130:0,7,1,6 chr1 154033329 . ATAAG A 1189.58 PASS AC=1;AF=0.5;AN=2;DP=423;MQ=60;set=variant5-variant8-variant9-variant12-variant14-variant17-variant20-variant22-variant35-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:18,12:30:99:450,0,1009:13,5,11,1 chr1 154061855 . T G 2099.84 PASS AC=2;AF=1;AN=2;DP=2668;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,69:69:99:2137,207,0:0,0,39,30 chr1 154072601 . G A 3173.27 PASS AC=1;AF=0.75;AN=2;DP=215;MQ=60;MQRankSum=-0.622;ReadPosRankSum=-0.193;set=variant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:52,54:106:99:1302,0,1325:24,28,22,32 chr1 154076366 . T C 256.24 PASS AC=2;AF=0.741;AN=2;DP=266;MQ=60;set=variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant20-variant21-variant23-variant24-variant25-variant29-variant31-variant32-variant33-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:217,15,0:0,0,5,0 chr1 154108387 . G A 1800.65 PASS AC=2;AF=1;AN=2;DP=2519;FS=0;MQ=60;MQRankSum=1.209;ReadPosRankSum=1.536;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:1879,180,0:0,0,22,38 chr1 154112166 . A AC 94.56 PASS AC=1;AF=0.5;AN=2;DP=49;set=variant7-variant35 GT:AD:DP:GQ:PL:SB 0/1:11,9:20:99:177,0,277:8,3,7,2 chr1 154112167 . A C 531.76 PASS AC=1;AF=0.713;AN=2;DP=806;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,6:23:86:86,0,386:11,6,5,1 chr1 154148813 . A G 579.8 PASS AC=1;AF=0.5;AN=2;DP=83;FractionInformativeReads=1;MQ=60;set=variant14-variant35 GT:AD:DP:GQ:PL:SB 0/1:27,13:40:99:290,0,639:11,16,5,8 chr1 154199543 . T C 767.12 PASS AC=2;AF=0.989;AN=2;DP=897;MQRankSum=-0.106;ReadPosRankSum=-0.951;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:487,42,0:0,0,10,4 chr1 154243115 . C T 841.83 PASS AC=2;AF=0.625;AN=2;DP=1851;MQ=60;set=variant2-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant23-variant24-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,89:89:99:2680,265,0:0,0,42,47 chr1 154243246 . G T,GTT 406.54 PASS AC=1,0;AF=0.4,0.2;AN=2;DP=169;set=variant12-variant15-variant28-variant31-variant35 GT:DP:GQ:SB 0/1:25:99:3,12,9,1 chr1 154243457 . A T 979.37 PASS AC=2;AF=0.611;AN=2;DP=743;FractionInformativeReads=1;MQ=60;set=variant5-variant12-variant14-variant17-variant24-variant29-variant31-variant35-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:2319,231,0:0,0,37,40 chr1 154245512 . A G 103.72 PASS AC=2;AF=0.63;AN=2;DP=455;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant14-variant15-variant17-variant23-variant24-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:893,81,0:0,0,10,17 chr1 154245626 . TAA TA,T 98.55 PASS AC=1,0;AF=0.411,0.089;AN=2;DP=1006;set=variant-variant2-variant3-filterInvariant5-variant7-variant8-variant9-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant26-variant27-variant29-filterInvariant31-variant32-variant33-filterInvariant35-variant36-variant37-variant39-variant40-variant41 GT:DP:GQ:SB 0/1:42:99:18,8,12,4 chr1 154245917 . T C 1196.45 PASS AC=2;AF=0.611;AN=2;DP=1032;MQ=60;set=variant5-variant12-variant14-variant17-variant24-variant29-variant31-variant35-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,139:139:99:4392,415,0:0,0,69,70 chr1 154285052 . G A 406.31 PASS AC=1;AF=0.646;AN=2;DP=1012;set=variant5-variant6-variant7-variant9-variant14-variant15-variant16-variant17-variant18-variant20-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:33,35:68:99:843,0,710:17,16,18,17 chr1 154285078 . T G 358.22 PASS AC=1;AF=0.697;AN=2;DP=1159;set=variant3-variant4-variant5-variant6-variant7-variant9-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:30,27:57:99:524,0,680:11,19,13,14 chr1 154293675 . G A 1281.17 PASS AC=1;AF=0.543;AN=2;DP=2147;set=variant4-variant5-variant7-variant9-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant25-variant26-variant27-variant31-variant34-variant35-variant36-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:59,54:113:99:1286,0,1468:31,28,26,28 chr1 154294656 . T C 935.05 PASS AC=1;AF=0.7;AN=2;DP=3271;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:47,66:113:99:1617,0,1191:16,31,27,39 chr1 154295592 . C T 2294.09 PASS AC=1;AF=0.543;AN=2;DP=3346;MQ=60;set=variant4-variant5-variant7-variant9-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant25-variant26-variant27-variant31-variant34-variant35-variant36-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:64,79:143:99:1955,0,1609:35,29,42,37 chr1 154303705 . C T 366.48 PASS AC=1;AF=0.543;AN=2;DP=358;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant7-variant9-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant25-variant26-variant27-variant31-variant34-variant35-variant36-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:3,10:13:95:339,0,95:0,3,2,8 chr1 154303976 . T C 1139.22 PASS AC=1;AF=0.543;AN=2;DP=2205;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant7-variant9-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant25-variant26-variant27-variant31-variant34-variant35-variant36-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:61,59:120:99:1531,0,1543:37,24,37,22 chr1 154305010 . A G 341.9 PASS AC=2;AF=0.909;AN=2;DP=913;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:598,57,0:0,0,13,6 chr1 154305190 . G C 993.53 PASS AC=1;AF=0.543;AN=2;DP=1626;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant7-variant9-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant25-variant26-variant27-variant31-variant34-variant35-variant36-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:27,23:50:99:556,0,706:14,13,10,13 chr1 154310048 . C G 5489.79 PASS AC=1;AF=0.65;AN=2;DP=4995;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:106,82:188:99:2191,0,2871:55,51,31,51 chr1 154310223 . G GA 3573.92 PASS AC=1;AF=0.646;AN=2;DP=6617;MQ=60;set=variant5-variant6-variant7-variant9-variant14-variant15-variant16-variant18-variant20-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:115,128:243:99:2937,0,2560:57,58,59,69 chr1 154313232 . T C 329.22 PASS AC=1;AF=0.75;AN=2;DP=686;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,11:23:99:365,0,274:8,4,7,4 chr1 154317153 . C T 3192.72 PASS AC=1;AF=0.633;AN=2;DP=4556;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:95,99:194:99:2621,0,2378:40,55,49,50 chr1 154317281 . G A 1574.36 PASS AC=1;AF=0.536;AN=2;DP=1775;MQ=60;set=variant5-variant7-variant9-variant14-variant16-variant18-variant20-variant27-variant31-variant34-variant35-variant36-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:85,60:145:99:1568,0,2329:40,45,26,34 chr1 154317418 . T C 1666.56 PASS AC=1;AF=0.633;AN=2;DP=1651;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,46:81:99:1350,0,1069:19,16,20,26 chr1 154318172 . A G 847.59 PASS AC=1;AF=0.536;AN=2;DP=978;MQ=60;set=variant5-variant7-variant9-variant14-variant16-variant18-variant20-variant27-variant31-variant34-variant35-variant36-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:43,38:81:99:1122,0,1309:32,11,26,12 chr1 154319349 . T TTTTA,TTTTATTTA 275.96 PASS AC=1,0;AF=0.636,0.045;AN=2;DP=575;MQ=60;set=variant-variant2-variant5-variant8-variant9-variant10-variant13-filterInvariant14-variant19-variant21-variant24-variant25-variant29-variant30-variant32-variant33-variant34-variant35-variant38-variant41-variant43-variant44 GT:DP:GQ:SB 0/1:13:99:0,6,1,6 chr1 154321072 . A G 1098.35 PASS AC=2;AF=0.977;AN=2;DP=2379;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:1903,180,0:0,0,28,32 chr1 154323548 . AT A 39.42 PASS AC=1;AF=0.735;AN=2;DP=132;MQ=60;set=variant4-variant8-variant9-variant10-variant13-variant19-variant21-variant22-variant23-variant24-variant29-variant32-variant35-variant37-variant38-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,6:10:92:153,0,92:2,2,2,4 chr1 154323772 . A G 704.59 PASS AC=1;AF=0.538;AN=2;DP=897;MQ=60;set=variant5-variant7-variant9-variant14-variant16-variant18-variant20-variant27-variant31-variant35-variant36-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:30,40:70:99:949,0,662:16,14,19,21 chr1 154377569 . C T 675.91 PASS AC=2;AF=0.989;AN=2;DP=1396;MQ=60;MQRankSum=0.217;ReadPosRankSum=-1.463;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1527,152,0:0,0,33,18 chr1 154401679 . G A 1964.49 PASS AC=1;AF=0.5;AN=2;DP=1706;MQ=60;set=variant5-variant7-variant10-variant14-variant23-variant25-variant29-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:125,95:220:99:2320,0,3089:76,49,58,37 chr1 154401972 . T C 813.15 PASS AC=2;AF=0.662;AN=2;DP=3129;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,122:122:99:3877,366,0:0,0,42,80 chr1 154407419 . A C 587.96 PASS AC=1;AF=0.629;AN=2;DP=598;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant6-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,14:22:99:470,0,237:5,3,8,6 chr1 154407713 . T C 627.89 PASS AC=1;AF=0.638;AN=2;DP=1480;MQ=60;set=variant3-variant4-variant5-variant6-variant12-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,27:54:99:691,0,683:9,18,9,18 chr1 154408340 . T C 241.58 PASS AC=2;AF=0.676;AN=2;DP=1066;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:939,84,0:0,0,21,7 chr1 154409730 . G A 283.83 PASS AC=1;AF=0.735;AN=2;DP=116;FractionInformativeReads=1;set=variant3-variant6-variant15-variant16-variant21-variant24-variant26-variant28-variant30-variant31-variant32-variant35-variant36-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,3:7:99:105,0,120:2,2,3,0 chr1 154409893 . A AT 378.81 PASS AC=1;AF=0.621;AN=2;DP=989;MQ=60;set=variant3-variant4-variant5-variant6-variant12-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-filterInvariant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,12:35:99:206,0,497:12,11,5,7 chr1 154420402 . G C 46.72 PASS AC=1;AF=0.641;AN=2;DP=255;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,4:5:31:124,0,31:1,0,3,1 chr1 154422580 . CTG CTGTGTGTGTGTGTGTG,CTGTGTG,CTGTGTGTGTG,CTGTGTGTGTGTG,C,CTGTGTGTGTGTGTG,CTGTGTGTG,CTGTGTGTGTGTGTGTGTG,CTGTGTGTGTGTGTGTGTGTGTG 114.07 PASS AC=0,0,0,0,0,0,2,0,0;AF=0.071,0.048,0.167,0.095,0.071,0.048,0.167,0.095,0.024;AN=2;DP=354;set=variant3-variant5-variant6-variant7-variant8-variant15-variant18-variant19-variant20-variant21-variant25-variant26-variant27-variant29-variant30-variant32-variant35-variant36-variant38-variant41-variant43 GT:DP:GQ:SB 7/7:10:32:0,0,3,7 chr1 154426947 . T A 424.61 PASS AC=1;AF=0.5;AN=2;DP=725;MQ=60;set=variant5-variant7-variant10-variant14-variant23-variant25-variant29-variant35-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:42,36:78:99:717,0,1068:24,18,22,14 chr1 154426970 . A C 1369.24 PASS AC=1;AF=0.638;AN=2;DP=2474;MQ=60;set=variant3-variant4-variant5-variant6-variant12-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,53:96:99:1336,0,930:23,20,32,21 chr1 154437896 . T C 3057 PASS AC=2;AF=0.866;AN=2;DP=4292;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,120:120:99:3805,360,0:0,0,58,62 chr1 154438084 . C T 1590.82 PASS AC=2;AF=0.866;AN=2;DP=2201;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1400,125,0:0,0,21,21 chr1 154438880 . T C 640.01 PASS AC=2;AF=0.854;AN=2;DP=1014;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:999,96,0:0,0,14,18 chr1 154439865 . T A 728.71 PASS AC=2;AF=0.866;AN=2;DP=1646;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1432,135,0:0,0,18,27 chr1 154441856 . GT G 3695.96 PASS AC=1;AF=0.75;AN=2;DP=12931;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:162,161:323:99:3852,0,3700:69,93,65,96 chr1 154442960 . G A 767.61 PASS AC=1;AF=0.744;AN=2;DP=2908;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,35:82:99:1012,0,1135:17,30,9,26 chr1 154452100 . A G 5325.8 PASS AC=2;AF=0.966;AN=2;DP=7087;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,155:155:99:4765,465,0:0,0,80,75 chr1 154452204 . T C 2987.26 PASS AC=1;AF=0.5;AN=2;DP=1947;MQ=60;set=variant5-variant7-variant14-variant23-variant25-variant29-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:111,116:227:99:2697,0,2683:61,50,62,54 chr1 154452218 . C T 8843.69 PASS AC=2;AF=0.955;AN=2;DP=11206;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,231:231:99:6751,691,0:0,0,122,109 chr1 154454674 . C G 320.92 PASS AC=2;AF=0.965;AN=2;DP=328;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:136,12,0:0,0,3,1 chr1 154455949 . T C 803.93 PASS AC=1;AF=0.744;AN=2;DP=2519;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,28:74:99:707,0,1219:25,21,13,15 chr1 154457855 . A C 932.26 PASS AC=1;AF=0.864;AN=2;DP=1621;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:13,20:33:99:509,0,330:5,8,10,10 chr1 154459197 . C G 1277.86 PASS AC=2;AF=0.966;AN=2;DP=3233;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,78:78:99:2339,234,0:0,0,37,41 chr1 154473726 . G A 1298.79 PASS AC=2;AF=0.955;AN=2;DP=1413;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1069,105,0:0,0,23,12 chr1 154474131 . C G 3252.7 PASS AC=1;AF=0.864;AN=2;DP=6314;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:109,76:185:99:1883,0,2541:50,59,38,38 chr1 154474557 . T C 1994.23 PASS AC=1;AF=0.864;AN=2;DP=2771;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:36,30:66:99:730,0,882:17,19,12,18 chr1 154474875 . G A 1081.84 PASS AC=1;AF=0.744;AN=2;DP=2722;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,34:71:99:1270,0,1793:19,18,18,16 chr1 154474900 . G A 1092.3 PASS AC=1;AF=0.744;AN=2;DP=2607;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,31:67:99:1226,0,1737:17,19,16,15 chr1 154475330 . T A 4216.11 PASS AC=1;AF=0.732;AN=2;DP=7962;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:132,106:238:99:3926,0,7128:63,69,55,51 chr1 154475331 . C A 4216.09 PASS AC=1;AF=0.732;AN=2;DP=7932;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:131,105:236:99:3926,0,7128:63,68,54,51 chr1 154479657 . C CAT 2842.87 PASS AC=2;AF=0.955;AN=2;DP=2202;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:2439,171,0:0,0,35,18 chr1 154479670 . C T 1062.85 PASS AC=1;AF=0.744;AN=2;DP=2341;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,37:69:99:896,0,835:17,15,23,14 chr1 154492702 . G A 758.62 PASS AC=1;AF=0.744;AN=2;DP=3311;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:74,49:123:99:1185,0,1930:49,25,31,18 chr1 154493721 . T C 1370.19 PASS AC=2;AF=0.955;AN=2;DP=1761;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:1748,162,0:0,0,36,18 chr1 154514331 . C A 279.03 PASS AC=1;AF=0.732;AN=2;DP=1085;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,17:25:99:421,0,251:5,3,12,5 chr1 154514338 . A T 148.8 PASS AC=1;AF=0.5;AN=2;DP=250;FractionInformativeReads=1;MQ=60;set=variant5-variant7-variant14-variant23-variant25-variant29-variant35-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:18,9:27:99:224,0,657:12,6,6,3 chr1 154516477 . G A 4488.85 PASS AC=1;AF=0.609;AN=2;DP=7261;MQ=60;set=variant3-variant4-variant5-variant7-variant9-variant12-variant15-variant18-variant20-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant32-variant35-variant36-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:147,158:305:99:3834,0,3623:79,68,76,82 chr1 154516571 . T C 9055.04 PASS AC=2;AF=0.955;AN=2;DP=10950;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,250:250:99:7986,749,0:0,0,105,145 chr1 154522248 . A G 2032.64 PASS AC=1;AF=0.837;AN=2;DP=2880;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,32:63:99:965,0,947:9,22,12,20 chr1 154523215 . C T 1205.87 PASS AC=2;AF=0.955;AN=2;DP=1871;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1576,131,0:0,0,38,6 chr1 154523562 . G T 953.36 PASS AC=1;AF=0.5;AN=2;DP=457;FractionInformativeReads=1;MQ=60;set=variant5-variant7-variant14-variant23-variant25-variant29-variant35-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:42,43:85:99:1358,0,1153:11,31,8,35 chr1 154523588 . T G 1141.54 PASS AC=2;AF=0.943;AN=2;DP=1427;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1671,123,0:0,0,4,37 chr1 154524973 . A G 2513.9 PASS AC=1;AF=0.604;AN=2;DP=4312;MQ=60;set=variant3-variant4-variant5-variant7-variant9-variant12-variant15-variant18-variant20-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant32-variant35-variant36-variant37-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:115,87:202:99:2134,0,2638:58,57,34,53 chr1 154528053 . G A 1382.25 PASS AC=1;AF=0.55;AN=2;DP=1058;FractionInformativeReads=1;MQ=60;set=variant5-variant7-variant14-variant23-variant25-variant29-variant35-variant37-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:52,48:100:99:1161,0,1150:26,26,23,25 chr1 154528086 . T C 3091.54 PASS AC=2;AF=0.943;AN=2;DP=4090;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,69:69:99:2149,207,0:0,0,30,39 chr1 154540865 . G T 310.59 PASS AC=1;AF=0.5;AN=2;DP=27;FS=0;FractionInformativeReads=0.963;MQ=60;MQRankSum=0.205;QD=11.5;ReadPosRankSum=2.205;SOR=0.693;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:13,13:26:99:339,0,340:4,9,4,9 chr1 154544662 . G A 622.18 PASS AC=1;AF=0.5;AN=2;DP=180;FractionInformativeReads=1;MQ=60;set=variant16-variant20-variant35 GT:AD:DP:GQ:PL:SB 0/1:22,31:53:99:932,0,597:10,12,10,21 chr1 154548721 . T C 2091.05 PASS AC=2;AF=0.826;AN=2;DP=3402;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,88:88:99:2911,264,0:0,0,37,51 chr1 154551368 . G A 655.63 PASS AC=1;AF=0.533;AN=2;DP=913;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant7-variant8-variant9-variant11-variant13-variant14-variant18-variant19-variant24-variant35-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:22,43:65:99:1053,0,545:11,11,19,24 chr1 154554951 . A AGGGGCATG 4821.24 PASS AC=2;AF=0.943;AN=2;DP=6112;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,123:123:99:5476,370,0:0,0,53,70 chr1 154555492 . T C 974.68 PASS AC=2;AF=0.738;AN=2;DP=1512;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1167,102,0:0,0,22,12 chr1 154556266 . G A 1350.4 PASS AC=2;AF=0.738;AN=2;DP=1754;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1041,101,0:0,0,19,15 chr1 154556425 . G A 650.58 PASS AC=1;AF=0.662;AN=2;DP=1822;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant14-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,27:49:99:655,0,597:10,12,14,13 chr1 154556663 . G A 787.03 PASS AC=1;AF=0.662;AN=2;DP=2447;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant14-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,27:61:99:654,0,972:13,21,12,15 chr1 154557685 . C T 971.02 PASS AC=1;AF=0.662;AN=2;DP=3616;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant14-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,69:134:99:1764,0,1655:37,28,46,23 chr1 154559036 . G C 289.98 PASS AC=2;AF=0.955;AN=2;DP=403;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:309,21,0:0,0,1,6 chr1 154561192 . G A 626.42 PASS AC=1;AF=0.5;AN=2;DP=68;FS=3.357;FractionInformativeReads=1;MQ=60;MQRankSum=-1.066;QD=9.21;ReadPosRankSum=-0.657;SOR=1.186;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:39,29:68:99:655,0,1014:19,20,11,18 chr1 154561261 . G C 2516.78 PASS AC=2;AF=0.943;AN=2;DP=2998;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,67:67:99:2132,201,0:0,0,30,37 chr1 154562617 . A AC,ACC 661.9 PASS AC=1,0;AF=0.421,0.079;AN=2;DP=1845;MQ=60;set=variant3-variant4-variant7-variant10-variant11-variant15-variant19-variant26-variant27-variant32-variant34-variant35-variant36-variant37-variant38-variant40-filterInvariant41-variant42-variant44 GT:DP:GQ:SB 0/1:73:99:24,24,7,18 chr1 154562625 . G C 1374.71 PASS AC=2;AF=0.875;AN=2;DP=4206;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:7,72:79:45:1878,45,0:4,3,28,44 chr1 154571174 . T TGGA 592.49 PASS AC=2;AF=0.989;AN=2;DP=604;FS=0;MQ=60;MQRankSum=0.751;ReadPosRankSum=0.751;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:667,45,0:0,0,3,12 chr1 154573967 . T C 5124.46 PASS AC=2;AF=0.726;AN=2;DP=6741;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,170:170:99:5504,508,0:0,0,82,88 chr1 154574820 . T C 2977.94 PASS AC=2;AF=1;AN=2;DP=5799;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,141:141:99:4413,422,0:0,0,72,69 chr1 154575040 . C T 3231.03 PASS AC=2;AF=1;AN=2;DP=5191;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,109:109:99:3374,327,0:0,0,55,54 chr1 154580458 . C A 1994.47 PASS AC=1;AF=0.553;AN=2;DP=5011;MQ=60;set=variant-variant2-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant19-variant24-variant33-variant34-variant35-variant37-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:138,125:263:99:2880,0,3136:68,70,58,67 chr1 154600372 . A G 3432.51 PASS AC=2;AF=1;AN=2;DP=5735;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,153:153:99:5030,461,0:0,0,81,72 chr1 154600394 . T C 380.44 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=547;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:99,29:128:99:247,0,3887:14,85,29,0 chr1 154600401 . A C 73.69 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=3833;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:106,39:145:99:872,0,3434:17,89,39,0 chr1 154600405 . T C 292.22 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=4080;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:112,37:149:99:859,0,3506:20,92,37,0 chr1 154600411 . A C 215.98 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=3003;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:136,25:161:99:112,0,5388:37,99,25,0 chr1 154600414 . A C 206.98 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=1604;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:138,25:163:99:115,0,5366:37,101,25,0 chr1 154679901 . CT CTT,C 109.63 PASS AC=1,0;AF=0.611,0.037;AN=2;DP=318;set=variant2-variant3-variant4-variant8-variant9-variant10-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant39-variant41-variant44 GT:DP:GQ:SB 0/1:17:83:4,2,9,2 chr1 154709682 . TG T,TGG 226.16 PASS AC=1,0;AF=0.742,0.048;AN=2;DP=655;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant21-variant22-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant37-variant39-variant40-variant42 GT:DP:GQ:SB 0/1:21:99:5,3,6,7 chr1 154744807 . C G,T 4201.69 PASS AC=1,0;AF=0.694,0.014;AN=2;DP=6275;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant42-variant44 GT:DP:GQ:SB 0/1:191:99:42,64,27,58 chr1 154744852 . A G 2723.32 PASS AC=2;AF=0.756;AN=2;DP=4531;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,129:129:99:4371,387,0:0,0,46,83 chr1 154832290 . C T 2147.61 PASS AC=1;AF=0.607;AN=2;DP=2423;MQ=60;set=variant4-variant7-variant11-variant17-variant19-variant22-variant32-variant34-variant35-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:113,100:213:99:2450,0,4007:46,67,41,59 chr1 154832304 . T C 6867.94 PASS AC=1;AF=0.744;AN=2;DP=6174;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:92,93:185:99:2520,0,3498:40,52,33,60 chr1 154832322 . A C 5906.09 PASS AC=2;AF=0.942;AN=2;DP=6036;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,146:146:99:5668,445,0:0,0,51,95 chr1 154840516 . C A 1018.26 PASS AC=1;AF=0.692;AN=2;DP=2571;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant19-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:55,49:104:99:1217,0,1408:30,25,27,22 chr1 154841415 . TCTCTCTCTCTCACA T 167.92 PASS AC=1;AF=0.7;AN=2;DP=489;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant19-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant33-variant34-variant35-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,5:14:99:183,0,529:7,2,5,0 chr1 154842199 . GGCTGCTGCT GGCTGCTGCTGCTGCTGCTGCT,GGCTGCTGCTGCTGCTGCTGCTGCTGCT,GGCTGCTGCTGCTGCTGCTGCTGCTGCTGCT,GGCTGCTGCTGCTGCTGCTGCTGCT,GGCTGCT,G,GGCTGCTGCTGCTGCT,GGCTGCTGCTGCTGCTGCT,GGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCT 2072.81 PASS AC=0,0,0,1,0,0,1,0,0;AF=0.182,0.091,0.045,0.386,0.102,0.011,0.034,0.091,0.011;AN=2;DP=4436;set=Intersection GT:DP:GQ:SB 7/4:41:99:0,0,15,26 chr1 154909268 . A G 1499.6 PASS AC=1;AF=0.677;AN=2;DP=5266;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:76,112:188:99:2907,0,1902:32,44,45,67 chr1 154916992 . T TA 87.09 PASS AC=1;AF=0.63;AN=2;DP=821;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant19-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:14,11:25:99:196,0,314:7,7,8,3 chr1 154917314 . G A 830.93 PASS AC=1;AF=0.667;AN=2;DP=2350;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:58,37:95:99:854,0,1559:33,25,16,21 chr1 154917701 . A G 870.51 PASS AC=2;AF=0.92;AN=2;DP=2693;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,81:81:99:2530,243,0:0,0,30,51 chr1 154919080 . C T 693.91 PASS AC=1;AF=0.667;AN=2;DP=3923;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:81,69:150:99:1729,0,2152:39,42,30,39 chr1 154930303 . T C 838.92 PASS AC=1;AF=0.625;AN=2;DP=140;FractionInformativeReads=1;MQ=60;set=variant12-variant29-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:21,22:43:99:610,0,528:9,12,12,10 chr1 154941593 . C G 130.13 PASS AC=1;AF=0.648;AN=2;DP=473;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant19-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,12:20:99:293,0,180:5,3,8,4 chr1 154965908 . A C 309.39 PASS AC=1;AF=0.5;AN=2;DP=185;MQ=60;set=variant4-variant8-variant9-variant11-variant17-variant21-variant25-variant35-variant36-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,14:31:99:400,0,945:9,8,14,0 chr1 154965912 . T C 306.38 PASS AC=1;AF=0.5;AN=2;DP=205;MQ=60;set=variant4-variant8-variant9-variant11-variant21-variant25-variant31-variant35-variant36-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,14:31:99:394,0,1014:9,8,14,0 chr1 154965916 . A C 30.05 PASS AC=1;AF=0.5;AN=2;DP=127;MQ=60;set=filterInvariant4-variant8-filterInvariant21-variant25-variant35-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,11:32:99:225,0,1078:12,9,11,0 chr1 154983539 . C T 708.19 PASS AC=1;AF=0.704;AN=2;DP=746;MQ=60;set=variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant19-variant22-variant23-variant25-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,13:34:99:265,0,619:9,12,5,8 chr1 154987526 . C T 2344.39 PASS AC=1;AF=0.69;AN=2;DP=6755;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant22-variant23-variant24-variant25-variant29-variant30-variant31-variant33-variant34-variant35-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:153,145:298:99:3278,0,3732:82,71,79,66 chr1 154988957 . A G 2153.8 PASS AC=2;AF=0.788;AN=2;DP=5719;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,169:169:99:5266,505,0:0,0,71,98 chr1 154989595 . T C 1252.79 PASS AC=2;AF=0.779;AN=2;DP=2975;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,103:103:99:3407,309,0:0,0,53,50 chr1 154995503 . G A 524.44 PASS AC=1;AF=0.69;AN=2;DP=1264;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant22-variant23-variant24-variant25-variant29-variant30-variant31-variant33-variant34-variant35-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:26,20:46:99:547,0,671:16,10,14,6 chr1 154995920 . G A 555.4 PASS AC=1;AF=0.5;AN=2;DP=186;FractionInformativeReads=1;MQ=60;set=variant7-variant17-variant35 GT:AD:DP:GQ:PL:SB 0/1:24,29:53:99:645,0,581:11,13,14,15 chr1 155001929 . T C 838.82 PASS AC=1;AF=0.646;AN=2;DP=1471;MQ=60;set=variant-variant2-variant3-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant22-variant23-variant24-variant25-variant29-variant30-variant31-variant34-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:23,32:55:99:839,0,598:8,15,11,21 chr1 155003954 . G A 181.82 PASS AC=1;AF=0.545;AN=2;DP=268;FractionInformativeReads=1;MQ=60;set=variant4-variant7-variant9-variant17-variant21-variant22-variant27-variant35-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:16,10:26:99:298,0,530:7,9,4,6 chr1 155003991 . T TTCC,TTCCCC,TTC,TTCCCCC,TTCCC 89.63 PASS AC=0,1,0,0,0;AF=0.147,0.088,0.029,0.176,0.059;AN=2;DP=421;set=variant2-variant3-variant6-variant8-variant10-variant11-variant13-variant21-variant26-variant28-variant29-variant33-variant34-filterInvariant35-variant36-variant38-variant42 GT:DP:GQ:SB 0/2:28:97:6,15,7,0 chr1 155003995 . A C 46.08 PASS AC=1;AF=0.5;AN=2;DP=814;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-filterInvariant11-variant12-variant13-filterInvariant15-variant17-variant19-variant21-variant22-variant25-variant26-variant27-variant28-filterInvariant29-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:24,10:34:99:285,0,898:7,17,10,0 chr1 155004000 . A C 71.65 PASS AC=1;AF=0.5;AN=2;DP=987;set=variant2-filterInvariant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant17-variant19-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant33-variant34-variant35-filterInvariant36-variant38-variant39-variant40-variant41-filterInvariant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:30,8:38:99:218,0,1269:12,18,8,0 chr1 155004005 . A C 41.99 PASS AC=1;AF=0.5;AN=2;DP=1119;set=filterInvariant2-filterInvariant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant17-variant19-variant21-filterInvariant22-variant23-variant26-variant28-variant29-variant33-variant34-variant35-variant38-filterInvariant39-filterInvariant40-variant41-filterInvariant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:34,10:44:99:264,0,1090:15,19,10,0 chr1 155006091 . A G 1040.09 PASS AC=1;AF=0.64;AN=2;DP=4927;MQ=60;set=variant-variant2-variant3-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant22-variant23-variant24-variant25-variant29-variant30-variant31-variant34-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:105,97:202:99:2243,0,2432:51,54,50,47 chr1 155006999 . C T 2255.89 PASS AC=1;AF=0.64;AN=2;DP=4517;MQ=60;set=variant-variant2-variant3-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant22-variant23-variant24-variant25-variant29-variant30-variant31-variant34-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:109,93:202:99:2393,0,2771:52,57,46,47 chr1 155007293 . C T 235.59 PASS AC=1;AF=0.64;AN=2;DP=401;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant22-variant23-variant24-variant25-variant29-variant30-variant31-variant34-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,5:16:99:177,0,698:2,9,1,4 chr1 155007302 . C A 235.59 PASS AC=1;AF=0.64;AN=2;DP=331;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant22-variant23-variant24-variant25-variant29-variant30-variant31-variant34-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:10,4:14:99:138,0,674:2,8,1,3 chr1 155019710 . A C 1270.49 PASS AC=1;AF=0.64;AN=2;DP=2820;MQ=60;set=variant-variant2-variant3-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant22-variant23-variant24-variant25-variant29-variant30-variant31-variant34-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:73,48:121:99:1073,0,1691:38,35,28,20 chr1 155021893 . AT A,ATT,ATTT 216.1 PASS AC=0,1,0;AF=0.188,0.328,0.016;AN=2;DP=1095;set=variant-variant2-filterInvariant3-variant5-variant6-variant7-filterInvariant8-variant9-variant10-variant11-variant12-variant14-filterInvariant15-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant25-variant27-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant43 GT:DP:GQ:SB 0/2:24:99:2,5,1,16 chr1 155023634 . G A 165.89 PASS AC=1;AF=0.533;AN=2;DP=157;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant7-variant8-variant10-variant15-variant17-variant20-variant22-variant25-variant26-variant28-variant31-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:99:112,0,108:1,3,1,3 chr1 155025361 . T C 111.86 PASS AC=1;AF=0.542;AN=2;DP=236;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant7-variant8-variant10-variant15-variant19-variant22-variant25-variant31-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:15,17:32:99:422,0,464:3,12,6,11 chr1 155026114 . C T 251.59 PASS AC=1;AF=0.718;AN=2;DP=1203;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,14:39:99:402,0,938:5,20,3,11 chr1 155026942 . A C 1449.58 PASS AC=2;AF=0.86;AN=2;DP=3265;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,89:89:99:2847,267,0:0,0,42,47 chr1 155028522 . G A 1490.7 PASS AC=1;AF=0.641;AN=2;DP=6519;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant13-variant14-variant16-variant18-variant20-variant21-variant22-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:118,114:232:99:2906,0,2864:62,56,56,58 chr1 155030557 . A C 3883.48 PASS AC=1;AF=0.625;AN=2;DP=12397;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant13-variant14-variant16-variant18-variant20-variant21-variant22-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:231,228:459:99:5729,0,5606:107,124,96,132 chr1 155031376 . C T 827.64 PASS AC=1;AF=0.529;AN=2;DP=1689;MQ=60;set=variant-variant2-variant7-variant8-variant10-variant11-variant15-variant17-variant19-variant20-variant22-variant25-variant26-variant28-variant31-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:47,43:90:99:1119,0,1326:22,25,24,19 chr1 155033317 . T C 2836.76 PASS AC=2;AF=0.718;AN=2;DP=3644;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,93:93:99:3054,279,0:0,0,30,63 chr1 155033918 . C T 808.6 PASS AC=1;AF=0.5;AN=2;DP=866;MQ=60;set=variant5-variant11-variant12-variant13-variant18-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:22,37:59:99:987,0,565:14,8,22,15 chr1 155034632 . C G 438.47 PASS AC=1;AF=0.5;AN=2;DP=363;FractionInformativeReads=1;MQ=60;set=variant5-variant12-variant13-variant18-variant28-variant29-variant30-variant33-variant35-variant36-variant37-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:17,14:31:99:440,0,496:8,9,4,10 chr1 155057499 . A G,C 741.62 PASS AC=1,0;AF=0.611,0.042;AN=2;DP=2474;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:DP:GQ:SB 0/1:76:99:34,12,23,7 chr1 155059851 . A G 624.07 PASS AC=1;AF=0.633;AN=2;DP=2299;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant10-variant12-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:42,42:84:99:1091,0,866:19,23,17,25 chr1 155100265 . A G 543.4 PASS AC=1;AF=0.607;AN=2;DP=776;MQ=60;set=variant2-variant4-variant5-variant7-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant28-variant29-variant30-variant32-filterInvariant33-variant34-variant35-variant37-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:19,19:38:99:426,0,595:10,9,10,9 chr1 155106054 . A G 3686.31 PASS AC=1;AF=0.703;AN=2;DP=5306;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:81,73:154:99:2013,0,2100:43,38,39,34 chr1 155106227 . A T 5014.01 PASS AC=1;AF=0.703;AN=2;DP=6709;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:105,124:229:99:3040,0,2516:44,61,55,69 chr1 155106550 . A G 748.79 PASS AC=1;AF=0.58;AN=2;DP=2937;MQ=60;set=variant2-variant4-variant5-variant7-variant10-variant12-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant28-variant30-variant32-variant33-variant35-variant37-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:73,55:128:99:1466,0,1872:38,35,31,24 chr1 155106697 . G A 1219.94 PASS AC=1;AF=0.58;AN=2;DP=2680;MQ=60;set=variant2-variant4-variant5-variant7-variant10-variant12-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant28-variant30-variant32-variant33-variant35-variant37-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:57,50:107:99:1366,0,1582:26,31,22,28 chr1 155108287 . G A 1312.9 PASS AC=1;AF=0.58;AN=2;DP=2383;MQ=60;set=variant2-variant4-variant5-variant7-variant10-variant12-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant28-variant30-variant32-variant33-variant35-variant37-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:57,51:108:99:1342,0,1728:38,19,30,21 chr1 155108663 . A AG 437.18 PASS AC=2;AF=1;AN=2;DP=926;FS=0;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:455,45,0:0,0,14,1 chr1 155113104 . G T 619.66 PASS AC=1;AF=0.565;AN=2;DP=1403;MQ=60;set=variant2-variant5-variant7-variant10-variant12-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant28-variant30-variant32-variant33-variant35-variant37-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:24,32:56:99:778,0,731:4,20,12,20 chr1 155142210 . A G 1287.36 PASS AC=1;AF=0.625;AN=2;DP=3067;MQ=60;set=variant2-variant5-variant7-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:87,49:136:99:1223,0,2373:40,47,25,24 chr1 155142229 . G A 1217.37 PASS AC=1;AF=0.625;AN=2;DP=3076;MQ=60;set=variant2-variant5-variant7-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:83,48:131:99:1183,0,2171:37,46,26,22 chr1 155148781 . G A 277.04 PASS AC=1;AF=0.571;AN=2;DP=728;MQ=60;set=variant2-variant5-variant7-variant10-variant12-variant15-variant17-variant18-variant19-variant20-variant22-variant24-variant26-variant28-variant30-variant32-variant35-variant37-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:17,19:36:99:605,0,499:4,13,3,16 chr1 155149718 . G A 2247.16 PASS AC=1;AF=0.591;AN=2;DP=3800;MQ=60;set=variant2-variant5-variant7-variant10-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant22-variant24-variant26-variant28-variant30-variant32-variant35-variant37-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:82,104:186:99:2528,0,1926:34,48,49,55 chr1 155151219 . A C 57.19 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=133;FractionInformativeReads=1;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:47,14:61:99:404,0,1874:4,43,14,0 chr1 155151223 . A C 316.83 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=64;FS=77.239;FractionInformativeReads=0.984;MQ=60;MQRankSum=-0.919;QD=4.95;ReadPosRankSum=-0.779;SOR=5.13;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:51,12:63:99:345,0,3990:7,44,12,0 chr1 155151224 . G C 316.83 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=64;FS=73.26;FractionInformativeReads=0.984;MQ=60;MQRankSum=-0.674;QD=4.95;ReadPosRankSum=-1.111;SOR=5.13;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:51,12:63:99:345,0,3990:8,43,12,0 chr1 155151228 . A C 264.19 PASS AC=1;AF=0.5;AN=2;DP=65;FS=58.209;FractionInformativeReads=1;MQ=60;MQRankSum=-1.548;QD=4.06;ReadPosRankSum=-1.093;SOR=4.97;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:54,11:65:99:292,0,3909:12,42,11,0 chr1 155151232 . T C 249.14 PASS AC=1;AF=0.5;AN=2;DP=65;FS=54.422;FractionInformativeReads=1;MQ=60;MQRankSum=2.573;QD=3.83;ReadPosRankSum=-1.736;SOR=4.797;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:55,10:65:99:277,0,4119:12,43,10,0 chr1 155151233 . G C 249.14 PASS AC=1;AF=0.5;AN=2;DP=68;FS=54.051;FractionInformativeReads=1;MQ=60;MQRankSum=-1.307;QD=3.66;ReadPosRankSum=-1.861;SOR=4.797;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:58,10:68:99:277,0,4119:13,45,10,0 chr1 155151236 . A C 199.01 PASS AC=1;AF=0.5;AN=2;DP=71;FS=49.392;FractionInformativeReads=1;MQ=60;MQRankSum=0.256;QD=2.8;ReadPosRankSum=-2.67;SOR=4.797;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:61,10:71:99:227,0,4332:16,45,10,0 chr1 155151238 . A C 202.02 PASS AC=1;AF=0.5;AN=2;DP=72;FS=48.032;FractionInformativeReads=1;MQ=60;MQRankSum=1.604;QD=2.81;ReadPosRankSum=-3.265;SOR=4.797;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:62,10:72:99:230,0,4129:17,45,10,0 chr1 155151241 . G A,C 363.96 PASS AC=0,1;AF=0.25,0.25;AN=2;DP=107;FractionInformativeReads=1;MQ=60;set=variant30-variant35 GT:DP:GQ:SB 0/2:70:99:18,45,7,0 chr1 155151242 . T C 115.03 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=69;FS=29.497;FractionInformativeReads=1;MQ=60;MQRankSum=1.501;QD=1.67;ReadPosRankSum=-3.141;SOR=3.895;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:63,6:69:99:143,0,4177:18,45,6,0 chr1 155162067 . C T 3459.22 PASS AC=1;AF=0.661;AN=2;DP=3959;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:73,57:130:99:1526,0,2066:41,32,28,29 chr1 155172379 . G A 703.81 PASS AC=1;AF=0.661;AN=2;DP=699;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:19,13:32:99:298,0,458:11,8,6,7 chr1 155174376 . CA C,CAA 82.9 PASS AC=1,0;AF=0.262,0.262;AN=2;DP=614;MQ=60;set=variant-variant2-filterInvariant3-variant7-variant10-filterInvariant11-variant12-variant15-variant16-filterInvariant18-variant20-variant21-variant22-variant26-variant29-variant30-variant34-filterInvariant35-variant36-variant42-filterInvariant43 GT:DP:GQ:SB 0/1:26:80:12,8,4,2 chr1 155178782 . A T 1325.64 PASS AC=1;AF=0.722;AN=2;DP=4062;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,73:140:99:1903,0,1620:27,40,31,42 chr1 155181843 . G T 877.97 PASS AC=1;AF=0.661;AN=2;DP=1140;set=variant2-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:26,24:50:99:707,0,766:20,6,18,6 chr1 155182164 . C T 6099.75 PASS AC=1;AF=0.661;AN=2;DP=7509;set=variant2-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:143,135:278:99:3265,0,3511:74,69,65,70 chr1 155184975 . A G 1998.93 PASS AC=1;AF=0.736;AN=2;DP=8584;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:144,123:267:99:2991,0,3478:67,77,59,64 chr1 155186729 . T C 3823.01 PASS AC=1;AF=0.661;AN=2;DP=4642;set=variant2-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:90,100:190:99:2275,0,1893:39,51,43,57 chr1 155186742 . G A 3452.05 PASS AC=1;AF=0.571;AN=2;DP=3662;set=variant2-variant4-variant5-variant7-variant8-variant10-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant22-variant24-variant26-variant28-variant29-variant30-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:82,88:170:99:1960,0,1867:34,48,38,50 chr1 155188197 . A G 3245.55 PASS AC=1;AF=0.5;AN=2;DP=282;FS=1.431;FractionInformativeReads=1;MQ=53.76;MQRankSum=-1.064;QD=11.51;ReadPosRankSum=0.337;SOR=0.598;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:145,137:282:99:3274,0,3743:62,83,62,75 chr1 155194980 . T C 373.66 PASS AC=2;AF=0.712;AN=2;DP=225;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant15-variant18-variant19-variant20-variant21-variant22-variant24-variant28-variant29-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:91,9,0:0,0,1,2 chr1 155202689 . A C 1031.05 PASS AC=1;AF=0.579;AN=2;DP=2339;set=variant2-variant5-variant7-variant10-variant12-variant13-variant17-variant18-variant20-variant22-variant24-variant26-variant28-variant30-variant35-variant37-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:87,61:148:99:1526,0,2362:48,39,32,29 chr1 155203060 . G A 1479.86 PASS AC=1;AF=0.575;AN=2;DP=2804;set=variant2-variant5-variant7-variant10-variant12-variant13-variant17-variant18-variant20-variant22-variant24-variant26-variant28-variant30-variant35-variant37-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:63,63:126:99:1458,0,1544:28,35,26,37 chr1 155205331 . T C 87.17 PASS AC=1;AF=0.583;AN=2;DP=368;FractionInformativeReads=1;set=variant2-variant5-variant7-variant10-variant12-variant13-variant17-variant18-variant20-variant22-variant24-variant26-variant28-variant30-variant35-variant37-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,8:19:99:277,0,373:8,3,8,0 chr1 155205669 . G T 4277.23 PASS AC=2;AF=0.989;AN=2;DP=9858;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,221:221:99:6913,660,0:0,0,92,129 chr1 155206341 . T G 1220.8 PASS AC=1;AF=0.579;AN=2;DP=1669;MQ=60;set=variant2-variant5-variant7-variant10-variant12-variant13-variant17-variant18-variant20-variant22-variant24-variant26-variant28-variant30-variant35-variant37-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:48,55:103:99:1366,0,1130:19,29,19,36 chr1 155209360 . C T 61.21 PASS AC=1;AF=0.571;AN=2;DP=435;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant7-variant10-variant11-filterInvariant12-variant13-variant17-variant18-variant20-variant22-variant24-variant26-variant28-variant30-variant34-variant35-variant37-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,11:22:99:349,0,388:9,2,10,1 chr1 155218301 . G C 673.82 PASS AC=1;AF=0.5;AN=2;DP=189;FractionInformativeReads=1;MQ=60;set=variant8-variant16-variant35 GT:AD:DP:GQ:PL:SB 0/1:34,40:74:99:1131,0,882:13,21,17,23 chr1 155225072 . G A 155.15 PASS AC=1;AF=0.5;AN=2;DP=22;FS=7.384;FractionInformativeReads=1;MQ=60;MQRankSum=-0.853;QD=7.05;ReadPosRankSum=0.785;SOR=1.759;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:14,8:22:99:183,0,402:9,5,2,6 chr1 155227642 . AT A 41.99 PASS AC=1;AF=0.714;AN=2;DP=67;MQ=60;set=variant22-variant26-variant28-variant35-variant37-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:3,7:10:54:168,0,54:0,3,1,6 chr1 155230131 . C T 1179.81 PASS AC=1;AF=0.583;AN=2;DP=2247;set=variant2-variant5-variant7-variant10-variant12-variant13-variant17-variant18-variant20-variant22-variant26-variant28-variant30-variant35-variant37-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:72,80:152:99:1872,0,1801:42,30,51,29 chr1 155230705 . GT G 233.66 PASS AC=1;AF=0.588;AN=2;DP=461;MQ=60;set=variant2-variant5-variant7-variant10-variant12-variant13-variant17-variant18-variant20-variant22-variant26-variant28-variant35-variant37-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:7,11:18:99:252,0,133:2,5,2,9 chr1 155231545 . T G 766.64 PASS AC=1;AF=0.575;AN=2;DP=1240;set=variant2-variant5-variant7-variant10-variant11-variant12-variant13-variant17-variant18-variant20-variant22-variant26-variant28-variant30-variant34-variant35-variant37-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:34,28:62:99:812,0,982:8,26,7,21 chr1 155232074 . C T 936.15 PASS AC=1;AF=0.583;AN=2;DP=2075;MQ=60;set=variant2-variant5-variant7-variant10-variant12-variant13-variant17-variant18-variant20-variant22-variant26-variant28-variant30-variant35-variant37-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:48,53:101:99:1378,0,1302:25,23,25,28 chr1 155239624 . G A 1246.85 PASS AC=1;AF=0.605;AN=2;DP=1822;MQ=60;set=variant2-variant5-variant7-variant10-variant12-variant13-variant17-variant18-variant20-variant22-variant26-variant28-variant30-variant34-variant35-variant37-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:41,35:76:99:884,0,1025:15,26,13,22 chr1 155255837 . T C 623.3 PASS AC=1;AF=0.605;AN=2;DP=714;MQ=60;set=variant2-variant5-variant7-variant10-variant12-variant13-variant17-variant18-variant20-variant22-variant26-variant28-variant30-variant34-variant35-variant37-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:31,13:44:99:236,0,886:6,25,5,8 chr1 155257343 . T G 134.89 PASS AC=1;AF=0.5;AN=2;DP=54;FractionInformativeReads=1;MQ=60;set=variant7-variant17-variant35 GT:AD:DP:GQ:PL:SB 0/1:10,7:17:99:185,0,319:5,5,4,3 chr1 155257492 . C G 755.97 PASS AC=1;AF=0.605;AN=2;DP=1358;MQ=60;set=variant2-variant5-variant7-variant10-variant12-variant13-variant17-variant18-variant20-variant22-variant26-variant28-variant30-variant34-variant35-variant37-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:49,47:96:99:1326,0,1297:24,25,28,19 chr1 155258752 . G A 1924.26 PASS AC=1;AF=0.614;AN=2;DP=2642;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant7-variant10-variant11-variant12-variant13-variant17-variant18-variant20-variant22-variant26-variant28-variant30-variant32-variant34-variant35-variant37-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:69,67:136:99:2541,0,3871:35,34,37,30 chr1 155258756 . C T 1896.68 PASS AC=1;AF=0.605;AN=2;DP=2274;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant7-variant10-variant12-variant13-variant17-variant18-variant20-variant22-variant26-variant28-variant30-variant34-variant35-variant37-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:67,68:135:99:2587,0,3832:35,32,37,31 chr1 155259323 . C T 614.76 PASS AC=1;AF=0.605;AN=2;DP=884;MQ=60;set=variant2-variant5-variant7-variant10-variant12-variant13-variant17-variant18-variant20-variant22-variant26-variant28-variant30-variant34-variant35-variant37-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:36,26:62:99:636,0,923:14,22,13,13 chr1 155260096 . G A 881.57 PASS AC=1;AF=0.605;AN=2;DP=985;MQ=60;set=variant2-variant5-variant7-variant10-variant12-variant13-variant17-variant18-variant20-variant22-variant26-variant28-variant30-variant34-variant35-variant37-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:38,21:59:99:481,0,1008:20,18,9,12 chr1 155260350 . A G 1028.15 PASS AC=1;AF=0.605;AN=2;DP=1525;MQ=60;set=variant2-variant5-variant7-variant10-variant12-variant13-variant17-variant18-variant20-variant22-variant26-variant28-variant30-variant34-variant35-variant37-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:43,44:87:99:1131,0,1015:20,23,27,17 chr1 155260383 . G T 1276.01 PASS AC=1;AF=0.605;AN=2;DP=1890;MQ=60;set=variant2-variant5-variant7-variant10-variant12-variant13-variant17-variant18-variant20-variant22-variant26-variant28-variant30-variant34-variant35-variant37-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:54,55:109:99:1310,0,1129:24,30,30,25 chr1 155265177 . A G 1853.59 PASS AC=1;AF=0.619;AN=2;DP=2995;MQ=60;set=variant2-variant3-variant5-variant7-variant10-variant11-variant12-variant13-variant17-variant18-variant20-variant22-variant26-variant28-variant30-variant34-variant35-variant37-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:90,78:168:99:1974,0,2475:42,48,35,43 chr1 155269776 . A G 471.96 PASS AC=1;AF=0.625;AN=2;DP=607;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant7-variant10-variant11-variant12-variant13-variant17-variant18-variant20-variant22-variant26-variant28-variant30-variant34-variant35-variant37-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,17:28:99:541,0,284:8,3,13,4 chr1 155279482 . T G 242.35 PASS AC=1;AF=0.611;AN=2;DP=306;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant7-variant10-variant11-variant12-variant13-variant17-variant18-variant20-variant22-variant26-variant28-variant30-variant34-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:1,8:9:19:269,0,19:1,0,7,1 chr1 155280104 . CT CTT,C 1069.41 PASS AC=1,0;AF=0.283,0.217;AN=2;DP=4058;set=variant2-filterInvariant4-variant5-variant7-filterInvariant8-variant10-variant12-variant13-filterInvariant14-variant17-variant18-filterInvariant19-variant20-filterInvariant21-variant22-variant26-filterInvariant27-variant28-filterInvariant29-variant30-filterInvariant31-filterInvariant32-variant34-variant35-filterInvariant36-variant37-filterInvariant38-variant41-variant43-filterInvariant44 GT:DP:GQ:SB 0/1:86:99:9,41,10,26 chr1 155280164 . T C 717.73 PASS AC=1;AF=0.611;AN=2;DP=571;MQ=60;set=variant2-variant5-variant7-variant10-variant11-variant12-variant13-variant17-variant18-variant20-variant22-variant26-variant28-variant30-variant34-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:16,17:33:99:603,0,556:1,15,0,17 chr1 155289545 . T G 547.75 PASS AC=1;AF=0.588;AN=2;DP=1544;MQ=60;set=variant2-variant5-variant7-variant10-variant12-variant13-variant17-variant18-variant20-variant22-variant26-variant28-variant30-variant34-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:63,42:105:99:1078,0,1793:26,37,18,24 chr1 155291431 . C T 924.47 PASS AC=1;AF=0.5;AN=2;DP=873;MQ=60;set=variant2-variant7-variant8-variant12-variant16-variant17-variant22-variant30-variant34-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:53,56:109:99:1525,0,1437:33,20,39,17 chr1 155294274 . A G 3433.09 PASS AC=2;AF=1;AN=2;DP=4774;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,144:144:99:4951,431,0:0,0,51,93 chr1 155294772 . A G 2337.36 PASS AC=2;AF=0.989;AN=2;DP=3207;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,81:81:99:2777,243,0:0,0,32,49 chr1 155306151 . T TACAC 97.61 PASS AC=2;AF=1;AN=2;DP=213;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:180,12,0:0,0,3,1 chr1 155306440 . T C 1573.83 PASS AC=1;AF=0.5;AN=2;DP=136;FS=2.442;FractionInformativeReads=1;MQ=60;MQRankSum=-1.731;QD=11.57;ReadPosRankSum=-2.744;SOR=0.979;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:80,56:136:99:1602,0,2458:54,26,41,15 chr1 155311658 . C T 175.6 PASS AC=1;AF=0.5;AN=2;DP=408;MQ=60;set=variant2-variant7-variant8-variant12-variant16-variant17-variant22-variant30-variant34-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:25,20:45:99:591,0,777:19,6,16,4 chr1 155313047 . T C 976.84 PASS AC=2;AF=0.989;AN=2;DP=2047;FS=0;MQ=60;MQRankSum=0.565;ReadPosRankSum=-0.188;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1816,153,0:0,0,36,15 chr1 155408635 . T C 3821.14 PASS AC=2;AF=1;AN=2;DP=5505;FS=0;MQ=60;MQRankSum=1.344;ReadPosRankSum=0.439;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,140:140:99:4474,418,0:0,0,68,72 chr1 155429490 . A T 361.82 PASS AC=1;AF=0.579;AN=2;DP=498;MQ=60;set=variant2-variant5-variant7-variant8-variant10-variant12-variant13-variant16-variant17-variant18-variant20-variant22-variant26-variant28-variant30-variant34-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:19,11:30:99:289,0,549:14,5,9,2 chr1 155429725 . A C 340.74 PASS AC=1;AF=0.579;AN=2;DP=493;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant7-variant8-variant10-variant12-variant13-variant16-variant17-variant18-variant20-variant22-variant26-variant28-variant30-variant34-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,8:21:99:256,0,350:4,9,2,6 chr1 155532316 . T C 5127.87 PASS AC=2;AF=1;AN=2;DP=6620;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,166:166:99:7453,506,0:0,0,84,82 chr1 155532325 . T C 5261.5 PASS AC=2;AF=1;AN=2;DP=6654;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,171:171:99:8069,542,0:0,0,88,83 chr1 155532332 . T C 5168.26 PASS AC=2;AF=1;AN=2;DP=6732;FS=0;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,173:173:99:8227,557,0:0,0,90,83 chr1 155532341 . T C 4954.61 PASS AC=2;AF=1;AN=2;DP=6774;FS=0;MQRankSum=1.407;ReadPosRankSum=1.617;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,184:184:99:8050,557,0:0,0,101,83 chr1 155581311 . T C 994.29 PASS AC=1;AF=0.579;AN=2;DP=1912;set=variant2-variant5-variant7-variant8-variant10-variant12-variant13-variant16-variant17-variant18-variant20-variant22-variant26-variant28-variant30-variant34-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:41,61:102:99:1447,0,905:16,25,23,38 chr1 155581757 . A G 63.05 DRAGENHardSNP AC=2;AF=1;AN=2;DP=11;FS=0;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:85,9,0:0,0,3,0 chr1 155583937 . A G 42.2 PASS AC=1;AF=0.6;AN=2;DP=70;FS=0;FractionInformativeReads=1;set=filterInvariant5-variant10-filterInvariant20-filterInvariant22-filterInvariant26-filterInvariant28-filterInvariant34-filterInvariant35-filterInvariant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,5:9:98:106,0,98:0,4,1,4 chr1 155618415 . CT C 6911.09 PASS AC=2;AF=0.989;AN=2;DP=7735;MQRankSum=-5.776;ReadPosRankSum=1.755;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,176:176:99:6035,529,0:0,0,85,91 chr1 155630752 . A G 4648.26 PASS AC=1;AF=0.579;AN=2;DP=6459;set=variant2-variant5-variant7-variant8-variant10-variant12-variant13-variant16-variant17-variant18-variant20-variant22-variant26-variant28-variant30-variant34-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:175,181:356:99:4905,0,4390:93,82,100,81 chr1 155631307 . AACACAC AACAC,AACACACACACACAC,AACACACACACACACAC,AACACACACAC,AAC,AACACACACACAC,A,AACACACACACACACACACACAC,AACACACAC 598.48 PASS AC=0,0,1,0,0,0,0,0,0;AF=0.324,0.027,0.081,0.081,0.081,0.095,0.041,0.014,0.014;AN=2;DP=1401;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-filterInvariant19-filterInvariant21-variant22-variant23-filterInvariant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-filterInvariant38-variant40-variant41-variant44 GT:DP:GQ:SB 0/3:27:99:5,14,2,6 chr1 155640115 . C T 2414.86 PASS AC=1;AF=0.5;AN=2;DP=1220;set=variant9-variant20-variant27-variant35-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:124,123:247:99:2900,0,3042:59,65,62,61 chr1 155658085 . T C 2799.86 PASS AC=1;AF=0.583;AN=2;DP=5826;MQ=60;set=variant2-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant16-variant17-variant18-variant20-variant22-variant26-variant28-variant30-variant32-variant34-variant35-variant37-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:147,124:271:99:2835,0,3572:77,70,56,68 chr1 155658341 . T C 2200.47 PASS AC=1;AF=0.6;AN=2;DP=4096;set=variant2-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant16-variant17-variant18-variant20-variant22-variant26-variant28-variant30-variant34-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:140,99:239:99:2569,0,3478:69,71,58,41 chr1 155658940 . T G 3121.83 PASS AC=1;AF=0.556;AN=2;DP=3880;MQ=60;set=variant2-variant5-variant7-variant8-variant12-variant13-variant16-variant17-variant18-variant20-variant22-variant26-variant28-variant30-variant34-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:136,114:250:99:2694,0,3562:54,82,52,62 chr1 155686739 . CA C 34.38 PASS AC=1;AF=0.5;AN=2;DP=818;set=variant-variant2-variant4-variant5-variant6-variant7-filterInvariant8-variant9-variant10-variant11-filterInvariant12-variant15-variant16-variant17-filterInvariant18-variant19-variant20-variant21-variant22-variant25-variant26-variant28-variant32-variant33-variant35-variant36-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,12:24:99:187,0,167:7,5,10,2 chr1 155701055 . CA C,CAA 98.95 PASS AC=1,0;AF=0.385,0.115;AN=2;DP=496;set=variant6-variant8-filterInvariant11-variant16-variant22-filterInvariant24-filterInvariant25-filterInvariant30-filterInvariant31-variant32-filterInvariant35-variant40-variant42 GT:DP:GQ:SB 0/1:36:74:19,10,4,3 chr1 155702024 . C CT,CTT 185.96 PASS AC=1,0;AF=0.558,0.019;AN=2;DP=1021;set=variant-variant2-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant22-variant26-variant27-variant28-variant32-variant34-variant35-variant37-variant40-variant43-variant44 GT:DP:GQ:SB 0/1:33:99:4,11,8,10 chr1 155715641 . G A 379.15 PASS AC=1;AF=0.591;AN=2;DP=696;set=variant2-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant16-variant17-variant18-variant20-variant22-variant26-variant28-variant30-variant34-variant35-variant37-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,14:35:99:259,0,561:7,14,7,7 chr1 155719111 . A C 536.38 PASS AC=1;AF=0.5;AN=2;DP=967;FractionInformativeReads=1;set=variant5-variant13-variant18-variant20-variant22-variant28-variant32-variant35-variant37-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:58,27:85:99:571,0,1525:36,22,17,10 chr1 155722506 . C G 67.15 PASS AC=1;AF=0.635;AN=2;DP=461;FractionInformativeReads=1;set=variant-variant3-variant4-variant6-variant9-variant11-variant14-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,8:25:99:244,0,426:6,11,1,7 chr1 155724315 . GTT GTTT,GT,GTTTT,G 176.54 PASS AC=0,1,0,0;AF=0.095,0.333,0.024,0.048;AN=2;DP=874;set=variant2-variant7-variant8-variant9-variant10-filterInvariant11-filterInvariant14-variant16-filterInvariant17-filterInvariant18-filterInvariant19-variant20-filterInvariant21-filterInvariant26-variant27-variant30-variant31-variant33-variant35-variant36-variant40 GT:DP:GQ:SB 0/2:23:99:4,9,2,8 chr1 155735012 . T C 2642.6 PASS AC=1;AF=0.591;AN=2;DP=4381;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant16-variant17-variant18-variant20-variant22-variant26-variant28-variant30-variant34-variant35-variant37-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:109,106:215:99:2944,0,2704:51,58,58,48 chr1 155737385 . C T 1130.13 PASS AC=2;AF=0.989;AN=2;DP=1424;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1171,116,0:0,0,22,17 chr1 155737425 . AACACAC AAC,AACACACAC,AACAC,A 1391.16 PASS AC=1,0,0,0;AF=0.628,0.081,0.023,0.023;AN=2;DP=1380;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-filterInvariant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:40:99:8,16,6,10 chr1 155746340 . CT C 932.22 PASS AC=2;AF=0.966;AN=2;DP=2939;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,67:67:99:1872,201,0:0,0,20,47 chr1 155754117 . G A 1149.91 PASS AC=2;AF=0.966;AN=2;DP=1479;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:633,60,0:0,0,7,13 chr1 155755097 . G A 3927.49 PASS AC=2;AF=0.989;AN=2;DP=5028;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,126:127:99:4016,343,0:1,0,64,62 chr1 155783763 . C T 627.34 PASS AC=2;AF=0.943;AN=2;DP=1277;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:744,66,0:0,0,6,16 chr1 155785578 . CAACT C 5632.05 PASS AC=2;AF=0.966;AN=2;DP=5675;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,113:113:99:5035,340,0:0,0,68,45 chr1 155822971 . C T 1019.56 PASS AC=1;AF=0.744;AN=2;DP=832;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,11:22:99:304,0,419:11,0,8,3 chr1 155823002 . T C 1807.63 PASS AC=2;AF=1;AN=2;DP=1860;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1287,117,0:0,0,28,11 chr1 155829140 . C G 2625.84 PASS AC=2;AF=0.989;AN=2;DP=4456;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,88:88:99:2590,263,0:0,0,51,37 chr1 155829360 . C A 3678.89 PASS AC=2;AF=0.989;AN=2;DP=7861;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,182:182:99:5517,543,0:0,0,102,80 chr1 155829511 . C T 1811.67 PASS AC=1;AF=0.6;AN=2;DP=3652;MQ=60;set=variant2-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant16-variant17-variant18-variant22-variant26-variant28-variant30-variant34-variant35-variant37-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:131,93:224:99:2282,0,3344:66,65,47,46 chr1 155837865 . G C 4099.2 PASS AC=2;AF=0.989;AN=2;DP=7587;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,208:208:99:6344,623,0:0,0,118,90 chr1 155838267 . T C 3496.57 PASS AC=2;AF=1;AN=2;DP=7452;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,191:191:99:5743,573,0:0,0,106,85 chr1 155850558 . T C 872.02 PASS AC=1;AF=0.756;AN=2;DP=1768;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,21:34:99:698,0,354:3,10,4,17 chr1 155850811 . G A 509.68 PASS AC=1;AF=0.763;AN=2;DP=322;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,3:11:85:85,0,287:7,1,2,1 chr1 155852123 . C T 3501.29 PASS AC=1;AF=0.744;AN=2;DP=3040;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,42:77:99:1541,0,1073:17,18,28,14 chr1 155868336 . C G,A 724.91 PASS AC=2,0;AF=0.702,0.226;AN=2;DP=694;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:25:75:0,0,22,3 chr1 155868984 . T C 3565.33 PASS AC=2;AF=0.942;AN=2;DP=3596;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,106:106:99:3603,317,0:0,0,37,69 chr1 155869435 . T TA 5014.3 PASS AC=2;AF=0.737;AN=2;DP=10002;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:16,168:184:99:3970,156,0:9,7,69,99 chr1 155870416 . G A 4068.07 PASS AC=2;AF=0.942;AN=2;DP=4714;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,101:101:99:3142,303,0:0,0,43,58 chr1 155880573 . C G 3825.71 PASS AC=2;AF=0.942;AN=2;DP=7056;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,188:188:99:5781,561,0:0,0,80,108 chr1 155880760 . C CA 1478.69 PASS AC=2;AF=0.93;AN=2;DP=2357;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1843,138,0:0,0,14,32 chr1 155880952 . G A 260.77 PASS AC=2;AF=0.794;AN=2;DP=320;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:129,15,0:0,0,1,4 chr1 155884832 . TTC T 240.39 DRAGENHardINDEL AC=1;AF=0.5;AN=2;DP=1678;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:161,18:179:99:146,0,5488:56,105,9,9 chr1 155891045 . A C 1409.45 PASS AC=2;AF=0.757;AN=2;DP=1337;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:979,90,0:0,0,20,10 chr1 155891877 . C CAG 490.13 PASS AC=2;AF=1;AN=2;DP=955;FS=0;MQRankSum=-1.404;ReadPosRankSum=1.404;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,27:27:84:1206,84,0:0,0,2,25 chr1 155899020 . A T 1701.22 PASS AC=2;AF=0.75;AN=2;DP=2173;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:1740,180,0:0,0,37,23 chr1 155903310 . T C 911.08 PASS AC=2;AF=1;AN=2;DP=1268;FS=0;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:897,69,0:0,0,20,3 chr1 155903408 . C T 2742.04 PASS AC=2;AF=0.75;AN=2;DP=3241;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,93:93:99:2779,278,0:0,0,53,40 chr1 155904177 . T C 7773.81 PASS AC=2;AF=0.942;AN=2;DP=17083;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,479:479:99:14204,1434,0:0,0,272,207 chr1 155904392 . G A 144.21 PASS AC=2;AF=0.942;AN=2;DP=1254;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1402,111,0:0,0,3,34 chr1 155912486 . T C 10817.5 PASS AC=2;AF=1;AN=2;DP=13870;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,348:348:99:10247,1042,0:0,0,153,195 chr1 155917880 . T A 1890.63 PASS AC=2;AF=0.93;AN=2;DP=6583;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,159:159:99:4414,473,0:0,0,70,89 chr1 155920280 . A G 998.33 PASS AC=1;AF=0.5;AN=2;DP=655;FractionInformativeReads=1;MQ=60;set=variant9-variant20-variant22-variant27-variant35-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,62:118:99:1586,0,1326:25,31,30,32 chr1 155928232 . T C 1685.8 PASS AC=2;AF=0.93;AN=2;DP=1594;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1495,102,0:0,0,10,23 chr1 155928242 . C T 1522.77 PASS AC=2;AF=0.942;AN=2;DP=1393;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:1297,87,0:0,0,10,19 chr1 155931368 . G A 558.76 PASS AC=2;AF=0.763;AN=2;DP=1481;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1755,167,0:0,0,38,18 chr1 155947875 . A G 2954.55 PASS AC=2;AF=0.808;AN=2;DP=5437;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,142:143:99:3981,385,0:1,0,67,75 chr1 155954084 . C G 597.02 PASS AC=1;AF=0.5;AN=2;DP=381;MQ=60;set=variant9-variant22-variant27-variant35-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,23:57:99:445,0,925:24,10,13,10 chr1 155955076 . A G 1479.3 PASS AC=2;AF=1;AN=2;DP=3029;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:2021,204,0:0,0,42,26 chr1 155981489 . C G 1348.09 PASS AC=2;AF=0.718;AN=2;DP=2897;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,92:92:99:2820,275,0:0,0,53,39 chr1 156011444 . T C 4095.02 PASS AC=1;AF=0.718;AN=2;DP=6475;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:88,70:158:99:1589,0,2017:47,41,36,34 chr1 156013718 . A AC 1076.41 PASS AC=1;AF=0.5;AN=2;DP=171;FS=0;MQ=60;set=variant5-variant35 GT:AD:DP:GQ:PL:SB 0/1:55,31:86:99:751,0,1559:28,27,16,15 chr1 156021079 . G A 1630.13 PASS AC=1;AF=0.5;AN=2;DP=304;FractionInformativeReads=1;MQ=60;set=variant5-variant35 GT:AD:DP:GQ:PL:SB 0/1:93,87:180:99:1896,0,2433:37,56,45,42 chr1 156040310 . A G 1113.09 PASS AC=1;AF=0.875;AN=2;DP=1227;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,28:40:99:764,0,267:3,9,12,16 chr1 156044938 . C G 601.45 PASS AC=1;AF=0.583;AN=2;DP=966;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant12-variant15-variant18-variant19-variant21-variant27-variant28-variant32-variant34-variant35-variant36-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,30:61:99:711,0,835:17,14,18,12 chr1 156045183 . T A 348.85 PASS AC=1;AF=0.559;AN=2;DP=791;MQ=60;set=variant-variant2-variant5-variant6-variant12-variant15-variant18-variant19-variant21-variant27-variant28-variant32-variant35-variant36-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,31:62:99:864,0,715:15,16,17,14 chr1 156045662 . A G 346.87 PASS AC=1;AF=0.672;AN=2;DP=1956;MQ=60;set=variant-variant2-variant5-variant6-variant10-variant11-variant12-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant30-variant32-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,38:73:99:938,0,947:19,16,21,17 chr1 156045973 . C T 236.99 PASS AC=1;AF=0.559;AN=2;DP=598;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant12-variant15-variant18-variant19-variant21-variant27-variant28-variant32-variant35-variant36-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,23:39:99:649,0,443:9,7,11,12 chr1 156052286 . A G 1191.31 PASS AC=2;AF=1;AN=2;DP=1648;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1266,108,0:0,0,26,10 chr1 156109951 . TACACACACACACACAC TACACACACACACACACACACACACACACACACAC,TACACACACACACAC,TACACACACACACACACACACACACACACACAC,TACACAC,TACACACACACACACACAC,TACACACACACACACACACACACACACACAC,TACACACACACAC,TACACACACACACACACACAC,TACACACACAC,TACACACAC,TACACACACACACACACACACACACAC,TACACACACACACACACACACACACACAC,T,TACACACACACACACACACACAC 165.3 PASS AC=0,0,0,0,0,0,0,0,0,0,1,1,0,0;AF=0.196,0.054,0.071,0.036,0.036,0.071,0.143,0.036,0.054,0.054,0.018,0.018,0.018,0.018;AN=2;DP=478;set=variant2-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant20-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant42-variant43-variant44 GT:DP:GQ:SB 11/12:9:78:0,0,4,5 chr1 156132909 . GCA G 1839.67 PASS AC=1;AF=0.571;AN=2;DP=2829;MQ=60;set=variant-variant2-variant5-variant6-variant10-variant13-variant15-variant18-variant19-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant35-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,69:134:99:2676,0,2539:30,35,36,33 chr1 156133038 . T C 750.81 PASS AC=1;AF=0.6;AN=2;DP=1823;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant16-variant17-variant21-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:43,33:76:99:747,0,1196:19,24,14,19 chr1 156146218 . C T 2292.56 PASS AC=2;AF=0.684;AN=2;DP=3427;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,96:96:99:2932,287,0:0,0,62,34 chr1 156147326 . T C 1352.98 PASS AC=2;AF=0.621;AN=2;DP=1749;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant10-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant35-variant37-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,82:82:99:2730,245,0:0,0,34,48 chr1 156147558 . C T 324.76 PASS AC=2;AF=0.617;AN=2;DP=338;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant35-variant37-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:450,45,0:0,0,5,10 chr1 156163906 . C T 1412.9 PASS AC=1;AF=0.54;AN=2;DP=2711;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant10-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant30-variant32-variant35-variant36-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,55:98:99:1401,0,1078:26,17,29,26 chr1 156169610 . A G 898.96 PASS AC=1;AF=0.548;AN=2;DP=3771;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,44:112:99:1128,0,1750:44,24,32,12 chr1 156180847 . TTGTGTGTGTGTGTGTGTGTG TTGTGTGTGTGTGTGTGTGTGTG,TTGTGTGTGTGTGTGTGTGTGTGTGTG,TTGTGTGTGTGTGTGTGTG,TTGTGTGTGTGTGTGTGTGTGTGTG,TTGTGTGTGTGTGTG,T,TTGTGTGTGTGTGTGTGTGTGTGTGTGTG,TTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 76.8 PASS AC=1,0,0,0,0,0,0,0;AF=0.382,0.105,0.039,0.079,0.026,0.013,0.026,0.013;AN=2;DP=1070;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-filterInvariant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:16:33:2,1,7,6 chr1 156181007 . C G 411.34 PASS AC=1;AF=0.548;AN=2;DP=1351;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,17:50:99:485,0,917:19,14,9,8 chr1 156181615 . AC A 648.61 PASS AC=1;AF=0.54;AN=2;DP=1305;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant10-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant30-variant32-variant35-variant36-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,20:42:99:681,0,750:13,9,8,12 chr1 156181770 . A G 675.07 PASS AC=1;AF=0.548;AN=2;DP=2250;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,36:71:99:901,0,1060:19,16,23,13 chr1 156182710 . T C 109.13 PASS AC=1;AF=0.548;AN=2;DP=775;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,10:27:99:247,0,511:9,8,7,3 chr1 156195205 . C T 838.93 PASS AC=1;AF=0.537;AN=2;DP=803;set=variant-variant3-variant5-variant6-variant7-variant8-variant10-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant30-variant31-variant32-variant35-variant36-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,14:33:99:519,0,598:15,4,14,0 chr1 156202173 . A G 2089.64 PASS AC=1;AF=0.578;AN=2;DP=5799;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:93,85:178:99:1902,0,2465:51,42,41,44 chr1 156206121 . G A 2788.98 PASS AC=1;AF=0.56;AN=2;DP=7582;MQ=60;set=variant-variant6-variant7-variant10-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant38-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:197,164:361:99:3659,0,4635:104,93,83,81 chr1 156209857 . C T 127.4 PASS AC=1;AF=0.533;AN=2;DP=506;MQ=60;set=variant-variant4-variant5-variant7-variant14-variant19-variant20-variant32-variant33-variant35-variant36-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:27,23:50:99:498,0,610:11,16,8,15 chr1 156213257 . G A 582.57 PASS AC=1;AF=0.756;AN=2;DP=1933;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,26:45:99:727,0,469:13,6,17,9 chr1 156213921 . C T 2672.34 PASS AC=1;AF=0.536;AN=2;DP=3051;MQ=60;set=variant-variant4-variant5-variant7-variant19-variant20-variant32-variant33-variant35-variant36-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:146,96:242:99:2449,0,3823:72,74,48,48 chr1 156215899 . G A 1085.4 PASS AC=1;AF=0.595;AN=2;DP=5039;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:86,90:176:99:2098,0,2087:47,39,48,42 chr1 156219450 . A G 511.14 PASS AC=1;AF=0.595;AN=2;DP=2594;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,34:62:99:775,0,634:12,16,17,17 chr1 156220056 . T C 2185.13 PASS AC=1;AF=0.583;AN=2;DP=4998;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:90,64:154:99:1653,0,2302:58,32,41,23 chr1 156222366 . T A 304.74 PASS AC=1;AF=0.5;AN=2;DP=37;FS=1.257;FractionInformativeReads=1;MQ=60;MQRankSum=0.659;QD=8.24;ReadPosRankSum=2.56;SOR=0.498;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:21,16:37:99:333,0,534:8,13,7,9 chr1 156230002 . G A 156.08 PASS AC=1;AF=0.583;AN=2;DP=115;MQ=60;set=variant-variant4-variant5-variant7-variant14-variant19-variant20-variant33-variant35-variant36-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:5,3:8:99:103,0,159:3,2,3,0 chr1 156230141 . T A 711.28 PASS AC=1;AF=0.533;AN=2;DP=749;MQ=60;set=variant-variant4-variant5-variant7-variant14-variant19-variant20-variant32-variant33-variant35-variant36-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:21,34:55:99:953,0,557:15,6,24,10 chr1 156230206 . C A 718.09 PASS AC=1;AF=0.533;AN=2;DP=1166;MQ=60;set=variant-variant4-variant5-variant7-variant14-variant19-variant20-variant32-variant33-variant35-variant36-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:26,50:76:99:1405,0,639:15,11,30,20 chr1 156230605 . C G 245.12 PASS AC=1;AF=0.533;AN=2;DP=266;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant7-variant14-variant19-variant20-variant32-variant33-variant35-variant36-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:6,11:17:99:356,0,135:2,4,2,9 chr1 156231266 . G C 79.7 PASS AC=1;AF=0.533;AN=2;DP=620;MQ=60;set=variant-variant4-variant5-variant7-variant14-variant19-variant20-variant32-variant33-variant35-variant36-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:34,6:40:99:133,0,965:12,22,0,6 chr1 156233479 . T C 121.45 PASS AC=1;AF=0.533;AN=2;DP=374;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant7-variant14-variant19-variant20-variant32-variant33-variant35-variant36-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:12,21:33:99:559,0,301:3,9,7,14 chr1 156236592 . CTT C,CT 99.73 PASS AC=0,1;AF=0.019,0.481;AN=2;DP=1252;set=variant-variant2-variant4-variant5-variant7-variant14-filterInvariant17-filterInvariant18-variant19-variant20-filterInvariant22-filterInvariant25-filterInvariant28-filterInvariant29-filterInvariant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-filterInvariant43-filterInvariant44 GT:DP:GQ:SB 0/2:31:99:4,12,2,13 chr1 156247907 . C T 395.6 PASS AC=1;AF=0.568;AN=2;DP=412;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant10-variant11-variant13-variant14-variant15-variant18-variant19-variant22-variant24-variant26-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,4:10:99:109,0,245:0,6,2,2 chr1 156255833 . G C 422.99 PASS AC=2;AF=1;AN=2;DP=1092;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:858,75,0:0,0,7,18 chr1 156261491 . G C 1027.81 PASS AC=1;AF=0.542;AN=2;DP=1212;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant7-variant14-variant19-variant32-variant33-variant35-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:69,55:124:99:1269,0,1939:28,41,24,31 chr1 156262167 . AGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT AGTGTGTGTGTGTGTGT,AGTGTGTGTGTGTGTGTGTGTGTGTGTGT,AGTGTGTGTGTGTGTGTGTGTGT,AGTGTGTGTGTGTGTGTGTGTGTGT,AGTGT,AGTGTGTGTGTGTGT,AGTGTGTGTGTGTGTGTGTGTGTGTGT,A,AGTGTGTGTGTGTGTGTGT,AGTGTGTGTGTGTGTGTGTGT 302.36 PASS AC=1,1,0,0,0,0,0,0,0,0;AF=0.268,0.22,0.159,0.085,0.012,0.024,0.024,0.024,0.024,0.024;AN=2;DP=1301;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-filterInvariant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/2:18:99:0,1,4,13 chr1 156279210 . T C 2222.81 PASS AC=2;AF=1;AN=2;DP=3229;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,80:80:99:2754,240,0:0,0,23,57 chr1 156280296 . GATAA G 193.45 PASS AC=1;AF=0.575;AN=2;DP=249;MQ=60;set=variant-variant6-variant11-variant13-variant14-variant15-variant18-variant22-variant24-variant26-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,5:9:99:170,0,150:4,0,4,1 chr1 156282224 . A G 66.22 PASS AC=2;AF=0.865;AN=2;DP=235;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:279,24,0:0,0,3,5 chr1 156287360 . C T 775.81 PASS AC=1;AF=0.565;AN=2;DP=1411;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant10-variant11-variant13-variant14-variant15-variant18-variant19-variant22-variant24-variant26-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant37-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,42:76:99:1059,0,753:14,20,17,25 chr1 156287403 . T C 683.2 PASS AC=1;AF=0.574;AN=2;DP=1362;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,17:50:99:409,0,869:12,21,5,12 chr1 156288906 . G GT 100.92 PASS AC=1;AF=0.524;AN=2;DP=655;set=variant7-variant8-variant9-variant10-filterInvariant11-variant12-variant13-variant16-variant17-filterInvariant19-variant20-variant22-variant24-variant25-variant27-variant30-variant35-filterInvariant37-filterInvariant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,8:22:99:110,0,232:1,13,3,5 chr1 156303527 . C T,A 568.37 PASS AC=1,0;AF=0.548,0.024;AN=2;DP=594;MQ=60;set=variant-variant6-variant10-variant11-variant13-variant14-variant15-variant18-variant19-variant22-variant24-variant26-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant42-variant44 GT:DP:GQ:SB 0/1:36:99:6,12,7,11 chr1 156304782 . A G 160.08 PASS AC=1;AF=0.574;AN=2;DP=665;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,6:20:94:94,0,516:1,13,2,4 chr1 156307593 . C CA 843.12 PASS AC=1;AF=0.538;AN=2;DP=1264;set=variant-variant4-variant5-variant6-variant7-variant14-variant19-variant32-variant33-variant35-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:44,41:85:99:903,0,986:13,31,14,27 chr1 156347131 . G A 7369.35 PASS AC=2;AF=0.652;AN=2;DP=7431;MQ=60;set=variant-variant2-variant4-variant7-variant12-variant14-variant15-variant16-variant18-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,378:378:99:10875,1126,0:0,0,195,183 chr1 156348344 . C T 582.1 PASS AC=2;AF=0.652;AN=2;DP=621;MQ=60;set=variant-variant2-variant4-variant7-variant12-variant14-variant15-variant16-variant18-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:758,78,0:0,0,10,16 chr1 156351066 . C A 5962.56 PASS AC=2;AF=0.652;AN=2;DP=4320;MQ=60;set=variant-variant2-variant4-variant7-variant12-variant14-variant15-variant16-variant18-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,160:160:99:4824,478,0:0,0,94,66 chr1 156374256 . C T 597.74 PASS AC=1;AF=0.522;AN=2;DP=1531;MQ=60;set=variant-variant4-variant6-variant7-variant11-variant15-variant16-variant17-variant18-variant20-variant22-variant24-variant25-variant28-variant31-variant32-variant34-variant35-variant37-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:43,28:71:99:695,0,970:24,19,18,10 chr1 156376680 . A G 379.68 PASS AC=2;AF=1;AN=2;DP=445;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:397,33,0:0,0,9,2 chr1 156434703 . G T 1495 PASS AC=2;AF=0.733;AN=2;DP=2427;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:1961,180,0:0,0,31,29 chr1 156435151 . C T 749.38 PASS AC=1;AF=0.5;AN=2;DP=128;FractionInformativeReads=1;MQ=60;set=variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,33:62:99:778,0,693:15,14,18,15 chr1 156446242 . C A 3100.41 PASS AC=2;AF=0.733;AN=2;DP=6790;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,181:181:99:5346,540,0:0,0,115,66 chr1 156446450 . C T 1702.92 PASS AC=2;AF=0.733;AN=2;DP=2317;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,66:66:99:2294,196,0:0,0,13,53 chr1 156446903 . T C 3769.86 PASS AC=2;AF=0.733;AN=2;DP=5800;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,144:144:99:4261,431,0:0,0,66,78 chr1 156450740 . G A 3131.12 PASS AC=2;AF=0.733;AN=2;DP=5019;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,125:125:99:3867,374,0:0,0,54,71 chr1 156450873 . T C 663.47 PASS AC=2;AF=0.761;AN=2;DP=1206;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1172,105,0:0,0,9,26 chr1 156452870 . G A 1570.29 PASS AC=2;AF=0.733;AN=2;DP=3056;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,86:86:99:2684,257,0:0,0,58,28 chr1 156453096 . G T 1738.76 PASS AC=1;AF=0.5;AN=2;DP=307;MQ=60;set=variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:89,78:167:99:1767,0,2205:39,50,34,44 chr1 156453247 . T A 930.24 PASS AC=2;AF=0.733;AN=2;DP=1873;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:1425,139,0:0,0,16,31 chr1 156460308 . T A 817.35 PASS AC=2;AF=0.955;AN=2;DP=1407;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1064,105,0:0,0,22,13 chr1 156495521 . CAAAAAAAA CAAAAAA,C,CAAAAAAAAAAAAA,CAAAAAAAAAAA,CAAAAAAAAAA,CAAAAAAA,CAAAAAAAAAAAA,CAAAAA,CAAAAAAAAAAAAAAA,CAAAAAAAAAAAAAA 132.92 PASS AC=0,0,0,0,0,1,0,0,0,0;AF=0.052,0.017,0.155,0.103,0.086,0.086,0.103,0.034,0.034,0.017;AN=2;DP=1562;set=filterInvariant-variant2-variant3-variant5-filterInvariant6-variant7-variant9-filterInvariant10-variant11-variant12-variant14-variant15-variant17-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant31-variant33-variant34-variant35-variant36-variant40-variant42-variant43-filterInvariant44 GT:DP:GQ:SB 0/6:22:46:3,4,8,7 chr1 156496188 . A G 2526.96 PASS AC=2;AF=0.989;AN=2;DP=4111;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,111:111:99:3401,331,0:0,0,59,52 chr1 156503541 . T C 191.63 PASS AC=2;AF=1;AN=2;DP=1014;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:737,75,0:0,0,17,8 chr1 156509552 . C G 2473.02 PASS AC=2;AF=1;AN=2;DP=3215;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,91:91:99:3271,273,0:0,0,61,30 chr1 156520173 . T A 2040.58 PASS AC=2;AF=0.989;AN=2;DP=4821;MQ=60;MQRankSum=-1.518;ReadPosRankSum=1.552;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,121:121:99:3365,360,0:0,0,64,57 chr1 156526234 . C T 1099.55 PASS AC=2;AF=0.989;AN=2;DP=2749;MQ=60;MQRankSum=-1.114;ReadPosRankSum=0.841;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:1715,179,0:0,0,33,27 chr1 156526387 . C G 548.35 PASS AC=2;AF=0.688;AN=2;DP=3610;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,111:111:99:3180,333,0:0,0,58,53 chr1 156526444 . T C 982.89 PASS AC=2;AF=0.989;AN=2;DP=2762;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,91:91:99:2631,272,0:0,0,39,52 chr1 156531474 . A G 354.04 PASS AC=2;AF=0.989;AN=2;DP=1269;FractionInformativeReads=1;MQ=60;MQRankSum=0.216;ReadPosRankSum=-0.216;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,31:31:93:968,93,0:0,0,18,13 chr1 156531871 . A G 2709.11 PASS AC=2;AF=0.989;AN=2;DP=4341;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,117:117:99:3609,350,0:0,0,41,76 chr1 156532344 . T G 1079.68 PASS AC=2;AF=0.761;AN=2;DP=2896;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,92:92:99:2916,275,0:0,0,62,30 chr1 156532908 . C A 1215.7 PASS AC=2;AF=0.761;AN=2;DP=6750;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,132:132:99:3779,394,0:0,0,70,62 chr1 156532977 . T C 3172.06 PASS AC=2;AF=0.989;AN=2;DP=5831;MQ=60;MQRankSum=1.536;ReadPosRankSum=-0.347;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,109:109:99:3366,325,0:0,0,45,64 chr1 156534525 . A C 524.85 PASS AC=2;AF=0.726;AN=2;DP=1200;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,50:51:99:1506,143,0:1,0,17,33 chr1 156534539 . G A 405.61 PASS AC=2;AF=0.761;AN=2;DP=1039;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1288,120,0:0,0,12,28 chr1 156536123 . T C 331.77 PASS AC=2;AF=0.989;AN=2;DP=739;FractionInformativeReads=1;MQ=60;MQRankSum=-1.359;ReadPosRankSum=-0.453;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,13:13:42:630,42,0:0,0,11,2 chr1 156536133 . A G 331.77 PASS AC=2;AF=0.989;AN=2;DP=861;MQ=60;MQRankSum=-1.244;ReadPosRankSum=-2.096;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:630,42,0:0,0,12,2 chr1 156536221 . G C 1213.39 PASS AC=2;AF=0.989;AN=2;DP=2879;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:2112,180,0:0,0,43,17 chr1 156536251 . T C 1823.63 PASS AC=2;AF=0.989;AN=2;DP=4016;FractionInformativeReads=1;MQ=60;MQRankSum=0.527;ReadPosRankSum=0.776;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,85:85:99:2825,255,0:0,0,55,30 chr1 156536353 . A G 3544.08 PASS AC=2;AF=0.989;AN=2;DP=7088;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,165:165:99:4740,494,0:0,0,78,87 chr1 156536480 . T C 1840.63 PASS AC=2;AF=0.989;AN=2;DP=2431;MQ=60;MQRankSum=0.184;ReadPosRankSum=0.282;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:1779,171,0:0,0,21,36 chr1 156538973 . A G 292.45 PASS AC=2;AF=0.988;AN=2;DP=285;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.736;ReadPosRankSum=0.736;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:139,12,0:0,0,3,1 chr1 156539019 . CA C 519.09 PASS AC=2;AF=0.988;AN=2;DP=538;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:306,33,0:0,0,9,2 chr1 156539154 . T C 1198.79 PASS AC=2;AF=0.989;AN=2;DP=1942;MQ=60;MQRankSum=1.549;ReadPosRankSum=1.062;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1631,150,0:0,0,33,17 chr1 156551848 . A G 1548.27 PASS AC=2;AF=0.731;AN=2;DP=3956;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,99:100:99:3195,254,0:1,0,34,65 chr1 156552720 . T G 468.2 PASS AC=2;AF=0.932;AN=2;DP=807;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:753,63,0:0,0,14,7 chr1 156553494 . T C 345.46 PASS AC=1;AF=0.5;AN=2;DP=1592;MQ=60;set=filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant10-filterInvariant13-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant19-filterInvariant22-variant24-filterInvariant25-filterInvariant27-filterInvariant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant35-filterInvariant38-filterInvariant39-filterInvariant41-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:46,20:66:99:331,0,3585:13,33,20,0 chr1 156553501 . T C 41.14 PASS AC=1;AF=0.5;AN=2;DP=2791;MQ=60;set=filterInvariant2-filterInvariant3-variant4-filterInvariant5-filterInvariant6-filterInvariant8-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant13-filterInvariant14-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-variant24-filterInvariant25-filterInvariant27-filterInvariant28-filterInvariant29-filterInvariant30-filterInvariant35-filterInvariant37-filterInvariant38-filterInvariant39-filterInvariant40-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:54,19:73:99:301,0,4263:15,39,19,0 chr1 156553504 . CTTT C 251.4 PASS AC=1;AF=0.5;AN=2;DP=216;MQ=60;set=filterInvariant3-variant35 GT:AD:DP:GQ:PL:SB 0/1:64,19:83:99:281,0,4576:23,41,19,0 chr1 156553762 . A C 228.73 PASS AC=2;AF=0.932;AN=2;DP=813;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:728,57,0:0,0,4,15 chr1 156556321 . G A 3048.23 PASS AC=2;AF=0.907;AN=2;DP=5567;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,159:159:99:4753,477,0:0,0,95,64 chr1 156556606 . A G 345.74 PASS AC=2;AF=1;AN=2;DP=918;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:677,60,0:0,0,7,13 chr1 156561414 . T C 655.34 PASS AC=2;AF=0.932;AN=2;DP=1207;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:979,96,0:0,0,18,14 chr1 156561557 . G GGGGCCGGGCC,GGGGTCGGGCC,GGGGCCGGGCCGGGCC 2495.94 PASS AC=2,0,0;AF=0.648,0.295,0.057;AN=2;DP=2606;FS=0;set=Intersection GT:DP:GQ:SB 1/1:55:99:0,0,43,12 chr1 156561651 . G C 5478.29 PASS AC=2;AF=0.932;AN=2;DP=9206;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,240:240:99:7277,719,0:0,0,138,102 chr1 156562008 . G A 2694.55 PASS AC=2;AF=0.932;AN=2;DP=3184;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,73:73:99:2476,218,0:0,0,25,48 chr1 156562143 . G A 605.04 PASS AC=2;AF=0.932;AN=2;DP=1372;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1533,120,0:0,0,28,12 chr1 156563375 . G A 1266.67 PASS AC=2;AF=0.932;AN=2;DP=3712;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,97:97:99:3050,290,0:0,0,50,47 chr1 156563726 . A C 3362.84 PASS AC=2;AF=0.932;AN=2;DP=6323;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,144:144:99:4512,432,0:0,0,72,72 chr1 156563813 . G A 2921.79 PASS AC=2;AF=0.932;AN=2;DP=4851;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,104:104:99:3042,311,0:0,0,47,57 chr1 156563852 . C T 2101.31 PASS AC=2;AF=0.932;AN=2;DP=3649;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:2525,237,0:0,0,35,44 chr1 156563898 . T C 1450.6 PASS AC=2;AF=0.932;AN=2;DP=2398;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1587,138,0:0,0,17,29 chr1 156563992 . C G 840.81 PASS AC=2;AF=0.932;AN=2;DP=2028;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1439,138,0:0,0,19,27 chr1 156564640 . G A 921.4 PASS AC=2;AF=0.744;AN=2;DP=2331;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,61:61:99:2085,183,0:0,0,34,27 chr1 156564922 . C T 3605.25 PASS AC=2;AF=0.737;AN=2;DP=11168;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,302:302:99:9526,904,0:0,0,152,150 chr1 156565049 . A AAC 12589 PASS AC=2;AF=1;AN=2;DP=11760;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,292:292:99:13058,881,0:0,0,135,157 chr1 156567496 . C T 240.81 PASS AC=2;AF=0.744;AN=2;DP=2163;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:2270,215,0:0,0,49,23 chr1 156594656 . C A 649.67 PASS AC=2;AF=0.737;AN=2;DP=1733;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,47:48:99:1419,116,0:0,1,13,34 chr1 156595447 . G A 2377.9 PASS AC=2;AF=0.895;AN=2;DP=3527;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,105:105:99:3178,312,0:0,0,50,55 chr1 156616814 . C G 2748.69 PASS AC=1;AF=0.5;AN=2;DP=491;FractionInformativeReads=1;MQ=60;set=variant22-variant35 GT:AD:DP:GQ:PL:SB 0/1:144,116:260:99:2935,0,3895:62,82,51,65 chr1 156626920 . T C 5920.85 PASS AC=2;AF=1;AN=2;DP=10102;FS=0;MQ=60;MQRankSum=1.313;ReadPosRankSum=0.853;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,234:234:99:6785,701,0:0,0,101,133 chr1 156638495 . A G 66.22 PASS AC=2;AF=0.853;AN=2;DP=300;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:302,27,0:0,0,4,5 chr1 156639000 . A G 1253.48 PASS AC=1;AF=0.604;AN=2;DP=2461;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant13-variant14-variant20-variant21-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:54,47:101:99:1180,0,1277:26,28,23,24 chr1 156639636 . G A 1444.23 PASS AC=1;AF=0.604;AN=2;DP=4733;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant13-variant14-variant20-variant21-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:117,90:207:99:2321,0,2923:61,56,45,45 chr1 156639753 . G A 1584.85 PASS AC=2;AF=0.763;AN=2;DP=7833;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,209:209:99:6720,619,0:0,0,86,123 chr1 156640156 . G A 3147.98 PASS AC=2;AF=0.763;AN=2;DP=11341;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,310:310:99:9109,922,0:0,0,177,133 chr1 156640308 . C T 3212.29 PASS AC=1;AF=0.604;AN=2;DP=6874;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant13-variant14-variant20-variant21-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:158,152:310:99:3833,0,3776:75,83,61,91 chr1 156640503 . C T 1470.13 PASS AC=1;AF=0.604;AN=2;DP=3821;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant13-variant14-variant20-variant21-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:68,75:143:99:1969,0,1813:29,39,40,35 chr1 156640678 . G A,C 355.1 PASS AC=2,0;AF=0.75,0.013;AN=2;DP=2443;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant43 GT:DP:GQ:SB 1/1:68:99:0,0,9,59 chr1 156646668 . A G 2610.86 PASS AC=2;AF=0.989;AN=2;DP=3930;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,106:106:99:3379,317,0:0,0,56,50 chr1 156670545 . C T 1399.26 PASS AC=2;AF=0.977;AN=2;DP=1226;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1329,99,0:0,0,15,18 chr1 156692678 . T C 628.5 PASS AC=2;AF=1;AN=2;DP=863;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:778,87,0:0,0,16,13 chr1 156693018 . C G 917.52 PASS AC=1;AF=0.5;AN=2;DP=359;FractionInformativeReads=1;MQ=60;set=variant8-variant15-variant22-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:29,30:59:99:898,0,871:16,13,17,13 chr1 156696603 . G A 768.33 PASS AC=1;AF=0.5;AN=2;DP=286;FractionInformativeReads=1;MQ=60;set=variant8-variant15-variant22-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:44,25:69:99:704,0,1304:30,14,21,4 chr1 156698265 . C T 960.69 PASS AC=1;AF=0.615;AN=2;DP=1918;MQ=60;set=variant2-variant5-variant6-variant9-variant10-variant13-variant14-variant15-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:48,41:89:99:891,0,1110:18,30,15,26 chr1 156705593 . G C 5312.18 PASS AC=2;AF=1;AN=2;DP=10444;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,253:253:99:7260,757,0:0,0,125,128 chr1 156706559 . A C,G 5984.76 PASS AC=1,1;AF=0.33,0.67;AN=2;DP=6753;FS=0;MQ=60;set=Intersection GT:DP:GQ:SB 1/2:122:99:0,0,70,52 chr1 156707775 . T G 767.56 PASS AC=2;AF=1;AN=2;DP=2119;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,47:48:99:1563,134,0:1,0,33,14 chr1 156713512 . C T 1226.57 PASS AC=2;AF=1;AN=2;DP=2623;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,67:67:99:2112,201,0:0,0,30,37 chr1 156713558 . G A 813.85 PASS AC=1;AF=0.615;AN=2;DP=1474;set=variant2-variant5-variant6-variant9-variant10-variant13-variant14-variant15-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:27,27:54:99:684,0,831:13,14,12,15 chr1 156752048 . C G 1933.58 PASS AC=1;AF=0.776;AN=2;DP=2406;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,26:63:99:616,0,1028:19,18,13,13 chr1 156752231 . AT A 355.76 PASS AC=1;AF=0.818;AN=2;DP=359;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,6:13:99:175,0,210:0,7,0,6 chr1 156760887 . C A 1096.39 PASS AC=1;AF=0.633;AN=2;DP=2554;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,42:75:99:988,0,759:19,14,23,19 chr1 156761618 . C T 2054.29 PASS AC=1;AF=0.579;AN=2;DP=1438;MQ=60;set=variant5-variant9-variant10-variant14-variant15-variant20-variant21-variant24-variant25-variant26-variant30-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:35,47:82:99:1076,0,771:13,22,22,25 chr1 156784982 . T C 1586.99 PASS AC=1;AF=0.737;AN=2;DP=2032;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,23:60:99:506,0,1118:17,20,13,10 chr1 156785356 . T C 1060.39 PASS AC=2;AF=0.976;AN=2;DP=2016;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:1655,144,0:0,0,36,12 chr1 156785617 . G A 2774.7 PASS AC=1;AF=0.776;AN=2;DP=5562;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:93,58:151:99:1613,0,2497:45,48,24,34 chr1 156785762 . AG A 2179.51 PASS AC=1;AF=0.724;AN=2;DP=3819;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:62,65:127:99:2554,0,3709:24,38,26,39 chr1 156785771 . A G 2364.75 PASS AC=1;AF=0.737;AN=2;DP=3755;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:62,66:128:99:2627,0,3712:26,36,26,40 chr1 156785779 . G A 2067.87 PASS AC=1;AF=0.776;AN=2;DP=3671;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,60:115:99:2279,0,3245:24,31,24,36 chr1 156786839 . T TTCTCTCTCTCTCTC,TTCTCCCTCTCTCTCTCTC,TTCTCTCTCTCTCTCTCTCTCTC,TTCTCTC,TTCTCTCTCTCTCTCTCTC,TTCTC,TTCTCTCTCTCTCTCTC,TTCTCTCTCTCTCTCTCTCTC,TTCTCTCTCTCTC,TTCTCTCTCTCTCTCTCTCTCTCTC 251.09 PASS AC=0,0,0,2,0,0,0,0,0,0;AF=0.1,0.017,0.067,0.3,0.25,0.033,0.05,0.067,0.033,0.033;AN=2;DP=608;set=variant-variant3-variant4-variant5-variant7-variant10-variant13-variant15-variant16-variant17-variant18-variant20-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-filterInvariant43-variant44 GT:DP:GQ:SB 4/4:11:32:0,0,0,11 chr1 156810090 . A G 1025.05 PASS AC=2;AF=0.886;AN=2;DP=1537;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1127,108,0:0,0,23,13 chr1 156810219 . GA G 353.89 PASS AC=1;AF=0.531;AN=2;DP=587;set=variant5-variant11-variant14-variant15-variant17-variant20-variant24-variant25-variant26-variant30-variant33-variant35-variant36-variant37-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:18,25:43:99:950,0,1045:6,12,10,15 chr1 156810221 . G GCC 353.89 PASS AC=1;AF=0.531;AN=2;DP=573;MQ=60;set=variant5-variant11-variant14-variant15-variant17-variant20-variant24-variant25-variant26-variant30-variant33-variant35-variant36-variant37-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:17,25:42:99:950,0,1045:6,11,10,15 chr1 156813650 . T C 178.26 PASS AC=1;AF=0.522;AN=2;DP=329;FractionInformativeReads=1;MQ=60;set=variant5-variant9-variant11-variant14-variant15-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,8:14:99:259,0,190:5,1,7,1 chr1 156815921 . C T 2565.55 PASS AC=1;AF=0.583;AN=2;DP=902;MQ=60;set=variant11-variant15-variant17-variant35-variant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:78,78:156:99:2020,0,1950:35,43,35,43 chr1 156816612 . G C 395.58 PASS AC=1;AF=0.583;AN=2;DP=183;FractionInformativeReads=1;MQ=60;set=variant11-variant15-variant17-variant35-variant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:22,20:42:99:566,0,670:6,16,5,15 chr1 156818647 . T C 1635.41 PASS AC=1;AF=0.5;AN=2;DP=1316;MQ=60;set=variant3-variant4-variant6-variant7-variant8-variant16-variant18-variant21-variant22-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:54,54:108:99:1389,0,1452:36,18,36,18 chr1 156845492 . AGTGTGTGTGTGT AGTGTGTGTGTGTGTGT,A,AGTGTGTGTGTGTGTGTGT,AGTGTGTGTGT,AGTGTGTGTGTGTGT,AGTGTGTGTGTGTGTGTGTGT 809.19 PASS AC=1,0,0,1,0,0;AF=0.489,0.023,0.125,0.125,0.114,0.011;AN=2;DP=3699;set=Intersection GT:DP:GQ:SB 4/1:61:99:0,0,23,38 chr1 156846233 . G A,T 1683.58 PASS AC=1,0;AF=0.526,0.026;AN=2;DP=3274;MQ=60;set=variant2-variant3-variant4-variant9-variant11-variant14-variant15-variant20-variant22-variant24-variant25-variant26-variant32-variant33-variant34-variant35-variant36-variant38-variant43 GT:DP:GQ:SB 0/1:191:99:50,42,50,49 chr1 156848995 . C T 1218.43 PASS AC=2;AF=0.763;AN=2;DP=6074;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,183:183:99:5498,546,0:0,0,104,79 chr1 156863532 . T C 1122.87 PASS AC=2;AF=1;AN=2;DP=1833;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1382,129,0:0,0,27,16 chr1 156863617 . G T 503.43 PASS AC=2;AF=0.895;AN=2;DP=2218;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:1691,179,0:0,0,27,33 chr1 156872149 . G A 418.52 PASS AC=2;AF=0.768;AN=2;DP=2080;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:1685,177,0:0,0,24,35 chr1 156875092 . G A 1297.23 PASS AC=2;AF=0.762;AN=2;DP=3249;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:3057,207,0:0,0,39,29 chr1 156875097 . G A 1375.13 PASS AC=2;AF=0.786;AN=2;DP=3408;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,69:69:99:3158,213,0:0,0,40,29 chr1 156875107 . C A 1357.89 PASS AC=2;AF=0.762;AN=2;DP=3736;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,80:81:99:3466,236,0:0,1,49,31 chr1 156875377 . G C 506.74 PASS AC=2;AF=0.955;AN=2;DP=837;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:549,42,0:0,0,3,11 chr1 156875985 . G A 1692.65 PASS AC=2;AF=1;AN=2;DP=3677;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,96:96:99:3071,289,0:0,0,62,34 chr1 156877457 . T C 2211.71 PASS AC=2;AF=1;AN=2;DP=6402;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,142:142:99:4190,425,0:0,0,63,79 chr1 156880190 . C A 613.31 PASS AC=1;AF=0.5;AN=2;DP=123;FractionInformativeReads=1;MQ=60;set=variant26-variant35 GT:AD:DP:GQ:PL:SB 0/1:21,35:56:99:978,0,481:7,14,14,21 chr1 156883493 . G A 614.06 PASS AC=1;AF=0.533;AN=2;DP=847;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant9-variant10-variant12-variant13-variant14-variant17-variant21-variant23-variant26-variant35-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:38,31:69:99:877,0,1018:25,13,23,8 chr1 156883546 . A G 1205.75 PASS AC=1;AF=0.603;AN=2;DP=3030;MQ=60;set=variant-variant2-variant3-variant5-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant19-variant21-variant22-variant23-variant25-variant26-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:74,67:141:99:1658,0,1753:43,31,43,24 chr1 156884365 . T C 1011.98 PASS AC=1;AF=0.738;AN=2;DP=1823;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,17:45:99:448,0,742:19,9,13,4 chr1 156885491 . T G 612.06 PASS AC=1;AF=0.589;AN=2;DP=1669;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant21-variant22-variant23-variant26-variant28-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,39:71:99:946,0,783:17,15,16,23 chr1 156894006 . C G 66.5 PASS AC=1;AF=0.65;AN=2;DP=1023;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,18:26:99:541,0,158:3,5,7,11 chr1 156894367 . G C 227.18 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=735;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:68,22:90:99:275,0,3449:20,48,22,0 chr1 156894372 . A C 197.47 PASS AC=1;AF=0.5;AN=2;DP=308;FractionInformativeReads=1;MQ=60;set=variant10-filterInvariant34-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:71,13:84:99:249,0,3582:24,47,13,0 chr1 156902259 . G A 198.21 PASS AC=1;AF=0.641;AN=2;DP=1884;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,37:58:99:981,0,555:16,5,25,12 chr1 156906093 . C T 663.55 PASS AC=1;AF=0.5;AN=2;DP=101;FractionInformativeReads=1;MQ=60;set=variant15-variant35 GT:AD:DP:GQ:PL:SB 0/1:29,21:50:99:540,0,773:10,19,6,15 chr1 156907081 . T C 842.3 PASS AC=1;AF=0.65;AN=2;DP=3780;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,50:93:99:1286,0,1138:22,21,29,21 chr1 156907115 . T C 1008.77 PASS AC=1;AF=0.625;AN=2;DP=2083;MQ=60;set=variant-variant3-variant5-variant9-variant12-variant13-variant14-variant16-variant17-variant19-variant21-variant22-variant23-variant26-variant28-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,52:96:99:1386,0,1204:23,21,29,23 chr1 156914240 . CCATTCATT CCATT,C,CCATTCATTCATT 685.9 PASS AC=1,0,0;AF=0.423,0.244,0.038;AN=2;DP=3909;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:69:99:14,19,17,19 chr1 156939175 . C T 650.69 PASS AC=1;AF=0.59;AN=2;DP=3709;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,35:86:99:816,0,1244:24,27,17,18 chr1 156948956 . CCCT C 1060.3 PASS AC=1;AF=0.563;AN=2;DP=806;MQ=60;set=variant-variant3-variant5-variant9-variant12-variant13-variant14-variant17-variant21-variant22-variant23-variant26-variant28-variant35-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:22,25:47:99:965,0,993:16,6,16,9 chr1 156954267 . C T 765.9 PASS AC=1;AF=0.569;AN=2;DP=4574;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:84,67:151:99:1423,0,2030:36,48,31,36 chr1 156954384 . T C 353.24 PASS AC=1;AF=0.571;AN=2;DP=790;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:20,13:33:99:422,0,711:2,18,1,12 chr1 156956057 . T C 715.31 PASS AC=1;AF=0.563;AN=2;DP=573;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant9-variant12-variant13-variant14-variant17-variant21-variant22-variant23-variant26-variant28-variant35-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:20,13:33:99:353,0,705:3,17,3,10 chr1 157014702 . G A 2075.83 PASS AC=1;AF=0.608;AN=2;DP=7402;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:88,58:146:99:1329,0,2197:44,44,32,26 chr1 157014877 . A T 2072.96 PASS AC=1;AF=0.563;AN=2;DP=1896;MQ=60;set=variant-variant3-variant5-variant9-variant12-variant13-variant14-variant17-variant21-variant22-variant23-variant26-variant28-variant35-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:52,50:102:99:1278,0,1343:31,21,27,23 chr1 157014964 . T A 1822.06 PASS AC=1;AF=0.571;AN=2;DP=4813;set=variant-variant2-variant4-variant6-variant7-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant33-variant35-variant36-variant37-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:90,100:190:99:2317,0,2092:46,44,53,47 chr1 157015026 . C A 2046.49 PASS AC=1;AF=0.563;AN=2;DP=2140;MQ=60;set=variant-variant3-variant5-variant9-variant12-variant13-variant14-variant17-variant21-variant22-variant23-variant26-variant28-variant35-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:87,78:165:99:1766,0,2114:35,52,33,45 chr1 157043491 . A G 266.3 PASS AC=1;AF=0.619;AN=2;DP=2586;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,41:84:99:984,0,1156:22,21,23,18 chr1 157061973 . C T 435.23 PASS AC=1;AF=0.638;AN=2;DP=1415;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant33-variant35-variant36-variant37-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:18,21:39:99:546,0,484:10,8,12,9 chr1 157062364 . G A 2106.31 PASS AC=1;AF=0.635;AN=2;DP=2384;MQ=60;set=variant2-variant4-variant6-variant7-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant33-variant35-variant36-variant37-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:52,48:100:99:1163,0,1292:27,25,26,22 chr1 157062696 . G T 3934.78 PASS AC=1;AF=0.625;AN=2;DP=3372;MQ=60;set=variant2-variant4-variant6-variant7-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant33-variant35-variant36-variant37-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:64,50:114:99:1279,0,1789:31,33,21,29 chr1 157068533 . G A 590.8 PASS AC=1;AF=0.5;AN=2;DP=351;FractionInformativeReads=1;MQ=60;set=variant7-variant18-variant23-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:47,40:87:99:935,0,1175:28,19,25,15 chr1 157094030 . CAAA CAA,C,CA 886.14 PASS AC=1,0,1;AF=0.28,0.122,0.256;AN=2;DP=5534;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 3/1:103:99:8,13,69,13 chr1 157483440 . C T 168.71 PASS AC=2;AF=0.662;AN=2;DP=1346;set=variant-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,33:33:98:1074,98,0:0,0,18,15 chr1 157483563 . C T 640.69 PASS AC=1;AF=0.5;AN=2;DP=90;FractionInformativeReads=1;MQ=60;set=variant14-variant35 GT:AD:DP:GQ:PL:SB 0/1:17,22:39:99:549,0,526:9,8,12,10 chr1 157483865 . C T 224 PASS AC=2;AF=0.662;AN=2;DP=1220;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1422,120,0:0,0,17,23 chr1 157484453 . G A 567.79 PASS AC=1;AF=0.643;AN=2;DP=2493;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,38:86:99:963,0,1463:19,29,16,22 chr1 157484575 . A G 601.82 PASS AC=2;AF=0.662;AN=2;DP=2547;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,83:83:99:2670,249,0:0,0,42,41 chr1 157484698 . T C 1069.54 PASS AC=1;AF=0.5;AN=2;DP=340;FractionInformativeReads=1;MQ=60;set=variant13-variant14-variant15-variant35 GT:AD:DP:GQ:PL:SB 0/1:46,44:90:99:1245,0,1353:23,23,22,22 chr1 157485275 . T G 1167.2 PASS AC=1;AF=0.5;AN=2;DP=1194;MQ=60;set=variant8-variant10-variant11-variant13-variant14-variant15-variant18-variant20-variant35-variant37-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:55,50:105:99:1315,0,1378:28,27,27,23 chr1 157485429 . C G 1671.52 PASS AC=1;AF=0.5;AN=2;DP=734;MQ=60;set=variant11-variant13-variant14-variant15-variant35 GT:AD:DP:GQ:PL:SB 0/1:68,82:150:99:1853,0,1641:35,33,38,44 chr1 157485504 . G A 1440.19 PASS AC=1;AF=0.5;AN=2;DP=552;MQ=60;set=variant11-variant13-variant14-variant15-variant35 GT:AD:DP:GQ:PL:SB 0/1:52,50:102:99:1318,0,1326:29,23,16,34 chr1 157485561 . G A 666.67 PASS AC=1;AF=0.706;AN=2;DP=2283;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,36:56:99:1009,0,563:8,12,20,16 chr1 157485720 . T C 359.81 PASS AC=2;AF=0.989;AN=2;DP=660;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.241;ReadPosRankSum=-1.107;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:362,33,0:0,0,4,7 chr1 157489516 . T G 784.02 PASS AC=1;AF=0.5;AN=2;DP=1658;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant8-variant10-variant14-variant16-variant17-variant20-variant22-variant28-variant33-variant35-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,49:89:99:1361,0,953:20,20,27,22 chr1 157491173 . T A 1493.9 PASS AC=1;AF=0.779;AN=2;DP=2536;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,47:81:99:1151,0,802:11,23,20,27 chr1 157493685 . G C 11408.9 PASS AC=2;AF=0.826;AN=2;DP=14827;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,335:335:99:9798,1002,0:0,0,180,155 chr1 157497263 . T C 1526.54 PASS AC=2;AF=0.83;AN=2;DP=1930;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:1811,165,0:0,0,38,17 chr1 157501930 . G A 8554.59 PASS AC=2;AF=0.826;AN=2;DP=10365;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,243:243:99:7452,726,0:0,0,129,114 chr1 157502830 . T C 8142.3 PASS AC=2;AF=0.826;AN=2;DP=8663;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,198:198:99:6069,594,0:0,0,98,100 chr1 157503805 . G A 3671.65 PASS AC=1;AF=0.5;AN=2;DP=3595;MQ=60;set=variant3-variant5-variant8-variant9-variant10-variant14-variant16-variant17-variant20-variant22-variant28-variant31-variant33-variant35-variant37-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:99,93:192:99:2421,0,2451:38,61,33,60 chr1 157504466 . T C 1110.66 PASS AC=1;AF=0.5;AN=2;DP=142;FractionInformativeReads=1;MQ=60;set=variant10-variant35 GT:AD:DP:GQ:PL:SB 0/1:37,32:69:99:966,0,1050:15,22,14,18 chr1 157508882 . C T 412.08 PASS AC=2;AF=0.826;AN=2;DP=1080;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:902,69,0:0,0,15,8 chr1 157509025 . C T 995.4 PASS AC=2;AF=0.83;AN=2;DP=4689;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,109:109:99:3357,327,0:0,0,63,46 chr1 157514091 . C T 904.78 PASS AC=1;AF=0.633;AN=2;DP=1618;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant7-variant10-variant13-variant14-variant15-variant16-variant21-variant24-variant26-variant29-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:66,56:122:99:1294,0,1763:39,27,34,22 chr1 157514097 . A G 3256.18 PASS AC=2;AF=0.817;AN=2;DP=4498;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,129:129:99:4878,388,0:0,0,75,54 chr1 157517127 . C T 192.28 PASS AC=1;AF=0.643;AN=2;DP=1041;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant7-variant13-variant14-variant15-variant16-variant21-variant24-variant26-variant29-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:42,62:104:99:1471,0,972:25,17,32,30 chr1 157522016 . G A 530.6 PASS AC=1;AF=0.633;AN=2;DP=446;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant7-variant10-variant13-variant14-variant15-variant16-variant21-variant24-variant26-variant29-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:25,5:30:99:113,0,882:22,3,5,0 chr1 157543746 . C T 2066.08 PASS AC=1;AF=0.581;AN=2;DP=6909;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:132,93:225:99:2171,0,3119:66,66,46,47 chr1 157543762 . C T 6660.09 PASS AC=1;AF=0.83;AN=2;DP=9542;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:122,87:209:99:1933,0,2910:55,67,39,48 chr1 157543878 . G A 1591.65 PASS AC=1;AF=0.641;AN=2;DP=2229;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:41,32:73:99:1130,0,1338:14,27,13,19 chr1 157545047 . A G 698.8 PASS AC=1;AF=0.636;AN=2;DP=1848;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:38,25:63:99:612,0,1000:21,17,12,13 chr1 157545231 . G T 449.69 PASS AC=1;AF=0.636;AN=2;DP=1690;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:41,21:62:99:456,0,1155:21,20,10,11 chr1 157548669 . T A 809.56 PASS AC=1;AF=0.636;AN=2;DP=939;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:18,20:38:99:515,0,510:3,15,6,14 chr1 157557957 . T C 789.48 PASS AC=1;AF=0.603;AN=2;DP=1808;MQ=60;set=variant2-variant3-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:25,33:58:99:952,0,669:7,18,9,24 chr1 157566211 . A G 1112.82 PASS AC=1;AF=0.603;AN=2;DP=2550;MQ=60;set=variant2-variant3-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:63,49:112:99:1005,0,1391:27,36,23,26 chr1 157567751 . A G 293.08 PASS AC=1;AF=0.814;AN=2;DP=3228;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,31:73:99:825,0,1038:20,22,13,18 chr1 157647789 . C A 6471.1 PASS AC=2;AF=0.765;AN=2;DP=15914;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,466:466:99:14628,1397,0:0,0,250,216 chr1 157648098 . G A 2491.98 PASS AC=2;AF=0.611;AN=2;DP=5086;set=variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,175:175:99:5858,525,0:0,0,71,104 chr1 157651017 . T C 346.97 PASS AC=2;AF=0.615;AN=2;DP=637;MQ=60;set=variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant13-variant15-variant16-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:483,42,0:0,0,3,11 chr1 157652929 . TA T 581.22 PASS AC=2;AF=0.625;AN=2;DP=1612;MQ=60;set=variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:1988,204,0:0,0,48,20 chr1 157666256 . T C 797.9 PASS AC=2;AF=0.591;AN=2;DP=894;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant7-variant8-variant10-variant13-variant14-variant15-variant16-variant21-variant24-variant25-variant26-variant28-variant29-variant32-variant33-variant34-variant35-variant37-variant38-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1399,135,0:0,0,17,28 chr1 157666336 . C G 273.95 PASS AC=2;AF=0.595;AN=2;DP=353;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant7-variant8-variant10-variant13-variant14-variant15-variant16-variant21-variant24-variant25-variant26-variant29-variant32-variant33-variant34-variant35-variant37-variant38-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:581,66,0:0,0,10,12 chr1 157668390 . T C 1350.88 PASS AC=2;AF=0.71;AN=2;DP=2924;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,95:95:99:3101,285,0:0,0,36,59 chr1 157669580 . T A 1028.28 PASS AC=2;AF=0.591;AN=2;DP=1655;MQ=60;set=variant3-variant6-variant7-variant8-variant10-variant13-variant14-variant15-variant16-variant18-variant21-variant24-variant25-variant26-variant28-variant32-variant33-variant34-variant35-variant37-variant38-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,78:78:99:2254,234,0:0,0,34,44 chr1 157670290 . C G 624.2 PASS AC=2;AF=0.717;AN=2;DP=2626;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant21-variant22-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,98:98:99:2990,294,0:0,0,52,46 chr1 157680273 . T C 1081.83 PASS AC=1;AF=0.575;AN=2;DP=1455;set=variant3-variant6-variant7-variant8-variant13-variant14-variant15-variant16-variant21-variant24-variant25-variant26-variant28-variant32-variant33-variant34-variant35-variant37-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:49,40:89:99:1094,0,1350:17,32,13,27 chr1 157718283 . A T 1682.86 PASS AC=2;AF=0.881;AN=2;DP=2364;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:2436,186,0:0,0,46,14 chr1 157718325 . T G 832.43 PASS AC=1;AF=0.563;AN=2;DP=1549;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant7-variant10-variant13-variant14-variant15-variant21-variant25-variant28-variant29-variant32-variant33-variant35-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:63,62:125:99:1392,0,1524:41,22,37,25 chr1 157718430 . T G 857.61 PASS AC=1;AF=0.563;AN=2;DP=1470;MQ=60;set=variant-variant3-variant7-variant10-variant13-variant14-variant15-variant21-variant25-variant28-variant29-variant32-variant33-variant35-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:62,57:119:99:1327,0,1643:22,40,25,32 chr1 157718645 . T C 256.52 PASS AC=1;AF=0.563;AN=2;DP=800;MQ=60;set=variant-variant3-variant7-variant10-variant13-variant14-variant15-variant21-variant25-variant28-variant29-variant32-variant33-variant35-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:22,24:46:99:592,0,582:14,8,15,9 chr1 157718780 . A G 746.59 PASS AC=1;AF=0.563;AN=2;DP=1368;MQ=60;set=variant-variant3-variant7-variant10-variant13-variant14-variant15-variant21-variant25-variant28-variant29-variant32-variant33-variant35-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:51,48:99:99:1084,0,1120:24,27,20,28 chr1 157718835 . G A 575.69 PASS AC=1;AF=0.563;AN=2;DP=879;MQ=60;set=variant-variant3-variant7-variant10-variant13-variant14-variant15-variant21-variant25-variant28-variant29-variant32-variant33-variant35-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:32,29:61:99:690,0,749:13,19,11,18 chr1 157736431 . C A 6506.14 PASS AC=1;AF=0.553;AN=2;DP=9714;set=variant-variant3-variant7-variant8-variant10-variant13-variant14-variant15-variant18-variant21-variant25-variant28-variant29-variant32-variant33-variant35-variant37-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:231,269:500:99:6728,0,5519:129,102,156,113 chr1 157737504 . G A 738.31 PASS AC=1;AF=0.71;AN=2;DP=935;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,14:44:99:314,0,783:10,20,3,11 chr1 157740186 . GTC G 3247.16 PASS AC=1;AF=0.724;AN=2;DP=2111;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant11-variant13-variant14-variant15-variant16-variant17-variant21-variant22-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,59:115:99:2303,0,3813:34,22,32,27 chr1 157740189 . A G 3256.19 PASS AC=1;AF=0.724;AN=2;DP=2130;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant11-variant13-variant14-variant15-variant16-variant17-variant21-variant22-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,59:115:99:2303,0,3813:34,22,32,27 chr1 157764964 . C T 250.39 PASS AC=1;AF=0.567;AN=2;DP=357;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant7-variant13-variant14-variant15-variant21-variant25-variant28-variant32-variant33-variant35-variant37-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:12,11:23:99:291,0,430:3,9,5,6 chr1 157771880 . C T 2164.43 PASS AC=1;AF=0.667;AN=2;DP=3947;MQ=60;set=variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:72,73:145:99:1601,0,1924:36,36,31,42 chr1 157801578 . T A 599.18 PASS AC=1;AF=0.579;AN=2;DP=1159;MQ=60;set=variant-variant11-variant13-variant14-variant15-variant18-variant21-variant24-variant25-variant28-variant29-variant32-variant33-variant35-variant36-variant37-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:23,24:47:99:647,0,536:8,15,11,13 chr1 157802877 . T C 1050.89 PASS AC=1;AF=0.655;AN=2;DP=2539;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant6-variant8-variant9-variant12-variant13-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,69:115:99:1646,0,1099:26,20,35,34 chr1 157802979 . C T 1138.58 PASS AC=2;AF=0.775;AN=2;DP=4555;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,120:120:99:3656,359,0:0,0,66,54 chr1 157806006 . G A 1627.35 PASS AC=2;AF=0.775;AN=2;DP=7235;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,189:189:99:5935,564,0:0,0,71,118 chr1 157811392 . G A 540.65 PASS AC=2;AF=0.775;AN=2;DP=2433;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1663,159,0:0,0,33,20 chr1 158045655 . A G 317.23 PASS AC=2;AF=0.806;AN=2;DP=455;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:606,60,0:0,0,12,8 chr1 158045749 . A G 536.5 PASS AC=2;AF=0.803;AN=2;DP=1065;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:889,81,0:0,0,16,11 chr1 158047657 . G A 214.33 PASS AC=1;AF=0.5;AN=2;DP=202;MQ=60;set=variant11-variant15-variant17-variant20-variant23-variant31-variant35-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,16:24:99:539,0,248:7,1,11,5 chr1 158056213 . AAC AACACAC,AACAC,AACACACAC,A 646.33 PASS AC=2,0,0,0;AF=0.5,0.13,0.074,0.019;AN=2;DP=427;set=variant3-variant4-variant8-variant9-variant11-variant14-variant15-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:DP:GQ:SB 1/1:16:54:0,0,13,3 chr1 158056299 . C G 3599.96 PASS AC=2;AF=0.648;AN=2;DP=2287;set=variant3-variant4-variant9-variant11-variant14-variant15-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,84:84:99:2488,252,0:0,0,53,31 chr1 158057420 . A T 415.27 PASS AC=2;AF=0.667;AN=2;DP=2094;MQ=60;set=variant-variant2-variant3-variant5-variant9-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1656,147,0:0,0,35,14 chr1 158058109 . C A 2243.57 PASS AC=2;AF=0.683;AN=2;DP=4935;MQ=60;set=variant-variant2-variant3-variant5-variant9-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,173:173:99:5301,516,0:0,0,113,60 chr1 158058266 . CTTTT CT,CTTT,CTT,CTTTTT,C 337.49 PASS AC=1,0,1,0,0;AF=0.139,0.167,0.181,0.069,0.028;AN=2;DP=4119;set=variant2-filterInvariant3-filterInvariant4-variant5-filterInvariant6-variant7-variant9-filterInvariant10-variant11-variant12-variant13-variant14-variant15-filterInvariant16-variant18-variant19-variant20-variant21-filterInvariant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-filterInvariant38-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/3:49:99:4,6,4,35 chr1 158065762 . C T 129.16 PASS AC=2;AF=0.583;AN=2;DP=518;MQ=60;set=variant-variant3-variant5-variant12-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant31-variant34-variant35-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:476,39,0:0,0,5,8 chr1 158066042 . A G 636.69 PASS AC=2;AF=0.703;AN=2;DP=1380;MQ=60;set=variant-variant2-variant3-variant5-variant9-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:1675,162,0:0,0,28,26 chr1 158066834 . A G 2101.64 PASS AC=2;AF=0.703;AN=2;DP=5067;MQ=60;set=variant-variant2-variant3-variant5-variant9-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,168:168:99:5070,503,0:0,0,83,85 chr1 158067047 . A C 2370.69 PASS AC=2;AF=0.661;AN=2;DP=7141;MQ=60;set=variant-variant2-variant3-variant5-variant9-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,201:201:99:8941,608,0:0,0,106,95 chr1 158067060 . TG T 2718.86 PASS AC=2;AF=0.703;AN=2;DP=7796;MQ=60;set=variant-variant2-variant3-variant5-variant9-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,212:212:99:9297,644,0:0,0,113,99 chr1 158068344 . A G 338.05 PASS AC=2;AF=0.661;AN=2;DP=1051;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant9-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1540,138,0:0,0,22,24 chr1 158069099 . G A 209.43 PASS AC=2;AF=0.732;AN=2;DP=2094;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:1985,170,0:0,0,31,26 chr1 158069286 . G C 1009.44 PASS AC=1;AF=0.5;AN=2;DP=75;FS=6.086;FractionInformativeReads=1;MQ=60;MQRankSum=-1.246;QD=13.46;ReadPosRankSum=0.758;SOR=1.389;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:36,39:75:99:1038,0,826:17,19,13,26 chr1 158069787 . T A 1930.98 PASS AC=1;AF=0.694;AN=2;DP=4954;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant14-variant16-variant17-variant18-variant20-variant22-variant24-variant26-variant27-variant28-variant30-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:98,92:190:99:2075,0,2257:56,42,47,45 chr1 158069891 . T A 1278.69 PASS AC=1;AF=0.688;AN=2;DP=2706;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant16-variant17-variant18-variant20-variant24-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:47,42:89:99:880,0,1269:13,34,16,26 chr1 158153996 . T C 5190.18 PASS AC=2;AF=1;AN=2;DP=6675;FS=0;MQ=60;MQRankSum=0.133;ReadPosRankSum=0.763;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,148:148:99:4752,443,0:0,0,71,77 chr1 158224575 . CTGTGTGTGTGTGTGTGTG C,CTGTGTGTGTG,CTGTGTGTGTGTG,CTGTGTGTG,CTGTGTGTGTGTGTG,CTGTGTGTGTGTGTGTG,CTGTG,CTGTGTG 1394.96 PASS AC=0,0,1,0,0,0,0,1;AF=0.075,0.113,0.275,0.088,0.15,0.063,0.013,0.025;AN=2;DP=3223;set=variant-variant2-variant3-variant5-filterInvariant6-variant7-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 8/3:27:99:0,0,7,20 chr1 158297960 . C T 2442.15 PASS AC=1;AF=0.591;AN=2;DP=1117;FractionInformativeReads=1;MQ=60;set=variant14-variant16-variant17-variant22-variant24-variant26-variant29-variant32-variant33-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:56,44:100:99:1170,0,1557:29,27,26,18 chr1 158300306 . G C 1615.75 PASS AC=1;AF=0.591;AN=2;DP=795;FractionInformativeReads=1;MQ=60;set=variant14-variant16-variant17-variant22-variant24-variant26-variant29-variant32-variant33-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:28,34:62:99:891,0,741:17,11,23,11 chr1 158300604 . C T 1505.23 PASS AC=1;AF=0.5;AN=2;DP=505;FractionInformativeReads=1;MQ=60;set=variant22-variant26-variant35 GT:AD:DP:GQ:PL:SB 0/1:94,89:183:99:2348,0,2416:53,41,43,46 chr1 158322961 . T C 88.51 PASS AC=2;AF=0.988;AN=2;DP=279;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.307;ReadPosRankSum=-0.361;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:355,27,0:0,0,8,1 chr1 158324425 . A G 2880.07 PASS AC=1;AF=0.617;AN=2;DP=2918;MQ=60;set=variant-variant5-variant6-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:56,38:94:99:941,0,1539:26,30,18,20 chr1 158326898 . T C 17660.1 PASS AC=1;AF=0.591;AN=2;DP=6853;set=variant14-variant16-variant17-variant22-variant24-variant26-variant29-variant32-variant33-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:344,323:667:99:7844,0,8443:173,171,154,169 chr1 158368132 . G A 355.31 PASS AC=1;AF=0.5;AN=2;DP=226;FractionInformativeReads=1;MQ=60;set=variant14-variant18-variant22-variant24-variant26-variant32-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:12,10:22:99:313,0,379:9,3,9,1 chr1 158368309 . T G 1810.43 PASS AC=1;AF=0.5;AN=2;DP=1299;FractionInformativeReads=1;MQ=60;set=variant14-variant18-variant22-variant24-variant26-variant32-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:58,80:138:99:2019,0,1446:32,26,41,39 chr1 158368392 . C T 1773.24 PASS AC=1;AF=0.5;AN=2;DP=620;FractionInformativeReads=1;MQ=60;set=variant4-variant12-variant21-variant35 GT:AD:DP:GQ:PL:SB 0/1:82,83:165:99:2150,0,2247:47,35,44,39 chr1 158368541 . A G 3950.03 PASS AC=1;AF=0.583;AN=2;DP=3764;MQ=60;set=variant-variant5-variant6-variant9-variant13-variant14-variant15-variant18-variant20-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:90,83:173:99:2153,0,2394:43,47,36,47 chr1 158368846 . T C 2833.85 PASS AC=1;AF=0.583;AN=2;DP=2594;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant6-variant9-variant13-variant14-variant15-variant18-variant20-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:82,61:143:99:1533,0,1862:42,40,27,34 chr1 158368964 . C T 1321.68 PASS AC=1;AF=0.5;AN=2;DP=827;MQ=60;set=variant14-variant18-variant22-variant24-variant26-variant32-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:43,38:81:99:1464,0,2373:23,20,15,23 chr1 158368974 . A G 1367.17 PASS AC=1;AF=0.5;AN=2;DP=839;FractionInformativeReads=1;MQ=60;set=variant14-variant18-variant22-variant24-variant26-variant32-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:41,36:77:99:1387,0,2328:22,19,16,20 chr1 158369064 . A G 770.98 PASS AC=1;AF=0.5;AN=2;DP=874;MQ=60;set=variant14-variant18-variant22-variant24-variant26-variant32-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:45,39:84:99:1141,0,1109:23,22,21,18 chr1 158369319 . C A 486.75 PASS AC=1;AF=0.587;AN=2;DP=301;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant9-variant13-variant14-variant15-variant18-variant20-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,5:11:99:179,0,148:2,4,0,5 chr1 158389208 . G GA 1089.29 PASS AC=1;AF=0.579;AN=2;DP=454;MQ=60;set=variant3-variant5-variant11-variant13-variant15-variant16-variant17-variant21-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant35-variant37-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:8,10:18:99:236,0,185:3,5,3,7 chr1 158389630 . G C 268.71 PASS AC=1;AF=0.609;AN=2;DP=406;FractionInformativeReads=1;set=variant-variant5-variant6-variant9-variant13-variant14-variant15-variant17-variant20-variant21-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:7,4:11:99:147,0,184:5,2,4,0 chr1 158389659 . T C 252.6 PASS AC=1;AF=0.685;AN=2;DP=709;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant6-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,11:19:99:383,0,172:5,3,10,1 chr1 158390252 . T G 1683.78 PASS AC=1;AF=0.685;AN=2;DP=4075;set=variant-variant3-variant5-variant6-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:99,85:184:99:2244,0,2382:51,48,46,39 chr1 158390501 . G A 2100.26 PASS AC=1;AF=0.685;AN=2;DP=4692;set=variant-variant3-variant5-variant6-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:79,74:153:99:1930,0,2222:29,50,30,44 chr1 158390834 . C A 703.92 PASS AC=1;AF=0.685;AN=2;DP=1322;MQ=60;set=variant-variant3-variant5-variant6-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:20,19:39:99:455,0,485:8,12,7,12 chr1 158435250 . C T 843.16 PASS AC=1;AF=0.692;AN=2;DP=2043;MQ=60;set=variant-variant5-variant6-variant9-variant12-variant13-variant14-variant15-variant17-variant20-variant21-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,46:90:99:1210,0,1055:28,16,30,16 chr1 158435278 . G A 1254.96 PASS AC=1;AF=0.75;AN=2;DP=3259;MQ=60;set=variant-variant3-variant5-variant6-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,71:139:99:1660,0,1633:41,27,43,28 chr1 158436299 . T C 5514.94 PASS AC=1;AF=0.721;AN=2;DP=13955;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:193,222:415:99:5547,0,4574:94,99,104,118 chr1 158436354 . AT A 4662.5 PASS AC=1;AF=0.742;AN=2;DP=10780;MQ=60;set=variant-variant3-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:152,181:333:99:4528,0,3601:66,86,80,101 chr1 158450238 . G A 2282.77 PASS AC=1;AF=0.583;AN=2;DP=2728;FractionInformativeReads=1;set=variant-variant5-variant9-variant14-variant17-variant20-variant21-variant25-variant27-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:122,84:206:99:2051,0,3330:51,71,39,45 chr1 158450314 . A G 1883.16 PASS AC=1;AF=0.667;AN=2;DP=4008;MQ=60;set=variant-variant3-variant5-variant6-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:78,75:153:99:1914,0,1954:34,44,36,39 chr1 158450382 . C T 1134.68 PASS AC=1;AF=0.596;AN=2;DP=2941;MQ=60;set=variant-variant5-variant6-variant9-variant12-variant14-variant16-variant17-variant20-variant21-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,65:123:99:1723,0,1576:24,34,31,34 chr1 158507157 . A T 1974.63 PASS AC=1;AF=0.662;AN=2;DP=3085;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,29:78:99:1123,0,2263:26,23,16,13 chr1 158507160 . T G 1971.64 PASS AC=1;AF=0.662;AN=2;DP=3168;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,31:81:99:1123,0,2263:26,24,17,14 chr1 158507184 . A G 1623.52 PASS AC=1;AF=0.6;AN=2;DP=3373;MQ=60;set=variant-variant5-variant6-variant7-variant9-variant10-variant12-variant14-variant16-variant17-variant20-variant21-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,41:94:99:955,0,1252:26,27,23,18 chr1 158507222 . GA G 1674.31 PASS AC=1;AF=0.662;AN=2;DP=4352;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,37:92:99:848,0,1390:27,28,18,19 chr1 158507398 . G T 109.98 PASS AC=1;AF=0.667;AN=2;DP=757;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,10:20:99:328,0,258:3,7,3,7 chr1 158532295 . G C 203.44 PASS AC=1;AF=0.603;AN=2;DP=319;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant6-variant7-variant9-variant12-variant14-variant16-variant17-variant20-variant21-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,5:9:99:195,0,110:3,1,5,0 chr1 158532405 . T G 973.59 PASS AC=1;AF=0.603;AN=2;DP=1846;MQ=60;set=variant-variant5-variant6-variant7-variant9-variant12-variant14-variant16-variant17-variant20-variant21-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,22:42:99:636,0,543:14,6,14,8 chr1 158533140 . A G 1127.95 PASS AC=1;AF=0.603;AN=2;DP=3218;FractionInformativeReads=1;set=variant-variant5-variant6-variant7-variant9-variant12-variant14-variant16-variant17-variant20-variant21-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,56:108:99:1268,0,1349:27,25,23,33 chr1 158533224 . A G 676.84 PASS AC=1;AF=0.6;AN=2;DP=2395;MQ=60;set=variant-variant5-variant6-variant7-variant9-variant10-variant12-variant14-variant16-variant17-variant20-variant21-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,33:88:99:788,0,1363:29,26,14,19 chr1 158549264 . G A 843.28 PASS AC=1;AF=0.603;AN=2;DP=2159;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant6-variant7-variant9-variant12-variant14-variant16-variant17-variant20-variant21-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,47:95:99:1116,0,1260:25,23,26,21 chr1 158549420 . C T 934.64 PASS AC=1;AF=0.603;AN=2;DP=2983;MQ=60;set=variant-variant5-variant6-variant7-variant9-variant12-variant14-variant16-variant17-variant20-variant21-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,39:88:99:982,0,1486:28,21,19,20 chr1 158549492 . C T 836.6 PASS AC=1;AF=0.603;AN=2;DP=3245;MQ=60;set=variant-variant5-variant6-variant7-variant9-variant12-variant14-variant16-variant17-variant20-variant21-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:71,40:111:99:939,0,1839:39,32,18,22 chr1 158549511 . A G 756.81 PASS AC=1;AF=0.603;AN=2;DP=3342;MQ=60;set=variant-variant5-variant6-variant7-variant9-variant12-variant14-variant16-variant17-variant20-variant21-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,44:112:99:963,0,1703:36,32,20,24 chr1 158580477 . A G 2076.3 PASS AC=1;AF=0.64;AN=2;DP=3197;MQ=60;set=variant-variant3-variant5-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:59,60:119:99:1633,0,1597:28,31,32,28 chr1 158580759 . G A 2907.31 PASS AC=1;AF=0.688;AN=2;DP=8118;MQ=60;set=variant-variant3-variant5-variant6-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:119,119:238:99:2973,0,2886:60,59,61,58 chr1 158580887 . T C 2403.12 PASS AC=1;AF=0.64;AN=2;DP=4586;set=variant-variant3-variant5-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:88,95:183:99:2321,0,2029:44,44,46,49 chr1 158580921 . GCACA GCACACACACACACA,GCA,GCACACACACA,G,GCACACA,GCACACACACACACACA,GCGCACACA,GCACACACA,GCACACACACACA 1968.25 PASS AC=0,0,0,1,0,0,0,1,0;AF=0.128,0.267,0.081,0.07,0.047,0.012,0.012,0.116,0.105;AN=2;DP=5568;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 4/8:67:99:0,0,25,42 chr1 158582646 . T C 956.74 PASS AC=1;AF=0.688;AN=2;DP=3712;MQ=60;set=variant-variant3-variant5-variant6-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,71:127:99:1713,0,1356:30,26,37,34 chr1 158584091 . A G 1125.18 PASS AC=1;AF=0.688;AN=2;DP=1633;MQ=60;set=variant-variant3-variant5-variant6-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,18:50:99:515,0,1250:17,15,7,11 chr1 158584103 . GA GAA,GAAA,G 864.18 PASS AC=1,0,0;AF=0.471,0.176,0.044;AN=2;DP=1670;set=variant-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant40-variant41-variant42-filterInvariant43-variant44 GT:DP:GQ:SB 0/1:48:99:13,13,9,13 chr1 158587390 . C T 1073.97 PASS AC=1;AF=0.688;AN=2;DP=3022;MQ=60;set=variant-variant3-variant5-variant6-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,49:94:99:1235,0,1119:24,21,26,23 chr1 158587784 . T G 501.06 PASS AC=2;AF=1;AN=2;DP=1360;FS=0;MQ=60;MQRankSum=1.542;ReadPosRankSum=1.542;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1039,105,0:0,0,23,12 chr1 158587858 . G A 442.77 PASS AC=1;AF=0.615;AN=2;DP=1298;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:31,26:57:99:604,0,802:16,15,15,11 chr1 158588146 . G A 97.25 PASS AC=2;AF=0.8;AN=2;DP=64;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant9-variant10-variant13-variant17-variant25-variant27-variant28-variant29-variant31-variant35-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:135,9,0:0,0,0,3 chr1 158588916 . C G 260.37 PASS AC=1;AF=0.603;AN=2;DP=637;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,8:21:99:159,0,370:10,3,5,3 chr1 158592935 . G A 1436.49 PASS AC=1;AF=0.603;AN=2;DP=4201;MQ=60;set=variant-variant3-variant5-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:78,83:161:99:2080,0,1972:34,44,32,51 chr1 158595824 . T C 598.46 PASS AC=1;AF=0.615;AN=2;DP=798;MQ=60;set=variant-variant3-variant5-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,16:22:99:492,0,124:4,2,12,4 chr1 158595842 . C A 686.66 PASS AC=1;AF=0.615;AN=2;DP=1185;MQ=60;set=variant-variant3-variant5-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,23:35:99:646,0,355:10,2,16,7 chr1 158596524 . A G 546.22 PASS AC=1;AF=0.615;AN=2;DP=745;MQ=60;set=variant-variant3-variant5-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:16,20:36:99:542,0,391:11,5,14,6 chr1 158597309 . A G 742.04 PASS AC=1;AF=0.538;AN=2;DP=493;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant10-variant12-variant15-variant18-variant33-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:23,28:51:99:836,0,671:17,6,22,6 chr1 158597507 . G C 1164.56 PASS AC=1;AF=0.615;AN=2;DP=1881;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:54,30:84:99:722,0,1394:20,34,12,18 chr1 158606449 . G T 1347.87 PASS AC=1;AF=0.603;AN=2;DP=3277;MQ=60;set=variant-variant3-variant5-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:46,44:90:99:1155,0,1233:23,23,24,20 chr1 158607788 . T G 1494.46 PASS AC=2;AF=1;AN=2;DP=1906;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1695,158,0:0,0,37,16 chr1 158609300 . C G 861.98 PASS AC=1;AF=0.615;AN=2;DP=2181;MQ=60;set=variant-variant3-variant5-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:47,40:87:99:957,0,1086:26,21,23,17 chr1 158612236 . A G 841.26 PASS AC=1;AF=0.686;AN=2;DP=3087;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,30:73:99:646,0,938:24,19,17,13 chr1 158614198 . C T 805.06 PASS AC=1;AF=0.603;AN=2;DP=2111;MQ=60;set=variant-variant3-variant5-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:41,40:81:99:925,0,1069:15,26,15,25 chr1 158618223 . C T 205.39 PASS AC=1;AF=0.672;AN=2;DP=1055;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant20-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,17:33:99:489,0,489:13,3,13,4 chr1 158618480 . A T 286.31 PASS AC=1;AF=0.625;AN=2;DP=641;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant7-variant9-variant11-variant14-variant15-variant17-variant20-variant28-variant29-variant30-variant31-variant35-variant36-variant37-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:22,17:39:99:421,0,619:6,16,6,11 chr1 158619728 . A C 2741.21 PASS AC=2;AF=0.989;AN=2;DP=4186;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,108:108:99:3507,324,0:0,0,49,59 chr1 158624528 . G T 755.53 PASS AC=1;AF=0.5;AN=2;DP=184;FractionInformativeReads=1;MQ=60;set=variant4-variant35 GT:AD:DP:GQ:PL:SB 0/1:56,42:98:99:980,0,1363:25,31,17,25 chr1 158631257 . C T 442.56 PASS AC=1;AF=0.5;AN=2;DP=139;FractionInformativeReads=1;MQ=60;set=variant7-variant14-variant35 GT:AD:DP:GQ:PL:SB 0/1:23,25:48:99:796,0,649:5,18,4,21 chr1 158637865 . GAAA GAA,G,GA,GAAAA 149.5 PASS AC=1,0,0,0;AF=0.269,0.256,0.064,0.013;AN=2;DP=1106;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-filterInvariant21-variant22-filterInvariant23-variant24-filterInvariant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:23:99:5,8,4,6 chr1 158639601 . A G 1596.92 PASS AC=1;AF=0.7;AN=2;DP=3254;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:47,35:82:99:1030,0,1207:21,26,13,22 chr1 158644105 . T A 986.87 PASS AC=1;AF=0.667;AN=2;DP=2222;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:36,30:66:99:938,0,860:20,16,23,7 chr1 158646223 . T C 121.4 PASS AC=1;AF=0.563;AN=2;DP=63;FS=0;FractionInformativeReads=1;MQ=60;set=variant4-variant18-variant27-variant28-variant31-variant33-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:4,2:6:72:72,0,165:0,4,0,2 chr1 158647495 . A T 3091.88 PASS AC=2;AF=0.989;AN=2;DP=4278;MQ=60;MQRankSum=-1.285;ReadPosRankSum=1.176;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,102:102:99:3075,305,0:0,0,55,47 chr1 158647522 . A G 1269.49 PASS AC=1;AF=0.625;AN=2;DP=3050;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,54:107:99:1363,0,1139:25,28,27,27 chr1 158647631 . T A 1124.6 PASS AC=2;AF=0.989;AN=2;DP=1677;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:1700,165,0:0,0,17,38 chr1 158647669 . T C 188.93 PASS AC=1;AF=0.625;AN=2;DP=687;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,17:27:99:584,0,229:3,7,2,15 chr1 158654786 . C T 467.35 PASS AC=2;AF=1;AN=2;DP=505;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:264,21,0:0,0,7,0 chr1 158654852 . A G 707.28 PASS AC=1;AF=0.629;AN=2;DP=1504;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,19:42:99:544,0,674:18,5,13,6 chr1 158655036 . G A 6042.15 PASS AC=2;AF=1;AN=2;DP=7051;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,144:144:99:4197,429,0:0,0,71,73 chr1 158655162 . C A 2388.06 PASS AC=2;AF=1;AN=2;DP=3612;FS=0;MQ=60;MQRankSum=-0.17;ReadPosRankSum=0.713;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:2406,237,0:0,0,30,49 chr1 158656281 . T C 1859.38 PASS AC=2;AF=1;AN=2;DP=2020;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1424,129,0:0,0,31,12 chr1 158656347 . C CAGAG,CAGAGAGAG 4289.09 PASS AC=2,0;AF=0.989,0.011;AN=2;DP=4183;FS=0;set=Intersection GT:DP:GQ:SB 1/1:72:99:0,0,47,25 chr1 158656432 . G GA,GAA,GGA 1680.96 PASS AC=1,0,0;AF=0.613,0.016,0.048;AN=2;DP=6152;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:180:99:48,48,46,38 chr1 158656632 . G GA,GAA 1067.42 PASS AC=2,0;AF=0.455,0.489;AN=2;DP=1004;MQ=60;set=Intersection GT:DP:GQ:SB 1/1:15:48:0,0,4,11 chr1 158656641 . C A 861.09 PASS AC=2;AF=0.955;AN=2;DP=829;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:435,42,0:0,0,3,11 chr1 158656653 . A T 713.74 PASS AC=2;AF=1;AN=2;DP=610;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:35:328,35,0:0,0,3,9 chr1 158669342 . T TGTTTG 34.59 PASS AC=1;AF=0.638;AN=2;DP=519;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant22-variant24-variant27-variant28-variant29-variant30-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,17:21:99:702,0,200:3,1,11,6 chr1 158687896 . C T 892.36 PASS AC=1;AF=0.525;AN=2;DP=1849;MQ=60;set=variant-variant2-variant5-variant7-variant9-variant12-variant14-variant18-variant19-variant26-variant29-variant30-variant33-variant35-variant36-variant37-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:37,33:70:99:858,0,941:14,23,12,21 chr1 158735281 . G C 166.48 PASS AC=2;AF=0.638;AN=2;DP=289;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant11-variant13-variant14-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:279,24,0:0,0,6,2 chr1 158735595 . C T 1870.34 PASS AC=2;AF=0.813;AN=2;DP=7365;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,205:205:99:6484,613,0:0,0,118,87 chr1 158735691 . T C 1771.48 PASS AC=2;AF=0.813;AN=2;DP=7917;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,244:244:99:7550,732,0:0,0,121,123 chr1 158735740 . A G 1594.3 PASS AC=2;AF=0.813;AN=2;DP=7388;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,221:221:99:6702,662,0:0,0,99,122 chr1 158735892 . A G 1123.03 PASS AC=2;AF=0.813;AN=2;DP=4335;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,143:143:99:4538,428,0:0,0,68,75 chr1 158736215 . G A 2927.37 PASS AC=2;AF=0.92;AN=2;DP=5559;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,129:129:99:4049,386,0:0,0,62,67 chr1 158736445 . C T 923.58 PASS AC=1;AF=0.591;AN=2;DP=2121;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant11-variant13-variant14-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant34-variant35-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:53,63:116:99:1485,0,1248:22,31,27,36 chr1 158736517 . A T 514.45 PASS AC=1;AF=0.591;AN=2;DP=979;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant11-variant13-variant14-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant34-variant35-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:33,30:63:99:789,0,859:13,20,13,17 chr1 158747506 . C G 452.44 PASS AC=1;AF=0.5;AN=2;DP=714;FractionInformativeReads=1;MQ=60;set=variant-variant7-variant14-variant18-variant19-variant24-variant26-variant35-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,40:72:99:991,0,739:12,20,16,24 chr1 158813819 . A G 1141.1 PASS AC=1;AF=0.662;AN=2;DP=3793;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:71,65:136:99:1518,0,1534:39,32,40,25 chr1 158815342 . TTTTAAG T 667.38 PASS AC=1;AF=0.545;AN=2;DP=695;MQ=60;set=variant-variant3-variant7-variant10-variant13-variant16-variant17-variant26-variant28-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:47,33:80:99:1245,0,3576:28,19,20,13 chr1 158819324 . G C 1824.34 PASS AC=1;AF=0.662;AN=2;DP=4887;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:94,52:146:99:1000,0,2272:41,53,21,31 chr1 158909164 . C A 2376.71 PASS AC=2;AF=0.779;AN=2;DP=2180;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:2072,153,0:0,0,32,19 chr1 158913525 . A G 1950.08 PASS AC=2;AF=0.966;AN=2;DP=1581;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1939,132,0:0,0,27,15 chr1 158913532 . C T 1943.51 PASS AC=2;AF=0.685;AN=2;DP=1063;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant26-variant27-variant28-variant29-variant33-variant35-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:2048,141,0:0,0,29,18 chr1 158943295 . TCACACA TCACACACACA,TCACACACA,TCA,TCACA,T 527.17 PASS AC=0,1,1,0,0;AF=0.14,0.674,0.081,0.012,0.012;AN=2;DP=671;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 3/2:24:99:1,0,21,2 chr1 158943382 . C A 1019.9 PASS AC=1;AF=0.536;AN=2;DP=1461;FractionInformativeReads=1;MQ=60;set=variant6-variant9-variant10-variant14-variant16-variant20-variant23-variant24-variant26-variant27-variant28-variant35-variant36-variant41 GT:AD:DP:GQ:PL:SB 0/1:48,68:116:99:1740,0,1032:31,17,42,26 chr1 158946629 . A AATATATGTAT 687.62 PASS AC=2;AF=0.942;AN=2;DP=637;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant10-variant13-variant16-variant20-variant21-variant22-variant23-variant24-variant27-variant29-variant31-variant32-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:61:863,61,0:0,0,7,13 chr1 158946658 . CTATATATATATATATATATATATATATA C,CTA 457.73 PASS AC=2,0;AF=0.712,0.192;AN=2;DP=256;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant10-variant13-variant16-variant20-variant21-variant22-variant23-variant24-variant27-variant29-variant31-variant32-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:11:33:0,0,4,7 chr1 158946830 . C CT 514.19 PASS AC=2;AF=0.965;AN=2;DP=974;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:581,60,0:0,0,11,9 chr1 158986477 . G C 5689.27 PASS AC=1;AF=0.786;AN=2;DP=6054;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:106,84:190:99:2058,0,2773:64,42,52,32 chr1 158987941 . A G 906.91 PASS AC=2;AF=0.805;AN=2;DP=1021;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:988,96,0:0,0,22,10 chr1 159002222 . A G 825.42 PASS AC=2;AF=0.857;AN=2;DP=1243;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:919,75,0:0,0,20,5 chr1 159002301 . T C 2128.8 PASS AC=2;AF=0.857;AN=2;DP=4829;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,110:110:99:3266,330,0:0,0,64,46 chr1 159002377 . C A 2913.52 PASS AC=2;AF=0.857;AN=2;DP=7438;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,175:175:99:5046,524,0:0,0,88,87 chr1 159002389 . T A 2762.21 PASS AC=2;AF=0.857;AN=2;DP=7036;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,167:167:99:4713,498,0:0,0,79,88 chr1 159032255 . G T 1502.35 PASS AC=2;AF=0.905;AN=2;DP=2470;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,67:67:99:2072,200,0:0,0,41,26 chr1 159169641 . T C 1398.35 PASS AC=1;AF=0.744;AN=2;DP=4632;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:69,70:139:99:1913,0,1734:32,37,25,45 chr1 159171603 . C A 745.72 PASS AC=1;AF=0.5;AN=2;DP=517;FractionInformativeReads=1;MQ=60;set=variant4-variant9-variant12-variant17-variant24-variant29-variant31-variant35-variant36-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,26:64:99:600,0,950:17,21,17,9 chr1 159172854 . G A 184.45 PASS AC=1;AF=0.611;AN=2;DP=131;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant26-variant29-variant30-variant32-variant34-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,6:15:99:171,0,241:6,3,5,1 chr1 159173144 . C T 412.39 PASS AC=1;AF=0.583;AN=2;DP=637;MQ=60;set=variant-variant6-variant8-variant9-variant11-variant16-variant19-variant26-variant28-variant29-variant30-variant32-variant34-variant35-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:18,30:48:99:797,0,404:6,12,12,18 chr1 159174123 . C T 608.06 PASS AC=1;AF=0.583;AN=2;DP=1323;MQ=60;set=variant-variant6-variant8-variant9-variant11-variant16-variant19-variant26-variant28-variant29-variant30-variant32-variant34-variant35-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:42,51:93:99:1295,0,1072:29,13,35,16 chr1 159174605 . G A 1247.57 PASS AC=1;AF=0.5;AN=2;DP=157;FractionInformativeReads=1;MQ=60;set=variant-variant35 GT:AD:DP:GQ:PL:SB 0/1:42,45:87:99:1158,0,1213:21,21,19,26 chr1 159174824 . G C 5715.86 PASS AC=2;AF=1;AN=2;DP=8688;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,209:209:99:6260,627,0:0,0,100,109 chr1 159174920 . C T 3599.03 PASS AC=1;AF=0.611;AN=2;DP=2736;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant16-variant17-variant18-variant21-variant22-variant23-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:45,53:98:99:1487,0,1142:16,29,18,35 chr1 159175004 . CT C 1643.22 PASS AC=2;AF=0.814;AN=2;DP=1876;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1685,147,0:0,0,19,30 chr1 159175354 . G A 5261.06 PASS AC=1;AF=0.695;AN=2;DP=10966;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:127,137:264:99:3384,0,3263:68,59,72,65 chr1 159176490 . C T 83.73 PASS AC=1;AF=0.5;AN=2;DP=87;FractionInformativeReads=1;MQ=60;set=variant12-variant17-variant24-variant29-variant31-variant35-variant36-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,5:12:99:165,0,242:1,6,1,4 chr1 159249187 . G C 517.39 PASS AC=1;AF=0.5;AN=2;DP=155;FractionInformativeReads=1;MQ=60;set=variant4-variant12-variant17-variant31-variant35-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,10:22:99:332,0,368:7,5,5,5 chr1 159249451 . T TA 1979.27 PASS AC=1;AF=0.538;AN=2;DP=1469;MQ=60;set=variant4-variant10-variant12-variant17-variant26-variant29-variant31-variant33-variant34-variant35-variant37-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,48:92:99:1111,0,1044:24,20,28,20 chr1 159249743 . G T 1433.99 PASS AC=1;AF=0.55;AN=2;DP=746;FractionInformativeReads=1;MQ=60;set=variant4-variant10-variant12-variant17-variant31-variant34-variant35-variant37-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,31:79:99:1126,0,2839:18,30,12,19 chr1 159249745 . G T 1433.99 PASS AC=1;AF=0.55;AN=2;DP=732;FractionInformativeReads=1;MQ=60;set=variant4-variant10-variant12-variant17-variant31-variant34-variant35-variant37-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,30:77:99:1126,0,2839:17,30,11,19 chr1 159272764 . C T 483.53 PASS AC=1;AF=0.5;AN=2;DP=708;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant12-variant17-variant26-variant29-variant31-variant33-variant35-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,22:67:99:531,0,1129:15,30,8,14 chr1 159275706 . G A 973.74 PASS AC=1;AF=0.5;AN=2;DP=389;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant12-variant17-variant31-variant35-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,21:41:99:577,0,607:15,5,11,10 chr1 159283494 . T C 2681.24 PASS AC=1;AF=0.5;AN=2;DP=1291;MQ=60;set=variant4-variant6-variant12-variant17-variant31-variant35-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:68,77:145:99:1983,0,1703:42,26,50,27 chr1 159283746 . T C 2514.97 PASS AC=1;AF=0.5;AN=2;DP=1699;MQ=60;set=variant4-variant6-variant12-variant17-variant26-variant29-variant31-variant35-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:95,67:162:99:1741,0,2743:33,62,27,40 chr1 159401992 . C T 1235.81 PASS AC=1;AF=0.5;AN=2;DP=265;FractionInformativeReads=1;MQ=60;set=variant25-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:35,46:81:99:1290,0,856:23,12,33,13 chr1 159402584 . G GT 4436.21 PASS AC=2;AF=0.965;AN=2;DP=5779;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,135:135:99:4795,406,0:0,0,55,80 chr1 159402695 . A C 1568.95 PASS AC=2;AF=0.965;AN=2;DP=2364;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,61:61:99:2089,182,0:0,0,19,42 chr1 159409196 . T C 1466.9 PASS AC=2;AF=0.965;AN=2;DP=2092;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:1801,179,0:0,0,37,23 chr1 159409533 . G A 12692.7 PASS AC=2;AF=0.965;AN=2;DP=16125;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,369:369:99:11073,1104,0:0,0,191,178 chr1 159409734 . G T 7205.62 PASS AC=2;AF=0.989;AN=2;DP=9097;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,214:214:99:6852,641,0:0,0,99,115 chr1 159409857 . A G 4955.12 PASS AC=1;AF=0.819;AN=2;DP=5624;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:90,86:176:99:2214,0,2448:39,51,40,46 chr1 159505297 . C T 4735.51 PASS AC=1;AF=0.813;AN=2;DP=7453;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:96,85:181:99:2165,0,2745:57,39,48,37 chr1 159558258 . A G 1938.82 PASS AC=2;AF=0.833;AN=2;DP=6699;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,198:198:99:6219,593,0:0,0,99,99 chr1 159683091 . G A 5142.92 PASS AC=2;AF=0.619;AN=2;DP=2340;MQ=60;set=variant3-variant4-variant6-variant8-variant11-variant14-variant15-variant17-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant30-variant32-variant33-variant35-variant36-variant39 GT:AD:DP:GQ:PL:SB 1/1:0,112:112:99:3735,335,0:0,0,48,64 chr1 159684047 . CCACACACACACA CCACACACACACACA,CCACA,C,CCA,CCACACACA,CCACACACACACACACA,CCACACACACA 220.97 PASS AC=0,1,0,1,0,0,0;AF=0.122,0.488,0.049,0.098,0.012,0.024,0.012;AN=2;DP=1262;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant44 GT:DP:GQ:SB 4/2:32:99:1,0,17,14 chr1 159684121 . CT C 90.6 PASS AC=1;AF=0.5;AN=2;DP=1704;set=variant-variant2-variant3-variant4-variant5-filterInvariant6-variant7-variant9-variant10-variant11-filterInvariant14-variant15-variant16-variant18-filterInvariant19-variant20-filterInvariant21-filterInvariant23-filterInvariant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-filterInvariant32-variant33-variant34-filterInvariant35-filterInvariant37-filterInvariant38-variant39-filterInvariant40-variant41-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,11:53:90:90,0,757:23,19,6,5 chr1 159684186 . T A 1698.42 PASS AC=2;AF=0.619;AN=2;DP=1313;MQ=60;set=variant3-variant4-variant6-variant8-variant11-variant14-variant15-variant17-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant30-variant32-variant33-variant35-variant36-variant39 GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2160,207,0:0,0,39,31 chr1 159750731 . G GT 961.65 PASS AC=1;AF=0.583;AN=2;DP=1764;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant10-variant11-variant13-variant14-variant16-variant17-variant19-variant22-variant24-variant25-variant28-variant30-variant31-variant34-variant35-variant36-variant37-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,43:90:99:1681,0,2581:29,18,29,14 chr1 159750732 . A C 970.62 PASS AC=1;AF=0.583;AN=2;DP=1785;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant10-variant11-variant13-variant14-variant16-variant17-variant19-variant22-variant24-variant25-variant28-variant30-variant31-variant34-variant35-variant36-variant37-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,44:92:99:1681,0,2581:30,18,30,14 chr1 159752066 . G A 1712.57 PASS AC=1;AF=0.5;AN=2;DP=618;set=variant2-variant8-variant19-variant35 GT:AD:DP:GQ:PL:SB 0/1:86,89:175:99:2039,0,2032:47,39,47,42 chr1 159752419 . TG T 51.83 PASS AC=1;AF=0.5;AN=2;DP=6;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.406;QD=8.64;ReadPosRankSum=0.406;SOR=0.693;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:89:89,0,89:1,2,1,2 chr1 159799599 . C CA 4106.1 PASS AC=2;AF=0.872;AN=2;DP=5517;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,149:149:99:4993,448,0:0,0,103,46 chr1 159799910 . G A 2121.09 PASS AC=1;AF=0.5;AN=2;DP=1238;FractionInformativeReads=1;MQ=60;set=variant6-variant8-variant24-variant26-variant31-variant32-variant35 GT:AD:DP:GQ:PL:SB 0/1:93,109:202:99:2656,0,2192:42,51,44,65 chr1 159824205 . C T 435.61 PASS AC=1;AF=0.55;AN=2;DP=807;MQ=60;set=variant4-variant5-variant8-variant10-variant11-variant12-variant13-variant14-variant18-variant19-variant20-variant23-variant30-variant31-variant33-variant35-variant37-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:18,25:43:99:495,0,396:9,9,12,13 chr1 159824967 . G C 3498.3 PASS AC=2;AF=0.898;AN=2;DP=5083;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,112:112:99:3552,336,0:0,0,57,55 chr1 159825061 . G C 3078.59 PASS AC=1;AF=0.656;AN=2;DP=4003;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant28-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:92,44:136:99:940,0,2218:48,44,20,24 chr1 159825916 . C T 3476.26 PASS AC=1;AF=0.638;AN=2;DP=4076;MQ=60;set=variant-variant5-variant7-variant9-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:63,61:124:99:1439,0,1630:26,37,28,33 chr1 159826561 . CCA CCACA,C 282.6 PASS AC=1,0;AF=0.534,0.034;AN=2;DP=608;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant14-variant19-variant20-variant21-variant23-variant25-variant26-variant28-variant30-variant31-filterInvariant33-variant35-variant37-variant38-variant39-filterInvariant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:18:99:1,9,1,7 chr1 159827416 . C A 308.6 PASS AC=1;AF=0.558;AN=2;DP=847;FractionInformativeReads=1;set=variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant18-variant19-variant20-variant21-variant23-variant28-variant30-variant31-variant33-variant35-variant37-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,10:23:99:273,0,293:8,5,8,2 chr1 159827456 . A G 1626.58 PASS AC=2;AF=0.798;AN=2;DP=1970;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,31:31:93:1142,93,0:0,0,21,10 chr1 159827475 . G A 934.64 PASS AC=1;AF=0.558;AN=2;DP=1541;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant18-variant19-variant20-variant21-variant23-variant28-variant30-variant31-variant33-variant35-variant37-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:29,14:43:99:358,0,759:18,11,11,3 chr1 159828128 . A G 1318.27 PASS AC=2;AF=0.886;AN=2;DP=3005;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:2436,230,0:0,0,30,47 chr1 159828746 . G A 722.63 PASS AC=2;AF=0.793;AN=2;DP=1588;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,52:52:99:1769,156,0:0,0,22,30 chr1 159832425 . G A 2946.28 PASS AC=2;AF=0.757;AN=2;DP=3969;set=variant-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,119:120:99:4034,346,0:0,1,36,83 chr1 159842088 . T A 1607.92 PASS AC=2;AF=0.849;AN=2;DP=2246;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:1788,173,0:0,0,42,16 chr1 159842103 . C T 1857.33 PASS AC=2;AF=0.757;AN=2;DP=2295;MQ=60;set=variant-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,69:69:99:2147,207,0:0,0,46,23 chr1 159842566 . T A 323.54 PASS AC=2;AF=0.764;AN=2;DP=471;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:406,30,0:0,0,7,3 chr1 159842691 . C G 1318.08 PASS AC=2;AF=0.757;AN=2;DP=3335;MQ=60;set=variant-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,83:84:99:2507,241,0:1,0,50,33 chr1 159854392 . C A 1076.84 PASS AC=2;AF=0.849;AN=2;DP=1628;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1695,150,0:0,0,16,34 chr1 159860259 . G A 1520.3 PASS AC=1;AF=0.58;AN=2;DP=3442;MQ=60;set=variant-variant5-variant8-variant9-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:103,72:175:99:1822,0,2649:59,44,40,32 chr1 159860547 . CTT CTTT,C,CT,CTTTT,CTTTTT 192.53 PASS AC=1,0,0,0,0;AF=0.333,0.037,0.111,0.019,0.019;AN=2;DP=1006;set=variant-filterInvariant2-variant3-filterInvariant4-variant5-filterInvariant6-variant7-variant8-variant9-variant13-filterInvariant15-variant16-filterInvariant17-variant18-variant19-variant20-variant21-filterInvariant25-filterInvariant29-variant30-filterInvariant33-variant34-variant35-variant37-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:16:31:1,3,2,10 chr1 159889686 . G A 1034.35 PASS AC=1;AF=0.689;AN=2;DP=3422;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:77,49:126:99:1008,0,1913:31,46,23,26 chr1 159890459 . T C 1848.02 PASS AC=1;AF=0.65;AN=2;DP=1644;MQ=60;set=variant-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant19-variant20-variant23-variant24-variant26-variant27-variant33-variant35-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,47:96:99:1269,0,1263:17,32,19,28 chr1 159894146 . C T 563.25 PASS AC=2;AF=0.955;AN=2;DP=1380;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1303,102,0:0,0,29,5 chr1 159895536 . G A 414.23 PASS AC=2;AF=0.68;AN=2;DP=680;MQ=60;set=variant-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant30-variant33-variant35-variant37-variant38-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:989,105,0:0,0,15,20 chr1 159896866 . TCA TCACACA,TCACA,TCACACACACACA,T 376.13 PASS AC=0,0,0,1;AF=0.357,0.143,0.071,0.143;AN=2;DP=77;set=variant7-variant24-variant25-variant34-variant35-variant41-variant44 GT:DP:GQ:SB 0/4:10:99:3,1,4,2 chr1 159897126 . C T 2081.08 PASS AC=2;AF=0.672;AN=2;DP=1758;MQ=60;set=variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1683,145,0:0,0,37,12 chr1 159897388 . C T 922.58 PASS AC=2;AF=0.579;AN=2;DP=1129;MQ=60;set=variant3-variant5-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant19-variant20-variant23-variant29-variant30-variant32-variant35-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1657,148,0:0,0,16,34 chr1 159897681 . TAA TA,T 1861.76 PASS AC=0,2;AF=0.636,0.352;AN=2;DP=4367;set=Intersection GT:DP:GQ:SB 2/2:98:99:0,0,50,48 chr1 159898100 . A G 2177.89 PASS AC=2;AF=0.6;AN=2;DP=2470;MQ=60;set=variant3-variant5-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant19-variant20-variant23-variant29-variant30-variant31-variant32-variant35-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,124:124:99:4268,372,0:0,0,52,72 chr1 159898913 . A G 2627.92 PASS AC=2;AF=0.672;AN=2;DP=1764;MQ=60;set=variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,50:52:75:1710,75,0:1,1,21,29 chr1 159902526 . T C 2242.06 PASS AC=2;AF=0.661;AN=2;DP=1190;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1313,117,0:0,0,12,27 chr1 159906156 . A G 2637.61 PASS AC=2;AF=0.579;AN=2;DP=1440;MQ=60;set=variant3-variant5-variant8-variant9-variant10-variant11-variant12-variant16-variant19-variant20-variant21-variant23-variant24-variant28-variant29-variant35-variant38-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,83:83:99:2648,248,0:0,0,47,36 chr1 159906849 . A G 512.27 PASS AC=2;AF=0.714;AN=2;DP=394;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant32-variant35-variant37-variant38-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:844,72,0:0,0,7,17 chr1 159907362 . A G 1006.77 PASS AC=2;AF=0.69;AN=2;DP=616;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant19-variant20-variant21-variant23-variant24-variant28-variant29-variant35-variant38-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:90:1309,90,0:0,0,20,8 chr1 159907367 . T C 1091.44 PASS AC=2;AF=0.69;AN=2;DP=657;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant19-variant20-variant21-variant23-variant24-variant28-variant29-variant35-variant38-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1408,102,0:0,0,22,12 chr1 159913388 . G A 503.42 PASS AC=2;AF=0.691;AN=2;DP=1914;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant22-variant23-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:1862,174,0:0,0,23,35 chr1 159915168 . C T 217.61 PASS AC=1;AF=0.5;AN=2;DP=25;FS=0;FractionInformativeReads=0.96;MQ=60;MQRankSum=-1.848;QD=8.7;ReadPosRankSum=-1.371;SOR=0.804;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:15,9:24:99:246,0,477:11,4,7,2 chr1 159915424 . C A 564.07 PASS AC=2;AF=0.811;AN=2;DP=2232;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:2131,186,0:0,0,18,44 chr1 159922369 . C T 1751.65 PASS AC=2;AF=0.93;AN=2;DP=3406;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,81:81:99:2677,243,0:0,0,29,52 chr1 159923111 . T G 2758.73 PASS AC=2;AF=0.93;AN=2;DP=4717;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,96:96:99:2927,287,0:0,0,61,35 chr1 159998579 . TA T 9155.13 PASS AC=2;AF=0.768;AN=2;DP=13987;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,300:301:99:8359,875,0:0,1,155,145 chr1 159999185 . CTTT CTTTTT,CTTTT,CT,C 157.74 PASS AC=0,2,0,0;AF=0.141,0.282,0.154,0.013;AN=2;DP=1630;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-filterInvariant10-variant12-variant13-variant14-variant16-filterInvariant17-variant18-variant19-variant20-variant21-filterInvariant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-filterInvariant40-variant42-variant43-variant44 GT:DP:GQ:SB 2/2:19:7:0,3,3,13 chr1 160000435 . A T 1295.89 PASS AC=1;AF=0.5;AN=2;DP=1028;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant6-variant12-variant19-variant20-variant23-variant34-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:70,49:119:99:1193,0,1964:39,31,23,26 chr1 160009143 . G C 322.84 PASS AC=2;AF=1;AN=2;DP=526;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:492,39,0:0,0,8,5 chr1 160009163 . GACACACACACACAC GACACAC,GACAC,GACACACACACAC,GACACACACAC,GACACACACACACACAC,GACACACACACACACACACAC,GACACACAC,G,GAC 93.39 PASS AC=0,0,0,0,0,0,0,1,0;AF=0.313,0.047,0.047,0.156,0.063,0.016,0.031,0.063,0.016;AN=2;DP=441;set=variant-variant3-variant4-variant6-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant30-variant31-variant32-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/8:7:99:3,1,2,1 chr1 160009419 . A C 244.61 PASS AC=1;AF=0.841;AN=2;DP=1385;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:13,13:26:99:325,0,294:5,8,6,7 chr1 160054894 . G T 113.02 PASS AC=2;AF=0.595;AN=2;DP=210;MQ=60;set=variant-variant4-variant7-variant9-variant12-variant14-variant17-variant19-variant20-variant23-variant26-variant27-variant29-variant30-variant32-variant33-variant35-variant36-variant38-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:139,12,0:0,0,1,3 chr1 160057964 . C T 471.99 PASS AC=2;AF=0.583;AN=2;DP=1696;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant35-variant36-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1491,134,0:0,0,19,26 chr1 160058000 . C T 547.81 PASS AC=1;AF=0.5;AN=2;DP=555;MQ=60;set=variant11-variant15-variant21-variant24-variant29-variant31-variant35-variant36-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:21,16:37:99:363,0,570:10,11,8,8 chr1 160058252 . G A 818.1 PASS AC=1;AF=0.548;AN=2;DP=1128;MQ=60;set=variant-variant3-variant6-variant7-variant9-variant12-variant13-variant14-variant17-variant19-variant23-variant26-variant27-variant29-variant30-variant32-variant35-variant36-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,29:52:99:745,0,552:11,12,14,15 chr1 160058612 . C T 207.77 PASS AC=1;AF=0.543;AN=2;DP=1044;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant9-variant12-variant13-variant14-variant17-variant19-variant20-variant23-variant26-variant27-variant29-variant30-variant32-variant35-variant36-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,8:36:99:127,0,703:14,14,4,4 chr1 160060272 . G A 586.13 PASS AC=1;AF=0.545;AN=2;DP=876;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant9-variant12-variant13-variant14-variant17-variant19-variant20-variant23-variant27-variant29-variant30-variant32-variant35-filterInvariant36-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,13:36:99:349,0,599:9,14,5,8 chr1 160061853 . G A 312.92 PASS AC=1;AF=0.5;AN=2;DP=278;MQ=60;set=variant11-variant15-variant21-variant24-variant29-variant31-variant35-variant36-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,17:30:99:481,0,368:6,7,9,8 chr1 160061934 . T C 621.71 PASS AC=1;AF=0.5;AN=2;DP=901;MQ=60;set=variant3-variant6-variant11-variant12-variant15-variant21-variant23-variant24-variant26-variant29-variant31-variant35-variant36-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:30,23:53:99:847,0,1196:21,9,14,9 chr1 160061959 . C T 774.95 PASS AC=1;AF=0.5;AN=2;DP=1140;MQ=60;set=variant3-variant6-variant11-variant12-variant15-variant21-variant23-variant24-variant26-variant29-variant31-variant35-variant36-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:39,26:65:99:899,0,1402:26,13,15,11 chr1 160062472 . C T 2599.13 PASS AC=1;AF=0.5;AN=2;DP=2728;set=variant3-variant6-variant11-variant12-variant15-variant21-variant23-variant24-variant26-variant29-variant31-variant35-variant36-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:77,134:211:99:3194,0,1745:38,39,66,68 chr1 160062727 . A G 2801.15 PASS AC=1;AF=0.5;AN=2;DP=2500;MQ=60;set=variant3-variant6-variant11-variant12-variant15-variant21-variant23-variant24-variant26-variant29-variant31-variant35-variant36-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:74,80:154:99:2056,0,1910:40,34,41,39 chr1 160064592 . T C 468.08 PASS AC=1;AF=0.543;AN=2;DP=954;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant9-variant12-variant13-variant14-variant17-variant19-variant20-variant23-variant26-variant27-variant29-variant30-variant32-variant35-variant36-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,28:51:99:696,0,522:15,8,19,9 chr1 160068068 . A C 807.12 PASS AC=2;AF=0.641;AN=2;DP=2274;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,63:63:99:2124,189,0:0,0,45,18 chr1 160085868 . A C 297.42 PASS AC=1;AF=0.722;AN=2;DP=1252;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,23:39:99:579,0,458:5,11,6,17 chr1 160085955 . A C 94.66 PASS AC=1;AF=0.538;AN=2;DP=273;MQ=60;set=variant-variant3-variant6-variant7-variant9-variant12-variant13-variant14-variant15-variant17-variant19-variant23-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,7:12:99:195,0,147:1,4,4,3 chr1 160090674 . T C 1052.02 PASS AC=2;AF=1;AN=2;DP=2030;FS=0;MQ=60;MQRankSum=0.933;ReadPosRankSum=1.599;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1780,153,0:0,0,37,14 chr1 160090681 . CCCTT C 698.45 PASS AC=2;AF=0.81;AN=2;DP=2144;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:2446,171,0:0,0,42,15 chr1 160093222 . C T 3016.19 PASS AC=2;AF=0.989;AN=2;DP=8150;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,198:198:99:5976,591,0:0,0,82,116 chr1 160093648 . G A 1341.73 PASS AC=1;AF=0.5;AN=2;DP=1126;MQ=60;set=variant11-variant19-variant20-variant21-variant24-variant25-variant29-variant31-variant33-variant35-variant36-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:46,47:93:99:1233,0,1338:24,22,27,20 chr1 160093911 . T C 2743.33 PASS AC=2;AF=0.989;AN=2;DP=4686;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,111:111:99:3332,333,0:0,0,44,67 chr1 160093927 . T A 1459.54 PASS AC=1;AF=0.621;AN=2;DP=2861;MQ=60;set=variant4-variant5-variant7-variant9-variant11-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,48:108:99:1033,0,1550:22,38,23,25 chr1 160094458 . A G 237.04 PASS AC=2;AF=1;AN=2;DP=332;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:180,12,0:0,0,0,4 chr1 160095127 . T A 661.5 PASS AC=1;AF=0.694;AN=2;DP=1063;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,16:34:99:453,0,507:7,11,5,11 chr1 160097315 . C A 357.23 PASS AC=1;AF=0.5;AN=2;DP=387;FractionInformativeReads=1;MQ=60;set=variant11-variant19-variant20-variant21-variant24-variant25-variant29-variant33-variant35-variant36-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:19,16:35:99:486,0,618:16,3,15,1 chr1 160097666 . G A 2138.59 PASS AC=2;AF=0.821;AN=2;DP=3736;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,108:108:99:3491,324,0:0,0,51,57 chr1 160098927 . A AG 149.73 PASS AC=2;AF=0.845;AN=2;DP=659;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:633,51,0:0,0,7,10 chr1 160100201 . C G 2960.2 PASS AC=1;AF=0.5;AN=2;DP=1947;MQ=60;set=variant11-variant21-variant24-variant29-variant35-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:171,153:324:99:3334,0,4395:87,84,79,74 chr1 160111701 . G C 879.01 PASS AC=1;AF=0.526;AN=2;DP=1087;MQ=60;set=variant9-variant10-variant11-variant18-variant21-variant22-variant24-variant25-variant28-variant29-variant30-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:28,34:62:99:850,0,713:18,10,17,17 chr1 160111858 . C T 1172.5 PASS AC=1;AF=0.526;AN=2;DP=1431;MQ=60;set=variant9-variant10-variant11-variant18-variant21-variant22-variant24-variant25-variant28-variant29-variant30-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:30,43:73:99:1719,0,1475:14,16,21,22 chr1 160111860 . C T 1172.5 PASS AC=1;AF=0.526;AN=2;DP=1425;MQ=60;set=variant9-variant10-variant11-variant18-variant21-variant22-variant24-variant25-variant28-variant29-variant30-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:30,43:73:99:1719,0,1475:14,16,21,22 chr1 160112138 . A G 617.15 PASS AC=1;AF=0.526;AN=2;DP=1006;MQ=60;set=variant9-variant10-variant11-variant18-variant21-variant22-variant24-variant25-variant28-variant29-variant30-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:41,24:65:99:539,0,1025:18,23,14,10 chr1 160112207 . T A 355.51 PASS AC=1;AF=0.526;AN=2;DP=793;MQ=60;set=variant9-variant10-variant11-variant18-variant21-variant22-variant24-variant25-variant28-variant29-variant30-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:36,19:55:99:431,0,947:13,23,8,11 chr1 160112594 . CA C 270.94 PASS AC=1;AF=0.563;AN=2;DP=211;MQ=60;set=variant10-variant11-variant18-variant21-variant24-variant25-variant28-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,11:13:14:210,0,14:2,0,6,5 chr1 160112741 . T C 555.98 PASS AC=1;AF=0.526;AN=2;DP=792;FractionInformativeReads=1;MQ=60;set=variant9-variant10-variant11-variant18-variant21-variant22-variant24-variant25-variant28-variant29-variant30-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:29,17:46:99:343,0,737:14,15,10,7 chr1 160113371 . T A 1399.71 PASS AC=1;AF=0.528;AN=2;DP=1830;MQ=60;set=variant9-variant10-variant11-variant18-variant21-variant22-variant24-variant25-variant28-variant29-variant30-variant35-variant36-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:47,57:104:99:1658,0,1455:9,38,14,43 chr1 160113412 . CTT C 796.39 PASS AC=1;AF=0.528;AN=2;DP=807;MQ=60;set=variant9-variant10-variant11-variant18-variant21-variant22-variant24-variant25-variant28-variant29-variant30-variant35-variant36-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:15,24:39:99:963,0,559:0,15,5,19 chr1 160121488 . G T 1144.24 PASS AC=1;AF=0.579;AN=2;DP=1932;FractionInformativeReads=1;MQ=60;set=variant6-variant7-variant8-variant12-variant13-variant14-variant15-variant17-variant19-variant23-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,54:106:99:1264,0,1254:26,26,27,27 chr1 160121746 . C T 813.82 PASS AC=1;AF=0.579;AN=2;DP=1361;MQ=60;set=variant6-variant7-variant8-variant12-variant13-variant14-variant15-variant17-variant19-variant23-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,57:109:99:1540,0,1395:28,24,26,31 chr1 160122826 . G A 466.31 PASS AC=1;AF=0.579;AN=2;DP=1224;set=variant6-variant7-variant8-variant12-variant13-variant14-variant15-variant17-variant19-variant23-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,34:82:99:965,0,1365:34,14,26,8 chr1 160124875 . G A 2123.7 PASS AC=1;AF=0.788;AN=2;DP=3343;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,46:92:99:1102,0,1121:26,20,28,18 chr1 160128638 . C T 315.91 PASS AC=1;AF=0.5;AN=2;DP=18;FS=3.522;FractionInformativeReads=1;MQ=60;MQRankSum=-0.044;QD=17.55;ReadPosRankSum=-0.044;SOR=2.147;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:8,10:18:99:344,0,252:7,1,10,0 chr1 160128671 . G A 500.5 PASS AC=2;AF=0.658;AN=2;DP=1618;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1351,117,0:0,0,30,9 chr1 160128994 . C T 1046.66 PASS AC=2;AF=0.929;AN=2;DP=1492;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1386,117,0:0,0,12,27 chr1 160134205 . C T 810.02 PASS AC=2;AF=0.713;AN=2;DP=2754;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,91:91:99:3037,272,0:0,0,25,66 chr1 160136350 . G A 938.26 PASS AC=1;AF=0.786;AN=2;DP=2615;set=variant-variant2-variant4-variant5-variant8-variant9-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:52,39:91:99:908,0,1398:37,15,23,16 chr1 160137300 . A C 838.44 PASS AC=1;AF=0.685;AN=2;DP=1787;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant23-variant24-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,28:50:99:783,0,674:4,18,9,19 chr1 160140998 . G A 554.76 PASS AC=1;AF=0.655;AN=2;DP=378;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant17-variant19-variant22-variant24-variant26-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,4:10:99:132,0,156:3,3,4,0 chr1 160141196 . C T 3666.67 PASS AC=2;AF=0.977;AN=2;DP=4304;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,101:101:99:2927,301,0:0,0,55,46 chr1 160141285 . C T 5573.75 PASS AC=1;AF=0.633;AN=2;DP=1452;MQ=60;set=variant3-variant6-variant7-variant12-variant13-variant15-variant29-variant33-variant34-variant35-variant36-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,56:109:99:2185,0,3107:27,26,32,24 chr1 160141286 . C G 777.36 PASS AC=1;AF=0.646;AN=2;DP=2335;MQ=60;set=variant2-variant3-variant6-variant7-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant23-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,56:111:99:2185,0,3107:29,26,32,24 chr1 160141636 . C T 1342.01 PASS AC=1;AF=0.737;AN=2;DP=2555;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,37:73:99:982,0,837:15,21,14,23 chr1 160145688 . C G 449.7 PASS AC=2;AF=0.663;AN=2;DP=2571;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:1746,174,0:0,0,36,22 chr1 160145707 . C T 485.2 PASS AC=2;AF=0.531;AN=2;DP=1174;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant11-variant14-variant18-variant21-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,64:64:99:1868,192,0:0,0,38,26 chr1 160145977 . G A 2167.65 PASS AC=1;AF=0.5;AN=2;DP=212;FS=3.086;FractionInformativeReads=1;MQ=60;MQRankSum=-1.387;QD=10.22;ReadPosRankSum=1.171;SOR=0.695;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:113,99:212:99:2196,0,2714:53,60,52,47 chr1 160147065 . C T 178.44 PASS AC=2;AF=0.568;AN=2;DP=337;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant7-variant8-variant10-variant12-variant14-variant18-variant19-variant22-variant23-variant24-variant28-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:562,45,0:0,0,11,4 chr1 160147148 . A G 440.68 PASS AC=2;AF=0.568;AN=2;DP=1173;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant7-variant8-variant10-variant12-variant14-variant18-variant19-variant22-variant23-variant24-variant28-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:2153,204,0:0,0,40,28 chr1 160147502 . T G 690.82 PASS AC=2;AF=0.628;AN=2;DP=4233;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,96:96:99:2977,287,0:0,0,38,58 chr1 160147517 . A G 969.12 PASS AC=2;AF=0.567;AN=2;DP=1493;MQ=60;set=variant-variant14-variant18-variant19-variant22-variant23-variant24-variant28-variant30-variant31-variant33-variant34-variant35-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,88:89:99:3819,228,0:0,1,36,52 chr1 160147521 . C T 972.07 PASS AC=2;AF=0.567;AN=2;DP=1456;MQ=60;set=variant-variant14-variant18-variant19-variant22-variant23-variant24-variant28-variant30-variant31-variant33-variant34-variant35-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,90:91:99:3888,231,0:0,1,36,54 chr1 160151345 . CAA CA,C 42.41 PASS AC=2,0;AF=0.552,0.034;AN=2;DP=418;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant23-variant25-variant26-variant27-variant28-variant31-variant33-variant35-variant36-variant39-variant40-variant42-variant43 GT:DP:GQ:SB 1/1:20:34:1,0,17,2 chr1 160151450 . T C 2302.92 PASS AC=2;AF=0.671;AN=2;DP=3055;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,100:100:99:2934,298,0:0,0,54,46 chr1 160152382 . C T 1015.23 PASS AC=2;AF=0.542;AN=2;DP=977;FractionInformativeReads=1;MQ=60;set=variant-variant14-variant18-variant23-variant24-variant28-variant30-variant31-variant33-variant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,94:94:99:2896,281,0:0,0,49,45 chr1 160163446 . C T 267.8 PASS AC=2;AF=0.667;AN=2;DP=1045;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:1228,96,0:0,0,28,4 chr1 160163509 . C T 955.24 PASS AC=2;AF=0.64;AN=2;DP=2160;MQ=60;set=variant-variant3-variant4-variant6-variant8-variant9-variant12-variant14-variant15-variant18-variant23-variant25-variant26-variant28-variant30-variant31-variant32-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,96:96:99:2811,284,0:0,0,59,37 chr1 160164668 . T C 441.31 PASS AC=2;AF=0.989;AN=2;DP=725;FS=0;MQ=60;MQRankSum=0.684;ReadPosRankSum=0.322;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:668,69,0:0,0,16,7 chr1 160165442 . GC G,GCC,GCCC 96.09 PASS AC=0,1,0;AF=0.115,0.346,0.077;AN=2;DP=341;MQ=60;set=variant2-variant4-variant6-variant12-variant13-variant25-variant32-variant35-variant36-filterInvariant37-variant39-variant41-filterInvariant44 GT:DP:GQ:SB 0/2:23:99:0,12,3,8 chr1 160168368 . G A 1680.07 PASS AC=2;AF=0.648;AN=2;DP=3654;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant12-variant14-variant15-variant18-variant21-variant23-variant25-variant26-variant27-variant28-variant30-variant32-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,159:159:99:4723,476,0:0,0,100,59 chr1 160169473 . T C 811 PASS AC=2;AF=1;AN=2;DP=1205;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:960,81,0:0,0,21,6 chr1 160178356 . A G 2430.06 PASS AC=2;AF=1;AN=2;DP=4199;FS=0;MQ=60;MQRankSum=1.417;ReadPosRankSum=1.638;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,106:106:99:3303,318,0:0,0,61,45 chr1 160187173 . A G 1388.28 PASS AC=2;AF=0.886;AN=2;DP=2037;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,61:61:99:1940,182,0:0,0,35,26 chr1 160262706 . T C 153.06 PASS AC=1;AF=0.5;AN=2;DP=36;FractionInformativeReads=1;MQ=60;set=variant14-variant35 GT:AD:DP:GQ:PL:SB 0/1:10,5:15:99:139,0,277:5,5,4,1 chr1 160263286 . AT A 63.93 PASS AC=1;AF=0.5;AN=2;DP=588;MQ=60;set=filterInvariant-variant3-filterInvariant8-filterInvariant10-filterInvariant12-variant17-variant21-filterInvariant25-variant27-filterInvariant28-filterInvariant29-variant30-filterInvariant34-filterInvariant35-filterInvariant36-variant37-filterInvariant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,7:23:90:90,0,295:3,13,0,7 chr1 160265668 . G C 1588.86 PASS AC=1;AF=0.5;AN=2;DP=723;FractionInformativeReads=1;MQ=60;set=variant-variant14-variant30-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:93,70:163:99:1694,0,2218:41,52,32,38 chr1 160275434 . A G 6087.68 PASS AC=2;AF=0.955;AN=2;DP=9082;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,222:222:99:6686,665,0:0,0,111,111 chr1 160318940 . A G 1101.86 PASS AC=1;AF=0.7;AN=2;DP=2845;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,28:78:99:663,0,1236:22,28,9,19 chr1 160327203 . CT C 1573.81 PASS AC=1;AF=0.727;AN=2;DP=961;MQ=60;set=variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant16-variant19-variant22-variant24-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:14,14:28:99:344,0,342:3,11,4,10 chr1 160328804 . G A 2540.93 PASS AC=1;AF=0.717;AN=2;DP=2395;MQ=60;set=variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant16-variant19-variant22-variant24-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:55,55:110:99:1315,0,1162:23,32,28,27 chr1 160341876 . G A 1921.07 PASS AC=1;AF=0.712;AN=2;DP=1915;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant19-variant20-variant22-variant24-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:43,38:81:99:899,0,1153:20,23,19,19 chr1 160342015 . T G 366.22 PASS AC=1;AF=0.743;AN=2;DP=1335;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,17:29:99:497,0,257:4,8,4,13 chr1 160370356 . G C 137.07 PASS AC=2;AF=1;AN=2;DP=314;FS=0;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:344,30,0:0,0,8,2 chr1 160393905 . A G 661.21 PASS AC=1;AF=0.694;AN=2;DP=2512;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,48:87:99:1228,0,980:22,17,27,21 chr1 160394173 . A G 669.73 PASS AC=1;AF=0.604;AN=2;DP=2586;MQ=60;set=variant2-variant5-variant6-variant7-variant8-variant10-variant11-variant16-variant17-variant19-variant20-variant22-variant24-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant37-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,71:139:99:1690,0,1606:32,36,31,40 chr1 160394937 . A C 1301.44 PASS AC=1;AF=0.6;AN=2;DP=2439;MQ=60;set=variant2-variant5-variant6-variant7-variant8-variant11-variant16-variant17-variant19-variant20-variant22-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:74,61:135:99:1559,0,1932:36,38,33,28 chr1 160395003 . G A 1640.23 PASS AC=1;AF=0.619;AN=2;DP=2183;MQ=60;set=variant2-variant5-variant6-variant7-variant8-variant10-variant11-variant16-variant17-variant19-variant20-variant22-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:79,57:136:99:1414,0,2033:38,41,26,31 chr1 160395276 . C CT,CTT 352.49 PASS AC=1,0;AF=0.676,0.014;AN=2;DP=1700;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:50:99:18,12,10,10 chr1 160397254 . G T 3597.32 PASS AC=2;AF=1;AN=2;DP=5103;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,120:121:99:3397,352,0:0,1,56,64 chr1 160458782 . A G 1743.56 PASS AC=2;AF=0.793;AN=2;DP=4672;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,94:94:99:3118,282,0:0,0,65,29 chr1 160493178 . AT A,ATT 100.75 PASS AC=1,0;AF=0.559,0.059;AN=2;DP=309;MQ=60;set=variant-variant3-variant9-variant15-variant17-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant33-variant34-variant35-variant40-variant41 GT:DP:GQ:SB 0/1:7:5:0,1,1,5 chr1 160511648 . C T 306.43 PASS AC=1;AF=0.641;AN=2;DP=1290;MQ=60;set=variant-variant3-variant5-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,19:48:99:464,0,701:16,13,9,10 chr1 160512224 . G A 9813.49 PASS AC=1;AF=0.821;AN=2;DP=12640;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:171,174:345:99:4208,0,4184:84,87,86,88 chr1 160512616 . G A 14591.2 PASS AC=1;AF=0.821;AN=2;DP=17674;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:244,210:454:99:5104,0,5909:121,123,104,106 chr1 160512813 . T C 8329.3 PASS AC=1;AF=0.849;AN=2;DP=10962;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:117,127:244:99:3127,0,2929:48,69,57,70 chr1 160513183 . A G 9074.39 PASS AC=1;AF=0.826;AN=2;DP=9505;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:123,130:253:99:3229,0,2913:64,59,69,61 chr1 160513456 . G A 1958.51 PASS AC=1;AF=0.814;AN=2;DP=2591;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,26:41:99:779,0,461:12,3,21,5 chr1 160513626 . G A 10862.5 PASS AC=1;AF=0.802;AN=2;DP=12955;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:175,163:338:99:3835,0,3919:97,78,89,74 chr1 160514859 . G A 406.71 PASS AC=1;AF=0.814;AN=2;DP=1211;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,13:34:99:387,0,579:14,7,7,6 chr1 160514955 . T C 660.48 PASS AC=1;AF=0.826;AN=2;DP=1342;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,15:35:99:344,0,497:10,10,7,8 chr1 160515266 . G A 2230.33 PASS AC=1;AF=0.821;AN=2;DP=3544;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,47:100:99:956,0,1251:27,26,24,23 chr1 160516049 . A G 66.22 PASS AC=1;AF=0.829;AN=2;DP=553;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,12:13:3:304,0,3:1,0,7,5 chr1 160516308 . A G 1147.09 PASS AC=1;AF=0.814;AN=2;DP=2102;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,20:42:99:585,0,592:14,8,13,7 chr1 160519593 . G A 1214.66 PASS AC=1;AF=0.5;AN=2;DP=99;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.808;QD=12.27;ReadPosRankSum=0.626;SOR=0.641;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:49,50:99:99:1243,0,1241:32,17,32,18 chr1 160577890 . T G 229.75 PASS AC=1;AF=0.826;AN=2;DP=613;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,14:22:99:420,0,208:6,2,10,4 chr1 160578541 . C CA 1697.91 PASS AC=1;AF=0.849;AN=2;DP=2309;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,15:54:99:441,0,1403:22,17,6,9 chr1 160580015 . A G 2130.04 PASS AC=1;AF=0.641;AN=2;DP=4736;MQ=60;set=variant-variant3-variant5-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:81,72:153:99:1771,0,2040:34,47,32,40 chr1 160582213 . C A 514.62 PASS AC=1;AF=0.571;AN=2;DP=866;MQ=60;set=variant-variant2-variant3-variant5-variant9-variant10-variant12-variant13-variant15-variant16-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,13:19:99:360,0,129:4,2,9,4 chr1 160582248 . C G 541.06 PASS AC=1;AF=0.571;AN=2;DP=1291;MQ=60;set=variant-variant2-variant3-variant5-variant9-variant10-variant12-variant13-variant15-variant16-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:16,22:38:99:539,0,395:10,6,13,9 chr1 160585554 . C G 1985.27 PASS AC=2;AF=0.989;AN=2;DP=4157;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,90:90:99:2842,269,0:0,0,49,41 chr1 160585706 . C T 153.68 PASS AC=2;AF=0.8;AN=2;DP=1512;MQ=60;set=variant-variant2-variant3-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1692,138,0:0,0,12,34 chr1 160589369 . A G 344.5 PASS AC=1;AF=0.5;AN=2;DP=38;FS=3.259;FractionInformativeReads=1;MQ=60;MQRankSum=1.195;QD=9.07;ReadPosRankSum=-1.498;SOR=1.508;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:24,14:38:99:373,0,634:15,9,11,3 chr1 160604172 . T G 62.99 PASS AC=1;AF=0.986;AN=2;DP=162;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.198;ReadPosRankSum=-0.922;set=variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,5:7:28:123,0,28:1,1,3,2 chr1 160604863 . A T 314.96 PASS AC=2;AF=0.75;AN=2;DP=622;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:951,75,0:0,0,5,20 chr1 160648549 . C T 251.9 PASS AC=1;AF=0.841;AN=2;DP=517;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,2:6:72:72,0,161:4,0,2,0 chr1 160650792 . GC G 126.16 PASS AC=2;AF=0.917;AN=2;DP=561;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:391,36,0:0,0,8,4 chr1 160650913 . A G 1536.21 PASS AC=2;AF=0.989;AN=2;DP=2728;MQ=60;MQRankSum=-0.944;ReadPosRankSum=-0.087;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,64:64:99:2688,201,0:0,0,42,22 chr1 160650918 . AC A 949.03 PASS AC=1;AF=0.5;AN=2;DP=670;MQ=60;set=variant4-variant12-variant19-variant20-variant24-variant26-variant31-variant35-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:28,41:69:99:1132,0,696:18,10,27,14 chr1 160653308 . CT C,CTT 973.88 PASS AC=1,0;AF=0.455,0.045;AN=2;DP=5109;set=Intersection GT:DP:GQ:SB 0/1:122:99:36,26,38,22 chr1 160681653 . G GA 1038.26 PASS AC=1;AF=0.533;AN=2;DP=772;MQ=60;set=variant3-variant6-variant7-variant9-variant13-variant16-variant21-variant28-variant29-variant30-variant33-filterInvariant35-variant36-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:28,8:36:90:90,0,605:13,15,4,4 chr1 160681775 . A G 280.63 PASS AC=1;AF=0.662;AN=2;DP=838;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant20-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,15:28:99:375,0,298:6,7,7,8 chr1 160681836 . C G 186.77 PASS AC=1;AF=0.579;AN=2;DP=225;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant9-variant10-variant12-variant15-variant24-variant25-variant27-variant28-variant29-variant31-variant34-variant35-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,7:14:99:221,0,192:3,4,1,6 chr1 160681863 . G T 81.49 PASS AC=1;AF=0.674;AN=2;DP=161;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant11-variant13-variant14-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant30-variant32-variant35-variant36-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,7:11:99:193,0,147:0,4,3,4 chr1 160717693 . G GT 185.1 PASS AC=2;AF=0.833;AN=2;DP=229;MQ=60;set=variant-variant2-variant3-variant4-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant19-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:285,27,0:0,0,7,2 chr1 160717872 . T G 2209.87 PASS AC=2;AF=1;AN=2;DP=3005;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1580,153,0:0,0,30,21 chr1 160722064 . A G 978.7 PASS AC=2;AF=1;AN=2;DP=1029;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:582,54,0:0,0,5,13 chr1 160723256 . A G 4997.43 PASS AC=2;AF=0.763;AN=2;DP=5413;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,151:151:99:4737,453,0:0,0,53,98 chr1 160723517 . A G 918.41 PASS AC=2;AF=0.763;AN=2;DP=1433;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:787,66,0:0,0,9,13 chr1 160723957 . T C 242.07 PASS AC=1;AF=0.568;AN=2;DP=238;FractionInformativeReads=1;set=variant2-variant3-variant4-variant5-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant21-variant24-variant25-variant26-variant28-variant30-variant35-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:99:112,0,117:2,2,2,2 chr1 160724305 . T C 653.38 PASS AC=2;AF=1;AN=2;DP=1456;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1318,117,0:0,0,26,13 chr1 160766179 . C CT 806.66 PASS AC=1;AF=0.756;AN=2;DP=1345;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,12:20:99:283,0,181:3,5,5,7 chr1 160771761 . C A 1375.29 PASS AC=1;AF=0.543;AN=2;DP=4180;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant9-variant11-variant12-variant16-variant17-variant20-variant24-variant25-variant26-variant28-variant30-variant35-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:111,135:246:99:3110,0,2760:52,59,63,72 chr1 160786670 . A G 700.86 PASS AC=1;AF=0.543;AN=2;DP=1199;MQ=60;set=variant2-variant4-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant19-variant21-variant22-variant24-variant27-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,27:57:99:660,0,822:12,18,8,19 chr1 160788131 . T C 825.92 PASS AC=1;AF=0.545;AN=2;DP=1048;MQ=60;set=variant2-variant3-variant4-variant5-variant9-variant11-variant12-variant16-variant17-variant20-variant24-variant25-variant26-variant28-variant30-variant35-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,22:50:99:625,0,677:11,17,5,17 chr1 160789196 . A C 3821.02 PASS AC=2;AF=1;AN=2;DP=5331;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,190:190:99:5920,568,0:0,0,69,121 chr1 160789308 . C T 530.03 PASS AC=2;AF=0.721;AN=2;DP=680;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant30-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:908,72,0:0,0,3,21 chr1 160793442 . A G 4013.83 PASS AC=2;AF=0.625;AN=2;DP=4573;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant30-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,141:141:99:4454,423,0:0,0,78,63 chr1 160793560 . A G 3171.71 PASS AC=2;AF=0.621;AN=2;DP=4224;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant30-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,140:140:99:4081,419,0:0,0,57,83 chr1 160793962 . G C 3134.57 PASS AC=2;AF=0.625;AN=2;DP=3807;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant30-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,115:115:99:3684,344,0:0,0,77,38 chr1 160797323 . T G 468.49 PASS AC=2;AF=0.65;AN=2;DP=462;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant24-variant25-variant26-variant27-variant28-variant30-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:597,48,0:0,0,12,4 chr1 160797514 . C G 3906.92 PASS AC=2;AF=0.633;AN=2;DP=3418;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant24-variant25-variant26-variant27-variant28-variant30-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,125:125:99:3552,374,0:0,0,60,65 chr1 160797684 . A G 2191.43 PASS AC=2;AF=0.633;AN=2;DP=1776;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant24-variant25-variant26-variant27-variant28-variant30-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2178,210,0:0,0,36,34 chr1 160798126 . A G 746.96 PASS AC=2;AF=0.633;AN=2;DP=713;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant24-variant25-variant26-variant27-variant28-variant30-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,33:33:98:1182,98,0:0,0,4,29 chr1 160800480 . T C 1573.1 PASS AC=2;AF=0.645;AN=2;DP=2033;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant24-variant25-variant26-variant27-variant28-variant30-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,84:84:99:2411,251,0:0,0,44,40 chr1 160800559 . A G 689.68 PASS AC=1;AF=0.568;AN=2;DP=1391;MQ=60;set=variant2-variant3-variant4-variant5-variant9-variant11-variant12-variant16-variant17-variant20-variant24-variant25-variant26-variant28-variant30-variant35-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,31:69:99:763,0,1082:15,23,16,15 chr1 160801046 . C G 3401.31 PASS AC=1;AF=0.542;AN=2;DP=3886;MQ=60;set=variant2-variant4-variant7-variant9-variant13-variant14-variant15-variant19-variant27-variant35-variant36-variant42 GT:AD:DP:GQ:PL:SB 0/1:197,177:374:99:4232,0,5101:88,109,79,98 chr1 160803802 . A G 495.81 PASS AC=1;AF=0.702;AN=2;DP=3998;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,52:100:99:1283,0,1203:25,23,31,21 chr1 160806019 . C G 1482.23 PASS AC=1;AF=0.5;AN=2;DP=233;FractionInformativeReads=1;MQ=60;set=variant4-variant35 GT:AD:DP:GQ:PL:SB 0/1:63,48:111:99:1207,0,1576:26,37,23,25 chr1 160809003 . G A 387.59 PASS AC=1;AF=0.688;AN=2;DP=742;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,12:24:99:454,0,348:2,10,0,12 chr1 160811669 . A G 788.39 PASS AC=1;AF=0.5;AN=2;DP=50;FS=1.142;FractionInformativeReads=0.98;MQ=60;MQRankSum=0.13;QD=15.77;ReadPosRankSum=-0.29;SOR=0.466;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:24,25:49:99:817,0,672:8,16,10,15 chr1 160832185 . C T 286.58 PASS AC=1;AF=0.5;AN=2;DP=78;FractionInformativeReads=1;MQ=60;set=variant4-variant25-variant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:12,13:25:99:419,0,424:10,2,11,2 chr1 160832212 . A G 142.7 PASS AC=1;AF=0.529;AN=2;DP=572;MQ=60;set=variant2-variant4-variant7-variant9-variant10-variant13-variant14-variant15-variant19-variant25-variant27-variant31-variant35-variant36-variant37-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:23,24:47:99:666,0,634:16,7,18,6 chr1 160832646 . A G 778.14 PASS AC=1;AF=0.533;AN=2;DP=800;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant7-variant9-variant10-variant13-variant14-variant15-variant19-variant25-variant27-variant31-variant35-variant36-variant42 GT:AD:DP:GQ:PL:SB 0/1:40,25:65:99:484,0,1050:16,24,12,13 chr1 160846284 . T G 310.29 PASS AC=1;AF=0.75;AN=2;DP=883;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,9:27:99:236,0,514:13,5,7,2 chr1 160849030 . T A 70.45 PASS AC=1;AF=0.75;AN=2;DP=817;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,9:19:99:264,0,354:10,0,8,1 chr1 160849060 . G A 193.9 PASS AC=1;AF=0.75;AN=2;DP=1582;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,21:35:99:612,0,512:14,0,15,6 chr1 160849082 . A G 606.39 PASS AC=1;AF=0.763;AN=2;DP=2491;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,44:75:99:1253,0,876:24,7,31,13 chr1 160849367 . G T 306.11 PASS AC=1;AF=0.75;AN=2;DP=927;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,10:19:99:283,0,171:3,6,2,8 chr1 160849420 . G A 91.66 PASS AC=1;AF=0.565;AN=2;DP=293;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant13-variant15-variant16-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,5:11:99:114,0,129:2,4,1,4 chr1 160850280 . G A 617.56 PASS AC=1;AF=0.763;AN=2;DP=2170;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,21:40:99:600,0,478:13,6,16,5 chr1 160850936 . T C 436.59 PASS AC=1;AF=0.763;AN=2;DP=7892;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:127,106:233:99:2339,0,3080:72,55,58,48 chr1 160851534 . A G 87.17 PASS AC=1;AF=0.842;AN=2;DP=303;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,5:7:70:184,0,70:2,0,5,0 chr1 160851564 . C G 37.72 PASS AC=1;AF=0.803;AN=2;DP=460;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,15:18:72:499,0,72:3,0,12,3 chr1 160851594 . GAAAAAAA G,GAAAAAA 82.47 PASS AC=1,0;AF=0.744,0.024;AN=2;DP=1069;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:DP:GQ:SB 0/1:36:99:9,1,21,5 chr1 160851619 . A G 294.37 PASS AC=1;AF=0.75;AN=2;DP=1753;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,33:47:99:1262,0,428:9,5,24,9 chr1 160851826 . A T 493.18 PASS AC=1;AF=0.75;AN=2;DP=3658;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,70:130:99:1917,0,1703:29,31,37,33 chr1 160851894 . G A 889.94 PASS AC=1;AF=0.763;AN=2;DP=4325;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:62,68:130:99:1782,0,1692:31,31,35,33 chr1 160852022 . C T 807.5 PASS AC=1;AF=0.75;AN=2;DP=6430;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:85,84:169:99:2033,0,2110:38,47,38,46 chr1 160852046 . T C 760.58 PASS AC=1;AF=0.75;AN=2;DP=5402;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:76,71:147:99:1783,0,1873:30,46,30,41 chr1 160854526 . G A 136.21 PASS AC=1;AF=0.763;AN=2;DP=874;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,7:20:99:211,0,447:10,3,5,2 chr1 160917902 . T C 804.76 PASS AC=1;AF=0.6;AN=2;DP=1787;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant16-variant18-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant30-variant35-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,47:90:99:1191,0,1082:15,28,15,32 chr1 160920809 . A G 747.31 PASS AC=1;AF=0.676;AN=2;DP=4795;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:74,55:129:99:1269,0,1885:44,30,30,25 chr1 160920813 . A G 985.22 PASS AC=2;AF=1;AN=2;DP=5780;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,140:140:99:5009,420,0:0,0,77,63 chr1 160920966 . C T 1595.06 PASS AC=1;AF=0.676;AN=2;DP=3824;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,58:126:99:1559,0,1845:34,34,34,24 chr1 160921230 . T G 531.7 PASS AC=1;AF=0.689;AN=2;DP=1146;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,17:34:99:567,0,544:2,15,2,15 chr1 160965537 . TCACACA TCACA,T,TCACACACA 1578.8 PASS AC=1,0,0;AF=0.537,0.293,0.012;AN=2;DP=2490;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:65:99:19,8,28,10 chr1 160967759 . C CT,CTT 346.44 PASS AC=1,0;AF=0.661,0.032;AN=2;DP=893;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant17-variant18-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42 GT:DP:GQ:SB 0/1:18:99:4,7,1,6 chr1 160969008 . T TG 875.75 PASS AC=1;AF=0.841;AN=2;DP=1735;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,23:42:99:604,0,495:12,7,13,10 chr1 160969585 . C T 1836.79 PASS AC=1;AF=0.854;AN=2;DP=4727;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:70,70:140:99:1692,0,1775:37,33,34,36 chr1 160971146 . A G 2313.03 PASS AC=1;AF=0.841;AN=2;DP=4475;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:63,43:106:99:929,0,1499:34,29,25,18 chr1 160990875 . T C 3215.33 PASS AC=1;AF=0.682;AN=2;DP=4915;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:90,93:183:99:3614,0,4541:37,53,39,54 chr1 160990876 . C A 3215.33 PASS AC=1;AF=0.682;AN=2;DP=4857;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:90,92:182:99:3614,0,4541:37,53,38,54 chr1 160990878 . C T 3166.48 PASS AC=1;AF=0.682;AN=2;DP=4783;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:89,90:179:99:3592,0,4544:37,52,36,54 chr1 161008535 . C G 2864.76 PASS AC=1;AF=0.55;AN=2;DP=1700;FractionInformativeReads=1;MQ=60;set=variant3-variant21-variant23-variant28-variant32-variant33-variant35-variant36-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:81,83:164:99:2237,0,2120:43,38,43,40 chr1 161010774 . A G 1630.86 PASS AC=1;AF=0.81;AN=2;DP=1593;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,18:42:99:548,0,750:4,20,3,15 chr1 161010791 . C T 508.28 PASS AC=1;AF=0.692;AN=2;DP=1150;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,16:33:99:461,0,514:3,14,3,13 chr1 161011051 . CAAA CAA,CAAAA,C,CA 130.32 PASS AC=1,0,0,0;AF=0.231,0.192,0.038,0.058;AN=2;DP=1054;set=filterInvariant3-variant4-variant5-variant6-variant7-variant9-filterInvariant10-variant13-variant14-variant16-filterInvariant17-variant18-variant20-filterInvariant21-variant22-filterInvariant23-variant25-variant26-variant29-variant30-variant32-variant35-filterInvariant38-variant39-variant41-filterInvariant42 GT:DP:GQ:SB 0/1:52:99:16,15,19,2 chr1 161011716 . G C 1834.64 PASS AC=1;AF=0.81;AN=2;DP=2688;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,33:66:99:883,0,830:15,18,12,21 chr1 161013121 . C T 1328.76 PASS AC=1;AF=0.705;AN=2;DP=5515;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:82,88:170:99:2053,0,2061:38,44,45,43 chr1 161014727 . A G 129.14 PASS AC=1;AF=0.716;AN=2;DP=570;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,6:10:69:193,0,69:2,2,2,4 chr1 161017556 . C T 664.33 PASS AC=1;AF=0.62;AN=2;DP=2711;MQ=60;set=variant-variant4-variant7-variant8-variant11-variant12-variant14-variant17-variant18-variant21-variant22-variant24-variant25-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:45,60:105:99:1562,0,1154:24,21,32,28 chr1 161019040 . G C 1460.5 PASS AC=1;AF=0.705;AN=2;DP=6941;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:70,74:144:99:1895,0,1859:37,33,44,30 chr1 161021807 . AC A 88.46 PASS AC=1;AF=0.5;AN=2;DP=8;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.067;QD=11.06;ReadPosRankSum=0.572;SOR=0.105;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:2,6:8:99:126,0,257:0,2,3,3 chr1 161021810 . ACCACCACCACCACCACCACCACCACCACCACCACC A 88.46 PASS AC=1;AF=0.5;AN=2;DP=8;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.589;QD=11.06;ReadPosRankSum=0.572;SOR=0.105;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:2,6:8:99:126,0,257:0,2,3,3 chr1 161022380 . G A 1519.95 PASS AC=1;AF=0.857;AN=2;DP=3408;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,42:83:99:1005,0,1072:18,23,20,22 chr1 161022639 . C G 58.54 PASS AC=1;AF=0.75;AN=2;DP=185;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant16-variant17-variant18-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant35-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,4:5:17:116,0,17:0,1,2,2 chr1 161023252 . TTCTCTCTCTCTCTCTCTCTCTCTC TTCTCTCTCTC,TTCTCTCTCTCTCTCTCTC,TTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC,TTCTCTCTCTCTCTCTCTCTC,TTCTCTCTCTCTCTCTCTCTCTCTCTCTC,TTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC,TTCTCTCTCTCTCTCTCTCTCTC,TTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC,TTCTCTCTCTCTCTCTCTCTCTCTCTC,TTC,TTCTCTCTCTCTCTC,T,TTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 430.25 PASS AC=0,1,0,0,1,0,0,0,0,0,0,0,0;AF=0.018,0.179,0.071,0.071,0.054,0.054,0.054,0.036,0.071,0.018,0.036,0.018,0.036;AN=2;DP=941;set=variant4-variant5-variant7-variant8-variant9-variant10-filterInvariant12-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant24-variant25-variant26-variant27-variant28-variant31-variant32-filterInvariant33-variant35-variant36-variant37-variant40-variant43-variant44 GT:DP:GQ:SB 2/5:17:99:0,1,4,12 chr1 161024782 . C T 123.2 PASS AC=1;AF=0.705;AN=2;DP=597;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,10:19:99:312,0,247:3,6,2,8 chr1 161042063 . C A 631.12 PASS AC=1;AF=0.553;AN=2;DP=1792;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant7-variant14-variant17-variant18-variant21-variant24-variant25-variant27-variant28-variant31-variant32-variant34-variant35-variant37-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:40,49:89:99:1300,0,1103:24,16,26,23 chr1 161042874 . AGCAGAGATGCGGT A 562.97 PASS AC=1;AF=0.5;AN=2;DP=337;MQ=60;set=variant3-variant7-variant21-variant23-variant28-variant33-variant35-variant36-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,20:41:99:764,0,2918:16,5,16,4 chr1 161043735 . A C 227.97 PASS AC=1;AF=0.838;AN=2;DP=953;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:17,10:27:99:280,0,451:7,10,4,6 chr1 161043764 . G A 183.99 PASS AC=1;AF=0.838;AN=2;DP=723;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:15,10:25:99:328,0,442:8,7,5,5 chr1 161044383 . T C 2691.39 PASS AC=1;AF=0.5;AN=2;DP=810;FractionInformativeReads=1;MQ=60;set=variant21-variant24-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:108,120:228:99:2908,0,2512:53,55,64,56 chr1 161047125 . CTATA C 97.73 PASS AC=1;AF=0.872;AN=2;DP=342;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,4:10:99:145,0,320:4,2,4,0 chr1 161047220 . T C 501.22 PASS AC=1;AF=0.556;AN=2;DP=410;FractionInformativeReads=1;MQ=60;set=variant3-variant21-variant23-variant28-variant33-variant35-variant36-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,30:51:99:900,0,542:14,7,22,8 chr1 161049358 . G A 5053.74 PASS AC=2;AF=0.93;AN=2;DP=5957;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,158:158:99:4865,473,0:0,0,88,70 chr1 161058927 . T C 1034.73 PASS AC=1;AF=0.5;AN=2;DP=1410;MQ=60;set=variant-variant3-variant21-variant23-variant33-variant35-variant36-variant37-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,72:128:99:1699,0,1244:31,25,40,32 chr1 161068240 . G A 790.1 PASS AC=2;AF=0.63;AN=2;DP=2222;MQ=60;set=variant-variant3-variant4-variant5-variant9-variant12-variant14-variant15-variant18-variant19-variant20-variant21-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,89:89:99:2855,263,0:0,0,56,33 chr1 161068836 . A C 3095.59 PASS AC=2;AF=0.579;AN=2;DP=4640;set=variant-variant3-variant4-variant5-variant14-variant18-variant21-variant24-variant25-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,254:255:99:7638,718,0:1,0,134,120 chr1 161089450 . C CTAAACT 923.64 PASS AC=2;AF=0.63;AN=2;DP=1765;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant9-variant13-variant14-variant15-variant18-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:3291,225,0:0,0,33,42 chr1 161090591 . A C 214.51 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=190;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:70,19:89:99:198,0,1428:8,62,17,2 chr1 161093425 . CAA CA,C 46.03 PASS AC=1,0;AF=0.571,0.214;AN=2;DP=46;FS=0;set=variant4-variant14-variant19-variant21-variant24-variant35-variant41 GT:DP:GQ:SB 0/1:6:3:0,1,5,0 chr1 161094834 . C T 160.4 PASS AC=2;AF=0.635;AN=2;DP=517;FractionInformativeReads=1;set=variant-variant3-variant4-variant5-variant7-variant9-variant13-variant15-variant18-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:940,84,0:0,0,22,6 chr1 161101890 . A C 144.11 PASS AC=2;AF=0.659;AN=2;DP=215;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant7-variant9-variant13-variant14-variant15-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:166,15,0:0,0,3,2 chr1 161126975 . C G 1116.56 PASS AC=2;AF=0.63;AN=2;DP=2389;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant9-variant13-variant14-variant15-variant18-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,110:110:99:3263,329,0:0,0,59,51 chr1 161135559 . A G 62.99 PASS AC=2;AF=0.844;AN=2;DP=97;FractionInformativeReads=1;MQ=60;set=variant4-variant9-variant11-variant13-variant15-variant18-variant21-variant22-variant24-variant25-variant29-variant32-variant33-variant34-variant35-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:216,18,0:0,0,1,5 chr1 161136224 . C A 734.67 PASS AC=2;AF=0.63;AN=2;DP=1971;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant9-variant13-variant14-variant15-variant18-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:2099,194,0:0,0,47,18 chr1 161136843 . C G 1201.41 PASS AC=2;AF=0.63;AN=2;DP=3164;set=variant-variant3-variant4-variant5-variant7-variant9-variant13-variant14-variant15-variant18-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:2,124:126:99:3932,330,0:1,1,61,63 chr1 161138121 . C T 685.49 PASS AC=1;AF=0.5;AN=2;DP=293;FractionInformativeReads=1;MQ=60;set=variant21-variant24-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:44,25:69:99:668,0,1240:27,17,17,8 chr1 161138933 . C G 1149.97 PASS AC=1;AF=0.5;AN=2;DP=481;FractionInformativeReads=1;MQ=60;set=variant21-variant24-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:57,79:136:99:1972,0,1394:29,28,38,41 chr1 161141086 . A G 759.24 PASS AC=1;AF=0.5;AN=2;DP=169;FractionInformativeReads=1;MQ=60;set=variant21-variant24-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:10,24:34:99:654,0,193:6,4,10,14 chr1 161141432 . C G 509.51 PASS AC=2;AF=0.583;AN=2;DP=783;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant14-variant18-variant21-variant24-variant25-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1446,147,0:0,0,27,22 chr1 161143312 . T C 539.89 PASS AC=2;AF=0.568;AN=2;DP=635;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant13-variant14-variant15-variant18-variant21-variant22-variant24-variant25-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1301,114,0:0,0,28,10 chr1 161143969 . A G 241.2 PASS AC=2;AF=0.63;AN=2;DP=767;FractionInformativeReads=1;set=variant-variant3-variant4-variant5-variant7-variant9-variant13-variant14-variant15-variant18-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1231,102,0:0,0,8,26 chr1 161160327 . GA G 860.99 PASS AC=2;AF=0.654;AN=2;DP=909;set=variant3-variant4-variant19-variant21-variant24-variant25-variant31-variant33-variant35-variant36-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,57:58:99:1457,147,0:1,0,37,20 chr1 161160872 . T C 2100.33 PASS AC=2;AF=0.654;AN=2;DP=1577;MQ=60;set=variant3-variant4-variant19-variant21-variant24-variant25-variant31-variant33-variant35-variant36-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,110:110:99:3489,329,0:0,0,66,44 chr1 161162173 . G A 714 PASS AC=2;AF=0.708;AN=2;DP=2080;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:2336,228,0:0,0,33,43 chr1 161163037 . T C 1040.6 PASS AC=2;AF=0.708;AN=2;DP=3163;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,85:85:99:2737,255,0:0,0,57,28 chr1 161163633 . C T 1117.85 PASS AC=2;AF=0.722;AN=2;DP=3829;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,104:104:99:3354,312,0:0,0,53,51 chr1 161165724 . GACAC GACACAC,G,GACACACAC,GAC 158.12 PASS AC=0,2,0,0;AF=0.353,0.25,0.029,0.015;AN=2;DP=527;set=variant-variant3-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 2/2:15:46:0,0,9,6 chr1 161166723 . G T 1002.78 PASS AC=2;AF=0.654;AN=2;DP=866;MQ=60;set=variant3-variant4-variant19-variant21-variant24-variant25-variant31-variant33-variant35-variant36-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,52:52:99:1698,156,0:0,0,14,38 chr1 161167698 . T G 602.47 PASS AC=2;AF=0.722;AN=2;DP=1332;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1470,114,0:0,0,32,6 chr1 161167989 . G A 2746.42 PASS AC=1;AF=0.6;AN=2;DP=838;MQ=60;set=variant21-variant24-variant35-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:79,91:170:99:2452,0,2320:38,41,43,48 chr1 161169165 . G T 366.26 PASS AC=2;AF=0.654;AN=2;DP=375;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant19-variant21-variant24-variant25-variant31-variant33-variant35-variant36-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:744,81,0:0,0,14,13 chr1 161172525 . C T 133.64 PASS AC=2;AF=0.654;AN=2;DP=184;MQ=60;set=variant3-variant4-variant19-variant21-variant24-variant25-variant31-variant33-variant35-variant36-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:537,36,0:0,0,0,12 chr1 161176137 . A G 2268.13 PASS AC=2;AF=0.722;AN=2;DP=5049;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,188:188:99:6020,563,0:0,0,124,64 chr1 161179877 . G A 1418.24 PASS AC=2;AF=0.65;AN=2;DP=1894;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant7-variant9-variant15-variant19-variant21-variant24-variant25-variant27-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:2545,237,0:0,0,47,32 chr1 161183516 . C T 821.73 PASS AC=2;AF=0.654;AN=2;DP=1034;MQ=60;set=variant3-variant4-variant19-variant21-variant24-variant25-variant31-variant33-variant35-variant36-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,105:105:99:3345,314,0:0,0,67,38 chr1 161184059 . CTGTGTGTGTG CTGTGTGTGTGTG,CTGTGTGTGTGTGTGTG,CTGTGTGTG,CTGTGTGTGTGTGTG,CTGTGTGTGTGTGTGTGTG,C,CTGTGTGTGTGTGTGTGTGTG 260.2 PASS AC=0,0,0,0,2,0,0;AF=0.205,0.205,0.026,0.154,0.077,0.013,0.013;AN=2;DP=1949;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:DP:GQ:SB 5/5:23:67:0,0,3,20 chr1 161188936 . T C 781.24 PASS AC=2;AF=0.571;AN=2;DP=637;MQ=60;set=variant4-variant11-variant13-variant15-variant19-variant21-variant22-variant24-variant25-variant31-variant35-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:2,40:42:77:1337,77,0:1,1,19,21 chr1 161191228 . G A 61.62 PASS AC=2;AF=0.605;AN=2;DP=318;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant11-variant13-variant15-variant19-variant21-variant22-variant24-variant25-variant27-variant31-variant33-variant35-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:615,51,0:0,0,14,3 chr1 161191450 . CTTTTTTTTTTTTT CTTTTTT,CTTTTTTTTTTT,CTTTTTTTTTT,CTTT,CTTTTTTT,CTTTTTTTTTTTT,C,CTTTTTTTT 336.83 PASS AC=2,0,0,0,0,0,0,0;AF=0.405,0.024,0.024,0.024,0.071,0.048,0.024,0.024;AN=2;DP=722;set=variant-variant2-variant4-variant7-variant10-variant11-variant13-variant15-variant19-variant21-variant22-variant24-variant25-variant27-filterInvariant29-variant33-variant35-variant38-variant39-variant40-variant43 GT:DP:GQ:SB 1/1:38:53:2,1,7,28 chr1 161191462 . T C 31.25 PASS AC=1;AF=0.5;AN=2;DP=432;set=filterInvariant-variant4-variant11-variant13-filterInvariant15-variant19-variant21-variant22-variant24-variant25-variant35-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:9,17:26:99:317,0,133:2,7,4,13 chr1 161191463 . T C 42.51 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=38;FS=5.524;FractionInformativeReads=0.684;MQ=60;MQRankSum=0.822;QD=1.12;ReadPosRankSum=0.274;SOR=2.457;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:20,6:26:71:71,0,420:6,14,0,6 chr1 161191522 . A G 59.7 PASS AC=2;AF=0.694;AN=2;DP=134;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant11-variant13-variant15-variant19-variant21-variant22-variant24-variant25-variant27-variant31-variant33-variant35-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:450,30,0:0,0,0,10 chr1 161192845 . CCACACACACACACA CCA,CCACACACA,CCACACACACACA,C,CCACACACACA,CCACA,CCACACACACACACACA,CCACACACACACACACACA,CCACACACACACACACACACACA,CCACACA 256.52 PASS AC=2,0,0,0,0,0,0,0,0,0;AF=0.174,0.233,0.058,0.023,0.012,0.093,0.035,0.012,0.012,0.012;AN=2;DP=3731;set=variant-variant2-filterInvariant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-filterInvariant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:DP:GQ:SB 1/1:73:95:0,1,26,46 chr1 161195709 . CTTTTTTTTT CTT,CT,CTTTTTTTT,CTTTT,C,CTTT 97.92 PASS AC=2,0,0,0,0,0;AF=0.452,0.167,0.024,0.095,0.024,0.024;AN=2;DP=169;set=variant4-variant7-variant8-variant10-variant12-variant14-variant15-variant21-variant22-variant25-variant27-variant29-variant31-variant33-variant34-variant35-variant38-variant39-variant40-variant41-variant42 GT:DP:GQ:SB 1/1:5:15:0,0,3,2 chr1 161196166 . A C 730.41 PASS AC=2;AF=0.587;AN=2;DP=1384;MQ=60;set=variant-variant4-variant7-variant8-variant11-variant13-variant14-variant15-variant19-variant21-variant22-variant24-variant25-variant27-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:2254,186,0:0,0,42,20 chr1 161197921 . G A 1772.66 PASS AC=1;AF=0.5;AN=2;DP=248;MQ=60;set=variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:52,67:119:99:1801,0,1395:31,21,32,35 chr1 161199078 . G A 610.3 PASS AC=1;AF=0.5;AN=2;DP=41;FS=6.816;FractionInformativeReads=1;MQ=60;MQRankSum=0.494;QD=14.89;ReadPosRankSum=1.777;SOR=0.925;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:16,25:41:99:639,0,426:6,10,15,10 chr1 161200487 . C A 353.21 PASS AC=2;AF=0.671;AN=2;DP=1868;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:2086,186,0:0,0,34,28 chr1 161200586 . T G 790.56 PASS AC=2;AF=0.607;AN=2;DP=1434;MQ=60;set=variant-variant4-variant11-variant13-variant16-variant21-variant24-variant25-variant31-variant35-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,125:125:99:3781,374,0:0,0,64,61 chr1 161201350 . G T 73.32 PASS AC=2;AF=0.587;AN=2;DP=271;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant7-variant8-variant13-variant14-variant15-variant16-variant19-variant21-variant22-variant24-variant25-variant27-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:757,51,0:0,0,5,12 chr1 161201352 . G A 73.32 PASS AC=2;AF=0.587;AN=2;DP=261;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant7-variant8-variant13-variant14-variant15-variant16-variant19-variant21-variant22-variant24-variant25-variant27-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:51:757,51,0:0,0,5,11 chr1 161202605 . G A 1953.98 PASS AC=2;AF=0.583;AN=2;DP=3273;MQ=60;set=variant-variant4-variant7-variant8-variant11-variant13-variant14-variant15-variant16-variant19-variant21-variant22-variant24-variant25-variant27-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,149:149:99:4602,447,0:0,0,80,69 chr1 161205046 . GTTTTTT GT,GTTT,G,GTTTCTTTTTTT 294.67 PASS AC=0,0,2,0;AF=0.409,0.045,0.182,0.045;AN=2;DP=212;MQ=60;set=variant-variant4-variant15-variant16-variant25-variant35-variant36-variant38-variant39-variant40-variant43 GT:DP:GQ:SB 3/3:5:15:0,0,1,4 chr1 161205056 . T C 128.62 PASS AC=2;AF=0.667;AN=2;DP=43;MQ=60;set=variant25-variant35-variant38 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:169,15,0:0,0,1,4 chr1 161206230 . T C 1980.48 PASS AC=1;AF=0.5;AN=2;DP=310;FractionInformativeReads=1;MQ=60;set=variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:87,86:173:99:2009,0,2217:50,37,43,43 chr1 161228800 . C T 467.02 PASS AC=2;AF=0.588;AN=2;DP=968;MQ=60;set=variant-variant4-variant5-variant14-variant15-variant16-variant19-variant21-variant22-variant24-variant25-variant31-variant35-variant37-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,67:67:99:2297,201,0:0,0,23,44 chr1 161253657 . C T 350.51 PASS AC=1;AF=0.638;AN=2;DP=1009;MQ=60;set=variant2-variant3-variant6-variant9-variant10-variant12-variant13-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:30,18:48:99:425,0,862:10,20,6,12 chr1 161254280 . G C 1309.32 PASS AC=1;AF=0.526;AN=2;DP=1276;MQ=60;set=variant3-variant9-variant10-variant13-variant15-variant17-variant21-variant24-variant25-variant27-variant28-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:31,43:74:99:1104,0,768:15,16,21,22 chr1 161254634 . G C 868.09 PASS AC=1;AF=0.526;AN=2;DP=1325;MQ=60;set=variant3-variant9-variant10-variant13-variant15-variant17-variant21-variant24-variant25-variant27-variant28-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:34,44:78:99:1067,0,991:15,19,20,24 chr1 161274618 . T A 34.67 PASS AC=1;AF=0.5;AN=2;DP=12;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.825;QD=2.89;ReadPosRankSum=0.289;SOR=0.368;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:8,4:12:63:63,0,242:3,5,2,2 chr1 161274755 . T TTCTC 298.36 PASS AC=1;AF=0.5;AN=2;DP=245;MQ=60;set=variant3-variant13-variant15-variant17-variant25-variant27-variant28-variant31-variant33-variant35-variant36-variant37-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:8,14:22:99:543,0,406:3,5,7,7 chr1 161276376 . G A 406.42 PASS AC=1;AF=0.56;AN=2;DP=1290;MQ=60;set=variant3-variant9-variant11-variant12-variant13-variant15-variant17-variant21-variant24-variant25-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:31,35:66:99:952,0,823:12,19,13,22 chr1 161276434 . A G 1030.4 PASS AC=2;AF=1;AN=2;DP=1742;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1592,131,0:0,0,25,19 chr1 161279882 . A G 123.15 PASS AC=1;AF=0.603;AN=2;DP=457;MQ=60;set=variant2-variant3-variant5-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant21-variant22-variant24-variant25-variant27-variant28-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,11:19:99:408,0,258:4,4,4,7 chr1 161309452 . GTTTTT GT,G 93.11 PASS AC=0,2;AF=0.5,0.5;AN=2;DP=17;FS=0;MQ=60;SOR=2.833;set=variant21-variant35 GT:DP:GQ:SB 2/2:3:10:0,0,0,3 chr1 161332091 . CT C 500.91 PASS AC=1;AF=0.5;AN=2;DP=849;set=variant3-filterInvariant5-filterInvariant10-variant11-variant13-variant15-variant17-variant19-variant21-variant25-filterInvariant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant40-filterInvariant42 GT:AD:DP:GQ:PL:SB 0/1:12,23:35:99:438,0,247:9,3,16,7 chr1 161475173 . C T 1312.6 PASS AC=1;AF=0.5;AN=2;DP=304;FractionInformativeReads=1;MQ=60;set=variant4-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:46,51:97:99:1216,0,1230:32,14,30,21 chr1 161475750 . G A 3650.19 PASS AC=1;AF=0.533;AN=2;DP=2274;MQ=60;set=variant2-variant3-variant11-variant13-variant16-variant21-variant27-variant28-variant35-variant36-variant37-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:85,89:174:99:2242,0,1937:47,38,48,41 chr1 161476204 . C T 6130.19 PASS AC=1;AF=0.533;AN=2;DP=2332;FractionInformativeReads=1;set=variant2-variant3-variant11-variant13-variant16-variant21-variant27-variant28-variant35-variant36-variant37-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:87,82:169:99:3138,0,4335:44,43,44,38 chr1 161476205 . A G 6130.19 PASS AC=1;AF=0.533;AN=2;DP=2338;FractionInformativeReads=1;set=variant2-variant3-variant11-variant13-variant16-variant21-variant27-variant28-variant35-variant36-variant37-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:88,82:170:99:3138,0,4335:45,43,44,38 chr1 161476533 . T C 2221.02 PASS AC=1;AF=0.533;AN=2;DP=891;MQ=60;set=variant2-variant3-variant11-variant13-variant16-variant21-variant27-variant28-variant35-variant36-variant37-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:31,36:67:99:939,0,846:9,22,12,24 chr1 161479438 . C T 361.43 PASS AC=1;AF=0.536;AN=2;DP=188;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant11-variant13-variant16-variant27-variant28-variant35-variant36-variant37-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,7:18:99:168,0,327:9,2,5,2 chr1 161479599 . G A 2716.12 PASS AC=1;AF=0.533;AN=2;DP=1545;set=variant2-variant3-variant11-variant13-variant16-variant21-variant27-variant28-variant35-variant36-variant37-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:62,59:121:99:1492,0,1673:37,25,40,19 chr1 161480649 . A G 11876.5 PASS AC=1;AF=0.533;AN=2;DP=6500;set=variant2-variant3-variant11-variant13-variant16-variant21-variant27-variant28-variant35-variant36-variant37-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:264,202:466:99:4699,0,6266:120,144,99,103 chr1 161494311 . G C 3117.52 PASS AC=2;AF=0.826;AN=2;DP=3970;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,129:129:99:3877,387,0:0,0,59,70 chr1 161495477 . A T 10864.1 PASS AC=2;AF=0.707;AN=2;DP=21389;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,567:567:99:16648,1691,0:0,0,262,305 chr1 161495885 . T C 2487.4 PASS AC=2;AF=0.821;AN=2;DP=7349;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,209:209:99:6871,627,0:0,0,98,111 chr1 161514542 . A C 954.66 PASS AC=2;AF=0.672;AN=2;DP=2421;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant6-variant7-variant11-variant12-variant13-variant14-variant16-variant21-variant22-variant23-variant25-variant27-variant28-variant30-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,85:85:99:2530,255,0:0,0,52,33 chr1 161514759 . C CAG 192.36 PASS AC=1;AF=0.5;AN=2;DP=15;FS=0;FractionInformativeReads=0.533;MQ=39.69;MQRankSum=-1.589;QD=12.82;ReadPosRankSum=-1.067;SOR=3.912;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:2,6:8:65:230,0,65:1,1,0,6 chr1 161518333 . A T,C 3579.06 PASS AC=0,2;AF=0.313,0.219;AN=2;DP=6322;set=variant2-variant3-variant11-variant13-variant14-variant16-variant21-variant28-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:DP:GQ:SB 2/2:370:99:2,0,176,192 chr1 161561832 . C T 44.4 PASS AC=2;AF=0.545;AN=2;DP=317;FractionInformativeReads=1;set=filterInvariant2-filterInvariant11-variant17-variant21-variant27-variant28-variant35-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:255,27,0:0,0,5,4 chr1 161563281 . A AG 1323.45 PASS AC=2;AF=0.567;AN=2;DP=988;set=variant2-variant11-variant13-variant14-variant16-variant21-variant25-variant28-variant35-variant36-variant37-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1433,123,0:0,0,24,16 chr1 161565314 . C T 344.22 PASS AC=2;AF=0.583;AN=2;DP=705;FractionInformativeReads=1;set=variant2-variant11-variant14-variant16-variant21-variant25-variant28-variant35-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:33:468,33,0:0,0,8,2 chr1 161565324 . C T 1306.35 PASS AC=2;AF=0.811;AN=2;DP=3675;set=variant-filterInvariant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:51:646,51,0:0,0,12,4 chr1 161565381 . A G 949.35 PASS AC=2;AF=0.567;AN=2;DP=2498;set=variant2-variant11-variant13-variant14-variant16-variant21-variant25-variant28-variant35-variant36-variant37-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:1774,171,0:0,0,35,22 chr1 161576227 . C G 494.82 PASS AC=2;AF=0.817;AN=2;DP=1750;set=filterInvariant2-filterInvariant3-variant4-variant5-filterInvariant6-variant7-variant8-variant9-variant10-filterInvariant11-variant12-variant13-variant14-filterInvariant15-variant16-filterInvariant17-filterInvariant18-variant19-filterInvariant20-filterInvariant21-filterInvariant22-variant24-variant25-variant26-filterInvariant27-variant28-filterInvariant29-variant30-variant31-variant32-variant33-filterInvariant34-filterInvariant35-variant36-variant37-variant38-variant39-filterInvariant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:952,90,0:0,0,26,4 chr1 161577657 . G A 1730.75 PASS AC=2;AF=0.685;AN=2;DP=2826;set=variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant14-variant16-variant21-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,44:45:99:1371,125,0:1,0,23,21 chr1 161577669 . G A 1767.52 PASS AC=2;AF=0.793;AN=2;DP=4283;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1318,125,0:0,0,21,21 chr1 161593349 . C T 3834.99 PASS AC=2;AF=1;AN=2;DP=3690;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1762,152,0:0,0,13,38 chr1 161593397 . C G 2162.19 PASS AC=2;AF=1;AN=2;DP=2186;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:1067,81,0:0,0,10,17 chr1 161593468 . A G 1619.72 PASS AC=2;AF=1;AN=2;DP=2795;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1012,99,0:0,0,15,18 chr1 161593551 . T G 1475.74 PASS AC=2;AF=1;AN=2;DP=1690;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:999,72,0:0,0,1,23 chr1 161593571 . A G 1255.78 PASS AC=2;AF=1;AN=2;DP=1473;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:651,48,0:0,0,1,15 chr1 161594226 . C T 540.2 PASS AC=2;AF=1;AN=2;DP=1062;FS=0;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:392,36,0:0,0,9,3 chr1 161594246 . G T 697.63 PASS AC=2;AF=1;AN=2;DP=1483;FS=0;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:428,39,0:0,0,10,3 chr1 161594525 . G C 2990.38 PASS AC=2;AF=1;AN=2;DP=2956;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1601,108,0:0,0,12,23 chr1 161594526 . T G 2990.38 PASS AC=2;AF=1;AN=2;DP=2856;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1601,108,0:0,0,12,24 chr1 161594561 . C G 1263.63 PASS AC=2;AF=0.988;AN=2;DP=1854;FS=0;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:691,66,0:0,0,5,17 chr1 161596072 . T C 260.36 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=141;FS=20.933;FractionInformativeReads=1;MQ=52;MQRankSum=-5.73;QD=1.85;ReadPosRankSum=-6.107;SOR=2.785;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:120,21:141:99:289,0,3280:66,54,18,3 chr1 161596283 . G A 1419.83 PASS AC=2;AF=0.966;AN=2;DP=2667;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,78:78:99:2611,233,0:0,0,19,59 chr1 161599693 . T C 1257.96 PASS AC=2;AF=0.987;AN=2;DP=3367;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:1406,144,0:0,0,30,18 chr1 161600104 . A T 34.82 PASS AC=1;AF=0.5;AN=2;DP=433;set=filterInvariant2-variant3-filterInvariant16-variant35-filterInvariant40 GT:AD:DP:GQ:PL:SB 0/1:50,21:71:99:494,0,1294:34,16,19,2 chr1 161600189 . A C 1171.4 PASS AC=1;AF=0.5;AN=2;DP=1224;set=variant8-variant14-variant25-variant27-variant33-variant35-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:90,66:156:99:1375,0,1758:44,46,33,33 chr1 161600345 . C T 69.04 PASS AC=1;AF=0.662;AN=2;DP=343;set=filterInvariant-filterInvariant2-filterInvariant3-variant4-filterInvariant5-filterInvariant6-filterInvariant7-variant8-filterInvariant10-filterInvariant11-filterInvariant14-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant20-variant21-filterInvariant22-filterInvariant23-filterInvariant25-filterInvariant26-variant27-filterInvariant28-filterInvariant29-filterInvariant32-filterInvariant33-filterInvariant34-filterInvariant35-variant36-filterInvariant37-filterInvariant38-variant39-filterInvariant40-filterInvariant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:2,7:9:29:198,0,29:0,2,1,6 chr1 161600832 . G T 765.63 PASS AC=2;AF=0.776;AN=2;DP=1157;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:736,57,0:0,0,17,2 chr1 161601133 . T C 1411.26 PASS AC=2;AF=1;AN=2;DP=1785;FS=0;MQRankSum=-1.264;ReadPosRankSum=0.234;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:694,63,0:0,0,6,15 chr1 161643125 . T C 904.22 PASS AC=1;AF=0.5;AN=2;DP=336;FractionInformativeReads=1;set=variant8-variant27-variant35-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:48,16:64:99:493,0,1529:17,31,8,8 chr1 161643269 . C T 698.01 PASS AC=1;AF=0.5;AN=2;DP=1042;FractionInformativeReads=1;set=variant3-variant4-variant6-variant10-variant11-variant26-variant27-variant28-variant29-variant31-variant35-variant36-variant39 GT:AD:DP:GQ:PL:SB 0/1:71,53:124:99:1114,0,1662:35,36,29,24 chr1 161643798 . T C 319.36 PASS AC=2;AF=0.885;AN=2;DP=78;FS=0;FractionInformativeReads=1;set=variant3-variant4-variant6-variant10-variant11-variant26-variant27-variant28-variant29-variant31-variant35-variant36-variant39 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:123,9,0:0,0,0,3 chr1 161644955 . G A 164.94 PASS AC=1;AF=0.545;AN=2;DP=160;FractionInformativeReads=1;set=variant3-variant4-variant6-variant10-variant11-variant26-variant27-variant28-variant31-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:13,10:23:99:238,0,261:7,6,7,3 chr1 161645010 . C A 341.07 PASS AC=1;AF=0.538;AN=2;DP=284;set=variant3-variant4-variant6-variant10-variant11-variant26-variant27-variant28-variant29-variant31-variant35-variant36-variant39 GT:AD:DP:GQ:PL:SB 0/1:16,14:30:99:297,0,387:9,7,8,6 chr1 161645259 . T G 227.59 PASS AC=2;AF=0.872;AN=2;DP=1391;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1100,108,0:0,0,13,23 chr1 161647533 . A G 343.73 PASS AC=2;AF=0.793;AN=2;DP=2820;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,67:67:99:1944,200,0:0,0,40,27 chr1 161676904 . T C 8677.85 PASS AC=2;AF=0.756;AN=2;DP=13474;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,352:354:99:10657,1009,0:1,1,211,141 chr1 161676970 . A G 10093.8 PASS AC=2;AF=0.756;AN=2;DP=14889;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,381:381:99:11383,1142,0:0,0,189,192 chr1 161677350 . A G 196.77 PASS AC=2;AF=0.786;AN=2;DP=263;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:136,12,0:0,0,1,3 chr1 161680258 . G A 4606.22 PASS AC=1;AF=0.732;AN=2;DP=6063;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:86,69:155:99:1717,0,2014:45,41,39,30 chr1 161680413 . GA G 704.34 PASS AC=1;AF=0.5;AN=2;DP=587;MQ=60;set=variant10-variant21-variant32-variant33-variant35-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:53,33:86:99:664,0,2516:21,32,15,18 chr1 161680432 . A G 1710.38 PASS AC=1;AF=0.5;AN=2;DP=461;FractionInformativeReads=1;MQ=60;set=variant21-variant32-variant33-variant35-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:54,42:96:99:1417,0,1570:25,29,18,24 chr1 161680518 . T A 985.61 PASS AC=1;AF=0.5;AN=2;DP=445;FractionInformativeReads=1;MQ=60;set=variant21-variant32-variant33-variant35-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:43,35:78:99:782,0,1160:21,22,18,17 chr1 161680786 . T C 166.67 PASS AC=1;AF=0.5;AN=2;DP=71;FractionInformativeReads=1;MQ=60;set=variant21-variant32-variant35-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,7:11:99:282,0,144:2,2,5,2 chr1 161680791 . T C 198.88 PASS AC=1;AF=0.5;AN=2;DP=74;FractionInformativeReads=1;MQ=60;set=variant21-variant32-variant35-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,7:11:99:279,0,177:3,1,5,2 chr1 161680868 . T C 254.9 PASS AC=1;AF=0.676;AN=2;DP=728;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,7:15:99:226,0,173:4,4,5,2 chr1 161681848 . C T 1827.4 PASS AC=1;AF=0.5;AN=2;DP=801;FractionInformativeReads=1;MQ=60;set=variant21-variant32-variant33-variant35-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:69,64:133:99:1770,0,1889:34,35,25,39 chr1 161683136 . G A 9395.66 PASS AC=1;AF=0.681;AN=2;DP=9513;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:182,141:323:99:3537,0,4732:106,76,88,53 chr1 161691366 . C A 349.59 PASS AC=2;AF=0.875;AN=2;DP=725;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:588,51,0:0,0,13,4 chr1 161691433 . C T 610.68 PASS AC=1;AF=0.762;AN=2;DP=1212;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,6:27:99:108,0,596:12,9,4,2 chr1 161695381 . G C 61.77 PASS AC=2;AF=0.731;AN=2;DP=168;MQ=60;set=variant-variant3-variant4-variant6-variant8-variant9-variant11-variant12-variant13-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant29-variant30-variant33-variant34-variant35-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:271,21,0:0,0,6,1 chr1 161695639 . G T 3137.09 PASS AC=2;AF=0.852;AN=2;DP=5681;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,162:162:99:5083,485,0:0,0,105,57 chr1 161696088 . T C 5370.74 PASS AC=2;AF=0.768;AN=2;DP=8882;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,202:202:99:6337,606,0:0,0,104,98 chr1 161696782 . G C 1298.61 PASS AC=1;AF=0.662;AN=2;DP=2451;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,29:60:99:672,0,804:9,22,11,18 chr1 161696998 . C G 488.36 PASS AC=1;AF=0.662;AN=2;DP=740;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,8:22:99:210,0,482:10,4,5,3 chr1 161697547 . T C 2569.38 PASS AC=1;AF=0.5;AN=2;DP=988;MQ=60;set=variant21-variant32-variant33-variant35-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:99,81:180:99:2086,0,2665:49,50,41,40 chr1 161698011 . CGGGGG CG,CGGG,C,CGG,CGGGG 7611.69 PASS AC=1,0,0,1,0;AF=0.607,0.036,0.06,0.036,0.012;AN=2;DP=4926;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/4:118:99:0,4,47,67 chr1 161698019 . G C 7619.45 PASS AC=1;AF=0.676;AN=2;DP=4104;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,87:130:99:3193,0,1367:22,21,33,54 chr1 161721267 . G A 153.15 PASS AC=1;AF=0.625;AN=2;DP=34;FS=0;FractionInformativeReads=1;MQ=60;set=variant21-variant32-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:8,3:11:99:102,0,238:6,2,3,0 chr1 161721351 . A G 959.06 PASS AC=1;AF=0.732;AN=2;DP=840;MQ=60;set=variant-variant2-variant3-variant4-variant8-variant10-variant12-variant13-variant15-variant16-variant20-variant21-variant22-variant23-variant24-variant27-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,11:44:99:239,0,853:20,13,8,3 chr1 161721403 . T TG 706.3 PASS AC=1;AF=0.5;AN=2;DP=323;MQ=60;set=variant21-variant32-variant33-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:48,22:70:99:527,0,1545:26,22,15,7 chr1 161722272 . C A 620.69 PASS AC=1;AF=0.6;AN=2;DP=2026;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant22-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:40,30:70:99:656,0,967:16,24,15,15 chr1 161722779 . C CAAA,CAA 848.2 PASS AC=1,1;AF=0.795,0.08;AN=2;DP=1237;set=Intersection GT:DP:GQ:SB 2/1:24:99:0,0,21,3 chr1 161722805 . T G 1397.11 PASS AC=1;AF=0.5;AN=2;DP=282;FractionInformativeReads=1;MQ=60;set=variant21-variant32-variant33-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:31,21:52:99:523,0,990:25,6,15,6 chr1 161736035 . A G 1732.16 PASS AC=2;AF=0.875;AN=2;DP=3231;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:2059,204,0:0,0,34,34 chr1 161736052 . C A 1175.96 PASS AC=1;AF=0.5;AN=2;DP=73;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.189;QD=16.11;ReadPosRankSum=-1.514;SOR=0.653;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:27,46:73:99:1204,0,631:15,12,25,21 chr1 161736209 . T C 861.7 PASS AC=1;AF=0.5;AN=2;DP=77;FS=1.94;FractionInformativeReads=1;MQ=60;MQRankSum=0.29;QD=11.19;ReadPosRankSum=1.167;SOR=1.004;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:39,38:77:99:890,0,909:16,23,13,25 chr1 161736272 . C T 470.79 PASS AC=1;AF=0.5;AN=2;DP=50;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.002;QD=9.42;ReadPosRankSum=-2.575;SOR=0.586;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:29,21:50:99:499,0,780:9,20,7,14 chr1 161754004 . T A 207.59 PASS AC=1;AF=0.5;AN=2;DP=51;FractionInformativeReads=1;MQ=60;set=variant9-variant13-variant30-variant35 GT:AD:DP:GQ:PL:SB 0/1:14,5:19:99:156,0,482:3,11,0,5 chr1 161761099 . C T 79.68 PASS AC=1;AF=0.5;AN=2;DP=39;FS=0;FractionInformativeReads=1;MQ=60;set=variant9-variant13-variant30-variant35 GT:AD:DP:GQ:PL:SB 0/1:12,5:17:99:164,0,389:10,2,5,0 chr1 161771812 . C T 778.45 PASS AC=1;AF=0.5;AN=2;DP=74;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.457;QD=10.52;ReadPosRankSum=-1.961;SOR=0.779;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:43,31:74:99:807,0,1263:24,19,18,13 chr1 161772143 . T G 240.99 PASS AC=1;AF=0.5;AN=2;DP=24;FS=2.706;FractionInformativeReads=1;MQ=60;MQRankSum=-1.194;QD=10.04;ReadPosRankSum=-1.5;SOR=1.445;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:16,8:24:99:269,0,551:2,14,0,8 chr1 161789625 . C G 1038.29 PASS AC=1;AF=0.5;AN=2;DP=288;MQ=60;set=variant9-variant13-variant30-variant35 GT:AD:DP:GQ:PL:SB 0/1:35,38:73:99:904,0,863:13,22,14,24 chr1 161790714 . AT ATTT,A,ATTTT,ATT 139.37 PASS AC=0,0,0,1;AF=0.2,0.1,0.1,0.1;AN=2;DP=75;set=variant9-variant13-filterInvariant20-variant30-variant35 GT:DP:GQ:SB 0/4:15:99:6,1,8,0 chr1 161822959 . C T 85.2 PASS AC=2;AF=0.963;AN=2;DP=266;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:144,15,0:0,0,2,3 chr1 161823197 . G GT 2657.26 PASS AC=1;AF=0.738;AN=2;DP=2864;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,22:55:99:617,0,1004:15,18,10,12 chr1 161928614 . C G 384.25 PASS AC=1;AF=0.5;AN=2;DP=24;FS=3.892;FractionInformativeReads=1;MQ=60;MQRankSum=-0.927;QD=16.01;ReadPosRankSum=-0.579;SOR=1.555;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:11,13:24:99:412,0,303:5,6,9,4 chr1 161928771 . G A 2290.86 PASS AC=1;AF=0.5;AN=2;DP=1490;MQ=60;set=variant9-variant10-variant13-variant16-variant21-variant30-variant34-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:106,63:169:99:1555,0,3034:73,33,40,23 chr1 161929235 . T C 234.82 PASS AC=2;AF=0.917;AN=2;DP=375;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:343,27,0:0,0,1,8 chr1 161929459 . CAAAAAAA CAA,CA,C,CAAA,CAAAAA,CAAAA 1635.02 PASS AC=0,0,0,0,0,1;AF=0.355,0.211,0.026,0.079,0.013,0.013;AN=2;DP=3047;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/6:51:99:14,12,25,0 chr1 161929761 . C T 10036.9 PASS AC=2;AF=0.875;AN=2;DP=11887;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,231:231:99:7542,692,0:0,0,122,109 chr1 161929878 . TAA TA,TAAA,T 6397.56 PASS AC=1,1,0;AF=0.761,0.068,0.011;AN=2;DP=11482;set=Intersection GT:DP:GQ:SB 1/2:215:99:17,17,91,90 chr1 161929937 . G A 3830.27 PASS AC=1;AF=0.5;AN=2;DP=262;FS=2.105;FractionInformativeReads=0.996;MQ=60;MQRankSum=1.867;QD=14.62;ReadPosRankSum=-0.807;SOR=0.551;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:120,141:261:99:3859,0,3281:71,49,78,63 chr1 161930873 . A G 1101.25 PASS AC=1;AF=0.5;AN=2;DP=518;MQ=60;set=variant10-variant16-variant21-variant34-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:41,55:96:99:1308,0,850:19,22,28,27 chr1 161931049 . C G 751.83 PASS AC=1;AF=0.5;AN=2;DP=297;FractionInformativeReads=1;MQ=60;set=variant10-variant16-variant21-variant34-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:40,23:63:99:527,0,977:19,21,10,13 chr1 161931361 . ATT AT,A,ATTT 447.62 PASS AC=0,2,0;AF=0.419,0.081,0.012;AN=2;DP=7293;set=variant-variant2-filterInvariant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-filterInvariant11-variant12-variant13-variant14-variant15-variant16-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant20-variant21-filterInvariant22-filterInvariant23-variant24-variant25-variant27-variant28-variant29-filterInvariant30-variant31-variant32-variant33-variant34-variant35-variant36-filterInvariant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 2/2:170:99:0,1,75,94 chr1 161931502 . G A 1365.55 PASS AC=1;AF=0.5;AN=2;DP=672;MQ=60;set=variant10-variant16-variant21-variant34-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:62,42:104:99:963,0,1689:27,35,17,25 chr1 161932148 . T C 1379.77 PASS AC=1;AF=0.5;AN=2;DP=555;MQ=60;set=variant10-variant16-variant21-variant34-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:35,65:100:99:2141,0,969:13,22,22,43 chr1 161933066 . G C 14283.5 PASS AC=2;AF=0.83;AN=2;DP=14017;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,336:336:99:10341,1007,0:0,0,162,174 chr1 161933324 . G A 613.58 PASS AC=1;AF=0.5;AN=2;DP=292;FractionInformativeReads=1;MQ=60;set=variant10-variant16-variant21-variant34-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:31,17:48:99:530,0,943:11,20,6,11 chr1 161953004 . T TA,TAA 1548.05 PASS AC=1,0;AF=0.531,0.031;AN=2;DP=1977;MQ=60;set=variant5-variant10-variant14-variant15-variant20-variant21-variant30-variant31-variant33-variant35-variant37-variant38-variant40-variant41-variant42-variant44 GT:DP:GQ:SB 0/1:133:99:43,29,40,21 chr1 161967681 . A G 2066.81 PASS AC=1;AF=0.762;AN=2;DP=5199;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:70,77:147:99:1667,0,1550:34,36,40,37 chr1 161970224 . AC A 205.2 PASS AC=1;AF=0.667;AN=2;DP=39;MQ=60;set=variant2-variant5-variant35 GT:AD:DP:GQ:PL:SB 0/1:5,10:15:99:354,0,151:1,4,4,6 chr1 161976234 . A G 2940.75 PASS AC=1;AF=0.821;AN=2;DP=5027;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:76,62:138:99:1411,0,1761:41,35,28,34 chr1 161976272 . G GA 2556.64 PASS AC=2;AF=0.932;AN=2;DP=5464;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:9,115:124:99:2964,121,0:5,4,52,63 chr1 161987385 . G A 638.99 PASS AC=1;AF=0.583;AN=2;DP=119;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant30-variant35-variant36-variant40 GT:AD:DP:GQ:PL:SB 0/1:9,13:22:99:450,0,281:1,8,1,12 chr1 162257033 . C G 1146.83 PASS AC=1;AF=0.65;AN=2;DP=730;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant12-variant17-variant21-variant23-variant24-variant26-variant31-variant33-variant35-variant37-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,18:37:99:433,0,523:14,5,10,8 chr1 162302635 . T C 444.74 PASS AC=1;AF=0.727;AN=2;DP=761;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant13-variant14-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,7:13:99:192,0,189:5,1,4,3 chr1 162302689 . C T 776.95 PASS AC=1;AF=0.719;AN=2;DP=1833;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant13-variant14-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:17,26:43:99:706,0,381:10,7,16,10 chr1 162313597 . T C 4452.38 PASS AC=2;AF=0.989;AN=2;DP=7655;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,149:149:99:4605,446,0:0,0,74,75 chr1 162313735 . C T 872.61 PASS AC=1;AF=0.635;AN=2;DP=2470;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant21-variant23-variant25-variant26-variant27-variant29-variant33-variant35-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,39:95:99:957,0,1441:25,31,14,25 chr1 162330927 . C G 49.73 PASS AC=1;AF=0.588;AN=2;DP=90;FS=0;FractionInformativeReads=1;MQ=60;set=variant5-variant8-variant9-variant13-variant19-variant23-variant24-variant25-variant26-variant29-variant30-variant32-variant35-variant36-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:99:117,0,115:1,2,0,3 chr1 162333181 . C T 147.58 PASS AC=1;AF=0.5;AN=2;DP=122;MQ=60;set=variant-variant7-variant14-variant26-variant35-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:5,12:17:99:352,0,162:1,4,4,8 chr1 162333324 . T C 199.61 PASS AC=1;AF=0.5;AN=2;DP=65;FractionInformativeReads=1;MQ=60;set=variant7-variant26-variant35 GT:AD:DP:GQ:PL:SB 0/1:6,6:12:99:153,0,196:3,3,3,3 chr1 162333990 . A G 623.98 PASS AC=1;AF=0.538;AN=2;DP=1835;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant21-variant23-variant26-variant27-variant28-variant32-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,22:69:99:484,0,1464:28,19,14,8 chr1 162334100 . T C 2014.52 PASS AC=2;AF=0.731;AN=2;DP=2360;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,90:90:99:2813,270,0:0,0,39,51 chr1 162335052 . C T 1400.37 PASS AC=1;AF=0.577;AN=2;DP=3058;MQ=60;set=variant-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant32-variant34-variant35-variant36-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:59,93:152:99:2355,0,1700:40,19,54,39 chr1 162335424 . T C 471.1 PASS AC=2;AF=0.829;AN=2;DP=935;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:943,84,0:0,0,8,20 chr1 162338228 . CAAAAA C,CAAAAAAA,CAAA,CAAAAAAAA,CAAAAAAAAA 508.03 PASS AC=1,1,0,0,0;AF=0.349,0.279,0.209,0.047,0.012;AN=2;DP=1467;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/2:33:99:0,0,16,17 chr1 162338377 . C G 1017.66 PASS AC=2;AF=0.802;AN=2;DP=1806;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1788,126,0:0,0,23,19 chr1 162338397 . A C 881.43 PASS AC=2;AF=0.802;AN=2;DP=1620;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1686,114,0:0,0,24,14 chr1 162338485 . A G 1028.8 PASS AC=2;AF=0.802;AN=2;DP=1801;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1494,135,0:0,0,25,20 chr1 162338496 . G A 427.26 PASS AC=1;AF=0.574;AN=2;DP=1165;MQ=60;set=variant-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant32-variant34-variant35-variant36-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:23,24:47:99:531,0,641:12,11,14,10 chr1 162338581 . T C 1024.63 PASS AC=1;AF=0.594;AN=2;DP=2632;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant30-variant31-variant32-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,38:69:99:1052,0,985:19,12,25,13 chr1 162338853 . G A 1105.58 PASS AC=1;AF=0.574;AN=2;DP=2186;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant32-variant34-variant35-variant36-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:27,42:69:99:1319,0,895:15,12,24,18 chr1 162338962 . C T 8982.53 PASS AC=2;AF=0.802;AN=2;DP=10693;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,237:237:99:7264,711,0:0,0,136,101 chr1 162339103 . C T 1780.53 PASS AC=1;AF=0.542;AN=2;DP=3516;set=variant-variant3-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant17-variant21-variant23-variant26-variant27-variant28-variant32-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:80,74:154:99:1820,0,1999:29,51,28,46 chr1 162339260 . T TG 378.52 PASS AC=1;AF=0.713;AN=2;DP=1559;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,14:31:99:324,0,436:7,10,4,10 chr1 162339261 . G GA 215.78 PASS AC=1;AF=0.574;AN=2;DP=1086;MQ=60;set=variant-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant32-variant34-variant35-variant36-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:14,17:31:99:391,0,348:4,10,7,10 chr1 162339579 . T C 2552.2 PASS AC=2;AF=1;AN=2;DP=4394;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,93:93:99:2866,279,0:0,0,54,39 chr1 162343774 . A G 1242.02 PASS AC=1;AF=0.633;AN=2;DP=4252;MQ=60;set=variant-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant34-variant35-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:66,52:118:99:1333,0,1638:41,25,33,19 chr1 162344102 . C T 898.02 PASS AC=1;AF=0.625;AN=2;DP=3988;MQ=60;set=variant-variant6-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant34-variant35-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,75:139:99:1978,0,1603:33,31,41,34 chr1 162344390 . A G 1292.06 PASS AC=2;AF=1;AN=2;DP=3214;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:2045,195,0:0,0,20,45 chr1 162345091 . G A 2930.39 PASS AC=2;AF=0.966;AN=2;DP=4272;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,106:106:99:3430,318,0:0,0,70,36 chr1 162345199 . T G 2481.39 PASS AC=1;AF=0.5;AN=2;DP=2456;MQ=60;set=variant-variant5-variant7-variant14-variant22-variant25-variant26-variant32-variant35-variant36-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:120,123:243:99:2773,0,2717:63,57,59,64 chr1 162345472 . C T 431.9 PASS AC=2;AF=0.966;AN=2;DP=954;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,22:22:65:707,65,0:0,0,5,17 chr1 162346433 . CA C 1249.58 PASS AC=1;AF=0.607;AN=2;DP=3614;MQ=60;set=variant-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant34-variant35-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,48:109:99:1138,0,1525:35,26,29,19 chr1 162348637 . C T 2022.01 PASS AC=1;AF=0.633;AN=2;DP=915;MQ=60;set=variant-variant6-variant7-variant8-variant13-variant18-variant22-variant25-variant26-variant27-variant29-variant33-variant35-variant36-variant40 GT:AD:DP:GQ:PL:SB 0/1:25,34:59:99:830,0,799:20,5,21,13 chr1 162348662 . C T 2282.49 PASS AC=2;AF=0.989;AN=2;DP=3162;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,66:66:99:2186,197,0:0,0,45,21 chr1 162351586 . G A 1303.3 PASS AC=1;AF=0.529;AN=2;DP=1746;MQ=60;set=variant4-variant7-variant8-variant9-variant12-variant14-variant20-variant24-variant27-variant30-variant31-variant34-variant35-variant37-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,70:127:99:1815,0,1715:43,14,48,22 chr1 162352111 . G A 152.64 PASS AC=1;AF=0.684;AN=2;DP=1054;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,18:34:99:485,0,473:6,10,7,11 chr1 162352163 . G A 40.73 PASS AC=1;AF=0.531;AN=2;DP=194;MQ=60;set=variant4-variant7-variant8-variant9-variant12-variant20-variant24-variant27-variant30-variant31-variant34-variant35-variant37-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,6:16:99:162,0,253:4,6,4,2 chr1 162352941 . G A 830.5 PASS AC=1;AF=0.525;AN=2;DP=1920;MQ=60;set=variant2-variant3-variant4-variant7-variant8-variant9-variant12-variant14-variant20-variant24-variant27-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,37:74:99:1033,0,1045:23,14,24,13 chr1 162353726 . T C 1182.86 PASS AC=1;AF=0.726;AN=2;DP=4053;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,45:96:99:1239,0,1365:27,24,24,21 chr1 162354150 . A T 480.78 PASS AC=1;AF=0.567;AN=2;DP=908;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant7-variant8-variant10-variant13-variant19-variant22-variant24-variant25-variant27-variant33-variant35-variant36-variant40 GT:AD:DP:GQ:PL:SB 0/1:31,33:64:99:856,0,818:19,12,18,15 chr1 162354196 . G T 1107.51 PASS AC=1;AF=0.525;AN=2;DP=1471;MQ=60;set=variant2-variant3-variant4-variant7-variant8-variant9-variant12-variant14-variant20-variant24-variant27-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,50:92:99:1974,0,1534:24,18,27,23 chr1 162354200 . AACAC A 1036.94 PASS AC=1;AF=0.525;AN=2;DP=1530;MQ=60;set=variant2-variant3-variant4-variant7-variant8-variant9-variant12-variant14-variant20-variant24-variant27-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,51:91:99:2017,0,1531:23,17,29,22 chr1 162354525 . A G 1575.22 PASS AC=2;AF=1;AN=2;DP=2868;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:2022,180,0:0,0,36,24 chr1 162354803 . G C 652.77 PASS AC=1;AF=0.525;AN=2;DP=1582;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant7-variant8-variant9-variant12-variant14-variant20-variant24-variant27-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,45:84:99:1152,0,976:18,21,18,27 chr1 162355489 . A G 566.75 PASS AC=1;AF=0.577;AN=2;DP=801;FractionInformativeReads=1;MQ=60;set=variant-variant8-variant10-variant13-variant19-variant22-variant24-variant25-variant27-variant33-variant35-variant36-variant40 GT:AD:DP:GQ:PL:SB 0/1:37,38:75:99:890,0,836:17,20,18,20 chr1 162356140 . G A 1991.18 PASS AC=1;AF=0.605;AN=2;DP=1482;MQ=60;set=variant-variant5-variant7-variant8-variant10-variant13-variant18-variant19-variant22-variant24-variant25-variant27-variant29-variant33-variant35-variant36-variant37-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:51,39:90:99:950,0,1412:22,29,20,19 chr1 162356324 . G T 1049.27 PASS AC=2;AF=1;AN=2;DP=1657;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1226,110,0:0,0,16,21 chr1 162356624 . TC T 1152.96 PASS AC=1;AF=0.5;AN=2;DP=100;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.425;QD=11.53;ReadPosRankSum=-1.312;SOR=0.724;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:60,40:100:99:1190,0,1937:29,31,19,21 chr1 162365659 . G A 4910.36 PASS AC=1;AF=0.609;AN=2;DP=3580;MQ=60;set=variant-variant4-variant5-variant7-variant8-variant10-variant13-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant28-variant29-variant33-variant35-variant36-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:94,81:175:99:2064,0,2369:55,39,43,38 chr1 162366121 . G A 11165.4 PASS AC=2;AF=1;AN=2;DP=13795;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,319:319:99:9705,957,0:0,0,163,156 chr1 162367235 . G A 838.25 PASS AC=2;AF=0.676;AN=2;DP=1408;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1418,126,0:0,0,11,31 chr1 162381833 . C G 924.66 PASS AC=1;AF=0.522;AN=2;DP=3903;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant8-variant9-variant12-variant14-variant15-variant17-variant20-variant24-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:130,103:233:99:2328,0,3009:63,67,48,55 chr1 162467014 . C G 1256.92 PASS AC=1;AF=0.617;AN=2;DP=2687;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant15-variant16-variant17-variant19-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,44:97:99:1148,0,1293:34,19,27,17 chr1 162467661 . G A 370.53 PASS AC=1;AF=0.5;AN=2;DP=34;FS=1.356;FractionInformativeReads=1;MQ=60;MQRankSum=0.155;QD=10.9;ReadPosRankSum=-1.57;SOR=0.803;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:18,16:34:99:399,0,465:8,10,9,7 chr1 162470961 . A AT 108.57 PASS AC=1;AF=0.609;AN=2;DP=347;set=variant-variant3-variant5-variant7-variant8-variant9-variant10-variant12-variant15-variant16-variant17-variant19-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant32-variant34-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:1,5:6:10:115,0,10:0,1,0,5 chr1 162473401 . CAAAA CAAA,CA,CAA,C 84.82 PASS AC=0,1,0,0;AF=0.063,0.25,0.292,0.063;AN=2;DP=252;set=variant-variant3-variant4-variant5-variant7-variant8-variant13-variant15-variant16-variant17-variant19-variant22-variant23-variant24-variant28-variant31-variant32-variant35-variant36-variant37-variant38-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:8:41:4,0,4,0 chr1 162493009 . C T 4593.63 PASS AC=1;AF=0.638;AN=2;DP=11377;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant12-variant15-variant16-variant17-variant19-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:233,153:386:99:3497,0,5692:125,108,88,65 chr1 162493123 . A G 5213.26 PASS AC=1;AF=0.633;AN=2;DP=10117;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant15-variant16-variant17-variant19-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:211,171:382:99:4291,0,5374:96,115,81,90 chr1 162493665 . T G 3589.18 PASS AC=1;AF=0.633;AN=2;DP=8249;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant12-variant15-variant16-variant17-variant19-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:140,141:281:99:3277,0,3287:77,63,72,69 chr1 162494683 . G T 1534.85 PASS AC=1;AF=0.633;AN=2;DP=3038;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant15-variant16-variant17-variant19-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,55:109:99:1469,0,1436:19,35,21,34 chr1 162495734 . T A 3530.15 PASS AC=1;AF=0.5;AN=2;DP=1741;MQ=60;set=variant4-variant9-variant12-variant14-variant19-variant20-variant29-variant32-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:83,97:180:99:2653,0,2358:45,38,55,42 chr1 162496065 . CTT CT,C 2174.09 PASS AC=0,1;AF=0.519,0.185;AN=2;DP=5477;MQ=60;set=variant-variant4-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41 GT:DP:GQ:SB 0/2:161:99:38,38,49,36 chr1 162497663 . G A 6399.52 PASS AC=1;AF=0.633;AN=2;DP=13572;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant15-variant16-variant17-variant19-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:220,236:456:99:6761,0,6033:124,96,142,94 chr1 162498459 . TA T 821.24 PASS AC=1;AF=0.638;AN=2;DP=2040;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant12-variant15-variant16-variant17-variant19-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,37:62:99:944,0,571:13,12,17,20 chr1 162498599 . T C 1849.31 PASS AC=1;AF=0.633;AN=2;DP=3383;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant15-variant16-variant17-variant19-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:75,58:133:99:1492,0,2078:49,26,35,23 chr1 162498946 . A G 3001.15 PASS AC=1;AF=0.633;AN=2;DP=5229;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant15-variant16-variant17-variant19-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:100,116:216:99:2937,0,2429:56,44,63,53 chr1 162558705 . C T 500.73 PASS AC=1;AF=0.525;AN=2;DP=1004;MQ=60;set=variant2-variant4-variant6-variant8-variant11-variant13-variant14-variant17-variant18-variant20-variant23-variant25-variant26-variant29-variant32-variant35-variant36-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,24:65:99:561,0,1122:14,27,9,15 chr1 162625020 . G A 286.33 PASS AC=2;AF=0.943;AN=2;DP=943;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:929,84,0:0,0,17,11 chr1 162675040 . T C 230.35 PASS AC=2;AF=0.872;AN=2;DP=390;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:213,15,0:0,0,0,5 chr1 162722846 . C G 2205.02 PASS AC=2;AF=0.989;AN=2;DP=3534;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:2454,237,0:0,0,50,29 chr1 162725655 . A C 774.68 PASS AC=2;AF=0.989;AN=2;DP=591;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.55;ReadPosRankSum=-0.937;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:485,36,0:0,0,1,11 chr1 162736851 . G GAAAA,GAA,GAAA 872.08 PASS AC=2,0,0;AF=0.705,0.273,0.011;AN=2;DP=638;FS=0;MQ=60;MQRankSum=1.106;ReadPosRankSum=0.715;set=Intersection GT:DP:GQ:SB 1/1:8:36:0,0,8,0 chr1 162736856 . C A 1020.16 PASS AC=2;AF=0.989;AN=2;DP=747;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.637;ReadPosRankSum=-1.331;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:597,42,0:0,0,13,1 chr1 162740327 . T C 2330.27 PASS AC=2;AF=0.989;AN=2;DP=6334;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,160:160:99:5172,480,0:0,0,62,98 chr1 162742180 . T C 1755.35 PASS AC=2;AF=0.989;AN=2;DP=2421;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:2181,195,0:0,0,26,39 chr1 162743418 . G T 1530.75 PASS AC=2;AF=0.989;AN=2;DP=2667;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,63:63:99:2079,189,0:0,0,22,41 chr1 162748588 . C A 878.67 PASS AC=2;AF=0.989;AN=2;DP=1314;FS=0;MQ=60;MQRankSum=0.902;ReadPosRankSum=0.332;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1384,116,0:0,0,7,32 chr1 162750208 . C T 674.58 PASS AC=2;AF=0.989;AN=2;DP=1111;MQ=60;MQRankSum=0.568;ReadPosRankSum=0.016;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,31:31:94:1263,94,0:0,0,10,21 chr1 162750210 . CTT C,CT 665.54 PASS AC=1,1;AF=0.693,0.295;AN=2;DP=1058;MQ=60;set=Intersection GT:DP:GQ:SB 1/2:20:99:0,0,6,14 chr1 162754049 . G A 904.69 PASS AC=2;AF=0.756;AN=2;DP=1043;FractionInformativeReads=1;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:910,87,0:0,0,20,9 chr1 162754244 . T G 904.22 PASS AC=2;AF=0.988;AN=2;DP=619;FS=0;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:598,42,0:0,0,3,11 chr1 162760551 . C T 5695.74 PASS AC=2;AF=0.756;AN=2;DP=8098;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,214:214:99:9889,683,0:0,0,138,76 chr1 162760554 . T C 5843.37 PASS AC=2;AF=0.989;AN=2;DP=9636;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,230:230:99:9987,692,0:0,0,147,83 chr1 162765475 . G C 1631.55 PASS AC=2;AF=0.989;AN=2;DP=1707;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1365,132,0:0,0,27,17 chr1 162765636 . AAGTCTTAGATGAAG A 767.4 PASS AC=2;AF=0.763;AN=2;DP=720;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:61:902,61,0:0,0,5,15 chr1 162766476 . C T 5111.7 PASS AC=2;AF=0.756;AN=2;DP=6390;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,176:176:99:5446,527,0:0,0,89,87 chr1 162768784 . CAAA CAA,CA,C 81.82 PASS AC=1,1,0;AF=0.512,0.369,0.036;AN=2;DP=479;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 2/1:16:93:0,0,10,6 chr1 162768939 . TA T 571.08 PASS AC=2;AF=0.94;AN=2;DP=504;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:262,21,0:0,0,2,5 chr1 162773493 . G A 227.2 PASS AC=1;AF=0.5;AN=2;DP=11;FS=4.393;FractionInformativeReads=1;MQ=54.41;MQRankSum=2.52;QD=20.65;ReadPosRankSum=-1.034;SOR=2.833;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:4,7:11:99:255,0,108:1,3,0,7 chr1 162822008 . C A 942.77 PASS AC=1;AF=0.5;AN=2;DP=72;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-2.036;QD=13.09;ReadPosRankSum=-0.976;SOR=0.798;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:34,38:72:99:971,0,1092:17,17,20,18 chr1 162824862 . C A 2234.89 PASS AC=1;AF=0.5;AN=2;DP=200;FS=2.44;FractionInformativeReads=1;MQ=60;MQRankSum=-1.479;QD=11.17;ReadPosRankSum=-1.671;SOR=0.649;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:109,91:200:99:2263,0,2666:58,51,44,47 chr1 163038613 . C A 770.75 PASS AC=2;AF=0.625;AN=2;DP=1939;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant32-variant35-variant36-variant37-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:1873,173,0:0,0,34,24 chr1 163038853 . G A 1101.79 PASS AC=2;AF=0.625;AN=2;DP=1673;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant32-variant35-variant36-variant37-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1852,150,0:0,0,14,36 chr1 163042020 . C CAA 589.59 PASS AC=2;AF=0.977;AN=2;DP=742;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:677,48,0:0,0,7,9 chr1 163043088 . A G 373.32 PASS AC=2;AF=0.677;AN=2;DP=695;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant29-variant30-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:1043,90,0:0,0,20,10 chr1 163044892 . TACACAC TAC,T 142.73 PASS AC=2,0;AF=0.902,0.085;AN=2;DP=386;FS=0;MQRankSum=0.751;ReadPosRankSum=-0.751;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:DP:GQ:SB 1/1:9:27:0,0,5,4 chr1 163045557 . T C 5599.46 PASS AC=2;AF=0.977;AN=2;DP=6522;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,164:164:99:5085,490,0:0,0,94,70 chr1 163045748 . GA G 7255.15 PASS AC=2;AF=0.955;AN=2;DP=12099;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,220:220:99:6277,661,0:0,0,109,111 chr1 163113260 . G T 2742.1 PASS AC=1;AF=0.536;AN=2;DP=6325;set=variant-variant3-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:116,113:229:99:2559,0,2830:56,60,57,56 chr1 163113375 . G C 2116.38 PASS AC=1;AF=0.725;AN=2;DP=5658;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:69,69:138:99:1853,0,1860:26,43,26,43 chr1 163113566 . A T 2843.74 PASS AC=1;AF=0.72;AN=2;DP=6090;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:87,75:162:99:1732,0,2205:45,42,44,31 chr1 163114605 . G A 962.62 PASS AC=1;AF=0.725;AN=2;DP=3344;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,43:88:99:1201,0,1152:12,33,13,30 chr1 163116030 . CT C,CTT 1573.59 PASS AC=1,0;AF=0.477,0.023;AN=2;DP=18162;set=variant-filterInvariant2-variant3-variant5-variant6-variant7-filterInvariant8-variant9-variant10-filterInvariant11-filterInvariant12-filterInvariant13-variant14-variant15-variant16-variant17-variant18-filterInvariant19-variant20-filterInvariant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-filterInvariant29-variant30-variant31-variant32-variant33-variant34-variant35-filterInvariant36-filterInvariant37-variant38-variant39-variant40-variant41-filterInvariant42-filterInvariant43-variant44 GT:DP:GQ:SB 0/1:382:99:125,130,58,69 chr1 163117351 . G T 647.34 PASS AC=1;AF=0.534;AN=2;DP=2068;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,40:73:99:995,0,997:11,22,15,25 chr1 163117599 . T TG 43.55 PASS AC=2;AF=1;AN=2;DP=156;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:81,6,0:0,0,0,2 chr1 163122528 . G C 998.72 PASS AC=1;AF=0.667;AN=2;DP=2141;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,19:50:99:513,0,764:13,18,5,14 chr1 163142537 . G A 744.28 PASS AC=2;AF=0.714;AN=2;DP=572;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant17-variant18-variant20-variant22-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:823,66,0:0,0,3,19 chr1 163187232 . T C 492.77 PASS AC=1;AF=0.5;AN=2;DP=208;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant9-variant22-variant23-variant27-variant35-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:10,11:21:99:368,0,306:8,2,9,2 chr1 163187263 . G A 1299.95 PASS AC=1;AF=0.793;AN=2;DP=1312;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,23:41:99:665,0,520:13,5,14,9 chr1 163307754 . A G 208.74 PASS AC=1;AF=0.5;AN=2;DP=152;FractionInformativeReads=1;MQ=60;set=variant6-variant18-variant28-variant35 GT:AD:DP:GQ:PL:SB 0/1:31,23:54:99:546,0,786:18,13,15,8 chr1 163309302 . C T 1102.68 PASS AC=2;AF=0.943;AN=2;DP=1784;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1557,152,0:0,0,16,35 chr1 164528870 . T C 193.39 PASS AC=2;AF=0.963;AN=2;DP=238;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:174,12,0:0,0,1,3 chr1 164529471 . G C 2634.49 PASS AC=2;AF=0.633;AN=2;DP=1372;set=variant7-variant14-variant15-variant16-variant20-variant22-variant23-variant24-variant29-variant30-variant32-variant35-variant37-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,96:96:99:2863,286,0:0,0,32,64 chr1 164529666 . G A 151.77 PASS AC=2;AF=0.75;AN=2;DP=118;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant10-variant13-variant14-variant15-variant16-variant18-variant20-variant27-variant29-variant31-variant32-variant35-variant37-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:167,12,0:0,0,1,3 chr1 164545960 . G A 41.98 PASS AC=2;AF=0.75;AN=2;DP=38;FS=0;FractionInformativeReads=1;MQ=60;set=variant5-variant30-variant35-variant38 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:494,54,0:0,0,8,10 chr1 164546160 . A T 883.97 PASS AC=2;AF=0.621;AN=2;DP=764;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant15-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:852,90,0:0,0,16,14 chr1 164559536 . A G 1363.49 PASS AC=1;AF=0.622;AN=2;DP=1480;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:26,17:43:99:558,0,843:22,4,14,3 chr1 164574684 . T C 527.24 PASS AC=1;AF=0.841;AN=2;DP=585;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,7:11:99:179,0,150:1,3,2,5 chr1 164595046 . TA T 75.16 PASS AC=1;AF=0.625;AN=2;DP=24;FS=0;MQ=60;set=variant35-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,6:9:47:112,0,47:2,1,4,2 chr1 164789444 . A G 1591.72 PASS AC=2;AF=1;AN=2;DP=1736;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1527,129,0:0,0,10,33 chr1 164816956 . G A 1406.19 PASS AC=1;AF=0.636;AN=2;DP=1105;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant11-variant14-variant16-variant19-variant21-variant22-variant24-variant27-variant28-variant29-variant33-variant35-variant36-variant37-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,18:45:99:448,0,674:12,15,9,9 chr1 164818907 . C T 1243.65 PASS AC=2;AF=0.989;AN=2;DP=1271;FS=0;MQ=60;MQRankSum=-1.357;ReadPosRankSum=-0.895;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:1036,75,0:0,0,23,2 chr1 164819704 . CA CAA,CAAA,C 2729.85 PASS AC=1,0,0;AF=0.563,0.021,0.042;AN=2;DP=3526;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant14-variant16-variant19-variant21-variant22-variant24-variant27-variant28-variant29-variant33-variant35-variant36-variant37-variant41-variant44 GT:DP:GQ:SB 0/1:117:99:58,21,28,10 chr1 164820162 . A G 2475.31 PASS AC=1;AF=0.615;AN=2;DP=2114;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant16-variant19-variant21-variant22-variant24-variant27-variant28-variant29-variant33-variant35-variant36-variant37-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,44:103:99:1135,0,1630:19,40,14,30 chr1 164853647 . G C 78.2 PASS AC=1;AF=0.579;AN=2;DP=343;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant11-variant14-variant16-variant19-variant21-variant22-variant27-variant29-variant31-variant33-variant34-variant35-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,6:16:99:170,0,270:7,3,5,1 chr1 165171059 . C T 244.21 PASS AC=1;AF=0.625;AN=2;DP=504;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant12-variant15-variant18-variant21-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,8:14:99:261,0,190:4,2,6,2 chr1 165171677 . T C 728.95 PASS AC=1;AF=0.62;AN=2;DP=1038;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant12-variant15-variant17-variant18-variant21-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,23:41:99:634,0,467:5,13,9,14 chr1 165171712 . G A 456.59 PASS AC=1;AF=0.62;AN=2;DP=644;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant12-variant15-variant17-variant18-variant21-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,15:27:99:417,0,329:3,9,7,8 chr1 165172158 . T A 664.47 PASS AC=1;AF=0.62;AN=2;DP=956;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant12-variant15-variant17-variant18-variant21-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,32:47:99:810,0,360:7,8,16,16 chr1 165173216 . A G 2438.43 PASS AC=2;AF=1;AN=2;DP=5627;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,120:120:99:3757,360,0:0,0,53,67 chr1 165175374 . G A 1374.06 PASS AC=1;AF=0.824;AN=2;DP=1902;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,27:52:99:723,0,723:8,17,9,18 chr1 165180089 . T A 2615.26 PASS AC=1;AF=0.845;AN=2;DP=3758;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,33:61:99:790,0,719:11,17,15,18 chr1 165180229 . TA T 502.57 PASS AC=1;AF=0.5;AN=2;DP=243;MQ=60;set=variant5-variant7-variant8-variant12-variant15-variant29-variant34-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,14:26:99:420,0,370:4,8,6,8 chr1 165218792 . G A 5128.51 PASS AC=1;AF=0.522;AN=2;DP=3537;set=variant5-variant6-variant7-variant8-variant11-variant14-variant15-variant18-variant20-variant24-variant25-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:74,75:149:99:1840,0,1773:41,33,42,33 chr1 165375835 . A G 41.43 PASS AC=2;AF=0.813;AN=2;DP=1326;MQ=60;set=filterInvariant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:908,81,0:0,0,19,8 chr1 165375895 . A C 410.32 PASS AC=2;AF=0.813;AN=2;DP=2122;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1614,138,0:0,0,30,16 chr1 165376043 . T C 1442.4 PASS AC=2;AF=0.813;AN=2;DP=5238;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,120:120:99:3660,359,0:0,0,64,56 chr1 165376227 . C CCG 889.36 PASS AC=2;AF=0.757;AN=2;DP=1223;MQ=60;set=variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:2115,141,0:0,0,13,34 chr1 165376231 . CTG C 847.37 PASS AC=2;AF=0.757;AN=2;DP=1124;MQ=60;set=variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:2115,141,0:0,0,12,34 chr1 165377389 . T C 903.3 PASS AC=2;AF=1;AN=2;DP=1029;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:955,75,0:0,0,22,3 chr1 165377552 . G A 4391.46 PASS AC=2;AF=0.838;AN=2;DP=5309;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,126:126:99:3686,374,0:0,0,62,64 chr1 165378729 . TACAC TAC,T 228.31 PASS AC=2,0;AF=0.58,0.42;AN=2;DP=1438;FS=0;set=Intersection GT:DP:GQ:SB 1/1:28:84:0,0,21,7 chr1 165378733 . C T 776.73 PASS AC=2;AF=0.604;AN=2;DP=833;set=variant2-variant5-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant21-variant25-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:93:1305,93,0:0,0,21,7 chr1 165378735 . C T 776.73 PASS AC=2;AF=0.587;AN=2;DP=809;FractionInformativeReads=1;set=variant2-variant5-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant21-variant25-variant27-variant28-variant29-variant32-variant35-variant36-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,31:31:93:1305,93,0:0,0,22,9 chr1 165386567 . C T 71.22 PASS AC=2;AF=0.594;AN=2;DP=513;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:622,48,0:0,0,2,14 chr1 165389129 . G A 1027.79 PASS AC=2;AF=0.558;AN=2;DP=2988;MQ=60;set=variant2-variant5-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant32-variant34-variant35-variant36-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,118:118:99:3550,353,0:0,0,73,45 chr1 165414511 . C A 313.5 PASS AC=1;AF=0.553;AN=2;DP=457;FractionInformativeReads=1;MQ=60;set=variant6-variant7-variant9-variant12-variant14-variant16-variant19-variant20-variant24-variant26-variant29-variant30-variant34-variant35-variant37-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:18,16:34:99:310,0,490:5,13,7,9 chr1 165513116 . T C 54.21 PASS AC=2;AF=0.961;AN=2;DP=220;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:139,12,0:0,0,2,2 chr1 165513417 . A G 300.51 PASS AC=1;AF=0.536;AN=2;DP=359;FractionInformativeReads=1;MQ=60;set=variant4-variant7-variant10-variant12-variant15-variant17-variant21-variant23-variant25-variant29-variant30-variant35-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:12,13:25:99:340,0,300:6,6,7,6 chr1 165513439 . A C 162.06 PASS AC=2;AF=0.955;AN=2;DP=887;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,22:22:65:706,65,0:0,0,12,10 chr1 165513456 . A T,C 160.65 PASS AC=2,0;AF=0.807,0.125;AN=2;DP=914;set=Intersection GT:DP:GQ:SB 1/1:15:8:4,0,6,5 chr1 165513463 . C G 151.64 PASS AC=2;AF=0.807;AN=2;DP=947;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:4,13:17:11:433,11,0:4,0,8,5 chr1 165532586 . C T 188.38 PASS AC=1;AF=0.571;AN=2;DP=83;FractionInformativeReads=1;MQ=60;set=variant6-variant8-variant9-variant23-variant34-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,5:11:99:127,0,229:5,1,4,1 chr1 165533005 . C A 1122.54 PASS AC=2;AF=0.604;AN=2;DP=3392;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant29-variant30-variant34-variant35-variant36-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,168:168:99:5150,504,0:0,0,86,82 chr1 165533188 . A C 343.08 PASS AC=2;AF=0.604;AN=2;DP=914;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant29-variant30-variant34-variant35-variant36-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1685,138,0:0,0,10,36 chr1 165533230 . G A 536.23 PASS AC=1;AF=0.538;AN=2;DP=347;FractionInformativeReads=1;MQ=60;set=variant4-variant7-variant12-variant15-variant17-variant21-variant23-variant25-variant29-variant30-variant35-variant36-variant42 GT:AD:DP:GQ:PL:SB 0/1:16,21:37:99:721,0,371:5,11,3,18 chr1 165601215 . G C 1137.21 PASS AC=1;AF=0.78;AN=2;DP=1328;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,20:42:99:680,0,608:16,6,18,2 chr1 165601466 . G A 3726.07 PASS AC=1;AF=0.736;AN=2;DP=4445;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:82,62:144:99:1534,0,2055:34,48,23,39 chr1 165601566 . T C 474.2 PASS AC=1;AF=0.636;AN=2;DP=394;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant13-variant19-variant32-variant34-variant35-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:12,20:32:99:588,0,247:2,10,6,14 chr1 165604991 . T C 10436.7 PASS AC=1;AF=0.603;AN=2;DP=11211;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant14-variant16-variant18-variant19-variant21-variant24-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:209,189:398:99:4241,0,4866:109,100,103,86 chr1 165605209 . C G 544.15 PASS AC=1;AF=0.635;AN=2;DP=973;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,11:20:99:404,0,289:1,8,0,11 chr1 165619424 . G T 91.91 PASS AC=2;AF=0.881;AN=2;DP=401;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:496,48,0:0,0,5,11 chr1 165621322 . TATTATC T 1339.4 PASS AC=2;AF=0.55;AN=2;DP=1245;MQ=60;set=variant-variant4-variant6-variant7-variant12-variant15-variant17-variant19-variant22-variant23-variant25-variant27-variant29-variant30-variant34-variant35-variant36-variant37-variant39-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,63:63:99:2796,190,0:0,0,17,46 chr1 165624799 . G T 713.15 PASS AC=2;AF=0.708;AN=2;DP=2313;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:2139,215,0:0,0,27,45 chr1 165630475 . C T 350.4 PASS AC=2;AF=0.793;AN=2;DP=981;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:624,48,0:0,0,14,2 chr1 165630495 . T C 570.72 PASS AC=2;AF=0.793;AN=2;DP=1718;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1320,123,0:0,0,29,12 chr1 165630698 . A G 515.57 PASS AC=2;AF=0.793;AN=2;DP=2595;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,59:60:99:1838,175,0:1,0,22,37 chr1 165630784 . C CA,CAA 111.78 PASS AC=1,0;AF=0.526,0.053;AN=2;DP=751;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant44 GT:DP:GQ:SB 0/1:14:7:2,0,6,6 chr1 165631123 . A G 132.68 PASS AC=2;AF=0.887;AN=2;DP=179;FS=0;MQ=60;set=variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:135,15,0:0,0,2,3 chr1 165634425 . C G 1153.23 PASS AC=2;AF=0.708;AN=2;DP=2494;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:2331,225,0:0,0,27,48 chr1 165636749 . A G 411.2 PASS AC=2;AF=0.681;AN=2;DP=648;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:580,48,0:0,0,3,13 chr1 165648559 . T G 222.24 PASS AC=2;AF=0.694;AN=2;DP=1182;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,31:31:93:1038,93,0:0,0,22,9 chr1 165648886 . G A 495.41 PASS AC=2;AF=0.694;AN=2;DP=991;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,29:29:90:1269,90,0:0,0,6,23 chr1 165648894 . C G 416.25 PASS AC=2;AF=0.694;AN=2;DP=845;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:84:1219,84,0:0,0,4,23 chr1 165651153 . T A 70.65 PASS AC=2;AF=0.718;AN=2;DP=713;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:823,66,0:0,0,18,4 chr1 165651502 . G C 389.95 PASS AC=2;AF=0.713;AN=2;DP=1263;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:904,84,0:0,0,7,21 chr1 165652273 . A G 2201.79 PASS AC=2;AF=0.713;AN=2;DP=6147;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,146:146:99:4505,438,0:0,0,78,68 chr1 165652445 . A G 1007.72 PASS AC=2;AF=0.713;AN=2;DP=1812;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1938,159,0:0,0,11,42 chr1 165721223 . T C 663.56 PASS AC=1;AF=0.769;AN=2;DP=751;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,13:29:99:446,0,591:14,2,11,2 chr1 165737704 . C G 3492.72 PASS AC=2;AF=0.977;AN=2;DP=5910;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,150:150:99:4755,449,0:0,0,91,59 chr1 165738311 . A T 1761.51 PASS AC=2;AF=0.966;AN=2;DP=2297;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,75:76:99:2167,215,0:1,0,34,41 chr1 165738463 . G C 606.79 PASS AC=2;AF=0.977;AN=2;DP=1211;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:636,51,0:0,0,3,14 chr1 165859630 . C G 3811.89 PASS AC=2;AF=1;AN=2;DP=6810;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,172:172:99:5181,514,0:0,0,85,87 chr1 166030079 . A AAG 493.72 PASS AC=2;AF=1;AN=2;DP=720;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:346,24,0:0,0,0,8 chr1 166124134 . A G 4307.23 PASS AC=2;AF=1;AN=2;DP=6220;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,156:156:99:5025,467,0:0,0,55,101 chr1 166136270 . TG T 58.62 PASS AC=2;AF=0.904;AN=2;DP=274;FS=0;MQ=60;set=variant2-variant3-variant5-variant6-variant8-variant9-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant26-variant27-variant28-variant29-variant33-variant35-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:141,15,0:0,0,3,2 chr1 166591043 . T C 1199.5 PASS AC=2;AF=0.763;AN=2;DP=1082;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1183,102,0:0,0,26,8 chr1 166809602 . C G 2022.88 PASS AC=2;AF=0.767;AN=2;DP=3110;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,87:87:99:2495,259,0:0,0,39,48 chr1 166820104 . G A 2249.59 PASS AC=2;AF=0.621;AN=2;DP=2236;set=variant-variant2-variant3-variant4-variant5-variant6-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:2158,212,0:0,0,46,25 chr1 166820731 . G T 1771.27 PASS AC=2;AF=0.621;AN=2;DP=1116;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant10-variant11-variant12-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant29-variant31-variant32-variant34-variant35-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1485,123,0:0,0,30,11 chr1 166821633 . C T 3430.6 PASS AC=2;AF=0.617;AN=2;DP=2727;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant10-variant11-variant12-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:2287,186,0:0,0,20,42 chr1 166822183 . G A 3242.36 PASS AC=2;AF=0.725;AN=2;DP=4416;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,118:118:99:3482,351,0:0,0,64,54 chr1 166822929 . G GA 1507 PASS AC=2;AF=0.617;AN=2;DP=1631;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant10-variant11-variant12-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:2283,207,0:0,0,42,26 chr1 166823726 . ATTTC A 20037.4 PASS AC=2;AF=0.617;AN=2;DP=11893;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant10-variant11-variant12-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,412:412:99:18418,1241,0:0,0,199,213 chr1 166824176 . C G 3461.41 PASS AC=2;AF=0.617;AN=2;DP=2406;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant10-variant11-variant12-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,100:100:99:3768,301,0:0,0,67,33 chr1 166824580 . T C 5887.16 PASS AC=2;AF=0.617;AN=2;DP=4096;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant10-variant11-variant12-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,136:136:99:4127,407,0:0,0,54,82 chr1 166824846 . T C 1353.12 PASS AC=2;AF=0.617;AN=2;DP=2178;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant10-variant11-variant12-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,87:87:99:2579,261,0:0,0,40,47 chr1 166825127 . A AC 10713.1 PASS AC=2;AF=0.725;AN=2;DP=8889;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,221:221:99:8916,671,0:0,0,109,112 chr1 166825837 . A G 3479.81 PASS AC=2;AF=0.629;AN=2;DP=4154;set=variant-variant2-variant3-variant4-variant5-variant6-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,125:125:99:4027,375,0:0,0,80,45 chr1 166826655 . C T 10780 PASS AC=2;AF=0.617;AN=2;DP=9476;set=variant-variant2-variant3-variant4-variant5-variant6-variant10-variant11-variant12-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,324:324:99:10062,970,0:0,0,188,136 chr1 166826773 . C T 11066.5 PASS AC=2;AF=0.629;AN=2;DP=10834;set=variant-variant2-variant3-variant4-variant5-variant6-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,367:368:99:11202,1090,0:1,0,166,201 chr1 166827674 . T C 394.59 PASS AC=2;AF=0.661;AN=2;DP=280;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant10-variant11-variant12-variant14-variant17-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant35-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:403,36,0:0,0,3,9 chr1 166831404 . A C 874.97 PASS AC=2;AF=0.617;AN=2;DP=630;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant10-variant11-variant12-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:1025,81,0:0,0,24,3 chr1 166831703 . C CA 1339.96 PASS AC=2;AF=0.617;AN=2;DP=1798;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant10-variant11-variant12-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1868,168,0:0,0,17,39 chr1 166833199 . C A 1912.18 PASS AC=2;AF=0.617;AN=2;DP=2776;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant10-variant11-variant12-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,98:98:99:2829,293,0:0,0,44,54 chr1 166944273 . TCACA T,ACACA 302.42 PASS AC=1,0;AF=0.645,0.097;AN=2;DP=409;set=variant2-variant3-variant5-variant6-variant10-variant11-variant12-variant-variant13-variant14-variant17-variant18-variant19-variant4-variant20-variant21-variant22-variant24-variant25-variant27-variant29-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:13:36:1,1,8,3 chr1 166958607 . C G 1842.99 PASS AC=1;AF=0.5;AN=2;DP=534;FractionInformativeReads=1;MQ=60;set=variant11-variant27-variant35 GT:AD:DP:GQ:PL:SB 0/1:91,85:176:99:2050,0,2125:48,43,40,45 chr1 166961857 . G A 903.34 PASS AC=1;AF=0.636;AN=2;DP=336;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant9-variant10-variant12-variant13-variant14-variant18-variant20-variant21-variant23-variant26-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,14:25:99:399,0,321:9,2,11,3 chr1 167022262 . T G 1359.32 PASS AC=1;AF=0.657;AN=2;DP=938;MQ=60;set=variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,11:23:99:301,0,261:7,5,7,4 chr1 167022381 . A G 1312.84 PASS AC=1;AF=0.629;AN=2;DP=1005;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,16:40:99:353,0,645:12,12,8,8 chr1 167022445 . G T 353.31 PASS AC=1;AF=0.577;AN=2;DP=387;MQ=60;set=variant3-variant7-variant10-variant12-variant13-variant14-variant20-variant21-variant31-variant32-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,14:36:99:360,0,557:11,11,4,10 chr1 167032796 . C T 576.98 PASS AC=1;AF=0.583;AN=2;DP=618;MQ=60;set=variant5-variant6-variant7-variant8-variant10-variant12-variant14-variant19-variant20-variant21-variant22-variant30-variant31-variant32-variant35-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,15:35:99:364,0,539:14,6,9,6 chr1 167042590 . C T 778.4 PASS AC=1;AF=0.595;AN=2;DP=1914;MQ=60;set=variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant20-variant21-variant22-variant26-variant27-variant31-variant33-variant35-variant37-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,51:98:99:1158,0,1162:27,20,27,24 chr1 167059336 . C T 411.53 PASS AC=2;AF=0.661;AN=2;DP=596;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:1024,75,0:0,0,23,2 chr1 167059462 . G C 2276.88 PASS AC=2;AF=0.671;AN=2;DP=5065;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,135:135:99:4298,405,0:0,0,84,51 chr1 167059575 . G T 4486.06 PASS AC=2;AF=0.656;AN=2;DP=5841;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,190:190:99:5681,568,0:0,0,93,97 chr1 167059760 . A G 1383.36 PASS AC=2;AF=0.661;AN=2;DP=1167;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1694,158,0:0,0,19,34 chr1 167059830 . A G 961.77 PASS AC=2;AF=0.661;AN=2;DP=774;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:1341,90,0:0,0,12,18 chr1 167059833 . A G 961.77 PASS AC=2;AF=0.676;AN=2;DP=942;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:1305,87,0:0,0,12,17 chr1 167063520 . A G 571.36 PASS AC=1;AF=0.611;AN=2;DP=631;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant11-variant12-variant13-variant17-variant18-variant19-variant22-variant23-variant24-variant25-variant27-variant31-variant32-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,15:27:99:402,0,375:5,7,9,6 chr1 167082869 . G A 2341.26 PASS AC=1;AF=0.726;AN=2;DP=1848;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant9-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:28,28:56:99:836,0,680:18,10,21,7 chr1 167094889 . GA G 1264.59 PASS AC=1;AF=0.569;AN=2;DP=923;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant14-variant16-variant17-variant19-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant35-variant37-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:16,20:36:99:701,0,538:12,4,13,7 chr1 167095163 . G C 1921.39 PASS AC=1;AF=0.691;AN=2;DP=3669;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant35-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:65,56:121:99:1429,0,1887:29,36,29,27 chr1 167097567 . G A 367.64 PASS AC=1;AF=0.5;AN=2;DP=1766;MQ=60;set=variant-variant5-variant11-variant14-variant17-variant19-variant23-variant25-variant26-variant27-variant28-variant30-variant32-variant35-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:72,54:126:99:1196,0,1901:31,41,25,29 chr1 167097739 . C A 787.39 PASS AC=1;AF=0.6;AN=2;DP=3021;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant11-variant13-variant14-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant35-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:66,53:119:99:1306,0,1668:32,34,30,23 chr1 167098095 . G A 779.02 PASS AC=1;AF=0.6;AN=2;DP=1599;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant11-variant13-variant14-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant35-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:36,42:78:99:1168,0,1157:23,13,25,17 chr1 167098129 . T C 941.39 PASS AC=1;AF=0.6;AN=2;DP=1849;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant11-variant13-variant14-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant35-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:41,47:88:99:1846,0,2504:25,16,31,16 chr1 167098131 . G A 2525.7 PASS AC=1;AF=0.857;AN=2;DP=3230;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,47:90:99:1846,0,2504:26,17,32,15 chr1 167098313 . AT A 4477.04 PASS AC=1;AF=0.691;AN=2;DP=7075;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant35-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:101,96:197:99:1921,0,2002:46,55,43,53 chr1 167210785 . G C 10256.6 PASS AC=2;AF=0.92;AN=2;DP=15246;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,357:357:99:10513,1070,0:0,0,154,203 chr1 167307356 . C T 69.21 PASS AC=1;AF=0.625;AN=2;DP=76;FractionInformativeReads=1;MQ=60;set=variant11-variant23-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:14,8:22:99:197,0,340:8,6,3,5 chr1 167353258 . AT A 190.63 PASS AC=1;AF=0.738;AN=2;DP=1145;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,14:24:99:318,0,202:2,8,5,9 chr1 167367193 . C T 278.6 PASS AC=1;AF=0.625;AN=2;DP=1287;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant6-variant9-variant11-variant12-variant14-variant15-variant18-variant19-variant21-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,29:54:99:767,0,564:16,9,18,11 chr1 167370988 . C A 133.71 PASS AC=1;AF=0.817;AN=2;DP=216;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant15-variant16-variant19-variant20-variant21-variant24-variant25-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,4:10:99:150,0,245:0,6,0,4 chr1 167382374 . A C 817.91 PASS AC=1;AF=0.75;AN=2;DP=4154;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:79,63:142:99:1446,0,1748:35,44,27,36 chr1 167382399 . AGTGTGT AGT,AGTGTGTGTGT,AGTGT,A 684.97 PASS AC=1,0,0,0;AF=0.622,0.024,0.049,0.049;AN=2;DP=3189;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:67:99:10,23,10,24 chr1 167385178 . G GA,GAA 1117.67 PASS AC=1,0;AF=0.5,0.088;AN=2;DP=9631;set=variant-filterInvariant2-variant3-filterInvariant4-variant5-variant6-filterInvariant7-filterInvariant8-variant9-filterInvariant10-variant11-variant12-filterInvariant13-variant14-variant15-filterInvariant16-variant18-variant19-filterInvariant20-variant21-filterInvariant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-filterInvariant32-variant33-variant34-variant35-variant36-filterInvariant38-variant39-filterInvariant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:214:99:59,54,57,44 chr1 167385324 . TAAAAA TAAA,TAAAA,TAAAAAA,T 2220.98 PASS AC=0,1,0,0;AF=0.182,0.489,0.011,0.011;AN=2;DP=6680;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-filterInvariant8-variant9-variant10-variant11-variant12-filterInvariant13-variant14-variant15-filterInvariant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:76:99:10,23,19,24 chr1 167389405 . CTT C,CT 1467.81 PASS AC=0,2;AF=0.261,0.568;AN=2;DP=4343;set=Intersection GT:DP:GQ:SB 2/2:52:33:2,4,8,38 chr1 167389423 . T C 1235.98 PASS AC=1;AF=0.58;AN=2;DP=1672;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant16-variant17-variant18-variant21-variant22-variant23-variant26-variant27-variant29-variant31-variant35-variant37-variant38-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,21:55:99:565,0,914:9,25,1,20 chr1 167389463 . T C 1559.58 PASS AC=2;AF=0.943;AN=2;DP=1110;FS=0;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1448,99,0:0,0,2,31 chr1 167389619 . G T 183.1 PASS AC=1;AF=0.722;AN=2;DP=906;FractionInformativeReads=1;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,14:25:99:338,0,376:10,1,8,6 chr1 167389761 . G T 1346.28 PASS AC=1;AF=0.722;AN=2;DP=2929;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,38:89:99:806,0,1247:23,28,18,20 chr1 167389821 . A G 1560.44 PASS AC=1;AF=0.58;AN=2;DP=1800;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant16-variant17-variant18-variant21-variant22-variant23-variant26-variant27-variant29-variant31-variant35-variant37-variant38-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,30:62:99:709,0,749:15,17,14,16 chr1 167389822 . C T 2979.9 PASS AC=2;AF=0.92;AN=2;DP=2946;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,61:61:99:2272,186,0:0,0,28,33 chr1 167391498 . G A 1410.04 PASS AC=1;AF=0.54;AN=2;DP=2628;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant16-variant17-variant18-variant21-variant22-variant23-variant26-variant27-variant29-variant31-variant35-variant37-variant38-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,56:95:99:1560,0,970:26,13,38,18 chr1 167391904 . C T 5833 PASS AC=2;AF=0.92;AN=2;DP=5929;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,130:130:99:4108,389,0:0,0,79,51 chr1 167392216 . C G 6848.75 PASS AC=2;AF=0.932;AN=2;DP=7967;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,193:193:99:6190,578,0:0,0,95,98 chr1 167392342 . A G 10035 PASS AC=2;AF=0.898;AN=2;DP=12138;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,260:260:99:7970,777,0:0,0,138,122 chr1 167392558 . A G 6359.56 PASS AC=2;AF=0.989;AN=2;DP=7155;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,147:148:99:4967,402,0:1,0,67,80 chr1 167392702 . A G 3272.96 PASS AC=1;AF=0.611;AN=2;DP=8934;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:112,104:216:99:2532,0,2691:55,57,53,51 chr1 167393128 . T C 673.47 PASS AC=1;AF=0.625;AN=2;DP=1317;MQ=60;set=variant-variant3-variant5-variant6-variant9-variant11-variant12-variant14-variant15-variant18-variant19-variant21-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,24:48:99:709,0,727:8,16,8,16 chr1 167393635 . G A 905.42 PASS AC=1;AF=0.611;AN=2;DP=4453;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:69,57:126:99:1313,0,1710:35,34,32,25 chr1 167394282 . T TTAC 912.48 PASS AC=1;AF=0.58;AN=2;DP=1854;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant16-variant17-variant18-variant21-variant22-variant23-variant26-variant27-variant29-variant31-variant35-variant37-variant38-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,26:53:99:841,0,1143:8,19,10,16 chr1 167394491 . C T 1426.92 PASS AC=2;AF=0.943;AN=2;DP=2335;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,61:61:99:1792,183,0:0,0,34,27 chr1 167395474 . TAA T,TA 11557.6 PASS AC=2,0;AF=0.92,0.023;AN=2;DP=12429;MQ=60;set=Intersection GT:DP:GQ:SB 1/1:270:99:0,0,117,153 chr1 167396643 . A ACT 8727.54 PASS AC=2;AF=0.989;AN=2;DP=9178;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,197:197:99:8820,593,0:0,0,81,116 chr1 167399868 . T TAG 6447.04 PASS AC=2;AF=0.989;AN=2;DP=6060;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,106:106:99:4833,325,0:0,0,66,40 chr1 167399962 . T C 6243.87 PASS AC=2;AF=0.989;AN=2;DP=9534;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,170:170:99:5263,508,0:0,0,85,85 chr1 167400074 . T A 2962.52 PASS AC=2;AF=0.852;AN=2;DP=4053;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,89:89:99:3007,266,0:0,0,37,52 chr1 167403504 . A G 513.47 PASS AC=2;AF=0.886;AN=2;DP=812;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:749,66,0:0,0,6,16 chr1 167404078 . G A 525.81 PASS AC=2;AF=0.886;AN=2;DP=2347;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:1504,164,0:0,0,28,27 chr1 167404179 . G A 340.71 PASS AC=1;AF=0.605;AN=2;DP=575;set=variant3-variant9-variant14-variant15-variant18-variant20-variant21-variant23-variant24-variant25-variant28-variant30-variant32-variant33-variant35-variant36-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,12:23:99:220,0,285:4,7,5,7 chr1 167408073 . C A 612.14 PASS AC=2;AF=0.886;AN=2;DP=918;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:845,66,0:0,0,4,18 chr1 167408670 . C T 766.02 PASS AC=1;AF=0.7;AN=2;DP=1676;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant16-variant17-variant19-variant22-variant24-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,35:60:99:932,0,640:10,15,13,22 chr1 167510837 . T C 13965.6 PASS AC=2;AF=0.955;AN=2;DP=15723;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,354:354:99:10693,1060,0:0,0,179,175 chr1 167510996 . G A 8941.82 PASS AC=2;AF=0.955;AN=2;DP=10693;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,238:238:99:7700,714,0:0,0,110,128 chr1 167515132 . C T 61.77 PASS AC=2;AF=0.733;AN=2;DP=98;FractionInformativeReads=1;MQ=60;set=variant5-variant7-variant8-variant9-variant17-variant21-variant22-variant24-variant25-variant27-variant29-variant33-variant35-variant36-variant39 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:184,15,0:0,0,4,1 chr1 167515272 . T C 1957.31 PASS AC=2;AF=0.898;AN=2;DP=2714;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:2116,213,0:0,0,43,28 chr1 167522453 . C T 515.73 PASS AC=2;AF=0.89;AN=2;DP=692;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:468,42,0:0,0,9,5 chr1 167523004 . G A 870.42 PASS AC=1;AF=0.5;AN=2;DP=834;MQ=60;set=variant2-variant6-variant8-variant9-variant11-variant21-variant27-variant29-variant30-variant35-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:42,28:70:99:618,0,1026:22,20,14,14 chr1 167599340 . C T 221.35 PASS AC=1;AF=0.5;AN=2;DP=99;FractionInformativeReads=1;MQ=60;set=variant6-variant14-variant23-variant35 GT:AD:DP:GQ:PL:SB 0/1:9,12:21:99:355,0,219:3,6,4,8 chr1 167673738 . T TA 298.57 PASS AC=2;AF=0.536;AN=2;DP=831;MQ=60;set=variant-variant2-variant4-variant6-variant8-variant10-variant12-variant14-variant15-variant16-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:84:783,84,0:0,0,24,3 chr1 167674287 . CAGCTAATTT C 884.3 PASS AC=2;AF=0.536;AN=2;DP=1636;MQ=60;set=variant-variant2-variant4-variant6-variant8-variant10-variant12-variant14-variant15-variant16-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:2231,151,0:0,0,31,18 chr1 167674303 . T C 1187.1 PASS AC=2;AF=0.536;AN=2;DP=1669;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant8-variant10-variant12-variant14-variant15-variant16-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:2410,163,0:0,0,34,19 chr1 167674306 . CTAATTT C 1258.41 PASS AC=2;AF=0.536;AN=2;DP=1794;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant8-variant10-variant12-variant14-variant15-variant16-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:2525,172,0:0,0,35,20 chr1 167674312 . T TCG 1216.42 PASS AC=2;AF=0.536;AN=2;DP=1778;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant8-variant10-variant12-variant14-variant15-variant16-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:2525,172,0:0,0,35,20 chr1 167674569 . T TAA 1215.22 PASS AC=2;AF=0.536;AN=2;DP=3065;MQ=60;set=variant-variant2-variant4-variant6-variant8-variant10-variant12-variant14-variant15-variant16-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:3,82:85:99:2815,145,0:0,3,26,56 chr1 167674653 . C G 368.79 PASS AC=2;AF=0.536;AN=2;DP=1089;MQ=60;set=variant-variant2-variant4-variant6-variant8-variant10-variant12-variant14-variant15-variant16-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1652,129,0:0,0,12,31 chr1 167675535 . A G 157.69 PASS AC=2;AF=0.556;AN=2;DP=394;FractionInformativeReads=1;set=variant-variant2-variant4-variant6-variant8-variant10-variant12-variant14-variant15-variant16-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:583,42,0:0,0,1,13 chr1 167758116 . CTT CT,C 111.93 PASS AC=2,0;AF=0.61,0.037;AN=2;DP=984;set=variant-variant2-variant3-filterInvariant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-filterInvariant40-variant41-variant43-variant44 GT:DP:GQ:SB 1/1:23:38:3,0,11,9 chr1 167758901 . A G 875.37 PASS AC=2;AF=0.744;AN=2;DP=1628;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1405,138,0:0,0,23,23 chr1 167758998 . C G 61.64 PASS AC=1;AF=0.5;AN=2;DP=209;FractionInformativeReads=1;MQ=60;set=variant-variant8-variant10-variant22-variant24-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,25:33:99:753,0,162:5,3,13,12 chr1 167759281 . T C 251.84 PASS AC=1;AF=0.706;AN=2;DP=1339;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,15:29:99:408,0,375:8,6,9,6 chr1 167759419 . C G 652.89 PASS AC=1;AF=0.667;AN=2;DP=716;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant8-variant10-variant22-variant24-variant25-variant30-variant34-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:41,35:76:99:1019,0,1119:26,15,24,11 chr1 167760165 . T G 5068.61 PASS AC=1;AF=0.607;AN=2;DP=4488;MQ=60;set=variant2-variant4-variant5-variant6-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant31-variant35-variant36-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:101,85:186:99:1891,0,2541:39,62,35,50 chr1 167760522 . G C 905.9 PASS AC=2;AF=0.833;AN=2;DP=1910;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,33:33:98:1070,98,0:0,0,15,18 chr1 167760635 . A G 666.73 PASS AC=1;AF=0.5;AN=2;DP=364;FractionInformativeReads=1;MQ=60;set=variant-variant8-variant10-variant22-variant24-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:23,29:52:99:814,0,677:14,9,19,10 chr1 167760731 . T C 3254.42 PASS AC=2;AF=0.833;AN=2;DP=4322;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,104:104:99:3175,311,0:0,0,60,44 chr1 167760807 . A G 1362.85 PASS AC=1;AF=0.718;AN=2;DP=3560;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,49:90:99:1266,0,937:18,23,19,30 chr1 167778843 . G A 2506.82 PASS AC=2;AF=0.719;AN=2;DP=6188;MQ=60;set=variant-variant3-variant4-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,181:181:99:5783,542,0:0,0,115,66 chr1 167787265 . C T 1839.75 PASS AC=1;AF=0.577;AN=2;DP=426;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant10-variant11-variant13-variant15-variant18-variant19-variant21-variant25-variant32-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,20:36:99:607,0,453:13,3,16,4 chr1 167793670 . C T 2175.23 PASS AC=1;AF=0.654;AN=2;DP=2072;MQ=60;set=variant2-variant3-variant4-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant28-variant31-variant32-variant35-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,27:71:99:587,0,1103:26,18,16,11 chr1 167803896 . T A 223.61 PASS AC=1;AF=0.6;AN=2;DP=318;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant13-variant14-variant18-variant19-variant20-variant21-variant25-variant26-variant30-variant35-variant37-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,3:11:99:102,0,309:0,8,1,2 chr1 167805439 . G A 449.54 PASS AC=2;AF=0.672;AN=2;DP=1477;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant30-variant33-variant34-variant35-variant37-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1119,111,0:0,0,22,15 chr1 167806642 . C G 1458.22 PASS AC=1;AF=0.542;AN=2;DP=813;MQ=60;set=variant-variant4-variant12-variant16-variant24-variant33-variant34-variant35-variant37-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:41,30:71:99:739,0,966:18,23,15,15 chr1 167806647 . T A 1421.72 PASS AC=2;AF=0.803;AN=2;DP=2494;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:2402,201,0:0,0,29,36 chr1 167806696 . T C 1308.48 PASS AC=2;AF=0.841;AN=2;DP=1514;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1618,120,0:0,0,12,28 chr1 167806714 . G A 483.43 PASS AC=2;AF=0.672;AN=2;DP=782;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant30-variant33-variant34-variant35-variant37-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:1260,84,0:0,0,5,23 chr1 167815514 . G A 1217.95 PASS AC=1;AF=0.5;AN=2;DP=1263;MQ=60;set=variant3-variant4-variant8-variant9-variant10-variant11-variant14-variant18-variant19-variant21-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,37:94:99:872,0,1545:19,38,16,21 chr1 167817639 . A G 3206.75 PASS AC=1;AF=0.769;AN=2;DP=3222;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,54:96:99:1282,0,1000:23,19,30,24 chr1 167886835 . CAAA CA,CAAAA,CAA,C 315.22 PASS AC=0,0,1,0;AF=0.136,0.091,0.258,0.03;AN=2;DP=3434;set=variant-filterInvariant2-filterInvariant3-variant6-variant7-variant9-variant10-variant11-variant12-variant13-filterInvariant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-filterInvariant36-variant37-variant40-filterInvariant43 GT:DP:GQ:SB 0/3:76:99:25,17,29,5 chr1 167906239 . A C 2896.11 PASS AC=2;AF=1;AN=2;DP=3745;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,107:107:99:3232,321,0:0,0,57,50 chr1 167988590 . A T 847.05 PASS AC=1;AF=0.5;AN=2;DP=516;MQ=60;set=variant3-variant4-variant8-variant9-variant11-variant12-variant13-variant18-variant19-variant21-variant35-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,25:38:99:913,0,397:11,2,22,3 chr1 168013850 . T C 1015.15 PASS AC=2;AF=0.658;AN=2;DP=1307;MQ=60;set=variant-variant2-variant4-variant7-variant12-variant14-variant15-variant16-variant18-variant20-variant22-variant24-variant25-variant26-variant28-variant35-variant36-variant38-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1345,138,0:0,0,24,22 chr1 168025538 . T C 61.77 PASS AC=1;AF=0.591;AN=2;DP=1506;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:22,35:57:99:901,0,470:10,12,17,18 chr1 168025628 . G A 164.93 PASS AC=1;AF=0.583;AN=2;DP=733;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,15:35:99:430,0,455:8,12,3,12 chr1 168025664 . C A 72.27 PASS AC=1;AF=0.592;AN=2;DP=501;FractionInformativeReads=1;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,12:28:99:437,0,376:6,10,0,12 chr1 168035104 . G C 55.31 PASS AC=2;AF=0.976;AN=2;DP=301;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:163,15,0:0,0,1,4 chr1 168106716 . T C 579.6 PASS AC=2;AF=0.872;AN=2;DP=3665;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,105:105:99:3323,314,0:0,0,43,62 chr1 168200733 . T C 830.27 PASS AC=1;AF=0.7;AN=2;DP=1618;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,17:34:99:490,0,517:10,7,13,4 chr1 168206118 . GTTTAA G 424.7 PASS AC=1;AF=0.694;AN=2;DP=835;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,17:23:99:687,0,365:1,5,2,15 chr1 168208308 . T C 1152.78 PASS AC=1;AF=0.694;AN=2;DP=4081;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,71:132:99:1753,0,1363:28,33,37,34 chr1 168212234 . G A 1058.32 PASS AC=1;AF=0.694;AN=2;DP=2995;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,37:105:99:883,0,1692:33,35,19,18 chr1 168215499 . C A 6203.99 PASS AC=1;AF=0.689;AN=2;DP=9990;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:163,154:317:99:5856,0,7151:86,77,75,79 chr1 168215505 . A G 6124.26 PASS AC=1;AF=0.694;AN=2;DP=9938;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:175,148:323:99:5729,0,7400:93,82,75,73 chr1 168215575 . G A 5035.52 PASS AC=1;AF=0.694;AN=2;DP=12462;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:239,170:409:99:3962,0,5901:114,125,83,87 chr1 168260377 . A AGTTTC 1630.64 PASS AC=1;AF=0.563;AN=2;DP=1022;MQ=60;set=variant2-variant14-variant21-variant29-variant35-variant38-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:74,64:138:99:2486,0,4232:38,36,41,23 chr1 168262289 . A G 815.1 PASS AC=2;AF=0.756;AN=2;DP=1109;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:980,69,0:0,0,20,3 chr1 168262299 . C T 869.6 PASS AC=1;AF=0.688;AN=2;DP=1105;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:14,12:26:99:297,0,512:13,1,8,4 chr1 168262522 . AGTGTGT AGTGTGTGT,AGTGTGTGTGT,AGTGT,AGTGTTTGTGTGT,AGT,AGTGTGTGTGTGT,A 284.09 PASS AC=2,0,0,0,0,0,0;AF=0.375,0.141,0.031,0.031,0.016,0.047,0.016;AN=2;DP=1262;set=variant3-variant4-variant6-variant7-variant8-variant9-filterInvariant10-filterInvariant12-filterInvariant13-variant16-filterInvariant17-filterInvariant18-variant19-variant21-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:9:27:0,0,0,9 chr1 168513067 . C A,T 1717.89 PASS AC=1,0;AF=0.5,0.031;AN=2;DP=2642;set=variant2-variant4-variant8-variant9-variant12-variant13-variant14-variant15-variant18-variant21-variant33-variant35-variant37-variant38-variant40-variant41 GT:DP:GQ:SB 0/1:222:99:85,59,47,31 chr1 168513109 . A G 1587.77 PASS AC=1;AF=0.533;AN=2;DP=2595;set=variant2-variant4-variant8-variant9-variant13-variant14-variant15-variant18-variant21-variant33-variant35-variant37-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:157,84:241:99:1899,0,3780:81,76,50,34 chr1 168545758 . C T 160.19 PASS AC=2;AF=0.697;AN=2;DP=546;FractionInformativeReads=1;set=variant-variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:545,42,0:0,0,13,1 chr1 168545949 . G A 1485.07 PASS AC=2;AF=0.775;AN=2;DP=6571;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:4,148:152:99:4474,356,0:2,2,76,72 chr1 168549422 . C T 599.05 PASS AC=1;AF=0.731;AN=2;DP=7255;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:113,82:195:99:1827,0,2673:54,59,37,45 chr1 168550512 . G C,A 404.44 PASS AC=1,0;AF=0.455,0.091;AN=2;DP=470;FractionInformativeReads=1;set=variant5-variant13-variant18-variant20-variant28-variant29-variant31-variant33-variant35-variant37-variant43 GT:DP:GQ:SB 0/1:35:99:1,19,4,11 chr1 168550785 . A G 610.27 PASS AC=1;AF=0.55;AN=2;DP=203;FractionInformativeReads=1;set=variant5-variant13-variant18-variant28-variant29-variant31-variant33-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,14:26:99:566,0,933:12,0,14,0 chr1 168550789 . T A 610.27 PASS AC=1;AF=0.55;AN=2;DP=216;FractionInformativeReads=1;set=variant5-variant13-variant18-variant28-variant29-variant31-variant33-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,17:30:99:629,0,960:13,0,16,1 chr1 168551236 . C T 4511.23 PASS AC=1;AF=0.571;AN=2;DP=3189;MQ=60;set=variant5-variant18-variant28-variant29-variant33-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:274,207:481:99:4798,0,6870:146,128,110,97 chr1 168664588 . G A 1237.98 PASS AC=1;AF=0.556;AN=2;DP=355;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant16-variant19-variant28-variant29-variant33-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:26,19:45:99:551,0,852:21,5,15,4 chr1 168665256 . T C 682.99 PASS AC=1;AF=0.55;AN=2;DP=544;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant16-variant19-variant28-variant29-variant33-variant35-variant37-variant42 GT:AD:DP:GQ:PL:SB 0/1:38,21:59:99:532,0,1066:15,23,9,12 chr1 168665346 . A C 367.89 PASS AC=1;AF=0.55;AN=2;DP=359;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant16-variant19-variant28-variant29-variant33-variant35-variant37-variant42 GT:AD:DP:GQ:PL:SB 0/1:24,18:42:99:465,0,666:10,14,9,9 chr1 168665747 . C CT 1052.4 PASS AC=1;AF=0.75;AN=2;DP=2983;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:56,41:97:99:1357,0,1910:30,26,21,20 chr1 168665974 . T C 79.93 PASS AC=1;AF=0.75;AN=2;DP=414;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,5:16:99:177,0,412:1,10,0,5 chr1 168670140 . TGTGTGG T 382.87 PASS AC=1;AF=0.593;AN=2;DP=752;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant19-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:8,13:21:99:499,0,454:7,1,10,3 chr1 168698173 . C T 874.26 PASS AC=2;AF=0.673;AN=2;DP=2479;MQ=60;set=variant-variant5-variant6-variant11-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,97:97:99:3111,290,0:0,0,69,28 chr1 169075857 . C CCCG,CCCGCCGCCG,CCCGCCG 379.84 PASS AC=2,0,0;AF=0.75,0.05,0.033;AN=2;DP=260;set=variant2-variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant25-variant27-variant28-variant29-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:DP:GQ:SB 1/1:10:50:0,0,9,1 chr1 169080837 . C T 186.63 PASS AC=1;AF=0.833;AN=2;DP=1325;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,12:38:99:308,0,715:9,17,2,10 chr1 169094100 . T A 717 PASS AC=1;AF=0.797;AN=2;DP=2639;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,47:83:99:1156,0,1042:16,20,25,22 chr1 169099061 . G A 259.1 PASS AC=1;AF=0.792;AN=2;DP=629;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,5:21:99:122,0,526:11,5,4,1 chr1 169101257 . AT ATT,ATTTTTTTTTT,A,ATTTT 908.41 PASS AC=1,0,0,0;AF=0.486,0.014,0.057,0.014;AN=2;DP=6434;set=variant-variant3-variant4-variant5-variant7-filterInvariant9-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-filterInvariant24-variant25-variant27-variant28-variant29-variant32-variant33-filterInvariant34-variant35-filterInvariant36-variant37-variant38-variant39-variant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:DP:GQ:SB 0/1:150:99:25,53,35,37 chr1 169102223 . G C 333.34 PASS AC=1;AF=0.661;AN=2;DP=873;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant9-variant10-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant32-variant33-variant34-variant35-variant37-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,16:23:99:510,0,232:1,6,2,14 chr1 169138027 . A G 872.04 PASS AC=1;AF=0.717;AN=2;DP=2063;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,41:64:99:986,0,459:10,13,24,17 chr1 169138307 . C A 597.69 PASS AC=1;AF=0.717;AN=2;DP=1330;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,18:52:99:423,0,822:19,15,9,9 chr1 169138318 . T A 519.43 PASS AC=1;AF=0.717;AN=2;DP=1366;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,19:54:99:472,0,807:18,17,10,9 chr1 169138868 . C T 303.58 PASS AC=1;AF=0.717;AN=2;DP=886;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,18:33:99:505,0,410:4,11,5,13 chr1 169159866 . G T 483.35 PASS AC=1;AF=0.743;AN=2;DP=1767;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,18:46:99:451,0,717:18,10,12,6 chr1 169200111 . C T 431.64 PASS AC=1;AF=0.717;AN=2;DP=1217;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,29:47:99:619,0,427:7,11,13,16 chr1 169216412 . C G 222.17 PASS AC=2;AF=1;AN=2;DP=1043;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:848,78,0:0,0,7,19 chr1 169256501 . C T 810.09 PASS AC=1;AF=0.611;AN=2;DP=1262;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant9-variant10-variant14-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant32-variant33-variant34-variant35-variant37-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,19:39:99:491,0,560:13,7,13,6 chr1 169268077 . T C 160.43 PASS AC=1;AF=0.62;AN=2;DP=316;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant9-variant10-variant14-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant32-variant34-variant35-variant37-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,7:12:99:271,0,189:0,5,0,7 chr1 169272299 . A T 531.79 PASS AC=1;AF=0.657;AN=2;DP=2004;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,24:51:99:541,0,574:13,14,12,12 chr1 169272451 . A T 781.25 PASS AC=2;AF=0.989;AN=2;DP=739;FractionInformativeReads=1;MQ=60;MQRankSum=0.366;ReadPosRankSum=0.805;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:475,33,0:0,0,3,8 chr1 169272453 . G A 781.25 PASS AC=2;AF=0.989;AN=2;DP=700;FractionInformativeReads=1;MQ=60;MQRankSum=0.19;ReadPosRankSum=-1.822;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,10:10:33:475,33,0:0,0,2,8 chr1 169279196 . T TA 636.86 PASS AC=1;AF=0.657;AN=2;DP=1608;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,20:39:99:492,0,463:11,8,13,7 chr1 169293721 . G A 622.72 PASS AC=1;AF=0.657;AN=2;DP=2170;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,32:67:99:736,0,869:14,21,13,19 chr1 169337376 . C T 741.2 PASS AC=1;AF=0.658;AN=2;DP=2667;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,29:53:99:781,0,609:14,10,17,12 chr1 169337638 . C T 200.7 PASS AC=1;AF=0.658;AN=2;DP=772;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,12:21:99:344,0,260:3,6,3,9 chr1 169337677 . A ATTG 166.66 PASS AC=1;AF=0.667;AN=2;DP=377;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,3:12:99:99,0,404:2,7,0,3 chr1 169338520 . A AT,ATT,ATTT 80.75 PASS AC=1,0,0;AF=0.676,0.059,0.015;AN=2;DP=356;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:12:99:5,1,5,1 chr1 169345704 . G A 574.21 PASS AC=1;AF=0.658;AN=2;DP=1970;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,29:55:99:712,0,749:18,8,19,10 chr1 169346528 . AT A 899.93 PASS AC=1;AF=0.607;AN=2;DP=2200;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant14-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant32-variant33-variant34-variant35-variant37-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,31:71:99:947,0,1267:12,28,6,25 chr1 169349608 . C CTA 160.6 PASS AC=1;AF=0.744;AN=2;DP=491;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,6:14:99:228,0,318:8,0,6,0 chr1 169351596 . A G 302.6 PASS AC=1;AF=0.75;AN=2;DP=1540;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,16:33:99:384,0,404:6,11,5,11 chr1 169356216 . T C 235.58 PASS AC=1;AF=0.5;AN=2;DP=13;FS=3.041;FractionInformativeReads=1;MQ=60;MQRankSum=1.62;QD=18.12;ReadPosRankSum=-0.077;SOR=0.116;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:4,9:13:99:264,0,108:4,0,6,3 chr1 169356833 . G T 376.01 PASS AC=1;AF=0.75;AN=2;DP=1738;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,28:45:99:641,0,391:7,10,15,13 chr1 169364479 . T G 1126.21 PASS AC=1;AF=0.583;AN=2;DP=433;FractionInformativeReads=1;MQ=60;set=variant11-variant19-variant28-variant29-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:31,32:63:99:905,0,824:9,22,8,24 chr1 169365116 . GT GTTT,GTT,G 922.5 PASS AC=1,0,0;AF=0.459,0.149,0.041;AN=2;DP=2477;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:65:99:22,7,32,4 chr1 169390957 . A T 761.35 PASS AC=1;AF=0.607;AN=2;DP=1508;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant14-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant32-variant33-variant34-variant35-variant37-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,26:58:99:855,0,972:13,19,11,15 chr1 169391154 . A G 1013.41 PASS AC=1;AF=0.75;AN=2;DP=3255;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,26:63:99:597,0,1084:17,20,9,17 chr1 169394226 . A G 723.97 PASS AC=2;AF=0.791;AN=2;DP=2542;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,61:61:99:1821,183,0:0,0,25,36 chr1 169434120 . T C 1239.01 PASS AC=1;AF=0.55;AN=2;DP=1014;MQ=60;set=variant11-variant15-variant16-variant19-variant20-variant28-variant29-variant31-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:42,29:71:99:754,0,1237:10,32,12,17 chr1 169435027 . C T 4409.17 PASS AC=2;AF=1;AN=2;DP=5149;FS=0;MQ=60;MQRankSum=-0.485;ReadPosRankSum=0.679;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,119:119:99:3706,356,0:0,0,51,68 chr1 169455008 . G A 1497.14 PASS AC=1;AF=0.538;AN=2;DP=1946;MQ=60;set=variant8-variant13-variant17-variant18-variant19-variant24-variant27-variant28-variant29-variant33-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:92,87:179:99:1946,0,2353:48,44,41,46 chr1 169455435 . G C 2500.13 PASS AC=1;AF=0.62;AN=2;DP=4476;set=variant2-variant6-variant8-variant12-variant13-variant17-variant18-variant19-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:100,88:188:99:2185,0,2540:54,46,42,46 chr1 169484767 . A G 1003.09 PASS AC=1;AF=0.5;AN=2;DP=422;MQ=60;set=variant-variant33-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,67:127:99:1549,0,1607:23,37,29,38 chr1 169493953 . A C 901.59 PASS AC=1;AF=0.7;AN=2;DP=1891;MQ=60;set=variant-variant3-variant4-variant7-variant8-variant9-variant10-variant14-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,26:55:99:612,0,701:18,11,18,8 chr1 169498834 . T C 529.23 PASS AC=2;AF=0.966;AN=2;DP=1339;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:969,87,0:0,0,20,9 chr1 169510233 . G A 971.72 PASS AC=1;AF=0.68;AN=2;DP=6462;set=variant-variant3-variant4-variant7-variant8-variant9-variant10-variant16-variant17-variant18-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant32-variant33-variant35-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:131,137:268:99:3240,0,3559:77,54,69,68 chr1 169510475 . G T 4261.85 PASS AC=1;AF=0.636;AN=2;DP=3427;set=variant5-variant11-variant13-variant16-variant19-variant20-variant23-variant29-variant31-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:142,130:272:99:3104,0,3949:66,76,63,67 chr1 169519049 . T C 4195.74 PASS AC=2;AF=1;AN=2;DP=5894;FS=0;MQ=60;MQRankSum=-0.284;ReadPosRankSum=1.365;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,148:148:99:4601,443,0:0,0,85,63 chr1 169519671 . T C 408.02 PASS AC=1;AF=0.643;AN=2;DP=101;FractionInformativeReads=1;MQ=60;set=variant5-variant11-variant19-variant27-variant29-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:99:149,0,104:3,1,4,0 chr1 169521849 . T C 657.79 PASS AC=1;AF=0.625;AN=2;DP=547;FractionInformativeReads=1;MQ=60;set=variant5-variant11-variant13-variant19-variant27-variant29-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:38,35:73:99:692,0,864:21,17,17,18 chr1 169525766 . T C 515.54 PASS AC=2;AF=0.719;AN=2;DP=849;MQ=60;set=variant3-variant4-variant6-variant7-variant8-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:1012,78,0:0,0,23,3 chr1 169525808 . G A 1070.75 PASS AC=2;AF=0.565;AN=2;DP=1288;MQ=60;set=variant3-variant4-variant6-variant7-variant8-variant12-variant15-variant17-variant19-variant20-variant21-variant22-variant26-variant28-variant31-variant32-variant34-variant35-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1697,150,0:0,0,40,10 chr1 169551682 . T C 773.47 PASS AC=2;AF=0.568;AN=2;DP=904;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant6-variant7-variant8-variant12-variant15-variant17-variant19-variant20-variant21-variant22-variant26-variant28-variant31-variant32-variant34-variant35-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1124,123,0:0,0,20,21 chr1 169555367 . TA TAA,T 126.01 PASS AC=0,1;AF=0.083,0.417;AN=2;DP=258;MQ=60;set=variant-filterInvariant9-filterInvariant20-filterInvariant27-filterInvariant31-variant35 GT:DP:GQ:SB 0/2:30:99:5,5,16,4 chr1 169560727 . T TA,TAA,TAAA 497.04 PASS AC=2,0,0;AF=0.375,0.219,0.016;AN=2;DP=1488;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-filterInvariant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant34-variant35-variant38-variant39-variant40-variant41-variant43-variant44 GT:DP:GQ:SB 1/1:39:99:0,0,17,22 chr1 169563951 . T G 1195.65 PASS AC=2;AF=0.688;AN=2;DP=796;FractionInformativeReads=1;MQ=60;set=variant12-variant17-variant21-variant22-variant26-variant32-variant35-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,122:122:99:3643,365,0:0,0,57,65 chr1 169564167 . G C 366.1 PASS AC=2;AF=0.568;AN=2;DP=350;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant6-variant7-variant8-variant12-variant15-variant17-variant19-variant20-variant21-variant22-variant26-variant28-variant31-variant32-variant34-variant35-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:487,36,0:0,0,2,10 chr1 169566313 . C T 2482.45 PASS AC=2;AF=0.744;AN=2;DP=4949;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,148:148:99:4268,443,0:0,0,68,80 chr1 169572545 . CTGTGTGTG CTGTGTGTGTG,C,CTGTGTGTGTGTG,CTGTGTGTGTGTGTG,CTGTGTGTGTGTGTGTGTGTGTGTG,CTGTG,CTGTGTGTGTGTGTGTGTG,CTGTGTGTGTGTGTGTGTGTGTGTGTG,CTGTGTG,CTCTGTGTGTGTGTGTGTGTG 34.15 PASS AC=0,2,0,0,0,0,0,0,0,0;AF=0.114,0.357,0.129,0.071,0.043,0.029,0.029,0.014,0.029,0.014;AN=2;DP=1195;set=filterInvariant-variant3-variant4-filterInvariant9-variant10-variant11-variant13-variant7-variant15-variant8-variant17-variant12-variant21-variant23-variant25-variant19-variant26-variant27-variant20-variant28-variant29-filterInvariant30-variant22-variant31-variant32-variant34-variant36-variant37-variant2-variant38-variant35-variant39-variant40-variant43-variant44 GT:DP:GQ:SB 2/2:27:81:0,0,7,20 chr1 169572555 . G C 301.54 PASS AC=2;AF=0.543;AN=2;DP=753;set=variant3-variant4-variant6-variant7-variant8-variant12-variant15-variant17-variant19-variant20-variant21-variant22-variant26-variant28-variant31-variant32-variant34-variant35-variant36-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:1187,81,0:0,0,7,20 chr1 169572557 . G C 945.4 PASS AC=2;AF=0.568;AN=2;DP=696;set=variant3-variant4-variant6-variant7-variant8-variant12-variant15-variant17-variant19-variant20-variant21-variant22-variant26-variant28-variant31-variant32-variant34-variant35-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:81:1187,81,0:0,0,7,19 chr1 169580717 . T C 81.21 PASS AC=1;AF=0.588;AN=2;DP=431;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant9-variant12-variant17-variant20-variant21-variant24-variant25-variant26-variant30-variant32-variant34-variant35-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,5:13:99:132,0,201:5,3,4,1 chr1 169580972 . C CAT 174.2 PASS AC=1;AF=0.707;AN=2;DP=1027;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant20-variant21-variant24-variant25-variant26-variant29-variant30-variant32-variant34-variant35-variant36-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,13:28:99:467,0,616:5,10,5,8 chr1 169599254 . T C 1810.55 PASS AC=2;AF=0.697;AN=2;DP=4851;MQ=60;set=variant-variant2-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant20-variant21-variant22-variant24-variant25-variant26-variant29-variant30-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,152:152:99:4517,455,0:0,0,85,67 chr1 169660002 . G T 435.3 PASS AC=1;AF=0.667;AN=2;DP=921;MQ=60;set=variant-variant6-variant7-variant9-variant10-variant11-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant29-variant30-variant32-variant34-variant35-variant37-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,13:24:99:403,0,307:9,2,9,4 chr1 169660781 . A G 2263.15 PASS AC=1;AF=0.684;AN=2;DP=2479;MQ=60;set=variant-variant6-variant9-variant11-variant16-variant17-variant19-variant20-variant21-variant22-variant26-variant29-variant30-variant32-variant34-variant35-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:62,67:129:99:1851,0,1633:28,34,33,34 chr1 169665551 . G T 690.42 PASS AC=1;AF=0.675;AN=2;DP=1200;MQ=60;set=variant-variant6-variant9-variant11-variant13-variant16-variant17-variant19-variant20-variant21-variant22-variant26-variant29-variant30-variant32-variant34-variant35-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:34,27:61:99:696,0,770:19,15,16,11 chr1 169665632 . T C 974.14 PASS AC=1;AF=0.654;AN=2;DP=1950;MQ=60;set=variant-variant6-variant8-variant9-variant11-variant13-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:42,50:92:99:1169,0,886:18,24,25,25 chr1 169676486 . A G 584.42 PASS AC=1;AF=0.643;AN=2;DP=1575;MQ=60;set=variant-variant6-variant7-variant9-variant11-variant17-variant19-variant20-variant21-variant22-variant23-variant26-variant29-variant30-variant32-variant34-variant35-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:41,48:89:99:1315,0,1035:24,17,28,20 chr1 169679553 . C T 1433.83 PASS AC=1;AF=0.65;AN=2;DP=2640;MQ=60;set=variant-variant6-variant7-variant9-variant11-variant17-variant19-variant20-variant21-variant22-variant23-variant26-variant29-variant30-variant32-variant34-variant35-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:73,52:125:99:1075,0,1818:45,28,30,22 chr1 169698825 . T G 1549.79 PASS AC=2;AF=0.857;AN=2;DP=5220;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,123:123:99:3873,369,0:0,0,57,66 chr1 169698921 . C T 938.93 PASS AC=2;AF=0.685;AN=2;DP=1726;MQ=60;set=variant-variant6-variant7-variant9-variant10-variant11-variant13-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant32-variant34-variant35-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,73:73:99:2212,217,0:0,0,24,49 chr1 169699819 . G A 342.57 PASS AC=2;AF=0.685;AN=2;DP=1631;MQ=60;set=variant-variant6-variant7-variant9-variant10-variant11-variant13-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant32-variant34-variant35-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,73:73:99:2483,219,0:0,0,22,51 chr1 169762807 . T G 2452.51 PASS AC=1;AF=0.556;AN=2;DP=1510;MQ=60;set=variant11-variant13-variant15-variant25-variant27-variant35-variant37-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:102,86:188:99:2252,0,2867:65,37,52,34 chr1 169763046 . GA G,GAA 32.08 PASS AC=1,0;AF=0.484,0.031;AN=2;DP=3705;set=filterInvariant-variant3-filterInvariant4-variant5-variant7-filterInvariant9-variant10-variant11-filterInvariant12-variant14-filterInvariant15-variant18-filterInvariant19-filterInvariant21-filterInvariant23-filterInvariant24-variant25-variant26-filterInvariant27-filterInvariant28-variant29-variant30-filterInvariant31-filterInvariant32-variant35-filterInvariant36-filterInvariant37-variant38-filterInvariant39-filterInvariant42-filterInvariant43-variant44 GT:DP:GQ:SB 0/1:71:99:16,31,7,17 chr1 169763139 . T C 285.87 PASS AC=2;AF=0.814;AN=2;DP=764;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:872,66,0:0,0,5,17 chr1 169764568 . C G 446.26 PASS AC=2;AF=0.814;AN=2;DP=2435;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:1555,141,0:0,0,27,20 chr1 169764992 . T TG 2629.44 PASS AC=2;AF=1;AN=2;DP=3251;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:2334,175,0:0,0,25,32 chr1 169765052 . C G 679.71 PASS AC=1;AF=0.638;AN=2;DP=1830;MQ=60;set=variant-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:25,31:56:99:779,0,586:11,14,15,16 chr1 169768033 . T C 1675.17 PASS AC=2;AF=0.75;AN=2;DP=5945;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,161:161:99:5037,481,0:0,0,95,66 chr1 169768080 . C A 1566.81 PASS AC=2;AF=0.75;AN=2;DP=7576;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,224:224:99:6463,670,0:0,0,110,114 chr1 169795214 . CT C 253.15 PASS AC=2;AF=0.75;AN=2;DP=1285;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1021,102,0:0,0,12,22 chr1 169795276 . A C 74.49 PASS AC=2;AF=0.821;AN=2;DP=418;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:361,30,0:0,0,1,9 chr1 169797127 . G A 2060.05 PASS AC=1;AF=0.556;AN=2;DP=850;MQ=60;set=variant11-variant13-variant15-variant25-variant27-variant35-variant37-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:53,34:87:99:1166,0,1994:1,52,0,34 chr1 169819605 . A G 523.92 PASS AC=2;AF=0.75;AN=2;DP=1720;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:1722,165,0:0,0,17,38 chr1 169823296 . G GCTTGA,GCTTGACTTGA 1479.22 PASS AC=1,0;AF=0.636,0.023;AN=2;DP=693;MQ=60;set=variant2-variant3-variant4-variant8-variant11-variant13-variant14-variant15-variant16-variant18-variant23-variant24-variant25-variant27-variant31-variant32-variant35-variant36-variant37-variant39-variant41-variant42 GT:DP:GQ:SB 0/1:21:99:5,4,1,11 chr1 169823660 . C T 1676.52 PASS AC=1;AF=0.646;AN=2;DP=3121;MQ=60;set=variant-variant6-variant7-variant9-variant10-variant11-variant12-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant26-variant28-variant29-variant30-variant34-variant35-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:60,74:134:99:1898,0,1372:32,28,35,39 chr1 169823718 . T C 1903.15 PASS AC=2;AF=0.75;AN=2;DP=5942;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,136:136:99:4222,407,0:0,0,68,68 chr1 169831690 . CTCTT C 781.27 PASS AC=1;AF=0.646;AN=2;DP=2011;MQ=60;set=variant-variant6-variant7-variant9-variant10-variant11-variant12-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant26-variant28-variant29-variant30-variant34-variant35-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:54,40:94:99:1506,0,2995:33,21,24,16 chr1 169831993 . A G 398.44 PASS AC=2;AF=0.814;AN=2;DP=1665;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1369,132,0:0,0,14,30 chr1 169833822 . T C 235.4 PASS AC=2;AF=0.814;AN=2;DP=1131;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:934,81,0:0,0,6,21 chr1 169835950 . A C 118.19 PASS AC=2;AF=0.838;AN=2;DP=244;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant21-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:305,21,0:0,0,7,0 chr1 169838278 . G A 361.7 PASS AC=1;AF=0.646;AN=2;DP=1207;MQ=60;set=variant-variant6-variant7-variant9-variant10-variant11-variant12-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant26-variant28-variant29-variant30-variant34-variant35-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:30,34:64:99:847,0,819:8,22,9,25 chr1 169839595 . A G 193.47 PASS AC=1;AF=0.611;AN=2;DP=117;FractionInformativeReads=1;MQ=60;set=variant11-variant13-variant15-variant25-variant27-variant35-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:4,9:13:99:282,0,102:1,3,3,6 chr1 169847683 . G A 198.09 PASS AC=2;AF=0.821;AN=2;DP=581;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:471,36,0:0,0,11,1 chr1 169890574 . T A 6921.45 PASS AC=2;AF=0.929;AN=2;DP=8574;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,178:178:99:5493,531,0:0,0,98,80 chr1 169890933 . A G 2525.83 PASS AC=2;AF=0.929;AN=2;DP=3761;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:2470,227,0:0,0,28,48 chr1 169891056 . CT C 249.25 PASS AC=2;AF=0.936;AN=2;DP=632;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:401,42,0:0,0,3,11 chr1 169941761 . A T 736.17 PASS AC=2;AF=0.939;AN=2;DP=772;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:243,18,0:0,0,0,6 chr1 169947146 . C CA,CAA 2062.53 PASS AC=2,0;AF=0.905,0.012;AN=2;DP=2037;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:48:99:1,0,35,12 chr1 169951748 . A G 359.74 PASS AC=2;AF=0.939;AN=2;DP=464;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:501,39,0:0,0,11,2 chr1 169952385 . G T 755.04 PASS AC=2;AF=0.929;AN=2;DP=833;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:543,45,0:0,0,11,4 chr1 170001151 . ATACTCATT A 773.7 PASS AC=1;AF=0.591;AN=2;DP=591;MQ=60;set=variant8-variant11-variant13-variant15-variant18-variant23-variant24-variant25-variant27-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:27,17:44:99:624,0,2538:6,21,3,14 chr1 170004508 . A T 58.54 PASS AC=1;AF=0.667;AN=2;DP=127;FractionInformativeReads=1;MQ=60;set=variant5-variant8-variant10-variant11-variant13-variant14-variant15-variant18-variant23-variant24-variant25-variant26-variant27-variant29-variant35-variant36-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,3:8:99:108,0,163:3,2,3,0 chr1 170015700 . T C 306.75 PASS AC=1;AF=0.591;AN=2;DP=180;MQ=60;set=variant8-variant11-variant13-variant15-variant18-variant23-variant24-variant25-variant27-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:7,5:12:99:186,0,238:6,1,5,0 chr1 170037279 . C A 3668.14 PASS AC=1;AF=0.591;AN=2;DP=2680;MQ=60;set=variant8-variant11-variant13-variant15-variant18-variant23-variant24-variant25-variant27-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:123,97:220:99:2263,0,3100:65,58,50,47 chr1 170037624 . C T 2036.45 PASS AC=1;AF=0.591;AN=2;DP=1973;MQ=60;set=variant8-variant11-variant13-variant15-variant18-variant23-variant24-variant25-variant27-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:132,78:210:99:1680,0,3524:81,51,42,36 chr1 170043904 . G C 415.48 PASS AC=1;AF=0.763;AN=2;DP=1236;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,20:44:99:504,0,538:12,12,8,12 chr1 170115156 . G A 851.33 PASS AC=1;AF=0.589;AN=2;DP=1843;MQ=60;set=variant-variant3-variant8-variant9-variant11-variant12-variant13-variant15-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:30,32:62:99:765,0,770:15,15,19,13 chr1 170120715 . T C 244.62 PASS AC=1;AF=0.5;AN=2;DP=36;FS=0;FractionInformativeReads=1;MQ=60;set=variant32-variant35 GT:AD:DP:GQ:PL:SB 0/1:10,6:16:99:170,0,274:3,7,2,4 chr1 170135510 . T C 479.86 PASS AC=2;AF=0.8;AN=2;DP=596;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:417,33,0:0,0,10,1 chr1 170135669 . C T 1638.13 PASS AC=1;AF=0.558;AN=2;DP=3655;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant11-variant12-variant14-variant16-variant17-variant21-variant23-variant25-variant26-variant28-variant29-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:96,64:160:99:1543,0,2371:55,41,39,25 chr1 170135760 . T C 2604.24 PASS AC=1;AF=0.558;AN=2;DP=4733;set=variant-variant4-variant5-variant6-variant7-variant11-variant12-variant14-variant16-variant17-variant21-variant23-variant25-variant26-variant28-variant29-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:104,89:193:99:3348,0,5515:48,56,48,41 chr1 170135765 . T C 2532.3 PASS AC=1;AF=0.543;AN=2;DP=4208;set=variant-variant4-variant5-variant6-variant7-variant11-variant12-variant16-variant17-variant21-variant23-variant25-variant26-variant28-variant33-variant34-variant35-variant36-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:103,88:191:99:3330,0,5518:47,56,48,40 chr1 170137112 . GA G 232.61 PASS AC=1;AF=0.735;AN=2;DP=143;FS=0;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant10-variant19-variant20-variant21-variant23-variant31-variant32-variant34-variant35-variant37-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:1,3:4:17:78,0,17:0,1,0,3 chr1 170501385 . A C 2864.52 PASS AC=2;AF=1;AN=2;DP=6948;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,152:152:99:4492,454,0:0,0,81,71 chr1 170501456 . C T 2940.5 PASS AC=2;AF=0.636;AN=2;DP=4815;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,148:148:99:4348,440,0:0,0,69,79 chr1 170501575 . A G 885.84 PASS AC=1;AF=0.667;AN=2;DP=105;FractionInformativeReads=1;MQ=60;set=variant8-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:20,14:34:99:436,0,623:4,16,3,11 chr1 170502517 . A G 418.36 PASS AC=2;AF=1;AN=2;DP=466;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:690,57,0:0,0,15,4 chr1 170514229 . G A 1819.13 PASS AC=2;AF=0.636;AN=2;DP=1539;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,52:52:99:1897,155,0:0,0,37,15 chr1 170632574 . AG A 686.09 PASS AC=2;AF=1;AN=2;DP=1067;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:685,60,0:0,0,10,10 chr1 170632622 . CTT CT,C 453.66 PASS AC=2,0;AF=0.988,0.012;AN=2;DP=658;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:6:18:0,0,4,2 chr1 170632965 . G A 475.77 PASS AC=1;AF=0.5;AN=2;DP=664;MQ=60;set=variant7-variant8-variant9-variant11-variant13-variant16-variant19-variant27-variant29-variant30-variant31-variant35-variant37-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:19,25:44:99:538,0,453:7,12,11,14 chr1 170633066 . C G 1289.42 PASS AC=2;AF=1;AN=2;DP=2018;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.141;ReadPosRankSum=0.042;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1282,129,0:0,0,18,25 chr1 170633111 . T G 1661.49 PASS AC=2;AF=1;AN=2;DP=1723;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1916,129,0:0,0,20,23 chr1 170633119 . T G 1636.77 PASS AC=2;AF=1;AN=2;DP=1701;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1924,129,0:0,0,21,22 chr1 170633142 . C G 1391.5 PASS AC=2;AF=1;AN=2;DP=1470;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:1350,90,0:0,0,11,19 chr1 170633173 . A G 814.9 PASS AC=2;AF=1;AN=2;DP=1174;FS=0;MQ=60;MQRankSum=1.664;ReadPosRankSum=1.597;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:834,72,0:0,0,9,15 chr1 170633186 . AT A,ATT 370.38 PASS AC=0,1;AF=0.548,0.286;AN=2;DP=1048;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:19:99:5,7,4,3 chr1 170633229 . C CCTCTCTCTCTCTCTCTCTCT,CCTCTCTCTCTCT,CCTCTCTCTCTCTCT,CCTCTCTCTCTCTCTCTCTCTCT,CCTCTCTCTCT,CCTCTCTCTCTCTCTCTCTCTCTCT,CCTCTCTCTCTCTCTCTCT 211.03 PASS AC=1,1,0,0,0,0,0;AF=0.162,0.382,0.029,0.044,0.044,0.029,0.029;AN=2;DP=778;set=variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-filterInvariant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 2/1:9:99:0,0,6,3 chr1 170696474 . A C 2175.62 PASS AC=1;AF=0.886;AN=2;DP=3190;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:29,37:66:99:845,0,671:17,12,18,19 chr1 170705618 . A C 2179.71 PASS AC=2;AF=1;AN=2;DP=2069;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1001,110,0:0,0,16,21 chr1 170705685 . CTATATATATATA CTA,CTATATA,CTATA,C,CTATATATA,CTATATATATA 2009.71 PASS AC=0,2,0,0,0,0;AF=0.167,0.571,0.083,0.024,0.012,0.012;AN=2;DP=1299;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 2/2:2:7:0,0,1,1 chr1 170708637 . C G 901.64 PASS AC=1;AF=0.886;AN=2;DP=1132;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:14,15:29:99:420,0,421:2,12,5,10 chr1 170927570 . CT C,CTT 808.36 PASS AC=1,0;AF=0.403,0.129;AN=2;DP=3484;set=variant-filterInvariant2-filterInvariant3-filterInvariant6-filterInvariant7-variant10-variant11-variant12-variant13-variant15-filterInvariant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-filterInvariant30-variant31-variant32-variant33-variant34-variant35-filterInvariant36-filterInvariant37-filterInvariant38-variant39-variant42-variant44 GT:DP:GQ:SB 0/1:112:99:17,27,31,37 chr1 170965596 . T G 1012.3 PASS AC=1;AF=0.5;AN=2;DP=224;FractionInformativeReads=1;MQ=60;set=variant23-variant35 GT:AD:DP:GQ:PL:SB 0/1:70,53:123:99:1300,0,1620:42,28,33,20 chr1 170993444 . G GGT,T 156.36 PASS AC=1,0;AF=0.707,0.034;AN=2;DP=268;set=variant2-variant4-variant8-variant9-variant11-variant14-variant15-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:DP:GQ:SB 0/1:11:33:2,0,5,4 chr1 171061990 . A G 1110.12 PASS AC=2;AF=0.586;AN=2;DP=2148;MQ=60;set=variant3-variant6-variant9-variant10-variant11-variant12-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:2193,216,0:0,0,28,44 chr1 171069959 . A G 43.52 PASS AC=2;AF=0.675;AN=2;DP=100;FS=0;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant10-variant11-variant12-variant16-variant18-variant21-variant23-variant24-variant27-variant28-variant31-variant32-variant34-variant35-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:229,18,0:0,0,5,1 chr1 171070176 . G T 660.42 PASS AC=1;AF=0.5;AN=2;DP=326;MQ=60;set=variant23-variant24-variant25-variant28-variant35-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:24,16:40:99:386,0,610:12,12,9,7 chr1 171076966 . G A 1534.38 PASS AC=2;AF=0.611;AN=2;DP=3136;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant9-variant10-variant11-variant12-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant32-variant33-variant35-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,111:111:99:3376,333,0:0,0,48,63 chr1 171077198 . G A 2219.64 PASS AC=2;AF=0.597;AN=2;DP=4940;MQ=60;set=variant3-variant6-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,156:156:99:4561,466,0:0,0,91,65 chr1 171077372 . C G 1697.4 PASS AC=2;AF=0.55;AN=2;DP=2900;MQ=60;set=variant6-variant9-variant10-variant11-variant15-variant16-variant18-variant21-variant23-variant24-variant25-variant28-variant29-variant35-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,118:118:99:3684,353,0:0,0,49,69 chr1 171112490 . C T 578.15 PASS AC=2;AF=0.588;AN=2;DP=1386;MQ=60;set=variant3-variant4-variant6-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1776,153,0:0,0,14,37 chr1 171130236 . G A 1613.1 PASS AC=1;AF=0.5;AN=2;DP=1373;MQ=60;set=variant-variant10-variant12-variant13-variant15-variant16-variant35-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:81,67:148:99:1799,0,2016:48,33,39,28 chr1 171130346 . G A 2055.91 PASS AC=1;AF=0.5;AN=2;DP=2194;MQ=60;set=variant-variant6-variant9-variant10-variant12-variant15-variant16-variant18-variant35-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:102,96:198:99:2353,0,2612:55,47,54,42 chr1 171130539 . G C 1332.17 PASS AC=1;AF=0.5;AN=2;DP=1503;MQ=60;set=variant-variant6-variant9-variant10-variant12-variant15-variant16-variant18-variant35-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:68,70:138:99:1777,0,1810:21,47,25,45 chr1 171130598 . CACACA C 836.45 PASS AC=2;AF=0.556;AN=2;DP=1180;MQ=60;set=variant-variant6-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant32-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1524,106,0:0,0,6,29 chr1 171155103 . C T 447.77 PASS AC=1;AF=0.714;AN=2;DP=1086;MQ=60;set=variant-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,13:31:99:451,0,646:2,16,1,12 chr1 171168302 . G C 99.34 PASS AC=1;AF=0.697;AN=2;DP=355;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,6:14:99:185,0,185:6,2,5,1 chr1 171168584 . C T 1764.53 PASS AC=1;AF=0.633;AN=2;DP=2674;MQ=60;set=variant-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant18-variant20-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,67:122:99:2563,0,2837:26,29,33,34 chr1 171168585 . A G 1764.53 PASS AC=1;AF=0.686;AN=2;DP=3120;MQ=60;set=variant-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,64:119:99:2563,0,2837:26,29,31,33 chr1 171174531 . A G 906.57 PASS AC=1;AF=0.591;AN=2;DP=955;MQ=60;set=variant-variant10-variant12-variant15-variant18-variant27-variant34-variant35-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,45:71:99:1271,0,590:12,14,25,20 chr1 171178257 . C CT 318.21 PASS AC=1;AF=0.583;AN=2;DP=468;MQ=60;set=variant-variant10-variant12-variant13-variant15-variant18-variant27-variant34-variant35-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,25:40:99:630,0,338:8,7,16,9 chr1 171178490 . C T 1536.44 PASS AC=1;AF=0.583;AN=2;DP=1277;FractionInformativeReads=1;MQ=60;set=variant-variant10-variant12-variant13-variant15-variant18-variant27-variant34-variant35-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,52:116:99:1423,0,1653:31,33,25,27 chr1 171179351 . A T 1188.67 PASS AC=1;AF=0.583;AN=2;DP=1038;MQ=60;set=variant-variant10-variant12-variant13-variant15-variant18-variant27-variant34-variant35-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,37:102:99:933,0,1715:35,30,20,17 chr1 171217691 . C A 305.1 PASS AC=1;AF=0.583;AN=2;DP=306;MQ=60;set=variant-variant10-variant12-variant13-variant15-variant18-variant27-variant34-variant35-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,16:30:99:306,0,340:6,8,8,8 chr1 171301033 . C G 1008.33 PASS AC=1;AF=0.588;AN=2;DP=1906;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,34:82:99:1035,0,1706:18,30,13,21 chr1 171301043 . GA GAA,G 899.31 PASS AC=1,1;AF=0.581,0.016;AN=2;DP=1403;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:DP:GQ:SB 2/1:64:99:0,0,21,43 chr1 171303925 . C T 1054.15 PASS AC=1;AF=0.588;AN=2;DP=4308;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,76:140:99:1896,0,1585:27,37,28,48 chr1 171306323 . C T 256.64 PASS AC=1;AF=0.5;AN=2;DP=174;FractionInformativeReads=1;MQ=60;set=variant4-variant10-variant14-variant18-variant27-variant35 GT:AD:DP:GQ:PL:SB 0/1:12,18:30:99:436,0,367:8,4,11,7 chr1 171311003 . A C 1248.56 PASS AC=2;AF=0.649;AN=2;DP=4565;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,108:108:99:3450,323,0:0,0,51,57 chr1 171454777 . C T 3183.56 PASS AC=1;AF=0.533;AN=2;DP=1456;MQ=60;set=variant2-variant4-variant7-variant11-variant17-variant19-variant20-variant22-variant24-variant25-variant27-variant29-variant31-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:49,43:92:99:1071,0,1281:28,21,24,19 chr1 171482686 . A T 1291.28 PASS AC=1;AF=0.531;AN=2;DP=613;MQ=60;set=variant2-variant4-variant7-variant11-variant16-variant17-variant19-variant20-variant22-variant24-variant25-variant27-variant29-variant31-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:16,17:33:99:644,0,418:4,12,0,17 chr1 171482699 . G C 1059.38 PASS AC=1;AF=0.531;AN=2;DP=512;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant7-variant11-variant16-variant17-variant19-variant20-variant22-variant24-variant25-variant27-variant29-variant31-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:11,13:24:99:463,0,307:2,9,0,13 chr1 171483717 . A C 2779.6 PASS AC=1;AF=0.531;AN=2;DP=1517;MQ=60;set=variant2-variant4-variant7-variant11-variant16-variant17-variant19-variant20-variant22-variant24-variant25-variant27-variant29-variant31-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:37,69:106:99:1740,0,886:22,15,39,30 chr1 171487092 . TG T 329.5 PASS AC=1;AF=0.694;AN=2;DP=383;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant27-variant28-variant31-variant32-variant33-variant35-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,5:9:99:160,0,121:0,4,1,4 chr1 171491264 . T A 517.88 PASS AC=1;AF=0.703;AN=2;DP=355;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,6:8:54:150,0,54:1,1,4,2 chr1 171496875 . A G 79.66 PASS AC=1;AF=0.556;AN=2;DP=248;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant10-variant15-variant21-variant35-variant37-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,22:35:99:627,0,311:9,4,15,7 chr1 171496895 . A G 1134.93 PASS AC=2;AF=0.86;AN=2;DP=1587;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,43:45:86:1242,86,0:1,1,26,17 chr1 171505524 . G A 83.79 PASS AC=1;AF=0.5;AN=2;DP=170;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant7-variant11-variant16-variant17-variant19-variant20-variant22-variant24-variant25-variant27-variant29-variant31-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:8,7:15:99:218,0,246:1,7,0,7 chr1 171509014 . T C 65.44 PASS AC=1;AF=0.5;AN=2;DP=145;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant7-variant11-variant16-variant17-variant19-variant20-variant22-variant24-variant25-variant29-variant31-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:7,11:18:99:433,0,179:6,1,11,0 chr1 171509058 . G A 668.95 PASS AC=2;AF=0.86;AN=2;DP=971;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1421,108,0:0,0,31,5 chr1 171509327 . G A 3422.33 PASS AC=2;AF=0.86;AN=2;DP=5373;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,134:135:99:4097,393,0:0,1,65,69 chr1 171511039 . C G 2780.26 PASS AC=2;AF=0.86;AN=2;DP=4353;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,89:89:99:2657,266,0:0,0,43,46 chr1 171511442 . A G 769.53 PASS AC=1;AF=0.697;AN=2;DP=968;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,12:26:99:365,0,458:3,11,3,9 chr1 171514731 . C G 984.04 PASS AC=2;AF=0.86;AN=2;DP=1735;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1284,132,0:0,0,20,24 chr1 171514848 . TTTTATTTA TTTTATTTATTTA,T 51.95 PASS AC=2,0;AF=0.708,0.167;AN=2;DP=125;FS=0;MQ=60;set=variant3-variant7-variant15-variant21-variant25-variant27-variant32-variant34-variant35-variant38-variant41-variant42 GT:DP:GQ:SB 1/1:2:6:0,0,0,2 chr1 171519487 . A C 888.29 PASS AC=2;AF=0.86;AN=2;DP=1163;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1309,117,0:0,0,10,29 chr1 171526570 . G A 1493.54 PASS AC=2;AF=0.86;AN=2;DP=9043;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,206:207:99:6054,607,0:1,0,104,102 chr1 171527322 . A G 656.7 PASS AC=2;AF=0.86;AN=2;DP=1206;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-filterInvariant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:1073,84,0:0,0,4,24 chr1 171546833 . C A 1232.98 PASS AC=1;AF=0.7;AN=2;DP=1213;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,12:22:99:312,0,243:3,7,4,8 chr1 171548772 . A G 341.07 PASS AC=1;AF=0.5;AN=2;DP=219;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant7-variant11-variant16-variant17-variant19-variant20-variant22-variant24-variant25-variant27-variant29-variant31-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:8,10:18:99:341,0,256:3,5,4,6 chr1 171548868 . T C 540.57 PASS AC=2;AF=0.869;AN=2;DP=790;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:595,51,0:0,0,12,5 chr1 171553778 . A G 134.96 PASS AC=1;AF=0.5;AN=2;DP=111;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant7-variant11-variant16-variant17-variant20-variant22-variant25-variant27-variant29-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:4,2:6:69:69,0,129:2,2,0,2 chr1 171556165 . G C 5483.96 PASS AC=2;AF=0.837;AN=2;DP=7132;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,156:156:99:4469,468,0:0,0,79,77 chr1 171558447 . GTT GT,GTTT,G 139.99 PASS AC=1,0,0;AF=0.367,0.117,0.033;AN=2;DP=862;set=variant-variant3-variant5-variant7-filterInvariant12-variant13-variant14-variant16-variant18-variant19-variant21-filterInvariant22-variant23-variant25-filterInvariant26-variant27-variant28-filterInvariant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:DP:GQ:SB 0/1:20:91:7,2,8,3 chr1 171558516 . C T 1488.77 PASS AC=2;AF=0.837;AN=2;DP=2668;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:2018,168,0:0,0,33,23 chr1 171561225 . C T 6025.49 PASS AC=2;AF=0.837;AN=2;DP=6672;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,134:134:99:4264,401,0:0,0,52,82 chr1 171561250 . G A 5055.33 PASS AC=2;AF=0.837;AN=2;DP=5525;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,101:101:99:3452,303,0:0,0,37,64 chr1 171561307 . A G 3784.04 PASS AC=2;AF=0.837;AN=2;DP=3850;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:2781,225,0:0,0,52,23 chr1 171607702 . C T 3022.6 PASS AC=2;AF=0.845;AN=2;DP=4371;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,88:88:99:2786,264,0:0,0,50,38 chr1 171621525 . C T 2449.32 PASS AC=1;AF=0.545;AN=2;DP=2109;MQ=60;set=variant5-variant10-variant15-variant20-variant22-variant23-variant31-variant35-variant36-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:100,110:210:99:2931,0,2612:52,48,58,52 chr1 171621834 . C T 522.54 PASS AC=1;AF=0.545;AN=2;DP=416;FractionInformativeReads=1;MQ=60;set=variant5-variant10-variant15-variant20-variant22-variant23-variant31-variant35-variant36-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,16:40:99:472,0,557:7,17,3,13 chr1 171670237 . T C 5548.94 PASS AC=1;AF=0.5;AN=2;DP=2871;MQ=60;set=variant4-variant11-variant21-variant26-variant32-variant33-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:176,168:344:99:4191,0,4369:105,71,96,72 chr1 171670446 . C T 3124.85 PASS AC=1;AF=0.5;AN=2;DP=582;FractionInformativeReads=1;MQ=60;set=variant23-variant35 GT:AD:DP:GQ:PL:SB 0/1:164,142:306:99:3821,0,4630:77,87,68,74 chr1 171671463 . T G 4564.45 PASS AC=1;AF=0.567;AN=2;DP=12308;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:164,184:348:99:4622,0,3785:63,101,69,115 chr1 171672420 . AAGG A 4252.94 PASS AC=1;AF=0.5;AN=2;DP=1642;MQ=60;set=variant4-variant11-variant21-variant26-variant32-variant33-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:130,85:215:99:3169,0,6343:50,80,35,50 chr1 171672613 . A C 788.59 PASS AC=2;AF=1;AN=2;DP=1885;FS=0;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:638,54,0:0,0,15,3 chr1 171679958 . G A 922.37 PASS AC=1;AF=0.569;AN=2;DP=2438;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant11-variant12-variant13-variant15-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:46,52:98:99:1293,0,1037:18,28,18,34 chr1 171707272 . T C 147.99 PASS AC=2;AF=0.839;AN=2;DP=221;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant35-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:234,21,0:0,0,5,2 chr1 171750774 . C T 1297.53 PASS AC=1;AF=0.6;AN=2;DP=2243;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant11-variant12-variant15-variant20-variant21-variant25-variant26-variant31-variant32-variant33-variant35-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:54,49:103:99:1244,0,1650:40,14,29,20 chr1 171751051 . A G 5749.28 PASS AC=1;AF=0.643;AN=2;DP=6659;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:94,76:170:99:1854,0,2533:37,57,31,45 chr1 171751236 . T C 2150.52 PASS AC=1;AF=0.639;AN=2;DP=2611;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:37,30:67:99:732,0,891:15,22,15,15 chr1 171753039 . A G 1436.9 PASS AC=1;AF=0.6;AN=2;DP=2909;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant11-variant12-variant15-variant20-variant21-variant25-variant26-variant31-variant32-variant33-variant35-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:75,69:144:99:1684,0,1878:34,41,33,36 chr1 171754865 . A G 836.47 PASS AC=1;AF=0.643;AN=2;DP=888;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:14,18:32:99:464,0,353:10,4,12,6 chr1 171755170 . G A 850.84 PASS AC=1;AF=0.605;AN=2;DP=1266;MQ=60;set=variant3-variant4-variant5-variant6-variant11-variant12-variant15-variant20-variant21-variant25-variant26-variant31-variant32-variant33-variant35-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:39,32:71:99:826,0,1010:15,24,13,19 chr1 171757036 . C T 1382.75 PASS AC=1;AF=0.5;AN=2;DP=112;FS=1.561;FractionInformativeReads=1;MQ=60;MQRankSum=-0.792;QD=12.35;ReadPosRankSum=2.41;SOR=0.54;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:55,57:112:99:1411,0,1361:19,36,22,35 chr1 171763522 . C A 970.39 PASS AC=1;AF=0.6;AN=2;DP=1201;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant11-variant12-variant15-variant20-variant21-variant25-variant26-variant31-variant32-variant33-variant35-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:26,28:54:99:645,0,678:17,9,16,12 chr1 171763549 . C T 1197.99 PASS AC=1;AF=0.528;AN=2;DP=1539;MQ=60;set=variant-variant4-variant7-variant8-variant10-variant13-variant14-variant16-variant17-variant19-variant27-variant28-variant29-variant30-variant35-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:46,37:83:99:918,0,1120:27,19,21,16 chr1 171765591 . G A 1639.28 PASS AC=1;AF=0.605;AN=2;DP=3001;MQ=60;set=variant-variant3-variant5-variant6-variant11-variant12-variant15-variant20-variant21-variant25-variant26-variant31-variant32-variant33-variant35-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:74,61:135:99:1428,0,1950:42,32,34,27 chr1 171766580 . T G 2382.15 PASS AC=1;AF=0.611;AN=2;DP=1401;FractionInformativeReads=1;MQ=60;set=variant10-variant15-variant20-variant23-variant31-variant35-variant36-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,83:148:99:2218,0,1733:42,23,51,32 chr1 171766696 . A G 3912.76 PASS AC=1;AF=0.605;AN=2;DP=6415;MQ=60;set=variant-variant3-variant5-variant6-variant11-variant12-variant15-variant20-variant21-variant25-variant26-variant31-variant32-variant33-variant35-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:170,172:342:99:4343,0,4576:96,74,91,81 chr1 171810600 . G GC 454.74 PASS AC=1;AF=0.5;AN=2;DP=34;FS=3.041;FractionInformativeReads=1;MQ=60;MQRankSum=0.293;QD=13.37;ReadPosRankSum=0.569;SOR=0.317;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:16,18:34:99:492,0,449:11,5,10,8 chr1 171958073 . C T 673.25 PASS AC=1;AF=0.5;AN=2;DP=41;FS=3.27;FractionInformativeReads=1;MQ=60;MQRankSum=0.565;QD=16.42;ReadPosRankSum=1.116;SOR=1.371;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:18,23:41:99:701,0,464:13,5,19,4 chr1 172038079 . T C 1020.73 PASS AC=2;AF=0.589;AN=2;DP=2956;MQ=60;set=variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant26-variant30-variant31-variant33-variant35-variant36-variant37-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,93:94:99:2686,239,0:0,1,40,53 chr1 172222629 . TCTCTCCTCTCCTCTCCTCTC TCTCTC,TCTCTCCTCTC,T,TCTCTCCTCTCCTCTC 508.02 PASS AC=2,0,0,0;AF=0.439,0.045,0.076,0.167;AN=2;DP=672;set=variant3-variant5-variant6-variant8-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:6:18:0,0,5,1 chr1 172280452 . ATG A,ATGTGTGTG,ATGTG,ATGTGTGTGTG,ATGTGTG 68.53 PASS AC=1,0,0,0,0;AF=0.236,0.222,0.056,0.014,0.028;AN=2;DP=4723;set=filterInvariant-variant2-filterInvariant4-filterInvariant5-variant7-filterInvariant8-variant9-filterInvariant10-variant11-variant12-variant14-variant15-variant16-filterInvariant19-filterInvariant20-variant21-variant22-variant23-variant24-filterInvariant25-variant26-variant27-filterInvariant28-variant29-filterInvariant31-variant32-variant33-variant34-filterInvariant35-filterInvariant36-variant38-variant40-filterInvariant41-variant42-filterInvariant43-filterInvariant44 GT:DP:GQ:SB 0/1:82:99:17,53,2,10 chr1 172307678 . T C 311.23 PASS AC=1;AF=0.5;AN=2;DP=241;FractionInformativeReads=1;MQ=60;set=variant7-variant9-variant10-variant15-variant20-variant26-variant30-variant32-variant35-variant36-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,9:17:99:242,0,170:5,3,7,2 chr1 172308238 . C T 1504.45 PASS AC=1;AF=0.574;AN=2;DP=4193;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:76,68:144:99:1584,0,2027:42,34,31,37 chr1 172356437 . A G 1961.73 PASS AC=2;AF=1;AN=2;DP=3491;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,98:98:99:2831,294,0:0,0,43,55 chr1 172377046 . G A 1200.33 PASS AC=1;AF=0.5;AN=2;DP=336;FractionInformativeReads=1;MQ=60;set=variant11-variant30-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:42,38:80:99:998,0,1144:14,28,16,22 chr1 172380466 . G A 3053.15 PASS AC=1;AF=0.5;AN=2;DP=968;MQ=60;set=variant11-variant30-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:129,124:253:99:3195,0,3287:68,61,64,60 chr1 172380678 . TA TAA,T 1483.15 PASS AC=0,1;AF=0.263,0.238;AN=2;DP=11214;set=variant-variant2-variant3-variant4-variant5-filterInvariant6-variant7-variant8-filterInvariant9-variant10-filterInvariant11-variant12-variant14-filterInvariant15-filterInvariant16-filterInvariant17-variant18-filterInvariant19-variant20-filterInvariant23-filterInvariant24-variant25-filterInvariant26-filterInvariant27-variant28-variant29-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-variant34-filterInvariant35-variant36-filterInvariant37-variant38-variant39-variant40-variant41-filterInvariant43-filterInvariant44 GT:DP:GQ:SB 0/2:230:99:104,80,21,25 chr1 172380875 . C A 5065.23 PASS AC=2;AF=0.932;AN=2;DP=18344;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,417:417:99:12493,1248,0:0,0,199,218 chr1 172381383 . T C 5158.13 PASS AC=1;AF=0.593;AN=2;DP=10986;MQ=60;set=variant2-variant3-variant5-variant6-variant8-variant9-variant13-variant14-variant15-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant35-variant37-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:198,190:388:99:4987,0,5401:111,87,118,72 chr1 172400009 . AT A 139.57 PASS AC=2;AF=0.672;AN=2;DP=458;MQ=60;set=variant2-variant3-variant5-variant6-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:500,42,0:0,0,11,3 chr1 172410492 . TACACACACACACACACACAC TACACACACACAC,TACACAC,TACACACAC,T,TACACACACACACAC,TACACACACAC,TACACACACACACACACAC,TACACACACACACACAC 587.34 PASS AC=0,1,1,0,0,0,0,0;AF=0.279,0.384,0.128,0.012,0.047,0.012,0.023,0.012;AN=2;DP=935;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 2/3:26:99:0,0,22,4 chr1 172410967 . G A 2257.56 PASS AC=2;AF=0.676;AN=2;DP=5852;MQ=60;set=variant2-variant3-variant5-variant6-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,192:192:99:6058,574,0:0,0,104,88 chr1 172411496 . A G 207.34 PASS AC=2;AF=0.907;AN=2;DP=1405;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1349,117,0:0,0,17,22 chr1 172412995 . T C 1060.55 PASS AC=2;AF=0.676;AN=2;DP=3330;MQ=60;set=variant2-variant3-variant5-variant6-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,93:93:99:2863,278,0:0,0,45,48 chr1 172417558 . G A 1020.54 PASS AC=1;AF=0.5;AN=2;DP=414;FractionInformativeReads=1;MQ=60;set=variant11-variant30-variant35-variant37-variant42 GT:AD:DP:GQ:PL:SB 0/1:51,43:94:99:948,0,1235:29,22,22,21 chr1 172417781 . A G 79.71 PASS AC=2;AF=0.905;AN=2;DP=486;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:701,51,0:0,0,2,15 chr1 172422405 . G A 887.37 PASS AC=1;AF=0.5;AN=2;DP=385;FractionInformativeReads=1;MQ=60;set=variant11-variant30-variant35-variant37-variant42 GT:AD:DP:GQ:PL:SB 0/1:39,32:71:99:857,0,1155:19,20,9,23 chr1 172425529 . C G 1572.2 PASS AC=1;AF=0.645;AN=2;DP=6136;MQ=60;set=variant2-variant3-variant5-variant6-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant34-variant35-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:137,106:243:99:2361,0,3436:57,80,54,52 chr1 172431210 . G A 562.57 PASS AC=2;AF=0.878;AN=2;DP=895;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:693,51,0:0,0,16,1 chr1 172431333 . A G 974.78 PASS AC=1;AF=0.5;AN=2;DP=627;FractionInformativeReads=1;MQ=60;set=variant8-variant9-variant11-variant30-variant35-variant37-variant42 GT:AD:DP:GQ:PL:SB 0/1:49,49:98:99:1166,0,1220:29,20,31,18 chr1 172431386 . G A 1636.67 PASS AC=1;AF=0.5;AN=2;DP=841;MQ=60;set=variant8-variant9-variant11-variant30-variant35-variant37-variant42 GT:AD:DP:GQ:PL:SB 0/1:57,69:126:99:1651,0,1422:32,25,36,33 chr1 172434309 . G A 61.77 PASS AC=2;AF=1;AN=2;DP=27;FS=0;FractionInformativeReads=1;MQ=60;set=variant5-variant9-variant17-variant22-variant24-variant35-variant37-variant39 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:181,15,0:0,0,4,1 chr1 172434375 . G A 365.41 PASS AC=2;AF=0.869;AN=2;DP=1133;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:842,78,0:0,0,19,7 chr1 172434378 . C A 405.81 PASS AC=1;AF=0.5;AN=2;DP=212;FractionInformativeReads=1;MQ=60;set=variant8-variant9-variant11-variant30-variant35-variant37-variant42 GT:AD:DP:GQ:PL:SB 0/1:23,4:27:99:99,0,689:16,7,4,0 chr1 172434812 . C T 1084.98 PASS AC=1;AF=0.661;AN=2;DP=2595;MQ=60;set=variant2-variant3-variant5-variant6-variant8-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant34-variant35-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,44:108:99:977,0,1716:27,37,22,22 chr1 172437592 . G A 1068.44 PASS AC=2;AF=0.869;AN=2;DP=3812;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,103:103:99:2891,308,0:0,0,56,47 chr1 172437908 . G A 2133.99 PASS AC=1;AF=0.5;AN=2;DP=1396;FractionInformativeReads=1;MQ=60;set=variant8-variant9-variant11-variant30-variant35-variant37-variant42 GT:AD:DP:GQ:PL:SB 0/1:118,101:219:99:2193,0,2710:54,64,46,55 chr1 172501643 . T C 1846.42 PASS AC=1;AF=0.568;AN=2;DP=3902;MQ=60;set=variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant19-variant24-variant25-variant27-variant28-variant31-variant35-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:80,64:144:99:1570,0,2095:47,33,42,22 chr1 172502340 . T C 450.19 PASS AC=1;AF=0.614;AN=2;DP=734;FractionInformativeReads=1;MQ=60;set=variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant19-variant24-variant25-variant27-variant28-variant31-variant35-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:10,14:24:99:481,0,205:7,3,11,3 chr1 172502479 . T C 1220.4 PASS AC=2;AF=0.784;AN=2;DP=4066;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,122:122:99:4221,365,0:0,0,84,38 chr1 172502727 . TA T 1219.48 PASS AC=1;AF=0.568;AN=2;DP=1772;MQ=60;set=variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant19-variant24-variant25-variant27-variant28-variant31-variant35-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:38,43:81:99:1103,0,1203:15,23,18,25 chr1 172522249 . A G 164.91 PASS AC=1;AF=0.654;AN=2;DP=128;FS=0;FractionInformativeReads=1;MQ=60;set=variant6-variant12-variant15-variant21-variant23-variant24-variant26-variant32-variant34-variant35-variant36-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:6,9:15:99:338,0,217:6,0,9,0 chr1 172522602 . G A 133.71 PASS AC=1;AF=0.595;AN=2;DP=224;FractionInformativeReads=1;MQ=60;set=variant5-variant6-variant7-variant8-variant10-variant13-variant14-variant16-variant19-variant23-variant24-variant25-variant27-variant28-variant31-variant35-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,11:16:99:389,0,167:0,5,1,10 chr1 172546959 . G A 879.08 PASS AC=1;AF=0.5;AN=2;DP=66;FS=2.176;FractionInformativeReads=1;MQ=60;MQRankSum=-0.449;QD=13.32;ReadPosRankSum=0.68;SOR=1.136;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:33,33:66:99:907,0,810:13,20,10,23 chr1 172547465 . A G 785.2 PASS AC=1;AF=0.565;AN=2;DP=2104;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant16-variant19-variant23-variant24-variant25-variant27-variant28-variant31-variant35-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:47,35:82:99:785,0,1279:25,22,17,18 chr1 172554867 . T A 124.45 PASS AC=1;AF=0.575;AN=2;DP=179;FS=0;FractionInformativeReads=1;MQ=60;set=variant5-variant6-variant7-variant8-variant10-variant13-variant14-variant16-variant19-variant23-variant24-variant25-variant27-variant28-variant31-variant35-variant37-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,5:11:99:189,0,237:6,0,5,0 chr1 172577864 . CT C 55.76 PASS AC=1;AF=0.5;AN=2;DP=398;MQ=60;set=filterInvariant3-filterInvariant10-filterInvariant17-variant18-filterInvariant21-filterInvariant23-filterInvariant30-filterInvariant35 GT:AD:DP:GQ:PL:SB 0/1:48,10:58:88:88,0,1074:26,22,4,6 chr1 172634734 . T C 3710.21 PASS AC=2;AF=1;AN=2;DP=4637;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,123:123:99:4034,369,0:0,0,67,56 chr1 172635756 . GGTGTGT GGTGT,GGTGTGTGT,G,GGTGTGTGTGT 185.71 PASS AC=0,1,0,0;AF=0.197,0.242,0.015,0.045;AN=2;DP=1385;set=variant-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-filterInvariant14-variant16-variant17-variant21-variant22-variant23-filterInvariant24-filterInvariant25-filterInvariant26-variant27-variant28-filterInvariant29-variant30-variant31-variant34-variant35-variant36-variant37-filterInvariant38-variant39-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:22:99:9,6,4,3 chr1 173009536 . T A 3073.61 PASS AC=1;AF=0.525;AN=2;DP=4892;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant16-variant17-variant19-variant24-variant28-variant29-variant32-variant34-variant35-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:119,130:249:99:3678,0,3441:86,33,90,40 chr1 173009832 . G T 1272.36 PASS AC=1;AF=0.568;AN=2;DP=2863;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant16-variant17-variant19-variant24-variant27-variant28-variant29-variant32-variant34-variant35-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:78,52:130:99:1581,0,2365:33,45,20,32 chr1 173020230 . A AC 1077.8 PASS AC=1;AF=0.525;AN=2;DP=1087;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant16-variant17-variant19-variant24-variant28-variant29-variant32-variant34-variant35-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:32,43:75:99:1475,0,981:9,23,9,34 chr1 173472551 . T C 939.96 PASS AC=2;AF=0.536;AN=2;DP=865;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant24-variant29-variant30-variant31-variant33-variant35-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:1971,204,0:0,0,28,40 chr1 173474262 . G A 226.73 PASS AC=2;AF=0.536;AN=2;DP=219;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant24-variant29-variant30-variant31-variant33-variant35-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:622,54,0:0,0,14,4 chr1 173474429 . T C 1440.26 PASS AC=2;AF=0.536;AN=2;DP=1881;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant24-variant29-variant30-variant31-variant33-variant35-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,156:156:99:4408,466,0:0,0,76,80 chr1 173478648 . T C 75.73 PASS AC=2;AF=0.583;AN=2;DP=75;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant7-variant24-variant29-variant30-variant31-variant33-variant35-variant37-variant39-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:263,21,0:0,0,6,1 chr1 173490407 . TAA TA,T 94.44 PASS AC=2,0;AF=0.355,0.25;AN=2;DP=1031;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:17:50:0,0,12,5 chr1 173490616 . CTATATA C 144.5 PASS AC=2;AF=0.81;AN=2;DP=228;FS=0;MQ=60;set=variant2-variant3-variant6-variant7-variant8-variant11-variant16-variant17-variant20-variant21-variant24-variant26-variant27-variant31-variant33-variant35-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:295,21,0:0,0,2,5 chr1 173493312 . A G 244.53 PASS AC=2;AF=0.571;AN=2;DP=199;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant6-variant7-variant8-variant11-variant14-variant16-variant21-variant23-variant24-variant26-variant27-variant29-variant31-variant33-variant35-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:132,9,0:0,0,0,3 chr1 173503864 . A G 40.48 PASS AC=2;AF=0.667;AN=2;DP=47;FS=0;FractionInformativeReads=1;MQ=60;set=variant3-variant24-variant29-variant31-variant33-variant35-variant37-variant38-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:225,15,0:0,0,0,5 chr1 173516871 . G C 867.46 PASS AC=2;AF=0.538;AN=2;DP=1467;MQ=60;set=variant2-variant3-variant6-variant7-variant24-variant29-variant30-variant31-variant33-variant35-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,94:94:99:2717,281,0:0,0,46,48 chr1 173516903 . A G 603.37 PASS AC=2;AF=0.533;AN=2;DP=1358;MQ=60;set=variant2-variant3-variant6-variant7-variant24-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,70:71:99:2080,207,0:1,0,30,40 chr1 173552529 . A G 49.73 PASS AC=2;AF=0.583;AN=2;DP=70;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant6-variant17-variant24-variant25-variant26-variant29-variant33-variant34-variant35-variant38 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:94,9,0:0,0,2,1 chr1 173552783 . G A 536.63 PASS AC=2;AF=0.568;AN=2;DP=850;MQ=60;set=variant2-variant3-variant6-variant7-variant10-variant13-variant17-variant24-variant25-variant26-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:986,90,0:0,0,10,20 chr1 173556699 . G T 665.28 PASS AC=2;AF=0.955;AN=2;DP=543;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:274,21,0:0,0,6,1 chr1 173569176 . T C 474.17 PASS AC=2;AF=0.6;AN=2;DP=261;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant24-variant25-variant29-variant30-variant31-variant35-variant38-variant39 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:775,60,0:0,0,16,4 chr1 173626764 . CT CTTTTTTTTT,CTTTTTTT,CTTTTTTTT,CTTTT,CTTTTTTTTTT,CTTTTTTTTTTTT,C 33.69 PASS AC=0,1,0,0,0,0,0;AF=0.095,0.286,0.167,0.048,0.048,0.048,0.095;AN=2;DP=264;FS=0;set=variant-variant3-variant4-variant6-variant10-variant12-variant15-variant20-variant21-variant24-variant25-variant26-variant28-variant31-variant32-variant33-variant35-variant40-variant41-variant43-variant44 GT:DP:GQ:SB 0/2:7:9:0,2,1,4 chr1 173854660 . G A 303.63 PASS AC=1;AF=0.5;AN=2;DP=22;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.615;QD=13.8;ReadPosRankSum=-0.956;SOR=1.051;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:12,10:22:99:332,0,395:10,2,9,1 chr1 173900403 . A G 2174.33 PASS AC=1;AF=0.5;AN=2;DP=195;FS=0.542;FractionInformativeReads=1;MQ=60;MQRankSum=0.172;QD=11.15;ReadPosRankSum=3.677;SOR=0.773;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:103,92:195:99:2203,0,2723:63,40,58,34 chr1 173905901 . T A 133.08 PASS AC=2;AF=0.955;AN=2;DP=56;FS=0;set=variant4-variant7-variant11-variant12-variant20-variant21-variant24-variant25-variant27-variant35-variant38 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:134,12,0:0,0,4,0 chr1 174128914 . C T 223.35 PASS AC=1;AF=0.5;AN=2;DP=48;FractionInformativeReads=1;MQ=60;set=variant18-variant29-variant35 GT:AD:DP:GQ:PL:SB 0/1:13,7:20:99:195,0,396:4,9,2,5 chr1 174417231 . G A 3238.26 PASS AC=2;AF=0.955;AN=2;DP=6175;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,169:169:99:5039,506,0:0,0,98,71 chr1 174769068 . GCACACACACACACACACACACACA G,GCACACACACA,GCACACACACACA,GCA,GCACA,GCACACACACACACACACA,GCACACACA,GCACACACACACACA,GCACACA,GCACACACACACACACACACACACACA,GCACACACACACACACACACA 666.74 PASS AC=1,0,0,1,0,0,0,0,0,0,0;AF=0.174,0.035,0.093,0.465,0.093,0.012,0.023,0.012,0.012,0.012,0.012;AN=2;DP=1052;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/4:27:79:0,0,19,8 chr1 174843716 . CTTTTTTTTTTTTTT CTTTTTTTT,CTTTTTTTTTTTT,CTTTTT,CTTTTTTTTT,CTTTTTTTTTTT,CTTTTTTTTTT,CTTTTTTTTTTTTT,CT,C 143.61 PASS AC=0,0,0,0,1,0,0,0,0;AF=0.014,0.216,0.014,0.027,0.189,0.054,0.135,0.014,0.027;AN=2;DP=1269;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant17-filterInvariant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/5:16:23:1,2,4,9 chr1 174926860 . CTTTT CTT,CTTT,CT,C 109.3 PASS AC=0,1,0,0;AF=0.259,0.241,0.052,0.017;AN=2;DP=1103;set=variant-variant2-variant3-filterInvariant4-variant5-variant6-filterInvariant7-variant9-filterInvariant10-variant12-variant13-variant15-variant17-variant18-variant22-variant24-variant27-variant28-variant29-variant32-variant33-variant34-filterInvariant35-variant37-variant38-variant39-variant40-variant41-variant42 GT:DP:GQ:SB 0/2:37:99:17,5,8,7 chr1 174927388 . G C 1484.84 PASS AC=2;AF=0.955;AN=2;DP=1576;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:1295,96,0:0,0,4,28 chr1 174960461 . C T 2583.75 PASS AC=1;AF=0.588;AN=2;DP=3108;MQ=60;set=variant-variant2-variant3-variant7-variant13-variant14-variant16-variant19-variant23-variant27-variant32-variant33-variant34-variant35-variant37-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:92,73:165:99:1712,0,2488:51,41,37,36 chr1 174960911 . ATTTT AT,ATT,A,ATTTTT,ATTT 7514.61 PASS AC=1,0,0,0,0;AF=0.524,0.202,0.036,0.012,0.012;AN=2;DP=14350;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-filterInvariant24-filterInvariant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:287:99:76,72,50,89 chr1 174961987 . C T 8789.82 PASS AC=1;AF=0.838;AN=2;DP=11035;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:169,148:317:99:3646,0,3860:90,79,80,68 chr1 174968530 . T TC 1577.5 PASS AC=2;AF=1;AN=2;DP=2252;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1904,153,0:0,0,32,19 chr1 174969271 . C T 4788.55 PASS AC=1;AF=0.825;AN=2;DP=6764;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:74,85:159:99:2138,0,2105:39,35,44,41 chr1 174980242 . TAAAAAAAA T,TAAAAAAAAA,TAAAAAAA,TAAAAAA 1307.53 PASS AC=1,0,0,0;AF=0.25,0.075,0.2,0.038;AN=2;DP=3102;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-filterInvariant12-variant13-variant14-filterInvariant15-variant16-variant17-filterInvariant18-variant19-filterInvariant21-variant22-variant23-variant24-filterInvariant25-variant26-variant27-filterInvariant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:DP:GQ:SB 0/1:69:99:21,12,25,11 chr1 174980323 . T C 3812.68 PASS AC=1;AF=0.588;AN=2;DP=4711;MQ=60;set=variant-variant2-variant3-variant7-variant13-variant14-variant16-variant19-variant23-variant27-variant32-variant33-variant34-variant35-variant37-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:125,140:265:99:3740,0,3324:80,45,83,57 chr1 174983633 . T C 2823.96 PASS AC=1;AF=0.588;AN=2;DP=5031;MQ=60;set=variant-variant2-variant3-variant7-variant13-variant14-variant16-variant19-variant23-variant27-variant32-variant33-variant34-variant35-variant37-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:137,146:283:99:3428,0,3154:73,64,73,73 chr1 175046488 . G A 1249.92 PASS AC=1;AF=0.662;AN=2;DP=3046;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant28-variant29-variant30-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,38:89:99:898,0,1276:30,21,28,10 chr1 175046789 . A G 963.8 PASS AC=1;AF=0.662;AN=2;DP=4343;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant28-variant29-variant30-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,69:130:99:1821,0,1494:30,31,35,34 chr1 175052828 . G A 754.52 PASS AC=1;AF=0.545;AN=2;DP=1698;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant22-variant26-variant30-variant33-variant35-variant36-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:56,35:91:99:905,0,1411:33,23,23,12 chr1 175053101 . A T 1011.62 PASS AC=1;AF=0.662;AN=2;DP=4791;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant28-variant29-variant30-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:72,71:143:99:1879,0,1837:26,46,24,47 chr1 175054548 . C T 923.66 PASS AC=1;AF=0.662;AN=2;DP=2344;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant28-variant29-variant30-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,36:83:99:814,0,1175:29,18,24,12 chr1 175086373 . G A 3090.34 PASS AC=1;AF=0.5;AN=2;DP=146;FS=0.647;FractionInformativeReads=1;MQ=60;MQRankSum=-1.256;QD=21.17;ReadPosRankSum=-1.284;SOR=0.814;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:66,80:146:99:3119,0,2531:24,42,27,53 chr1 175086374 . C A 3090.34 PASS AC=1;AF=0.5;AN=2;DP=145;FS=1.385;FractionInformativeReads=1;MQ=60;MQRankSum=0.637;QD=21.31;ReadPosRankSum=-0.999;SOR=0.855;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:66,79:145:99:3119,0,2531:24,42,26,53 chr1 175086461 . A G 334.65 PASS AC=1;AF=0.691;AN=2;DP=1129;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant26-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,17:34:99:486,0,501:4,13,2,15 chr1 175087677 . G A 2508 PASS AC=1;AF=0.643;AN=2;DP=7444;set=variant-variant4-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant26-variant28-variant29-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:159,166:325:99:4234,0,3726:95,64,105,61 chr1 175087729 . T C 2734.54 PASS AC=1;AF=0.643;AN=2;DP=9164;set=variant-variant4-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant26-variant28-variant29-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:201,214:415:99:5128,0,4664:106,95,110,104 chr1 175092992 . GGAGT G 367.87 PASS AC=1;AF=0.881;AN=2;DP=755;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,16:21:99:637,0,239:1,4,6,10 chr1 175096333 . A G 740.44 PASS AC=1;AF=0.652;AN=2;DP=1770;set=variant-variant2-variant3-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant16-variant17-variant19-variant20-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,32:64:99:971,0,1038:4,28,5,27 chr1 175097331 . G A 760.92 PASS AC=1;AF=0.712;AN=2;DP=3649;MQ=60;set=variant-variant4-variant6-variant7-variant9-variant10-variant12-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:71,52:123:99:1159,0,1596:36,35,25,27 chr1 175097357 . C G 1303.49 PASS AC=1;AF=0.533;AN=2;DP=1584;MQ=60;set=variant6-variant7-variant20-variant24-variant25-variant28-variant30-variant32-variant33-variant34-variant35-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:69,49:118:99:1045,0,1568:36,33,21,28 chr1 175097864 . G A 840.48 PASS AC=1;AF=0.533;AN=2;DP=1027;MQ=60;set=variant6-variant7-variant20-variant24-variant28-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,42:90:99:1196,0,1157:19,29,14,28 chr1 175097991 . C T 422.96 PASS AC=1;AF=0.735;AN=2;DP=937;MQ=60;set=variant-variant4-variant6-variant7-variant9-variant10-variant12-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,16:31:99:430,0,381:4,11,4,12 chr1 175104796 . G T 934.74 PASS AC=1;AF=0.884;AN=2;DP=1241;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,11:29:99:361,0,554:15,3,10,1 chr1 175105778 . T C 119.1 PASS AC=1;AF=0.5;AN=2;DP=341;FractionInformativeReads=1;MQ=60;set=variant6-variant7-variant10-variant13-variant20-variant24-variant28-variant30-variant33-variant34-variant35-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,6:13:99:172,0,146:4,3,4,2 chr1 175105880 . G A 2346.78 PASS AC=1;AF=0.784;AN=2;DP=2690;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:26,30:56:99:719,0,626:16,10,17,13 chr1 175105942 . G A 3167.14 PASS AC=2;AF=0.966;AN=2;DP=3627;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:2281,224,0:0,0,44,31 chr1 175113578 . T C 2324.08 PASS AC=2;AF=0.966;AN=2;DP=4569;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,105:105:99:3390,314,0:0,0,65,40 chr1 175116046 . CT CTT,C 578.64 PASS AC=1,0;AF=0.489,0.011;AN=2;DP=3223;set=variant-variant2-variant3-variant4-filterInvariant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:74:99:16,22,16,20 chr1 175116252 . C G 1678.13 PASS AC=1;AF=0.864;AN=2;DP=3562;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:27,43:70:99:1065,0,749:11,16,18,25 chr1 175126073 . CAAAAAA CAAAA,C,CAAAAAAAAA,CAAAAA,CAAAAAAA,CAAAAAAAA,CAAAAAAAAAA 77.92 PASS AC=0,1,0,0,0,0,0;AF=0.036,0.196,0.018,0.071,0.143,0.054,0.018;AN=2;DP=1028;set=filterInvariant2-variant3-variant5-variant6-variant9-variant10-variant11-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant39-variant40-variant44 GT:DP:GQ:SB 0/2:42:99:12,8,19,3 chr1 175126644 . G A 4210.13 PASS AC=1;AF=0.86;AN=2;DP=5376;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:69,57:126:99:1367,0,1834:35,34,26,31 chr1 175126845 . T C 3503.55 PASS AC=1;AF=0.5;AN=2;DP=2427;MQ=60;set=variant3-variant11-variant13-variant14-variant18-variant20-variant24-variant25-variant27-variant33-variant35-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:117,78:195:99:1750,0,2836:53,64,34,44 chr1 175127582 . C T 489.51 PASS AC=1;AF=0.5;AN=2;DP=379;MQ=60;set=variant3-variant11-variant14-variant18-variant24-variant25-variant27-variant33-variant35-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:15,14:29:99:410,0,401:9,6,7,7 chr1 175127616 . C T 501.01 PASS AC=1;AF=0.5;AN=2;DP=371;MQ=60;set=variant3-variant11-variant14-variant18-variant24-variant25-variant27-variant33-variant35-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:13,13:26:99:327,0,320:8,5,6,7 chr1 175128444 . C A 976.62 PASS AC=1;AF=0.5;AN=2;DP=862;MQ=60;set=variant3-variant11-variant14-variant18-variant24-variant25-variant27-variant33-variant35-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:36,36:72:99:772,0,986:13,23,18,18 chr1 175128536 . G C 250.34 PASS AC=1;AF=0.594;AN=2;DP=1625;FractionInformativeReads=1;set=variant2-variant4-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,30:56:99:1178,0,2090:12,14,14,16 chr1 175128537 . G A 250.34 PASS AC=1;AF=0.594;AN=2;DP=1614;FractionInformativeReads=1;set=variant2-variant4-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,29:54:99:1178,0,2090:11,14,13,16 chr1 175128543 . C T 250.34 PASS AC=1;AF=0.594;AN=2;DP=1559;FractionInformativeReads=1;set=variant2-variant4-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,28:50:99:1110,0,1869:10,12,13,15 chr1 175128711 . C A 1555.21 PASS AC=1;AF=0.635;AN=2;DP=2086;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,31:67:99:767,0,1440:22,14,18,13 chr1 175128726 . A G 621.35 PASS AC=1;AF=0.594;AN=2;DP=2057;MQ=60;set=variant2-variant4-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,37:77:99:1029,0,1461:24,16,23,14 chr1 175129023 . CA C 155.74 PASS AC=1;AF=0.5;AN=2;DP=341;MQ=60;set=variant3-variant11-variant14-variant18-variant24-variant25-variant27-variant33-variant35-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:11,13:24:99:454,0,356:6,5,9,4 chr1 175129924 . C CCTT 966.91 PASS AC=1;AF=0.5;AN=2;DP=664;set=variant3-variant11-variant14-variant18-variant24-variant25-variant27-variant33-variant35-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:27,18:45:99:639,0,1085:13,14,10,8 chr1 175129945 . TC T 931.12 PASS AC=1;AF=0.594;AN=2;DP=1803;set=variant2-variant4-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,38:62:99:1327,0,849:13,11,18,20 chr1 175129947 . TTCTTCTTG T 922.28 PASS AC=1;AF=0.594;AN=2;DP=1910;set=variant2-variant4-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,38:68:99:1309,0,1039:17,13,18,20 chr1 175130204 . G A 594.78 PASS AC=1;AF=0.594;AN=2;DP=2401;MQ=60;set=variant2-variant4-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,50:79:99:1267,0,673:12,17,22,28 chr1 175130276 . G A 1611.25 PASS AC=2;AF=0.966;AN=2;DP=2500;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1401,137,0:0,0,20,26 chr1 175161849 . G T 581.59 PASS AC=2;AF=0.662;AN=2;DP=2160;MQ=60;set=variant2-variant3-variant4-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1396,149,0:0,0,20,30 chr1 175161930 . C G 274.57 PASS AC=2;AF=0.662;AN=2;DP=759;MQ=60;set=variant2-variant3-variant4-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:597,57,0:0,0,6,13 chr1 175293424 . T C 1134.39 PASS AC=2;AF=0.833;AN=2;DP=842;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:767,60,0:0,0,16,4 chr1 175299301 . T C 992.52 PASS AC=2;AF=0.842;AN=2;DP=3256;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,99:101:99:3064,253,0:1,1,57,42 chr1 175324518 . GCA G 3253.26 PASS AC=2;AF=0.78;AN=2;DP=2994;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,82:82:99:3722,250,0:0,0,54,28 chr1 175324521 . A T 3262.3 PASS AC=2;AF=0.78;AN=2;DP=3030;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,83:83:99:3722,250,0:0,0,55,28 chr1 175324651 . A G 1750.75 PASS AC=2;AF=0.724;AN=2;DP=5877;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,186:186:99:5580,555,0:0,0,87,99 chr1 175329083 . A C,T 336.22 PASS AC=0,2;AF=0.426,0.368;AN=2;DP=294;MQ=60;set=variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:DP:GQ:SB 2/2:9:27:0,0,2,7 chr1 175335412 . A C 1176.61 PASS AC=2;AF=0.805;AN=2;DP=1397;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1592,131,0:0,0,9,35 chr1 175336530 . T C 1364.14 PASS AC=2;AF=0.724;AN=2;DP=2903;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:2542,231,0:0,0,26,51 chr1 175336619 . T C 661.62 PASS AC=2;AF=0.711;AN=2;DP=1578;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1347,126,0:0,0,16,26 chr1 175348543 . T C 648.67 PASS AC=2;AF=0.775;AN=2;DP=1787;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,52:52:99:1765,156,0:0,0,34,18 chr1 175348723 . C T 1050.17 PASS AC=2;AF=0.775;AN=2;DP=4651;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,125:125:99:3925,375,0:0,0,60,65 chr1 175355128 . C G 168.92 PASS AC=2;AF=0.711;AN=2;DP=1704;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,49:50:99:1299,117,0:1,0,29,20 chr1 175355391 . A G 713.78 PASS AC=2;AF=0.893;AN=2;DP=3075;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,81:81:99:2789,243,0:0,0,43,38 chr1 175355618 . T C 615.88 PASS AC=2;AF=0.769;AN=2;DP=1127;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,23:25:26:716,26,0:1,1,7,16 chr1 175360690 . C T 997.02 PASS AC=2;AF=0.75;AN=2;DP=3070;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,74:74:99:2332,220,0:0,0,24,50 chr1 175362736 . G A 358.52 PASS AC=2;AF=0.763;AN=2;DP=780;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:77:910,77,0:0,0,21,5 chr1 175365663 . G A 943.7 PASS AC=2;AF=0.696;AN=2;DP=3362;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant16-variant17-variant18-variant21-variant22-variant23-variant25-variant27-variant32-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,144:144:99:4255,431,0:0,0,70,74 chr1 175375334 . C T 68.16 PASS AC=2;AF=0.64;AN=2;DP=811;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant9-variant12-variant13-variant16-variant17-variant21-variant22-variant23-variant25-variant27-variant31-variant32-variant34-variant35-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1204,111,0:0,0,24,13 chr1 175375469 . C A 1680.17 PASS AC=2;AF=0.583;AN=2;DP=2712;MQ=60;set=variant4-variant6-variant7-variant8-variant9-variant12-variant13-variant21-variant23-variant25-variant27-variant31-variant32-variant34-variant35-variant37-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,171:171:99:5186,511,0:0,0,103,68 chr1 175375683 . T C 2035.15 PASS AC=2;AF=0.776;AN=2;DP=8418;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,254:254:99:8030,761,0:0,0,135,119 chr1 175375802 . T C 2680.88 PASS AC=2;AF=0.776;AN=2;DP=9191;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,272:272:99:8459,816,0:0,0,122,150 chr1 175376019 . AG A,AGG 85.03 PASS AC=2,0;AF=0.756,0.026;AN=2;DP=1531;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:46:99:0,0,9,37 chr1 175712765 . GTCTCTCTCTCTCTCTCTCTCTCTC GTCTCTCTCTCTCTCTCTC,GTCTCTCTCTCTC,GTCTCTCTCTCTCTCTCTCTCTCTCTC,GTCTCTCTCTCTCTC,GTCTCTCTC,GTCTC,GTCTCTCTCTCTCTCTCTCTCTC,GTCTCTCTCTC,GTCTCTCTCTCTCTCTC,GTCTCTCTCTCTCTCTCTCTC,GTCTCTCTCTCTCTCTCTCTCTCTCTCTC,G 584.99 PASS AC=1,0,0,0,0,0,0,0,1,0,0,0;AF=0.159,0.146,0.024,0.073,0.012,0.061,0.073,0.024,0.134,0.098,0.049,0.012;AN=2;DP=1139;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 9/1:18:99:0,0,8,10 chr1 175916267 . T C 4402.9 PASS AC=2;AF=0.977;AN=2;DP=5536;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,131:131:99:4137,392,0:0,0,62,69 chr1 175916506 . AT A,ATT 66.93 PASS AC=1,0;AF=0.382,0.118;AN=2;DP=596;set=filterInvariant-filterInvariant3-filterInvariant4-filterInvariant5-variant13-variant15-variant16-variant18-variant22-filterInvariant25-variant26-filterInvariant28-filterInvariant31-variant33-filterInvariant35-variant40-filterInvariant42 GT:DP:GQ:SB 0/1:16:79:1,9,0,6 chr1 175937540 . C T 3672.47 PASS AC=2;AF=0.977;AN=2;DP=5430;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,122:122:99:3647,365,0:0,0,71,51 chr1 175951347 . T A 2714.67 PASS AC=2;AF=0.977;AN=2;DP=3543;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,81:81:99:2416,242,0:0,0,42,39 chr1 175955996 . T C 918.22 PASS AC=1;AF=0.542;AN=2;DP=825;FractionInformativeReads=1;MQ=60;set=variant-variant15-variant18-variant19-variant21-variant22-variant24-variant29-variant32-variant35-variant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:31,36:67:99:992,0,869:13,18,19,17 chr1 176012807 . G A 1171.01 PASS AC=2;AF=0.977;AN=2;DP=1001;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:678,57,0:0,0,14,5 chr1 176050430 . GA G,GAA 40.31 PASS AC=1,0;AF=0.424,0.076;AN=2;DP=2093;set=filterInvariant-filterInvariant3-filterInvariant4-variant5-variant6-variant7-filterInvariant8-variant9-variant10-variant12-variant14-variant15-variant17-filterInvariant21-variant22-variant23-variant26-variant27-variant29-variant30-filterInvariant31-variant32-filterInvariant33-variant34-filterInvariant35-filterInvariant36-filterInvariant37-variant38-filterInvariant40-variant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:DP:GQ:SB 0/1:55:79:14,31,4,6 chr1 176102974 . T C 1106.41 PASS AC=1;AF=0.5;AN=2;DP=1653;MQ=60;set=variant3-variant5-variant7-variant9-variant11-variant12-variant16-variant19-variant20-variant25-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,33:70:99:760,0,977:20,17,18,15 chr1 176103954 . C T 704.77 PASS AC=1;AF=0.5;AN=2;DP=1073;MQ=60;set=variant3-variant5-variant7-variant9-variant11-variant12-variant16-variant19-variant20-variant25-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,21:35:99:550,0,400:10,4,14,7 chr1 176129276 . G A 1939.37 PASS AC=1;AF=0.5;AN=2;DP=3325;MQ=60;set=variant3-variant5-variant7-variant9-variant11-variant12-variant16-variant19-variant20-variant25-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,73:140:99:1701,0,1529:37,30,39,34 chr1 176129391 . CTTTTT CTTT,CTTTT,CT,CTT,C,CTTTTTTT 168.88 PASS AC=0,0,0,0,1,0;AF=0.192,0.077,0.058,0.192,0.058,0.019;AN=2;DP=1572;set=variant-variant3-variant5-filterInvariant6-variant8-variant12-variant13-variant18-variant21-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-filterInvariant37-variant38-filterInvariant39-variant42-variant43-variant44 GT:DP:GQ:SB 0/5:44:99:12,12,3,17 chr1 176132292 . C T 1937.82 PASS AC=2;AF=0.977;AN=2;DP=1761;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1534,150,0:0,0,18,32 chr1 176137968 . G T 575.8 PASS AC=1;AF=0.5;AN=2;DP=676;MQ=60;set=variant-variant15-variant18-variant19-variant21-variant22-variant24-variant32-variant35 GT:AD:DP:GQ:PL:SB 0/1:48,25:73:99:530,0,1203:19,29,11,14 chr1 176153658 . T C 435.8 PASS AC=1;AF=0.837;AN=2;DP=1196;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,20:34:99:470,0,366:9,5,11,9 chr1 176176406 . T TGC 1086.82 PASS AC=1;AF=0.542;AN=2;DP=889;MQ=60;set=variant-variant15-variant18-variant19-variant21-variant22-variant24-variant29-variant32-variant35-variant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:40,43:83:99:1359,0,1278:21,19,24,19 chr1 176176495 . G A 1765.81 PASS AC=1;AF=0.5;AN=2;DP=2931;MQ=60;set=variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant16-variant19-variant20-variant25-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,67:128:99:1598,0,1597:32,29,32,35 chr1 176176659 . C G 776.17 PASS AC=2;AF=1;AN=2;DP=1408;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:733,66,0:0,0,7,15 chr1 176176674 . G A 369.28 PASS AC=1;AF=0.5;AN=2;DP=40;FS=0;FractionInformativeReads=1;MQ=60;set=variant24-variant35 GT:AD:DP:GQ:PL:SB 0/1:9,9:18:99:226,0,246:3,6,3,6 chr1 176525194 . G A 607.77 PASS AC=1;AF=0.643;AN=2;DP=1214;MQ=60;set=variant2-variant4-variant5-variant6-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant26-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,23:39:99:571,0,525:9,7,13,10 chr1 176660047 . TAA T,TA,TAAA,TAAAA 699.68 PASS AC=1,1,0,0;AF=0.167,0.417,0.131,0.095;AN=2;DP=2766;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/2:42:99:3,3,20,16 chr1 176660247 . C T 3433.57 PASS AC=2;AF=0.708;AN=2;DP=9207;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,274:274:99:7817,820,0:0,0,139,135 chr1 176665102 . ATGTGTGTGTGTGTGTGTGTG ATGTGTGTGTGTGTGTGTGTGTG,A,ATGTGTGTGTGTGTGTGTG,ATGTGTGTGTGTGTGTG,ATGTGTGTGTGTGTG,ATGTGTGTGTGTGTGTGTGTGTGTG,ATGTGTGTGTGTGTGTGTGTGTGTGTG 53.55 PASS AC=1,0,0,0,0,0,0;AF=0.097,0.355,0.21,0.016,0.016,0.016,0.016;AN=2;DP=675;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant23-variant28-variant29-variant30-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:12:99:0,6,1,5 chr1 176734756 . C T 2611.24 PASS AC=1;AF=0.659;AN=2;DP=3325;MQ=60;set=variant3-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant21-variant29-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,59:119:99:1474,0,1536:36,24,38,21 chr1 176759202 . A G 990.2 PASS AC=1;AF=0.5;AN=2;DP=213;FractionInformativeReads=1;MQ=60;set=variant32-variant35-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:20,39:59:99:1057,0,385:7,13,11,28 chr1 176762955 . T G 769.83 PASS AC=1;AF=0.5;AN=2;DP=200;FractionInformativeReads=1;MQ=60;set=variant32-variant35-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:38,21:59:99:531,0,974:13,25,5,16 chr1 176809042 . T C 123.17 PASS AC=1;AF=0.5;AN=2;DP=90;FractionInformativeReads=1;MQ=60;set=variant12-variant13-variant35-variant37-variant42 GT:AD:DP:GQ:PL:SB 0/1:9,14:23:99:392,0,255:7,2,10,4 chr1 176811338 . T A 548.45 PASS AC=1;AF=0.5;AN=2;DP=240;FractionInformativeReads=1;MQ=60;set=variant12-variant13-variant35-variant37-variant42 GT:AD:DP:GQ:PL:SB 0/1:19,22:41:99:651,0,509:14,5,16,6 chr1 176811873 . C T 2307.48 PASS AC=2;AF=0.731;AN=2;DP=6320;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,180:180:99:5500,539,0:0,0,73,107 chr1 176812896 . C T 212.25 PASS AC=2;AF=0.686;AN=2;DP=878;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:80:767,80,0:0,0,15,12 chr1 176813190 . A G 384.93 PASS AC=2;AF=0.756;AN=2;DP=999;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:953,90,0:0,0,14,16 chr1 176813300 . TGTGA T 904.35 PASS AC=2;AF=0.727;AN=2;DP=1302;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:2008,136,0:0,0,34,11 chr1 176813774 . T C 3904.73 PASS AC=2;AF=0.735;AN=2;DP=8706;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,240:240:99:9538,724,0:0,0,108,132 chr1 176813777 . A T 2117.85 PASS AC=1;AF=0.5;AN=2;DP=1369;MQ=60;set=variant12-variant13-variant19-variant35-variant37-variant42 GT:AD:DP:GQ:PL:SB 0/1:104,132:236:99:3549,0,2812:45,59,63,69 chr1 176826975 . C T 631.29 PASS AC=1;AF=0.5;AN=2;DP=247;FractionInformativeReads=1;MQ=60;set=variant12-variant19-variant35-variant37-variant42 GT:AD:DP:GQ:PL:SB 0/1:33,25:58:99:685,0,890:13,20,10,15 chr1 176830978 . C T 115.43 PASS AC=2;AF=0.917;AN=2;DP=1022;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:975,84,0:0,0,19,9 chr1 176832145 . T G 1750.87 PASS AC=1;AF=0.55;AN=2;DP=1274;FractionInformativeReads=1;MQ=60;set=variant6-variant9-variant12-variant15-variant19-variant34-variant35-variant37-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:62,85:147:99:2575,0,1801:22,40,35,50 chr1 176832552 . G A 570.9 PASS AC=1;AF=0.667;AN=2;DP=1514;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant35-variant36-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,41:76:99:1213,0,1088:9,26,12,29 chr1 176832613 . C T 115.39 PASS AC=2;AF=0.929;AN=2;DP=1519;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1658,138,0:0,0,22,24 chr1 176837817 . A G 281.17 PASS AC=1;AF=0.661;AN=2;DP=299;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant35-variant36-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,2:4:37:78,0,37:1,1,2,0 chr1 176845386 . C T 219.12 PASS AC=1;AF=0.667;AN=2;DP=533;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant35-variant36-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,12:24:99:329,0,288:8,4,9,3 chr1 176845410 . G C 456.87 PASS AC=2;AF=0.85;AN=2;DP=1063;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:793,72,0:0,0,17,7 chr1 176845528 . C T 629.25 PASS AC=2;AF=0.917;AN=2;DP=2778;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:2262,213,0:0,0,42,29 chr1 176851817 . C T 188.51 PASS AC=1;AF=0.5;AN=2;DP=58;FractionInformativeReads=1;MQ=60;set=variant12-variant19-variant35-variant37-variant42 GT:AD:DP:GQ:PL:SB 0/1:8,8:16:99:255,0,301:8,0,8,0 chr1 176857347 . A G 684.56 PASS AC=2;AF=0.917;AN=2;DP=3258;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,113:113:99:3455,339,0:0,0,60,53 chr1 176857498 . G A 356.64 PASS AC=1;AF=0.661;AN=2;DP=1158;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant35-variant36-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,29:61:99:732,0,853:11,21,11,18 chr1 176863836 . G C 377.45 PASS AC=2;AF=0.917;AN=2;DP=3307;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:2156,224,0:0,0,37,38 chr1 176863867 . T C 298.66 PASS AC=2;AF=0.917;AN=2;DP=3775;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,85:85:99:2527,255,0:0,0,44,41 chr1 176915022 . A G 1153.79 PASS AC=1;AF=0.65;AN=2;DP=1317;MQ=60;set=variant2-variant3-variant5-variant12-variant19-variant22-variant31-variant35-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:76,68:144:99:1602,0,1786:44,32,43,25 chr1 176918675 . T G 372.11 PASS AC=1;AF=0.636;AN=2;DP=295;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant12-variant19-variant22-variant31-variant35-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,15:23:99:545,0,247:1,7,2,13 chr1 176926763 . C G 79.71 PASS AC=1;AF=0.5;AN=2;DP=48;FractionInformativeReads=1;MQ=60;set=variant12-variant19-variant35 GT:AD:DP:GQ:PL:SB 0/1:10,10:20:99:278,0,343:8,2,6,4 chr1 176927093 . T A 787.56 PASS AC=1;AF=0.5;AN=2;DP=183;FS=0;FractionInformativeReads=1;MQ=60;set=variant12-variant19-variant35 GT:AD:DP:GQ:PL:SB 0/1:48,28:76:99:627,0,1216:16,32,9,19 chr1 176992553 . A G 3125.91 PASS AC=1;AF=0.688;AN=2;DP=4051;MQ=60;set=variant2-variant3-variant4-variant5-variant10-variant11-variant12-variant13-variant14-variant16-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:86,61:147:99:1497,0,2138:46,40,29,32 chr1 176992676 . C T 606.18 PASS AC=1;AF=0.611;AN=2;DP=1790;MQ=60;set=variant2-variant3-variant4-variant10-variant11-variant12-variant13-variant14-variant16-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant29-variant30-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,38:89:99:895,0,1218:20,31,15,23 chr1 176998368 . T A 203.39 PASS AC=1;AF=0.636;AN=2;DP=235;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant10-variant11-variant12-variant13-variant14-variant16-variant19-variant20-variant21-variant22-variant24-variant26-variant29-variant33-variant35-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,5:9:99:157,0,148:4,0,4,1 chr1 177000203 . C T 82.5 PASS AC=1;AF=0.656;AN=2;DP=97;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant10-variant12-variant13-variant14-variant16-variant20-variant21-variant22-variant24-variant26-variant33-variant35-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,3:4:34:123,0,34:0,1,0,3 chr1 177198818 . G T 285.13 PASS AC=1;AF=0.618;AN=2;DP=229;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant15-variant21-variant23-variant25-variant27-variant28-variant31-variant35-variant36-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:14,8:22:99:245,0,419:11,3,7,1 chr1 177198998 . T C 1620.78 PASS AC=1;AF=0.632;AN=2;DP=2861;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant12-variant15-variant21-variant23-variant25-variant27-variant28-variant31-variant34-variant35-variant36-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:73,72:145:99:1887,0,1786:38,35,39,33 chr1 177199426 . G A 346.59 PASS AC=1;AF=0.611;AN=2;DP=409;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant12-variant15-variant21-variant23-variant25-variant27-variant28-variant31-variant35-variant36-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,10:23:99:216,0,345:4,9,4,6 chr1 177247854 . C G 1083.79 PASS AC=1;AF=0.571;AN=2;DP=1882;MQ=60;set=variant3-variant5-variant7-variant9-variant10-variant11-variant12-variant15-variant16-variant18-variant20-variant22-variant26-variant30-variant32-variant33-variant34-variant35-variant38-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:49,45:94:99:1223,0,1227:19,30,16,29 chr1 177250670 . G A 1713.49 PASS AC=1;AF=0.6;AN=2;DP=2453;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant12-variant15-variant17-variant21-variant23-variant25-variant27-variant28-variant31-variant35-variant36-variant37-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:69,75:144:99:1820,0,1679:29,40,37,38 chr1 177251603 . GA G 952.1 PASS AC=1;AF=0.5;AN=2;DP=1010;set=variant9-variant10-variant11-variant15-variant26-variant30-variant32-variant33-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:43,45:88:99:1012,0,922:16,27,16,29 chr1 177898799 . C T 430.64 PASS AC=1;AF=0.645;AN=2;DP=1611;MQ=60;set=variant2-variant3-variant4-variant5-variant9-variant10-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,24:51:99:545,0,733:16,11,10,14 chr1 177901619 . G A 2076.77 PASS AC=1;AF=0.594;AN=2;DP=1696;FractionInformativeReads=1;MQ=60;set=variant3-variant13-variant15-variant16-variant18-variant19-variant20-variant22-variant25-variant27-variant30-variant31-variant32-variant33-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:49,48:97:99:1151,0,1130:29,20,30,18 chr1 177901655 . G A 4558.45 PASS AC=1;AF=0.594;AN=2;DP=2559;MQ=60;set=variant3-variant13-variant15-variant16-variant18-variant19-variant20-variant22-variant25-variant27-variant30-variant31-variant32-variant33-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:80,81:161:99:3181,0,1850:48,32,51,30 chr1 177901658 . C T 4586.2 PASS AC=1;AF=0.594;AN=2;DP=2655;FractionInformativeReads=1;MQ=60;set=variant3-variant13-variant15-variant16-variant18-variant19-variant20-variant22-variant25-variant27-variant30-variant31-variant32-variant33-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:85,86:171:99:2026,0,3356:52,33,53,33 chr1 177901713 . T C 2799.42 PASS AC=1;AF=0.625;AN=2;DP=6423;MQ=60;set=variant2-variant3-variant4-variant5-variant9-variant10-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:122,125:247:99:2804,0,2914:63,59,67,58 chr1 177901741 . A G 2792.04 PASS AC=1;AF=0.638;AN=2;DP=6727;MQ=60;set=variant2-variant3-variant4-variant5-variant9-variant10-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:128,130:258:99:3066,0,2898:66,62,66,64 chr1 177902387 . C A 2676.47 PASS AC=1;AF=0.594;AN=2;DP=2837;MQ=60;set=variant3-variant13-variant15-variant16-variant18-variant19-variant20-variant22-variant25-variant27-variant30-variant31-variant32-variant33-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:82,103:185:99:2343,0,1830:50,32,57,46 chr1 177902482 . G A 3438.87 PASS AC=1;AF=0.594;AN=2;DP=3782;MQ=60;set=variant3-variant13-variant15-variant16-variant18-variant19-variant20-variant22-variant25-variant27-variant30-variant31-variant32-variant33-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:105,142:247:99:3299,0,2316:52,53,67,75 chr1 177902725 . C T 2311.98 PASS AC=1;AF=0.594;AN=2;DP=2727;FractionInformativeReads=1;MQ=60;set=variant3-variant13-variant15-variant16-variant18-variant19-variant20-variant22-variant25-variant27-variant30-variant31-variant32-variant33-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:116,82:198:99:1977,0,2956:65,51,47,35 chr1 177902753 . G C 1482.9 PASS AC=1;AF=0.625;AN=2;DP=5276;MQ=60;set=variant2-variant3-variant4-variant5-variant9-variant10-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:134,96:230:99:2299,0,3157:70,64,53,43 chr1 177905469 . C A 1112.88 PASS AC=1;AF=0.607;AN=2;DP=1556;MQ=60;set=variant3-variant13-variant15-variant16-variant18-variant19-variant20-variant22-variant25-variant27-variant30-variant31-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:61,47:108:99:1090,0,1457:31,30,29,18 chr1 177906292 . C T 766.36 PASS AC=1;AF=0.607;AN=2;DP=641;MQ=60;set=variant3-variant13-variant15-variant16-variant18-variant19-variant20-variant22-variant25-variant27-variant30-variant31-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:23,32:55:99:804,0,684:15,8,19,13 chr1 177906657 . G A 1002.25 PASS AC=1;AF=0.56;AN=2;DP=3409;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant10-variant11-variant12-variant16-variant17-variant19-variant22-variant23-variant24-variant26-variant31-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:85,62:147:99:1498,0,2098:47,38,30,32 chr1 177913980 . T C 407.06 PASS AC=2;AF=0.942;AN=2;DP=393;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:164,12,0:0,0,2,2 chr1 177914728 . A G 972.19 PASS AC=1;AF=0.702;AN=2;DP=4349;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:73,43:116:99:1023,0,1945:43,30,29,14 chr1 177915020 . G A 1117.27 PASS AC=1;AF=0.536;AN=2;DP=1014;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant13-variant16-variant17-variant18-variant19-variant20-variant22-variant27-variant30-variant31-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:50,45:95:99:1154,0,1322:23,27,22,23 chr1 177915474 . A C 1299.27 PASS AC=2;AF=0.829;AN=2;DP=3731;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,85:85:99:2531,254,0:0,0,47,38 chr1 177916890 . A AAGGGACAGGGAGGGGAGGTGAGGGG 265.57 PASS AC=2;AF=0.931;AN=2;DP=257;FS=0;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:35:514,35,0:0,0,5,1 chr1 177917479 . G A 420.47 PASS AC=1;AF=0.533;AN=2;DP=505;MQ=60;set=variant3-variant4-variant13-variant16-variant17-variant18-variant19-variant20-variant22-variant25-variant27-variant30-variant31-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:23,19:42:99:520,0,571:14,9,13,6 chr1 177921434 . T A 691.15 PASS AC=1;AF=0.779;AN=2;DP=1506;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,17:46:99:496,0,687:11,18,4,13 chr1 177923440 . T G 3436.75 PASS AC=2;AF=0.609;AN=2;DP=3232;MQ=60;set=variant2-variant3-variant7-variant8-variant10-variant12-variant16-variant17-variant19-variant22-variant23-variant24-variant26-variant28-variant29-variant31-variant34-variant35-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,162:162:99:4988,486,0:0,0,96,66 chr1 177929554 . C T 2592.01 PASS AC=1;AF=0.633;AN=2;DP=3191;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant19-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant34-variant35-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,68:128:99:1421,0,1296:26,34,34,34 chr1 177929987 . T C 1780.75 PASS AC=2;AF=0.837;AN=2;DP=4865;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,115:115:99:3526,344,0:0,0,68,47 chr1 177930096 . T C 4704.69 PASS AC=2;AF=0.625;AN=2;DP=2933;MQ=60;set=variant2-variant3-variant8-variant10-variant12-variant16-variant17-variant22-variant23-variant24-variant26-variant28-variant29-variant31-variant35-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,157:157:99:4619,470,0:0,0,70,87 chr1 177930894 . C T 1670.61 PASS AC=2;AF=0.849;AN=2;DP=2201;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,69:69:99:2085,207,0:0,0,33,36 chr1 177935275 . A G 575.81 PASS AC=2;AF=0.849;AN=2;DP=1313;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,27:28:45:796,45,0:1,0,10,17 chr1 178062359 . G A 2058.31 PASS AC=1;AF=0.556;AN=2;DP=3492;MQ=60;set=variant-variant4-variant6-variant10-variant13-variant15-variant18-variant20-variant21-variant23-variant26-variant27-variant29-variant35-variant36-variant37-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:115,84:199:99:1808,0,2806:56,59,39,45 chr1 178063551 . A C 1152.8 PASS AC=2;AF=1;AN=2;DP=1822;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1496,123,0:0,0,22,19 chr1 178408795 . A G 170.41 PASS AC=1;AF=0.559;AN=2;DP=390;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant8-variant10-variant13-variant15-variant18-variant21-variant23-variant26-variant27-variant29-variant35-variant36-variant37-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:11,8:19:99:239,0,396:1,10,1,7 chr1 178421901 . T G 457.12 PASS AC=1;AF=0.559;AN=2;DP=1022;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant8-variant10-variant13-variant15-variant18-variant21-variant23-variant26-variant27-variant29-variant35-variant36-variant37-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:26,33:59:99:858,0,521:11,15,16,17 chr1 178433368 . C T 512.54 PASS AC=1;AF=0.542;AN=2;DP=772;MQ=60;set=variant-variant4-variant13-variant21-variant23-variant26-variant27-variant29-variant35-variant36-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:37,31:68:99:1147,0,1995:22,15,17,14 chr1 178433370 . G A 785.45 PASS AC=1;AF=0.5;AN=2;DP=200;FractionInformativeReads=1;MQ=60;set=variant13-variant26-variant35 GT:AD:DP:GQ:PL:SB 0/1:36,31:67:99:1147,0,1995:21,15,17,14 chr1 178442190 . C T 1366.12 PASS AC=1;AF=0.583;AN=2;DP=1531;MQ=60;set=variant-variant4-variant13-variant21-variant23-variant26-variant27-variant29-variant35-variant36-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:103,76:179:99:1752,0,2544:56,47,40,36 chr1 178442906 . T A 330.98 PASS AC=1;AF=0.542;AN=2;DP=434;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant13-variant21-variant23-variant26-variant27-variant29-variant35-variant36-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:17,17:34:99:387,0,450:7,10,9,8 chr1 178444907 . G A 1555.8 PASS AC=1;AF=0.583;AN=2;DP=1585;MQ=60;set=variant-variant4-variant13-variant21-variant23-variant26-variant27-variant29-variant35-variant36-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:53,52:105:99:1320,0,1525:29,24,29,23 chr1 178446272 . TTC T 964.69 PASS AC=1;AF=0.583;AN=2;DP=886;MQ=60;set=variant-variant4-variant13-variant21-variant23-variant26-variant27-variant29-variant35-variant36-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:49,31:80:99:1113,0,1969:27,22,14,17 chr1 178446659 . C T 1564.18 PASS AC=1;AF=0.571;AN=2;DP=1421;MQ=60;set=variant-variant4-variant13-variant18-variant21-variant23-variant26-variant27-variant29-variant35-variant36-variant37-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:41,62:103:99:1806,0,1066:16,25,27,35 chr1 178483231 . G A 627.96 PASS AC=2;AF=0.617;AN=2;DP=2435;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,100:100:99:3132,298,0:0,0,59,41 chr1 178484834 . A G 1436.14 PASS AC=2;AF=0.645;AN=2;DP=2124;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:2005,186,0:0,0,42,20 chr1 178489978 . T G 1511.29 PASS AC=2;AF=0.617;AN=2;DP=3788;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,157:157:99:5013,470,0:0,0,86,71 chr1 178491785 . C CT,CTT 143.93 PASS AC=2,0;AF=0.583,0.033;AN=2;DP=1319;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:DP:GQ:SB 1/1:35:99:0,0,12,23 chr1 178492447 . T A 1164.28 PASS AC=2;AF=0.654;AN=2;DP=2809;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2747,209,0:0,0,59,11 chr1 178492635 . T C 4060.39 PASS AC=2;AF=0.654;AN=2;DP=10209;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,280:280:99:8661,837,0:0,0,119,161 chr1 178511825 . A G 598.35 PASS AC=1;AF=0.756;AN=2;DP=1536;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,25:51:99:708,0,769:21,5,18,7 chr1 178511892 . G C 1290.64 PASS AC=1;AF=0.56;AN=2;DP=2665;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant12-variant13-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant33-variant35-variant36-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:73,47:120:99:1263,0,1871:44,29,29,18 chr1 178511924 . C T 1505.75 PASS AC=1;AF=0.558;AN=2;DP=3543;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant33-variant35-variant36-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:82,61:143:99:1719,0,2118:47,35,39,22 chr1 178514622 . C T 1232.93 PASS AC=1;AF=0.558;AN=2;DP=3394;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant33-variant35-variant36-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,71:136:99:1818,0,1634:32,33,38,33 chr1 178517591 . A G 3745.81 PASS AC=1;AF=0.814;AN=2;DP=3971;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,49:102:99:1188,0,1451:34,19,27,22 chr1 178518008 . A G 9211.03 PASS AC=1;AF=0.814;AN=2;DP=9323;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:141,90:231:99:1997,0,3425:62,79,33,57 chr1 178646748 . A T 580.2 PASS AC=1;AF=0.636;AN=2;DP=1269;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:24,7:31:99:139,0,598:15,9,4,3 chr1 178646752 . A C 1635.33 PASS AC=2;AF=1;AN=2;DP=1728;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,31:31:92:1029,92,0:0,0,19,12 chr1 178646815 . C T 509 PASS AC=1;AF=0.5;AN=2;DP=400;FractionInformativeReads=1;MQ=60;set=variant12-variant14-variant19-variant32-variant35-variant36-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:30,15:45:99:315,0,704:16,14,9,6 chr1 178646884 . C T 345.4 PASS AC=1;AF=0.5;AN=2;DP=310;FractionInformativeReads=1;MQ=60;set=variant10-variant13-variant14-variant29-variant31-variant35-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:19,22:41:99:486,0,405:8,11,8,14 chr1 178694196 . G A 114.87 PASS AC=1;AF=0.5;AN=2;DP=13;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.696;QD=8.84;ReadPosRankSum=0.817;SOR=1.179;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:8,5:13:99:143,0,226:7,1,5,0 chr1 178694279 . TGC T 1168.58 PASS AC=2;AF=0.989;AN=2;DP=2000;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:1819,144,0:0,0,36,12 chr1 178694402 . G GGCA 11199.8 PASS AC=2;AF=0.966;AN=2;DP=11222;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:2,308:310:99:13641,862,0:1,1,168,140 chr1 178745798 . CTT CT,C 176.18 PASS AC=2,0;AF=0.679,0.038;AN=2;DP=2048;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant28-filterInvariant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:55:99:0,0,36,19 chr1 178745947 . T G 1016.8 PASS AC=1;AF=0.5;AN=2;DP=951;FractionInformativeReads=1;MQ=60;set=variant9-variant10-variant14-variant18-variant23-variant29-variant35-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:64,38:102:99:881,0,1506:26,38,15,23 chr1 178776985 . G A 185.15 PASS AC=2;AF=1;AN=2;DP=188;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:127,9,0:0,0,3,0 chr1 178780650 . A G 260.04 PASS AC=2;AF=0.718;AN=2;DP=980;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:917,78,0:0,0,9,17 chr1 178818774 . G C 813.91 PASS AC=1;AF=0.5;AN=2;DP=103;FractionInformativeReads=1;MQ=60;set=variant32-variant35 GT:AD:DP:GQ:PL:SB 0/1:22,24:46:99:902,0,1204:18,4,24,0 chr1 178819064 . T A 4621.22 PASS AC=1;AF=0.5;AN=2;DP=700;FractionInformativeReads=1;MQ=60;set=variant32-variant35 GT:AD:DP:GQ:PL:SB 0/1:171,164:335:99:4475,0,4416:79,92,78,86 chr1 178819455 . A T 476.44 PASS AC=1;AF=0.5;AN=2;DP=68;FS=0;FractionInformativeReads=1;MQ=60;set=variant32-variant35 GT:AD:DP:GQ:PL:SB 0/1:7,19:26:99:613,0,195:4,3,12,7 chr1 178819553 . A G 496.44 PASS AC=1;AF=0.5;AN=2;DP=576;FractionInformativeReads=1;MQ=60;set=variant9-variant10-variant14-variant18-variant23-variant29-variant35-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:26,13:39:99:258,0,592:14,12,7,6 chr1 178819640 . G GT 679.08 PASS AC=1;AF=0.5;AN=2;DP=369;MQ=60;set=variant13-variant14-variant29-variant35-variant37-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:20,18:38:99:399,0,459:7,13,8,10 chr1 178820159 . C A 1094.16 PASS AC=2;AF=0.718;AN=2;DP=3832;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,104:104:99:3239,312,0:0,0,59,45 chr1 178834603 . T C 1742.48 PASS AC=1;AF=0.5;AN=2;DP=184;FS=1.852;FractionInformativeReads=1;MQ=60;MQRankSum=0.3;QD=9.47;ReadPosRankSum=-0.628;SOR=0.838;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:111,73:184:99:1771,0,2820:60,51,42,31 chr1 178838385 . G A 1727.94 PASS AC=1;AF=0.5;AN=2;DP=501;MQ=60;set=variant13-variant32-variant35 GT:AD:DP:GQ:PL:SB 0/1:81,69:150:99:1631,0,1879:37,44,32,37 chr1 178848223 . A G 831.78 PASS AC=1;AF=0.5;AN=2;DP=809;MQ=60;set=variant9-variant10-variant14-variant18-variant23-variant29-variant35-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:32,51:83:99:1243,0,802:11,21,21,30 chr1 178852800 . T A 292.08 PASS AC=1;AF=0.5;AN=2;DP=38;FS=0;FractionInformativeReads=1;MQ=60;set=variant32-variant35 GT:AD:DP:GQ:PL:SB 0/1:10,7:17:99:177,0,304:2,8,1,6 chr1 178854162 . C T 366.27 PASS AC=2;AF=0.718;AN=2;DP=954;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:71:777,71,0:0,0,17,7 chr1 178854769 . T C 396.78 PASS AC=1;AF=0.5;AN=2;DP=39;FractionInformativeReads=1;MQ=60;set=variant32-variant35 GT:AD:DP:GQ:PL:SB 0/1:11,13:24:99:364,0,419:0,11,3,10 chr1 178858711 . C A 223.69 PASS AC=2;AF=0.69;AN=2;DP=1384;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant22-variant23-variant24-variant29-variant30-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,29:29:86:894,86,0:0,0,20,9 chr1 178858759 . G A 613.5 PASS AC=2;AF=0.69;AN=2;DP=2359;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant22-variant23-variant24-variant29-variant30-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,52:53:99:1497,113,0:1,0,31,21 chr1 178861278 . G T 81.95 PASS AC=1;AF=0.5;AN=2;DP=14;FS=0;FractionInformativeReads=1;MQ=60;set=variant32-variant35 GT:AD:DP:GQ:PL:SB 0/1:4,3:7:99:111,0,122:3,1,3,0 chr1 178863266 . C T 93.19 PASS AC=1;AF=0.667;AN=2;DP=17;FS=0;FractionInformativeReads=1;MQ=60;set=variant10-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:2,3:5:76:117,0,76:0,2,0,3 chr1 178871217 . G A 793.98 PASS AC=2;AF=0.538;AN=2;DP=957;MQ=60;set=variant9-variant10-variant13-variant14-variant18-variant23-variant29-variant32-variant35-variant37-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:2340,216,0:0,0,50,22 chr1 178876054 . A G 1333.69 PASS AC=1;AF=0.5;AN=2;DP=225;FractionInformativeReads=1;MQ=60;set=variant32-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:25,31:56:99:785,0,639:8,17,13,18 chr1 178886266 . A C 3860.74 PASS AC=1;AF=0.5;AN=2;DP=386;FS=0.37;FractionInformativeReads=1;MQ=60;MQRankSum=2.698;QD=10;ReadPosRankSum=-0.637;SOR=0.726;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:219,167:386:99:3889,0,5464:111,108,86,81 chr1 178887023 . T C 1465.76 PASS AC=1;AF=0.5;AN=2;DP=1420;MQ=60;set=variant9-variant10-variant14-variant18-variant23-variant29-variant35-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:83,73:156:99:1748,0,2008:33,50,25,48 chr1 178887208 . A T 1515.45 PASS AC=2;AF=0.707;AN=2;DP=3665;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant22-variant23-variant24-variant29-variant30-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,128:128:99:4093,383,0:0,0,85,43 chr1 178887480 . A C 1733.49 PASS AC=1;AF=0.5;AN=2;DP=1007;FractionInformativeReads=1;MQ=60;set=variant10-variant14-variant29-variant35-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:94,92:186:99:2225,0,2399:34,60,38,54 chr1 178888856 . A G 4275.99 PASS AC=2;AF=0.707;AN=2;DP=8227;set=variant-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant22-variant23-variant24-variant29-variant30-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,321:322:99:9957,918,0:1,0,158,163 chr1 179023879 . T G 531.01 PASS AC=1;AF=0.604;AN=2;DP=422;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant8-variant9-variant11-variant12-variant16-variant17-variant18-variant21-variant22-variant23-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:10,11:21:99:345,0,339:1,9,2,9 chr1 179040930 . T C 386.76 PASS AC=1;AF=0.521;AN=2;DP=542;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant9-variant11-variant12-variant16-variant17-variant18-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,15:21:99:490,0,169:3,3,12,3 chr1 179041011 . A G 2048.84 PASS AC=1;AF=0.705;AN=2;DP=2338;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,36:68:99:886,0,795:18,14,20,16 chr1 179041398 . A G 1499.52 PASS AC=1;AF=0.705;AN=2;DP=2052;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,18:42:99:468,0,689:13,11,9,9 chr1 179041692 . CT C 3530.04 PASS AC=1;AF=0.705;AN=2;DP=5818;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,86:150:99:1923,0,1226:45,19,55,31 chr1 179042227 . T C 2911.19 PASS AC=1;AF=0.658;AN=2;DP=2798;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,36:77:99:1059,0,1014:15,26,9,27 chr1 179042300 . C A 1046.19 PASS AC=1;AF=0.625;AN=2;DP=1237;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant9-variant10-variant11-variant12-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,17:44:99:432,0,708:12,15,4,13 chr1 179042450 . T G 283.44 PASS AC=1;AF=0.645;AN=2;DP=313;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant9-variant10-variant11-variant12-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,5:17:99:130,0,309:4,8,2,3 chr1 179043539 . T G 6280.99 PASS AC=1;AF=0.705;AN=2;DP=5509;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:62,68:130:99:1975,0,1843:29,33,32,36 chr1 179045500 . C A 606.15 PASS AC=1;AF=0.694;AN=2;DP=1046;FractionInformativeReads=1;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,22:30:99:562,0,141:5,3,12,10 chr1 179051300 . T C 3207.82 PASS AC=1;AF=0.78;AN=2;DP=3437;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,46:106:99:1263,0,1782:32,28,24,22 chr1 179052006 . G T 1751.4 PASS AC=1;AF=0.574;AN=2;DP=2605;MQ=60;set=variant-variant2-variant4-variant6-variant9-variant11-variant12-variant16-variant17-variant18-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:57,68:125:99:1743,0,1469:25,32,33,35 chr1 179054557 . CA C,CAA 89.07 PASS AC=1,0;AF=0.409,0.106;AN=2;DP=2106;set=variant-variant2-variant3-filterInvariant4-filterInvariant5-variant6-variant7-filterInvariant9-variant10-variant11-variant13-filterInvariant14-filterInvariant15-filterInvariant18-variant20-filterInvariant21-filterInvariant22-variant24-variant25-variant27-variant28-filterInvariant29-filterInvariant30-variant31-variant32-filterInvariant33-filterInvariant35-variant37-variant38-filterInvariant40-variant41-variant42-variant44 GT:DP:GQ:SB 0/1:65:99:34,16,12,3 chr1 179054692 . T G 7903.21 PASS AC=1;AF=0.731;AN=2;DP=11288;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:137,173:310:99:4119,0,3170:73,64,92,81 chr1 179064560 . G GAGAT 289.38 PASS AC=1;AF=0.5;AN=2;DP=201;MQ=60;set=variant-variant4-variant12-variant26-variant28-variant35-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,6:14:99:227,0,436:5,3,3,3 chr1 179064875 . A G 546.63 PASS AC=1;AF=0.774;AN=2;DP=1025;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,7:27:99:207,0,568:9,11,4,3 chr1 179069429 . C T 3750.77 PASS AC=1;AF=0.705;AN=2;DP=3523;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,55:104:99:1626,0,1494:26,23,33,22 chr1 179070120 . C T 1134.13 PASS AC=1;AF=0.705;AN=2;DP=1883;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,24:59:99:652,0,996:18,17,9,15 chr1 179070334 . C G 1387.72 PASS AC=1;AF=0.705;AN=2;DP=1578;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,18:42:99:447,0,600:10,14,10,8 chr1 179070512 . C CT,CTT 167.15 PASS AC=1,0;AF=0.667,0.017;AN=2;DP=440;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant9-variant10-variant11-variant13-variant15-variant17-variant18-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:DP:GQ:SB 0/1:9:62:1,3,1,4 chr1 179071756 . G A 378.12 PASS AC=1;AF=0.667;AN=2;DP=944;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,18:31:99:449,0,305:5,8,6,12 chr1 179071865 . G A 157.45 PASS AC=1;AF=0.711;AN=2;DP=586;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,13:23:99:313,0,257:5,5,8,5 chr1 179071918 . G T 190.47 PASS AC=1;AF=0.774;AN=2;DP=661;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,9:24:99:211,0,375:9,6,6,3 chr1 179072966 . C T 1597.8 PASS AC=1;AF=0.705;AN=2;DP=1525;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,35:54:99:812,0,542:7,12,18,17 chr1 179073039 . C G 1075.65 PASS AC=1;AF=0.786;AN=2;DP=1329;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,30:47:99:910,0,410:10,7,13,17 chr1 179075755 . A G 390.56 PASS AC=1;AF=0.826;AN=2;DP=2014;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,16:44:99:334,0,613:14,14,5,11 chr1 179080115 . CTTTT CTT,CT,CTTT,C 982.21 PASS AC=1,0,1,0;AF=0.303,0.289,0.118,0.013;AN=2;DP=2451;set=variant-variant2-variant3-variant4-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/3:33:78:0,7,1,25 chr1 179087934 . T C 2770.85 PASS AC=1;AF=0.705;AN=2;DP=2578;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,29:75:99:695,0,1163:16,30,9,20 chr1 179089213 . C T 1225.42 PASS AC=1;AF=0.705;AN=2;DP=1269;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,9:35:99:248,0,761:18,8,8,1 chr1 179089475 . C G 1014.9 PASS AC=1;AF=0.705;AN=2;DP=1105;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,22:29:99:644,0,145:2,5,5,17 chr1 179089491 . A C 821.69 PASS AC=1;AF=0.705;AN=2;DP=879;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,12:18:99:401,0,136:2,4,2,10 chr1 179089518 . C G 450.08 PASS AC=1;AF=0.716;AN=2;DP=440;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,9:13:99:252,0,102:1,3,2,7 chr1 179102268 . A T 206.4 PASS AC=1;AF=0.5;AN=2;DP=81;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant12-variant28-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:8,8:16:99:265,0,276:6,2,7,1 chr1 179112145 . C G 591.53 PASS AC=1;AF=0.5;AN=2;DP=636;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant12-variant28-variant35-variant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:66,46:112:99:1083,0,1655:35,31,18,28 chr1 179198653 . T C 1336.7 PASS AC=2;AF=0.629;AN=2;DP=3961;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,162:162:99:4797,486,0:0,0,94,68 chr1 179198767 . ACGCCGCCGC ACGCCGCCGCCGCCGCCGC,ACGCCGCCGCCGCCGC,ACGCCGC,A,ACGCCGCCGCCGCCGCCGCCGC 1617.13 PASS AC=0,1,0,0,0;AF=0.05,0.383,0.167,0.017,0.017;AN=2;DP=3973;set=variant2-variant4-variant5-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant41 GT:DP:GQ:SB 0/2:115:99:18,33,21,43 chr1 179292442 . G A 218.24 PASS AC=1;AF=0.694;AN=2;DP=1076;MQ=60;set=variant2-variant4-variant5-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,18:39:99:406,0,456:12,9,11,7 chr1 179304892 . T C 468.23 PASS AC=1;AF=0.694;AN=2;DP=1145;MQ=60;set=variant2-variant4-variant5-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,14:37:99:400,0,631:6,17,2,12 chr1 179307047 . T A 236.84 PASS AC=1;AF=0.533;AN=2;DP=737;MQ=60;set=variant-variant2-variant5-variant7-variant12-variant17-variant18-variant22-variant29-variant31-variant35-variant36-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:31,24:55:99:602,0,748:12,19,11,13 chr1 179308803 . G A 582.43 PASS AC=1;AF=0.545;AN=2;DP=532;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant8-variant14-variant15-variant16-variant19-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:9,14:23:99:415,0,245:2,7,3,11 chr1 179310439 . C T 1426.34 PASS AC=1;AF=0.525;AN=2;DP=2280;MQ=60;set=variant4-variant5-variant8-variant14-variant15-variant16-variant19-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:57,55:112:99:1416,0,1432:23,34,19,36 chr1 179312102 . T C 1540.37 PASS AC=1;AF=0.735;AN=2;DP=4771;MQ=60;set=variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:62,64:126:99:1564,0,1395:24,38,33,31 chr1 179312235 . G A 768.33 PASS AC=1;AF=0.545;AN=2;DP=770;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant10-variant11-variant12-variant18-variant20-variant21-variant22-variant26-variant29-variant30-variant31-variant34-variant35-variant37-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:19,12:31:99:272,0,721:5,14,4,8 chr1 179312249 . AT A 404.92 PASS AC=1;AF=0.735;AN=2;DP=976;MQ=60;set=variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,15:25:99:496,0,354:4,6,3,12 chr1 179312525 . G A 452.72 PASS AC=1;AF=0.548;AN=2;DP=296;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant10-variant11-variant12-variant18-variant20-variant21-variant22-variant26-variant29-variant31-variant34-variant35-variant37-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,9:20:99:345,0,616:9,2,8,1 chr1 179312526 . GT G 360.92 PASS AC=1;AF=0.5;AN=2;DP=200;MQ=60;set=variant2-variant4-variant10-variant11-variant21-variant22-variant26-variant29-variant31-variant34-variant35-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:11,9:20:99:345,0,616:9,2,8,1 chr1 179312559 . A G 479.5 PASS AC=1;AF=0.5;AN=2;DP=99;FractionInformativeReads=1;MQ=60;set=variant31-variant34-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:25,12:37:99:304,0,744:19,6,9,3 chr1 179312752 . C T 603.25 PASS AC=1;AF=0.5;AN=2;DP=1180;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant10-variant11-variant21-variant22-variant26-variant29-variant30-variant31-variant34-variant35-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:47,49:96:99:1217,0,1206:18,29,19,30 chr1 179317895 . ATGTGTGTGTGTGTGTGTGTGTGTGTG ATGTGTGTGTGTGTG,ATGTGTGTGTGTGTGTG,A,ATGTGTGTGTGTGTGTGTGTGTG,ATG,ATGTGTGTGTGTGTGTGTGTG,ATGTG,AAGTGTGTGTGTGTGTGTGTGTGTGTGTG 932.01 PASS AC=0,0,1,0,1,0,0,0;AF=0.06,0.036,0.429,0.06,0.179,0.083,0.012,0.024;AN=2;DP=1333;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:DP:GQ:SB 3/5:23:99:0,0,19,4 chr1 179319541 . C G 2415.39 PASS AC=1;AF=0.5;AN=2;DP=607;FractionInformativeReads=1;MQ=60;set=variant31-variant34-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:62,69:131:99:1735,0,1549:29,33,34,35 chr1 179319580 . T C 3167.31 PASS AC=2;AF=0.829;AN=2;DP=3936;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,97:97:99:2888,290,0:0,0,43,54 chr1 179320578 . A G 916.98 PASS AC=1;AF=0.5;AN=2;DP=413;FS=0;FractionInformativeReads=1;MQ=60;set=variant31-variant34-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:57,37:94:99:826,0,1457:29,28,19,18 chr1 179320665 . A G 511.47 PASS AC=1;AF=0.667;AN=2;DP=1378;MQ=60;set=variant2-variant5-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant34-variant35-variant36-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,31:46:99:830,0,381:4,11,11,20 chr1 179323738 . C A 5454.01 PASS AC=2;AF=0.829;AN=2;DP=7381;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,209:209:99:6325,626,0:0,0,115,94 chr1 179323919 . A G 7878.38 PASS AC=1;AF=0.776;AN=2;DP=11737;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:165,158:323:99:3890,0,4342:87,78,84,74 chr1 179324553 . T G 2359.48 PASS AC=1;AF=0.5;AN=2;DP=2976;MQ=60;set=variant2-variant4-variant10-variant11-variant21-variant22-variant26-variant29-variant30-variant31-variant34-variant35-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:90,127:217:99:3048,0,2128:38,52,63,64 chr1 179324870 . C A 63.95 PASS AC=1;AF=0.5;AN=2;DP=142;FractionInformativeReads=1;set=variant2-variant4-variant10-variant11-variant21-variant22-variant26-variant29-variant30-variant31-variant34-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:7,4:11:99:144,0,195:5,2,3,1 chr1 179325506 . A G 2603.82 PASS AC=1;AF=0.721;AN=2;DP=7131;MQ=60;set=variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:116,86:202:99:2073,0,2942:45,71,33,53 chr1 179325633 . A G 939.58 PASS AC=2;AF=0.847;AN=2;DP=604;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:650,48,0:0,0,1,15 chr1 179325657 . GT G 249.13 PASS AC=1;AF=0.75;AN=2;DP=194;MQ=60;set=variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant27-variant28-variant32-variant35-variant36-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,4:7:65:94,0,65:0,3,0,4 chr1 179326065 . A C 690.08 PASS AC=1;AF=0.721;AN=2;DP=1771;MQ=60;set=variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,42:67:99:1175,0,745:20,5,30,12 chr1 179326323 . A G 3381.76 PASS AC=2;AF=0.829;AN=2;DP=5265;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,161:163:99:4964,454,0:1,1,56,105 chr1 179326350 . T C 1222.29 PASS AC=1;AF=0.5;AN=2;DP=392;FractionInformativeReads=1;set=variant31-variant34-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:45,58:103:99:1667,0,1227:13,32,19,39 chr1 179326393 . A G 551.16 PASS AC=1;AF=0.5;AN=2;DP=141;MQ=60;set=variant31-variant34-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:21,15:36:99:466,0,697:7,14,6,9 chr1 179326397 . C G 932.39 PASS AC=2;AF=0.829;AN=2;DP=1161;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,33:34:57:1351,57,0:0,1,12,21 chr1 179326587 . C T 2627.63 PASS AC=1;AF=0.5;AN=2;DP=668;FractionInformativeReads=1;set=variant31-variant34-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:96,103:199:99:2750,0,2605:66,30,70,33 chr1 179326708 . TAC T 5277.59 PASS AC=1;AF=0.721;AN=2;DP=9401;MQ=60;set=variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:180,168:348:99:6467,0,6938:80,100,72,96 chr1 179326747 . C A 6717.59 PASS AC=2;AF=0.829;AN=2;DP=7740;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,241:241:99:7610,721,0:0,0,84,157 chr1 179327017 . A G 1042.29 PASS AC=1;AF=0.721;AN=2;DP=3122;MQ=60;set=variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,41:102:99:1116,0,1609:39,22,27,14 chr1 179327591 . A T 4510.01 PASS AC=1;AF=0.5;AN=2;DP=1143;MQ=60;set=variant31-variant34-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:172,143:315:99:3796,0,4341:76,96,60,83 chr1 179334792 . A T 76.67 PASS AC=1;AF=0.5;AN=2;DP=8;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.747;QD=9.58;ReadPosRankSum=0.747;SOR=1.27;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:7,1:8:99:105,0,341:4,3,1,0 chr1 179334801 . C A 284.46 PASS AC=1;AF=0.712;AN=2;DP=383;MQ=60;set=variant2-variant3-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,4:10:99:147,0,299:4,2,4,0 chr1 179334840 . C T 325.96 PASS AC=1;AF=0.712;AN=2;DP=615;MQ=60;set=variant2-variant3-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,8:14:99:266,0,144:4,2,7,1 chr1 179334917 . G C 675.12 PASS AC=1;AF=0.706;AN=2;DP=1452;MQ=60;set=variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,26:42:99:620,0,357:10,6,15,11 chr1 179334934 . T G 811.04 PASS AC=1;AF=0.5;AN=2;DP=185;FractionInformativeReads=1;MQ=60;set=variant31-variant34-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:28,18:46:99:422,0,673:16,12,10,8 chr1 179334984 . A G 1231.22 PASS AC=2;AF=0.86;AN=2;DP=2237;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1621,168,0:0,0,28,28 chr1 179335058 . C T 528.99 PASS AC=1;AF=0.712;AN=2;DP=1541;MQ=60;set=variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,24:59:99:558,0,874:19,16,12,12 chr1 179335138 . A G 398.96 PASS AC=1;AF=0.6;AN=2;DP=742;MQ=60;set=variant5-variant8-variant9-variant13-variant14-variant15-variant16-variant19-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant32-variant34-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,14:44:99:293,0,698:15,15,5,9 chr1 179335158 . C T 490.56 PASS AC=1;AF=0.712;AN=2;DP=1039;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,12:39:99:392,0,1203:14,13,4,8 chr1 179335162 . G C 493.55 PASS AC=1;AF=0.712;AN=2;DP=1009;MQ=60;set=variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,10:36:99:339,0,1233:13,13,3,7 chr1 179335366 . C T 61.77 PASS AC=1;AF=0.852;AN=2;DP=135;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant8-variant10-variant11-variant12-variant13-variant16-variant17-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant35-variant36-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:2,5:7:63:123,0,63:2,0,2,3 chr1 179335499 . C CT,CTT 173.24 PASS AC=1,0;AF=0.485,0.015;AN=2;DP=744;set=variant2-variant3-variant5-filterInvariant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant31-variant32-filterInvariant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant44 GT:DP:GQ:SB 0/1:31:99:8,3,14,6 chr1 179339262 . C G 917.94 PASS AC=1;AF=0.571;AN=2;DP=479;FractionInformativeReads=1;MQ=60;set=variant17-variant18-variant31-variant34-variant35-variant36-variant40 GT:AD:DP:GQ:PL:SB 0/1:44,31:75:99:803,0,1181:16,28,9,22 chr1 179339334 . G A 500.32 PASS AC=1;AF=0.793;AN=2;DP=674;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,10:19:99:279,0,332:0,9,0,10 chr1 179347832 . T C 559.07 PASS AC=2;AF=0.722;AN=2;DP=3224;MQ=60;set=variant2-variant5-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant34-variant35-variant36-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,92:92:99:2505,276,0:0,0,46,46 chr1 179351606 . G C 103.53 PASS AC=2;AF=0.797;AN=2;DP=369;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:612,51,0:0,0,14,3 chr1 179352736 . T C 554.25 PASS AC=1;AF=0.571;AN=2;DP=485;MQ=60;set=variant17-variant18-variant31-variant34-variant35-variant36-variant40 GT:AD:DP:GQ:PL:SB 0/1:46,32:78:99:707,0,1044:21,25,15,17 chr1 179354304 . A G 759.32 PASS AC=2;AF=0.782;AN=2;DP=995;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:914,72,0:0,0,21,3 chr1 179364372 . G C 539.11 PASS AC=1;AF=0.571;AN=2;DP=372;FractionInformativeReads=1;set=variant17-variant18-variant31-variant34-variant35-variant36-variant40 GT:AD:DP:GQ:PL:SB 0/1:32,16:48:99:443,0,794:11,21,6,10 chr1 179364391 . A G 519.57 PASS AC=1;AF=0.674;AN=2;DP=1157;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant19-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant32-variant34-variant35-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,22:37:99:531,0,353:6,9,9,13 chr1 179380472 . GT G 1312.14 PASS AC=1;AF=0.803;AN=2;DP=1841;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,29:58:99:709,0,643:11,18,9,20 chr1 179380519 . G T 312.69 PASS AC=1;AF=0.563;AN=2;DP=173;FractionInformativeReads=1;MQ=60;set=variant17-variant18-variant25-variant28-variant31-variant34-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:13,14:27:99:443,0,420:2,11,4,10 chr1 179398563 . C G 452.04 PASS AC=2;AF=0.811;AN=2;DP=365;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:474,33,0:0,0,11,0 chr1 179401503 . G A 368.25 PASS AC=1;AF=0.563;AN=2;DP=488;MQ=60;set=variant17-variant18-variant25-variant28-variant31-variant34-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:26,28:54:99:599,0,723:14,12,16,12 chr1 179401564 . CT C 2211.43 PASS AC=2;AF=0.849;AN=2;DP=2353;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:4,44:48:36:1049,36,0:2,2,18,26 chr1 179401896 . G A 502.42 PASS AC=1;AF=0.806;AN=2;DP=484;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant32-variant35-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,12:18:99:324,0,136:4,2,6,6 chr1 179426175 . CCTGGT C 865.24 PASS AC=1;AF=0.556;AN=2;DP=550;set=variant17-variant18-variant23-variant25-variant28-variant31-variant34-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:46,29:75:99:1059,0,2563:23,23,14,15 chr1 179426240 . T C 484.65 PASS AC=1;AF=0.556;AN=2;DP=453;set=variant17-variant18-variant23-variant25-variant28-variant31-variant34-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:41,27:68:99:661,0,906:19,22,11,16 chr1 179437827 . G A 327.99 PASS AC=2;AF=0.878;AN=2;DP=434;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:381,30,0:0,0,1,9 chr1 179452194 . C T 71.4 PASS AC=2;AF=0.69;AN=2;DP=700;MQ=60;set=variant2-variant5-variant7-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:935,72,0:0,0,18,6 chr1 179452275 . G A 782.66 PASS AC=1;AF=0.556;AN=2;DP=790;MQ=60;set=variant17-variant18-variant23-variant25-variant28-variant31-variant34-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:45,36:81:99:840,0,1075:23,22,22,14 chr1 179452522 . G C 353.14 PASS AC=2;AF=0.712;AN=2;DP=321;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant7-variant8-variant9-variant11-variant13-variant14-variant16-variant17-variant19-variant21-variant22-variant23-variant25-variant26-variant27-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:405,39,0:0,0,4,9 chr1 179462149 . A G 991.46 PASS AC=2;AF=1;AN=2;DP=1158;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,31:31:93:1095,93,0:0,0,7,24 chr1 179494665 . C T 103.54 PASS AC=2;AF=0.913;AN=2;DP=400;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:349,24,0:0,0,0,8 chr1 179497359 . T C 422.99 PASS AC=2;AF=0.915;AN=2;DP=499;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:505,42,0:0,0,11,3 chr1 179503806 . G A 493.93 PASS AC=1;AF=0.652;AN=2;DP=598;MQ=60;set=variant-variant2-variant5-variant7-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant19-variant21-variant22-variant23-variant26-variant27-variant32-variant34-variant35-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,10:17:99:269,0,213:6,1,7,3 chr1 179504025 . AAAGAAG AAAG,A 1409.55 PASS AC=1,0;AF=0.63,0.022;AN=2;DP=2325;MQ=60;set=variant-variant2-variant5-variant7-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant19-variant21-variant22-variant23-variant26-variant27-variant32-variant34-variant35-variant39-variant40-variant44 GT:DP:GQ:SB 0/1:103:99:35,27,24,17 chr1 179504043 . C G 1716.82 PASS AC=1;AF=0.652;AN=2;DP=2563;MQ=60;set=variant-variant2-variant5-variant7-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant19-variant21-variant22-variant23-variant26-variant27-variant32-variant34-variant35-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,51:116:99:1790,0,4488:36,29,28,23 chr1 179504130 . G A 771.63 PASS AC=1;AF=0.652;AN=2;DP=2432;MQ=60;set=variant-variant2-variant5-variant7-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant19-variant21-variant22-variant23-variant26-variant27-variant32-variant34-variant35-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,44:95:99:1072,0,1304:18,33,17,27 chr1 179519608 . A G 1663.4 PASS AC=1;AF=0.604;AN=2;DP=885;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant6-variant9-variant11-variant12-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant28-variant31-variant33-variant34-variant35-variant36-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,14:36:99:413,0,741:19,3,13,1 chr1 179519880 . T C 3153.95 PASS AC=2;AF=0.94;AN=2;DP=4395;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,112:112:99:3903,335,0:0,0,42,70 chr1 179520050 . T C 3452.26 PASS AC=1;AF=0.658;AN=2;DP=4662;MQ=60;set=variant-variant2-variant5-variant7-variant8-variant13-variant14-variant15-variant16-variant19-variant22-variant23-variant27-variant32-variant34-variant35-variant37-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:138,120:258:99:2866,0,3274:74,64,61,59 chr1 179520108 . C T 2617.75 PASS AC=1;AF=0.536;AN=2;DP=3635;MQ=60;set=variant9-variant11-variant17-variant18-variant21-variant23-variant25-variant26-variant28-variant31-variant34-variant35-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:122,143:265:99:3514,0,3028:54,68,69,74 chr1 179520151 . C T 6711.92 PASS AC=2;AF=0.94;AN=2;DP=8825;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,238:238:99:7289,711,0:0,0,106,132 chr1 179520254 . C G 4563.96 PASS AC=1;AF=0.735;AN=2;DP=4910;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:75,77:152:99:2099,0,2196:40,35,40,37 chr1 179520506 . G A 3198.23 PASS AC=1;AF=0.735;AN=2;DP=3948;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:65,70:135:99:1794,0,1563:26,39,29,41 chr1 179521932 . G T 1342.84 PASS AC=1;AF=0.673;AN=2;DP=3004;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant19-variant21-variant22-variant23-variant26-variant27-variant29-variant30-variant32-variant34-variant35-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:55,53:108:99:1332,0,1223:24,31,21,32 chr1 179544898 . T C 3368.49 PASS AC=2;AF=0.965;AN=2;DP=5006;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,154:154:99:5703,466,0:0,0,76,78 chr1 179544913 . G C 2167.02 PASS AC=1;AF=0.5;AN=2;DP=169;FS=1.197;FractionInformativeReads=1;MQ=60;MQRankSum=-0.077;QD=12.82;ReadPosRankSum=0.88;SOR=0.809;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:80,89:169:99:2195,0,1846:40,40,47,42 chr1 179545115 . G A 186.39 PASS AC=1;AF=0.658;AN=2;DP=645;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant7-variant8-variant10-variant13-variant14-variant15-variant16-variant19-variant22-variant23-variant27-variant32-variant34-variant35-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:15,17:32:99:425,0,430:6,9,7,10 chr1 179560624 . T C 719.65 PASS AC=2;AF=0.965;AN=2;DP=1819;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1163,102,0:0,0,26,8 chr1 179561527 . C G 559.79 PASS AC=1;AF=0.556;AN=2;DP=845;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant9-variant11-variant17-variant18-variant21-variant25-variant26-variant28-variant31-variant34-variant35-variant36-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,21:36:99:635,0,370:5,10,8,13 chr1 179561645 . A C 597.61 PASS AC=2;AF=0.821;AN=2;DP=2125;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1829,168,0:0,0,38,18 chr1 179561683 . A T 275.61 PASS AC=2;AF=0.798;AN=2;DP=2730;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,68:70:99:1729,163,0:2,0,44,24 chr1 179562143 . G A 241.61 PASS AC=2;AF=0.731;AN=2;DP=853;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:680,63,0:0,0,7,14 chr1 179587569 . T C 40.73 PASS AC=1;AF=0.6;AN=2;DP=88;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant17-variant23-variant26-variant28-variant29-variant30-variant35-variant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:5,3:8:76:76,0,182:5,0,3,0 chr1 179599365 . G C 172.07 PASS AC=1;AF=0.5;AN=2;DP=262;set=variant2-variant4-variant11-variant17-variant21-variant23-variant26-variant28-variant29-variant30-variant35-variant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:2,11:13:10:334,0,10:1,1,8,3 chr1 179599423 . T C 606.62 PASS AC=1;AF=0.5;AN=2;DP=575;set=variant2-variant4-variant11-variant17-variant21-variant23-variant26-variant28-variant29-variant30-variant35-variant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:10,19:29:99:400,0,201:6,4,10,9 chr1 179599516 . C T 666.35 PASS AC=1;AF=0.5;AN=2;DP=593;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant11-variant17-variant21-variant23-variant26-variant28-variant29-variant30-variant35-variant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:20,18:38:99:481,0,408:11,9,6,12 chr1 179599985 . C T 1025.5 PASS AC=1;AF=0.5;AN=2;DP=92;FS=2.742;FractionInformativeReads=1;MQ=60;MQRankSum=0.012;QD=11.15;ReadPosRankSum=0.629;SOR=0.748;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:46,46:92:99:1054,0,1041:21,25,25,21 chr1 179600001 . A G 942.91 PASS AC=1;AF=0.5;AN=2;DP=1094;MQ=60;set=variant2-variant4-variant11-variant17-variant21-variant23-variant26-variant28-variant29-variant30-variant35-variant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:51,45:96:99:983,0,1237:26,25,21,24 chr1 179600042 . G A 963.65 PASS AC=1;AF=0.5;AN=2;DP=235;MQ=60;set=variant17-variant28-variant35 GT:AD:DP:GQ:PL:SB 0/1:51,38:89:99:771,0,1237:23,28,16,22 chr1 179604864 . C T 762.51 PASS AC=2;AF=0.86;AN=2;DP=3871;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,88:88:99:2577,263,0:0,0,46,42 chr1 179605058 . G A 123.08 PASS AC=1;AF=0.653;AN=2;DP=496;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,6:13:99:129,0,274:0,7,1,5 chr1 179609589 . G T 1725.38 PASS AC=1;AF=0.536;AN=2;DP=1965;FractionInformativeReads=1;MQ=60;set=variant9-variant11-variant17-variant18-variant21-variant25-variant26-variant28-variant31-variant34-variant35-variant36-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:72,64:136:99:1543,0,1811:34,38,34,30 chr1 179621224 . G A 418.45 PASS AC=1;AF=0.5;AN=2;DP=287;MQ=60;set=variant17-variant28-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:45,41:86:99:794,0,1009:20,25,23,18 chr1 179632536 . A G 685.68 PASS AC=1;AF=0.5;AN=2;DP=376;FractionInformativeReads=1;MQ=60;set=variant17-variant28-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:49,43:92:99:977,0,1215:24,25,23,20 chr1 179632727 . G A 122.47 PASS AC=1;AF=0.676;AN=2;DP=337;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,4:5:31:165,0,31:0,1,0,4 chr1 179712223 . A C 596.86 PASS AC=2;AF=0.596;AN=2;DP=1342;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant6-variant8-variant9-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant30-variant32-variant33-variant35-variant36-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:2093,213,0:0,0,42,29 chr1 179712480 . T G 215.02 PASS AC=2;AF=0.779;AN=2;DP=1553;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1347,120,0:0,0,11,29 chr1 179712616 . G T 152.64 PASS AC=2;AF=0.708;AN=2;DP=771;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,29:29:86:709,86,0:0,0,14,15 chr1 179776841 . A G 106.19 PASS AC=2;AF=0.581;AN=2;DP=585;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant21-variant22-variant23-variant24-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:572,60,0:0,0,11,9 chr1 179783922 . T A 1360.84 PASS AC=2;AF=0.597;AN=2;DP=3767;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant21-variant22-variant23-variant24-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,121:121:99:3628,360,0:0,0,57,64 chr1 179784230 . ACGCGCG ACG,A,ACGCG 75.55 PASS AC=1,0,0;AF=0.205,0.273,0.045;AN=2;DP=498;set=variant-variant2-variant3-variant4-filterInvariant6-variant10-variant13-variant18-variant21-variant23-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant40-variant42-variant43 GT:DP:GQ:SB 0/1:11:59:2,0,4,5 chr1 179784241 . CGCGCACAG C 48.57 PASS AC=1;AF=0.5;AN=2;DP=19;FS=6.368;FractionInformativeReads=0.684;MQ=60;MQRankSum=-0.085;QD=2.56;ReadPosRankSum=-0.761;SOR=2.833;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:10,3:13:86:86,0,384:5,5,3,0 chr1 179784249 . G C 205.79 PASS AC=1;AF=0.5;AN=2;DP=180;set=variant2-variant4-variant6-variant15-variant23-variant29-variant33-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:3,10:13:88:376,0,88:3,0,5,5 chr1 179785018 . CTG C 1150.36 PASS AC=2;AF=0.563;AN=2;DP=576;MQ=60;set=variant-variant2-variant4-variant22-variant24-variant34-variant35-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,81:81:99:3610,244,0:0,0,37,44 chr1 179810024 . TATAATAATAATA TATAATAATAATAATA,T,TATAATA,TATAATAATAATAATAATA 154.19 PASS AC=0,0,0,1;AF=0.227,0.045,0.182,0.091;AN=2;DP=138;MQ=60;set=variant4-variant8-variant9-variant17-filterInvariant21-variant22-variant28-variant34-variant35-variant42-variant43 GT:DP:GQ:SB 0/4:7:99:2,2,3,0 chr1 179810201 . A G 2906.73 PASS AC=2;AF=0.571;AN=2;DP=1496;MQ=60;set=variant-variant2-variant4-variant34-variant35-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:2,235:237:99:7343,660,0:1,1,150,85 chr1 179811337 . CA CAA,C 275.69 PASS AC=1,0;AF=0.375,0.125;AN=2;DP=722;MQ=60;set=variant-variant3-variant4-filterInvariant6-filterInvariant7-variant9-variant13-variant14-variant17-filterInvariant23-filterInvariant24-variant28-variant29-filterInvariant32-variant34-variant35-variant37-variant40-variant42-variant43 GT:DP:GQ:SB 0/1:26:99:5,2,18,1 chr1 179811936 . T C 545.2 PASS AC=2;AF=0.571;AN=2;DP=284;FractionInformativeReads=1;set=variant-variant2-variant4-variant34-variant35-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1517,123,0:0,0,10,31 chr1 179812163 . A G 95.78 PASS AC=2;AF=0.972;AN=2;DP=60;FS=0;FractionInformativeReads=1;MQRankSum=-2.017;ReadPosRankSum=-1.368;set=variant3-variant7-variant8-variant10-variant12-variant15-variant17-variant20-variant22-variant23-variant25-variant28-variant29-variant31-variant33-variant35-variant36-variant38 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:181,15,0:0,0,3,2 chr1 179812183 . CAAAAAA C,CAA 43.7 PASS AC=0,1;AF=0.143,0.5;AN=2;DP=42;set=variant-variant3-variant15-variant22-variant24-variant35-variant36 GT:DP:GQ:SB 0/2:6:83:1,2,3,0 chr1 179813352 . C T 1117.69 PASS AC=2;AF=0.591;AN=2;DP=1537;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant9-variant13-variant14-variant15-variant17-variant22-variant24-variant28-variant29-variant34-variant35-variant36-variant37-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,82:82:99:2924,246,0:0,0,60,22 chr1 179813499 . G A 4161.59 PASS AC=2;AF=0.591;AN=2;DP=5323;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant9-variant13-variant14-variant15-variant17-variant22-variant24-variant28-variant29-variant34-variant35-variant36-variant37-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,244:245:99:7736,724,0:1,0,126,118 chr1 179813613 . T C 5944.45 PASS AC=2;AF=0.611;AN=2;DP=9346;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant9-variant10-variant13-variant14-variant15-variant17-variant22-variant23-variant24-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,312:312:99:10085,936,0:0,0,161,151 chr1 179813716 . T TA 9147.8 PASS AC=2;AF=0.536;AN=2;DP=6456;MQ=60;set=variant-variant2-variant3-variant4-variant13-variant14-variant28-variant29-variant34-variant35-variant37-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:2,444:446:99:17870,1267,0:1,1,229,215 chr1 179814457 . A C 2845.85 PASS AC=2;AF=0.583;AN=2;DP=6234;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant9-variant10-variant13-variant14-variant15-variant17-variant22-variant24-variant28-variant29-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,260:260:99:8170,778,0:0,0,121,139 chr1 179816816 . T A 660.08 PASS AC=2;AF=0.571;AN=2;DP=243;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant34-variant35-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1382,117,0:0,0,11,28 chr1 179851159 . TG T 891.05 PASS AC=2;AF=0.943;AN=2;DP=2028;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1977,168,0:0,0,36,20 chr1 179854026 . A T 76.67 PASS AC=2;AF=0.588;AN=2;DP=194;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant15-variant18-variant22-variant24-variant28-variant34-variant35-variant36-variant37-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:552,42,0:0,0,1,13 chr1 179858292 . G A 79.46 PASS AC=2;AF=0.625;AN=2;DP=44;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant18-variant34-variant35-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:258,18,0:0,0,6,0 chr1 179887125 . G A 4147.48 PASS AC=2;AF=0.943;AN=2;DP=5392;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,126:126:99:4182,377,0:0,0,62,64 chr1 179992076 . A G 490.22 PASS AC=2;AF=0.878;AN=2;DP=551;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:754,57,0:0,0,2,17 chr1 179993793 . T C 283.47 PASS AC=2;AF=0.905;AN=2;DP=415;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:459,36,0:0,0,1,11 chr1 180000681 . A G 255.13 PASS AC=2;AF=1;AN=2;DP=9;FS=0;FractionInformativeReads=1;MQ=60;QD=28.35;SOR=1.402;set=variant35 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:283,27,0:0,0,3,6 chr1 180010702 . T C 148.54 PASS AC=2;AF=0.885;AN=2;DP=358;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:234,21,0:0,0,5,2 chr1 180013235 . T G 689.05 PASS AC=2;AF=0.667;AN=2;DP=152;FS=0;FractionInformativeReads=1;MQ=60;set=variant34-variant35-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,52:52:99:1435,155,0:0,0,27,25 chr1 180081856 . T A 3075.26 PASS AC=2;AF=0.625;AN=2;DP=1185;MQ=60;set=variant10-variant34-variant35-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,314:314:99:9319,940,0:0,0,170,144 chr1 180124288 . G C,T 801.38 PASS AC=1,0;AF=0.429,0.071;AN=2;DP=403;MQ=60;set=variant22-variant24-variant32-variant35-variant37-variant41-filterInvariant42 GT:DP:GQ:SB 0/1:77:99:15,22,19,21 chr1 180124379 . T C 255.13 PASS AC=2;AF=0.648;AN=2;DP=460;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant31-variant32-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:887,81,0:0,0,8,19 chr1 180135757 . TG T 890.42 PASS AC=2;AF=0.611;AN=2;DP=578;MQ=60;set=variant6-variant22-variant23-variant24-variant32-variant35-variant37-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,69:69:99:2463,208,0:0,0,27,42 chr1 180144291 . CAA CAAA,C 849 PASS AC=2,0;AF=0.634,0.012;AN=2;DP=1365;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:40:90:2,0,33,5 chr1 180144594 . A G 503.02 PASS AC=1;AF=0.5;AN=2;DP=178;FractionInformativeReads=1;MQ=60;set=variant6-variant23-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:30,25:55:99:751,0,936:5,25,6,19 chr1 180145088 . A G 1173.7 PASS AC=2;AF=0.989;AN=2;DP=3019;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,77:78:99:2248,198,0:1,0,35,42 chr1 180155376 . C G 373.55 PASS AC=2;AF=0.866;AN=2;DP=552;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:886,60,0:0,0,5,15 chr1 180155382 . AG A 187.41 PASS AC=2;AF=0.977;AN=2;DP=518;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:855,57,0:0,0,5,14 chr1 180159797 . TC T 234.66 PASS AC=2;AF=0.888;AN=2;DP=399;FS=0;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:627,54,0:0,0,6,12 chr1 180163578 . G T 708.81 PASS AC=1;AF=0.5;AN=2;DP=260;FractionInformativeReads=1;MQ=60;set=variant6-variant10-variant23-variant35 GT:AD:DP:GQ:PL:SB 0/1:52,35:87:99:733,0,1525:14,38,14,21 chr1 180165204 . A T 110.08 PASS AC=1;AF=0.5;AN=2;DP=168;MQ=60;set=variant6-variant10-variant22-variant23-variant24-variant32-variant35-variant37-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:12,7:19:99:169,0,341:9,3,5,2 chr1 180167440 . A G 898.91 PASS AC=1;AF=0.545;AN=2;DP=1194;MQ=60;set=variant6-variant10-variant22-variant23-variant24-variant31-variant32-variant35-variant37-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:54,45:99:99:1381,0,1458:26,28,24,21 chr1 180169330 . C T 2165.78 PASS AC=2;AF=0.8;AN=2;DP=2995;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,76:78:99:2396,214,0:1,1,38,38 chr1 180169367 . C T 459.38 PASS AC=1;AF=0.5;AN=2;DP=171;FractionInformativeReads=1;MQ=60;set=variant10-variant35 GT:AD:DP:GQ:PL:SB 0/1:59,36:95:99:958,0,1791:33,26,20,16 chr1 180170361 . C T 791.46 PASS AC=1;AF=0.817;AN=2;DP=1432;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,16:26:99:456,0,211:4,6,12,4 chr1 180171072 . A G 3519.3 PASS AC=2;AF=0.8;AN=2;DP=4813;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,146:146:99:4235,436,0:0,0,73,73 chr1 180171254 . T C 2636.36 PASS AC=2;AF=0.845;AN=2;DP=3237;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:2566,237,0:0,0,36,43 chr1 180171666 . A G 2955.62 PASS AC=2;AF=0.8;AN=2;DP=4652;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,108:108:99:3417,324,0:0,0,55,53 chr1 180171810 . CAA C,CA,CCAAAA,CAAA,CAAAA,CAAAAA 2053.67 PASS AC=0,0,0,0,1,0;AF=0.026,0.192,0.013,0.244,0.256,0.013;AN=2;DP=3483;set=variant-variant2-variant3-variant4-variant5-filterInvariant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-filterInvariant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 0/5:62:99:24,21,7,10 chr1 180172496 . A G 4313.93 PASS AC=2;AF=0.845;AN=2;DP=4383;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,121:121:99:5311,367,0:0,0,51,70 chr1 180172512 . T C 3343.23 PASS AC=2;AF=0.989;AN=2;DP=4299;FS=0;MQ=60;MQRankSum=-0.53;ReadPosRankSum=-0.598;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,120:120:99:5268,361,0:0,0,51,69 chr1 180173206 . A AATG,AATGATG,AATGATGATG 5038.4 PASS AC=2,0,0;AF=0.762,0.071,0.012;AN=2;DP=8012;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:179:99:2,2,73,102 chr1 180180669 . A G 1767.22 PASS AC=2;AF=0.791;AN=2;DP=2803;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,81:81:99:2338,243,0:0,0,37,44 chr1 180180756 . C T 512.71 PASS AC=1;AF=0.54;AN=2;DP=679;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant7-variant8-variant12-variant13-variant15-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,20:30:99:523,0,279:4,6,7,13 chr1 180240752 . C T 181.62 PASS AC=2;AF=0.691;AN=2;DP=650;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:743,60,0:0,0,8,12 chr1 180243524 . A G 1284.32 PASS AC=2;AF=0.681;AN=2;DP=4126;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,101:101:99:3594,303,0:0,0,49,52 chr1 180245228 . T TG 1801.2 PASS AC=2;AF=0.955;AN=2;DP=2837;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,66:66:99:2498,202,0:0,0,27,39 chr1 180245480 . TTAAG T 1081.54 PASS AC=2;AF=0.943;AN=2;DP=1139;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:1125,75,0:0,0,8,17 chr1 180245972 . G GC 829.26 PASS AC=2;AF=0.919;AN=2;DP=1776;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1930,153,0:0,0,25,26 chr1 180246013 . TGTAA T 973.76 PASS AC=2;AF=0.919;AN=2;DP=1899;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1510,102,0:0,0,18,16 chr1 180246261 . C T 1033.77 PASS AC=2;AF=0.925;AN=2;DP=1431;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1073,99,0:0,0,20,13 chr1 180246451 . G A 243.11 PASS AC=2;AF=0.85;AN=2;DP=1739;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1202,105,0:0,0,13,22 chr1 180247012 . T TG,TGG,TGGGG 1190.88 PASS AC=2,0,0;AF=0.841,0.049,0.012;AN=2;DP=5749;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:DP:GQ:SB 1/1:134:99:1,3,83,47 chr1 180247477 . CT C 561.96 PASS AC=2;AF=0.943;AN=2;DP=1190;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:849,69,0:0,0,15,8 chr1 180248436 . T A 70.66 PASS AC=2;AF=0.854;AN=2;DP=477;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:226,21,0:0,0,2,5 chr1 180257692 . A C 1132.66 PASS AC=2;AF=0.955;AN=2;DP=2032;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1831,168,0:0,0,21,35 chr1 180283659 . T C 295.67 PASS AC=2;AF=0.976;AN=2;DP=468;FS=0;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:470,54,0:0,0,10,8 chr1 180471053 . AC A 77.58 PASS AC=1;AF=0.5;AN=2;DP=407;set=variant5-variant6-filterInvariant9-variant14-variant17-variant21-variant24-variant26-variant27-filterInvariant30-variant31-variant35-variant36-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:16,11:27:99:159,0,241:13,3,9,2 chr1 180471054 . C A 43.97 PASS AC=1;AF=0.536;AN=2;DP=805;set=filterInvariant4-variant7-variant9-variant10-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-filterInvariant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,16:27:99:241,0,159:9,2,13,3 chr1 180757117 . G GT 253.02 PASS AC=2;AF=0.989;AN=2;DP=666;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:752,57,0:0,0,4,15 chr1 180772414 . G A 45.18 PASS AC=1;AF=0.536;AN=2;DP=313;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant23-variant25-variant26-variant27-variant28-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,6:18:99:213,0,354:10,2,6,0 chr1 180849494 . T C 229.3 PASS AC=1;AF=0.667;AN=2;DP=761;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,12:23:99:441,0,366:1,10,0,12 chr1 180854067 . A G 9496.59 PASS AC=2;AF=1;AN=2;DP=10414;FS=0;MQ=60;MQRankSum=1.677;ReadPosRankSum=1.654;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,238:238:99:7277,712,0:0,0,136,102 chr1 180855503 . A G 6260.72 PASS AC=1;AF=0.638;AN=2;DP=14435;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:180,163:343:99:4289,0,4630:99,81,92,71 chr1 180855529 . A C 5104.55 PASS AC=1;AF=0.5;AN=2;DP=403;FS=1.748;FractionInformativeReads=1;MQ=60;MQRankSum=1.071;QD=12.67;ReadPosRankSum=0.554;SOR=0.837;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:203,200:403:99:5133,0,5214:113,90,118,82 chr1 180856698 . G C 3269.17 PASS AC=1;AF=0.5;AN=2;DP=1297;FractionInformativeReads=1;MQ=60;set=variant29-variant31-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:175,149:324:99:3616,0,4340:80,95,75,74 chr1 180885430 . T C 3432.92 PASS AC=2;AF=0.989;AN=2;DP=7598;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,211:211:99:6702,632,0:0,0,106,105 chr1 180897521 . C T 1914.6 PASS AC=2;AF=1;AN=2;DP=4086;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:2,97:99:99:2931,247,0:1,1,58,39 chr1 180897569 . C T 755.63 PASS AC=1;AF=0.615;AN=2;DP=2797;MQ=60;set=variant2-variant3-variant4-variant5-variant8-variant10-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant34-variant35-variant36-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,51:111:99:1193,0,1517:29,31,27,24 chr1 180897792 . ATGC A 397.77 PASS AC=1;AF=0.679;AN=2;DP=1194;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,15:23:99:601,0,319:2,6,5,10 chr1 180905352 . C T 2425.71 PASS AC=1;AF=0.6;AN=2;DP=8920;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:159,146:305:99:3423,0,4195:77,82,74,72 chr1 180905448 . G T 2060.08 PASS AC=1;AF=0.625;AN=2;DP=10127;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:157,173:330:99:4419,0,4071:82,75,90,83 chr1 180913597 . A G 1553.13 PASS AC=2;AF=1;AN=2;DP=6204;FS=0;MQ=60;MQRankSum=-0.019;ReadPosRankSum=1.546;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,136:136:99:4183,407,0:0,0,64,72 chr1 180914304 . C T 489.01 PASS AC=2;AF=1;AN=2;DP=1001;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:916,84,0:0,0,16,12 chr1 180915244 . GA G 545.13 PASS AC=2;AF=0.932;AN=2;DP=1010;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:564,60,0:0,0,16,4 chr1 180915596 . T C 715.73 PASS AC=1;AF=0.703;AN=2;DP=1830;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,30:58:99:804,0,801:11,17,14,16 chr1 180917275 . A G 3442.05 PASS AC=1;AF=0.58;AN=2;DP=1994;MQ=60;set=variant3-variant6-variant7-variant8-variant10-variant13-variant15-variant16-variant18-variant19-variant21-variant22-variant26-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,47:96:99:1249,0,1232:24,25,23,24 chr1 180917342 . G A 706.94 PASS AC=1;AF=0.5;AN=2;DP=818;MQ=60;set=variant7-variant10-variant16-variant18-variant22-variant30-variant33-variant35-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:45,45:90:99:1198,0,1211:21,24,25,20 chr1 180918340 . C G 2831.05 PASS AC=2;AF=1;AN=2;DP=4887;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,127:127:99:3988,381,0:0,0,62,65 chr1 180918705 . C G 2472.2 PASS AC=1;AF=0.716;AN=2;DP=2926;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:63,34:97:99:666,0,1439:31,32,16,18 chr1 180920026 . T C 2185.49 PASS AC=1;AF=0.795;AN=2;DP=3191;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:35,29:64:99:685,0,799:18,17,19,10 chr1 180920177 . A G 3652.56 PASS AC=1;AF=0.795;AN=2;DP=4428;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:48,63:111:99:1476,0,1047:24,24,28,35 chr1 180920534 . G A 535.67 PASS AC=1;AF=0.5;AN=2;DP=744;FractionInformativeReads=1;MQ=60;set=variant6-variant7-variant10-variant12-variant15-variant16-variant18-variant21-variant22-variant29-variant30-variant33-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:35,32:67:99:906,0,956:21,14,17,15 chr1 180933498 . C T 1404.53 PASS AC=1;AF=0.737;AN=2;DP=1810;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,22:42:99:578,0,630:18,2,16,6 chr1 180974596 . C T 560.17 PASS AC=1;AF=0.5;AN=2;DP=57;FS=1.064;FractionInformativeReads=1;MQ=60;MQRankSum=0.789;QD=9.83;ReadPosRankSum=1.635;SOR=0.96;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:34,23:57:99:588,0,857:14,20,8,15 chr1 181018096 . T C 1601.65 PASS AC=1;AF=0.5;AN=2;DP=1541;set=variant3-variant5-variant9-variant12-variant14-variant16-variant22-variant26-variant28-variant33-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:83,71:154:99:1631,0,1903:48,35,42,29 chr1 181022517 . CAA CA,C,CAAA 377.49 PASS AC=1,0,0;AF=0.521,0.021,0.021;AN=2;DP=537;set=variant3-variant4-variant5-variant6-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant20-variant21-variant25-variant26-variant28-variant31-variant32-variant33-filterInvariant35-variant38-variant40-variant41-variant42 GT:DP:GQ:SB 0/1:18:69:10,3,3,2 chr1 181057874 . T G 7639.5 PASS AC=1;AF=0.744;AN=2;DP=9609;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:149,132:281:99:3247,0,3481:76,73,65,67 chr1 181058643 . A G 1336.9 PASS AC=2;AF=0.989;AN=2;DP=1389;FractionInformativeReads=1;MQ=60;MQRankSum=0;ReadPosRankSum=1.448;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:1586,141,0:0,0,22,25 chr1 181144597 . C G 331.12 PASS AC=1;AF=0.548;AN=2;DP=538;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant8-variant9-variant10-variant12-variant13-variant15-variant20-variant21-variant23-variant25-variant27-variant28-variant33-variant35-variant36-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,17:25:99:471,0,222:2,6,6,11 chr1 181452637 . CTTT C,CTT,CTTTT 32.04 PASS AC=0,1,0;AF=0.056,0.389,0.056;AN=2;DP=204;set=variant-variant2-filterInvariant4-variant20-variant23-variant26-variant29-variant35-filterInvariant36 GT:DP:GQ:SB 0/2:20:99:7,2,9,2 chr1 181549547 . T G 69.14 PASS AC=1;AF=0.703;AN=2;DP=808;MQ=60;set=variant3-variant4-variant5-variant6-variant9-variant10-variant12-variant13-variant14-variant16-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,11:17:99:402,0,215:6,0,10,1 chr1 181684605 . A G 731.08 PASS AC=2;AF=0.814;AN=2;DP=3113;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1495,147,0:0,0,20,29 chr1 181685432 . TA T,TAA 41.33 PASS AC=0,1;AF=0.075,0.45;AN=2;DP=311;set=variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant29-variant35-variant36-variant37-variant43 GT:DP:GQ:SB 0/2:9:7:0,2,2,5 chr1 181686216 . T C 1740.39 PASS AC=1;AF=0.744;AN=2;DP=6537;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:106,104:210:99:2587,0,2517:64,42,65,39 chr1 181688868 . G A 721.02 PASS AC=1;AF=0.5;AN=2;DP=263;FractionInformativeReads=1;MQ=60;set=variant4-variant24-variant27-variant31-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:34,25:59:99:657,0,846:18,16,16,9 chr1 181701799 . T A 2841.25 PASS AC=1;AF=0.5;AN=2;DP=1085;MQ=60;set=variant4-variant24-variant27-variant31-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:107,103:210:99:2641,0,2872:49,58,53,50 chr1 181706685 . C T 907.5 PASS AC=1;AF=0.563;AN=2;DP=609;FractionInformativeReads=1;MQ=60;set=variant4-variant13-variant18-variant24-variant27-variant31-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:47,39:86:99:851,0,1294:31,16,24,15 chr1 181708168 . A G 514.47 PASS AC=1;AF=0.556;AN=2;DP=325;FractionInformativeReads=1;MQ=60;set=variant4-variant13-variant18-variant24-variant27-variant31-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:15,22:37:99:692,0,464:13,2,18,4 chr1 181719679 . C T 884.14 PASS AC=1;AF=0.625;AN=2;DP=3168;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,47:91:99:1120,0,996:19,25,22,25 chr1 181721016 . C T 1208.97 PASS AC=1;AF=0.5;AN=2;DP=97;FS=2.717;FractionInformativeReads=1;MQ=60;MQRankSum=-2.205;QD=12.46;ReadPosRankSum=1.281;SOR=0.429;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:47,50:97:99:1237,0,1208:30,17,28,22 chr1 181725110 . T C 842.15 PASS AC=1;AF=0.521;AN=2;DP=2226;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant13-variant14-variant15-variant17-variant18-variant24-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:46,33:79:99:708,0,977:26,20,16,17 chr1 181726413 . G A 246.92 PASS AC=2;AF=0.814;AN=2;DP=1059;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:959,78,0:0,0,7,19 chr1 181727030 . A T 1796.69 PASS AC=1;AF=0.5;AN=2;DP=4029;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant14-variant15-variant17-variant24-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:110,87:197:99:2015,0,2791:55,55,42,45 chr1 181727273 . G A 595.08 PASS AC=1;AF=0.613;AN=2;DP=2418;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,57:112:99:1345,0,1396:22,33,27,30 chr1 181731667 . T TC 790.99 PASS AC=1;AF=0.5;AN=2;DP=1524;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant14-variant15-variant17-variant24-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:46,26:72:99:719,0,1317:29,17,20,6 chr1 181731940 . A G 1738.2 PASS AC=1;AF=0.5;AN=2;DP=499;MQ=60;set=variant3-variant6-variant16-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:52,60:112:99:1437,0,1404:18,34,26,34 chr1 181732695 . A G 324.16 PASS AC=1;AF=0.5;AN=2;DP=1468;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant14-variant15-variant17-variant24-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:49,43:92:99:1049,0,1094:20,29,17,26 chr1 181741301 . C T 1562.65 PASS AC=1;AF=0.523;AN=2;DP=4061;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant14-variant15-variant17-variant24-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:100,100:200:99:2564,0,2397:61,39,53,47 chr1 181745580 . G A 621.75 PASS AC=1;AF=0.523;AN=2;DP=1561;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant14-variant15-variant17-variant24-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:42,53:95:99:1253,0,1141:15,27,21,32 chr1 181750469 . G T 943.44 PASS AC=1;AF=0.603;AN=2;DP=1458;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant35-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,35:63:99:893,0,734:17,11,20,15 chr1 181752769 . AT ATT,A 628.85 PASS AC=1,0;AF=0.532,0.016;AN=2;DP=1816;set=variant-filterInvariant2-variant3-variant4-variant5-variant6-variant7-variant9-filterInvariant10-variant11-variant12-variant14-variant15-variant16-variant17-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant35-variant37-variant38-variant39-variant40-variant44 GT:DP:GQ:SB 0/1:49:99:13,13,16,7 chr1 181752783 . T TG,TTG 498.01 PASS AC=1,0;AF=0.5,0.045;AN=2;DP=709;MQ=60;set=variant9-variant15-variant18-variant24-variant27-variant34-variant35-variant36-variant41-variant42-variant43 GT:DP:GQ:SB 0/1:65:99:22,13,12,18 chr1 181752923 . AAGCTT A 1318.59 PASS AC=2;AF=0.775;AN=2;DP=3596;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,99:99:99:4370,298,0:0,0,42,57 chr1 181754314 . G C 90.96 PASS AC=1;AF=0.545;AN=2;DP=134;FractionInformativeReads=1;MQ=60;set=variant9-variant15-variant18-variant24-variant27-variant34-variant35-variant36-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,3:8:99:103,0,158:3,2,2,1 chr1 181754803 . C T 1798.79 PASS AC=1;AF=0.545;AN=2;DP=1652;FractionInformativeReads=1;MQ=60;set=variant9-variant15-variant18-variant24-variant27-variant34-variant35-variant36-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:75,96:171:99:2271,0,1580:44,31,55,41 chr1 181759443 . T TTA,TA,TTTA 101.44 PASS AC=0,0,1;AF=0.167,0.222,0.111;AN=2;DP=183;MQ=60;set=variant9-variant14-variant15-variant16-variant17-variant18-variant24-variant35-variant36 GT:DP:GQ:SB 0/3:18:99:9,3,5,1 chr1 181759473 . T A 719.62 PASS AC=1;AF=0.545;AN=2;DP=519;MQ=60;set=variant9-variant15-variant18-variant24-variant27-variant34-variant35-variant36-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:31,26:57:99:755,0,840:21,10,20,6 chr1 181759657 . G A 1986.51 PASS AC=1;AF=0.603;AN=2;DP=4278;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant35-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:86,96:182:99:2444,0,1981:37,49,49,47 chr1 181768947 . C CAG 703.27 PASS AC=2;AF=0.782;AN=2;DP=1818;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:2726,184,0:0,0,31,28 chr1 181768985 . G A 827.97 PASS AC=2;AF=0.763;AN=2;DP=2163;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:2502,227,0:0,0,45,31 chr1 181770735 . G T 1404.74 PASS AC=1;AF=0.667;AN=2;DP=584;MQ=60;set=variant2-variant5-variant7-variant10-variant11-variant13-variant14-variant18-variant23-variant24-variant25-variant27-variant29-variant33-variant34-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:22,19:41:99:427,0,611:13,9,8,11 chr1 181771225 . C T 611.1 PASS AC=1;AF=0.6;AN=2;DP=1153;MQ=60;set=variant-variant3-variant4-variant6-variant12-variant16-variant21-variant22-variant23-variant25-variant26-variant29-variant30-variant31-variant32-variant35-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,30:57:99:734,0,674:14,13,14,16 chr1 181771834 . A C 988.84 PASS AC=2;AF=0.75;AN=2;DP=3750;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,127:127:99:3952,381,0:0,0,60,67 chr1 181772300 . C T 1300.53 PASS AC=1;AF=0.6;AN=2;DP=1912;MQ=60;set=variant-variant3-variant4-variant6-variant12-variant16-variant21-variant22-variant23-variant25-variant26-variant29-variant30-variant31-variant32-variant35-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,58:109:99:1681,0,1262:26,25,31,27 chr1 181772714 . G C 1267.1 PASS AC=1;AF=0.5;AN=2;DP=432;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant16-variant31-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:38,35:73:99:846,0,1035:17,21,17,18 chr1 181773948 . A G 3932.46 PASS AC=1;AF=0.6;AN=2;DP=4071;MQ=60;set=variant-variant3-variant4-variant6-variant12-variant16-variant21-variant22-variant23-variant25-variant26-variant29-variant30-variant31-variant32-variant35-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:124,94:218:99:2444,0,3235:48,76,40,54 chr1 181774018 . A G 1372.62 PASS AC=1;AF=0.5;AN=2;DP=1223;MQ=60;set=variant2-variant11-variant13-variant18-variant23-variant24-variant27-variant34-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:72,77:149:99:2090,0,1694:35,37,33,44 chr1 181774271 . C G 1589.77 PASS AC=2;AF=0.706;AN=2;DP=3255;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,123:123:99:4242,369,0:0,0,55,68 chr1 181774370 . A C 2669.3 PASS AC=2;AF=0.8;AN=2;DP=5739;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,156:156:99:5374,468,0:0,0,98,58 chr1 181775052 . C A 64.62 PASS AC=2;AF=0.8;AN=2;DP=1529;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1108,105,0:0,0,13,22 chr1 181776078 . A AG 1234.07 PASS AC=2;AF=1;AN=2;DP=1699;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:1004,81,0:0,0,8,19 chr1 181776264 . TA TAA,T,TAAA 191.68 PASS AC=1,0,0;AF=0.485,0.03,0.03;AN=2;DP=1897;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant13-variant14-filterInvariant16-variant18-variant21-variant22-filterInvariant23-variant25-variant26-filterInvariant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-filterInvariant44 GT:DP:GQ:SB 0/1:38:99:11,8,10,9 chr1 182350896 . C G 3103.69 PASS AC=1;AF=0.794;AN=2;DP=5183;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,69:137:99:1945,0,1907:48,20,50,19 chr1 182350909 . C T 3434.27 PASS AC=1;AF=0.6;AN=2;DP=3581;MQ=60;set=variant-variant9-variant10-variant12-variant15-variant16-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant30-variant33-variant34-variant35-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:76,87:163:99:2341,0,2015:52,24,61,26 chr1 182351233 . G A 4006.98 PASS AC=1;AF=0.794;AN=2;DP=9429;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:122,120:242:99:2847,0,3005:57,65,58,62 chr1 182351422 . A G 1649.51 PASS AC=2;AF=1;AN=2;DP=3080;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,85:85:99:2722,253,0:0,0,45,40 chr1 182351627 . T A 4271.33 PASS AC=2;AF=0.909;AN=2;DP=4338;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,98:98:99:4483,301,0:0,0,55,43 chr1 182351630 . T TAAATGA 4566.23 PASS AC=2;AF=0.92;AN=2;DP=4415;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,100:100:99:4562,306,0:0,0,58,42 chr1 182352621 . T C 817.14 PASS AC=1;AF=0.794;AN=2;DP=2374;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,27:77:99:694,0,1315:26,24,12,15 chr1 182353198 . A T 95.61 PASS AC=1;AF=0.794;AN=2;DP=1297;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,17:37:99:419,0,545:8,12,8,9 chr1 182354850 . A G 330.57 PASS AC=1;AF=0.794;AN=2;DP=1017;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,17:41:99:529,0,870:12,12,8,9 chr1 182355046 . A G 823.87 PASS AC=1;AF=0.794;AN=2;DP=4951;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:91,107:198:99:2369,0,2078:45,46,56,51 chr1 182356247 . T C 109.44 PASS AC=1;AF=0.5;AN=2;DP=126;FractionInformativeReads=1;MQ=60;set=variant9-variant13-variant14-variant19-variant27-variant28-variant35-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:6,4:10:99:150,0,236:6,0,4,0 chr1 182356399 . A G 1466.96 PASS AC=1;AF=0.794;AN=2;DP=3389;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,48:104:99:1061,0,1268:31,25,23,25 chr1 182359578 . A C 95.31 PASS AC=1;AF=0.8;AN=2;DP=530;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,4:15:94:94,0,320:7,4,2,2 chr1 182360169 . T G 543.31 PASS AC=1;AF=0.794;AN=2;DP=1509;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,12:33:99:360,0,575:10,11,8,4 chr1 182360202 . A C 861.93 PASS AC=1;AF=0.794;AN=2;DP=1935;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,14:44:99:428,0,937:18,12,12,2 chr1 182360223 . G T 868.51 PASS AC=1;AF=0.794;AN=2;DP=2377;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,13:48:99:301,0,1044:22,13,12,1 chr1 182360315 . C T 1359.08 PASS AC=1;AF=0.6;AN=2;DP=2979;MQ=60;set=variant-variant9-variant10-variant12-variant15-variant16-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant30-variant33-variant34-variant35-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:95,60:155:99:1283,0,2445:57,38,34,26 chr1 182360632 . A G 4027.68 PASS AC=2;AF=0.898;AN=2;DP=5809;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,126:126:99:3903,377,0:0,0,58,68 chr1 182360843 . C G 1628.32 PASS AC=2;AF=0.92;AN=2;DP=2974;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2310,210,0:0,0,29,41 chr1 182360930 . A G 1324.68 PASS AC=2;AF=0.92;AN=2;DP=2114;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1565,146,0:0,0,18,31 chr1 182361478 . T C 485.57 PASS AC=2;AF=0.902;AN=2;DP=370;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:338,33,0:0,0,3,8 chr1 182367548 . G A 1928.73 PASS AC=1;AF=0.794;AN=2;DP=4630;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:73,69:142:99:1543,0,1944:26,47,31,38 chr1 182367643 . A G 634.2 PASS AC=1;AF=0.794;AN=2;DP=1565;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,20:44:99:602,0,679:11,13,8,12 chr1 182367877 . C G 1994.72 PASS AC=1;AF=0.5;AN=2;DP=1850;MQ=60;set=variant-variant9-variant13-variant14-variant19-variant27-variant28-variant35-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:105,71:176:99:1723,0,4015:51,54,33,38 chr1 182367893 . A G 2267.5 PASS AC=1;AF=0.794;AN=2;DP=7196;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:73,104:177:99:2464,0,2614:33,40,46,58 chr1 182369078 . G A 3157.46 PASS AC=2;AF=0.909;AN=2;DP=6398;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,162:162:99:5082,485,0:0,0,89,73 chr1 182369233 . A G 2847.08 PASS AC=1;AF=0.794;AN=2;DP=9525;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:163,113:276:99:2754,0,4319:93,70,59,54 chr1 182369738 . G A 489.03 PASS AC=2;AF=0.909;AN=2;DP=1240;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,31:31:93:1024,93,0:0,0,9,22 chr1 182429728 . T C 694.02 PASS AC=2;AF=0.692;AN=2;DP=2103;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1510,137,0:0,0,29,17 chr1 182441446 . G A 2616.37 PASS AC=1;AF=0.75;AN=2;DP=142;FractionInformativeReads=1;MQ=60;MQRankSum=0.761;ReadPosRankSum=-1.106;set=variant20-variant35 GT:AD:DP:GQ:PL:SB 0/1:27,40:67:99:1243,0,751:19,8,32,8 chr1 182441835 . C A 2057.8 PASS AC=1;AF=0.75;AN=2;DP=133;FractionInformativeReads=1;MQ=60;MQRankSum=1.298;ReadPosRankSum=1.271;set=variant20-variant35 GT:AD:DP:GQ:PL:SB 0/1:30,34:64:99:828,0,787:10,20,13,21 chr1 182443014 . G C 3991.65 PASS AC=1;AF=0.75;AN=2;DP=287;FractionInformativeReads=1;MQ=60;MQRankSum=0.83;ReadPosRankSum=1.665;set=variant20-variant35 GT:AD:DP:GQ:PL:SB 0/1:79,82:161:99:2065,0,2121:36,43,40,42 chr1 182443462 . T C 1397.59 PASS AC=1;AF=0.685;AN=2;DP=2713;MQ=60;set=variant3-variant4-variant5-variant6-variant8-variant10-variant12-variant13-variant18-variant19-variant20-variant22-variant25-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,69:123:99:1800,0,1290:28,26,30,39 chr1 182491107 . A C 1107.38 PASS AC=1;AF=0.886;AN=2;DP=1261;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:16,18:34:99:483,0,492:14,2,13,5 chr1 182496829 . A G 1146.38 PASS AC=1;AF=0.615;AN=2;DP=2691;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant14-variant15-variant16-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant34-variant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,57:118:99:1426,0,1565:23,38,24,33 chr1 182501933 . C A 5592.27 PASS AC=1;AF=0.736;AN=2;DP=6474;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:114,97:211:99:2120,0,2634:56,58,50,47 chr1 182502033 . G T 3237.63 PASS AC=1;AF=0.86;AN=2;DP=3704;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,49:107:99:1259,0,1525:18,40,16,33 chr1 182509269 . G A 1588.09 PASS AC=1;AF=0.875;AN=2;DP=1728;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:14,18:32:99:714,0,953:11,3,12,6 chr1 182509292 . A G 652.15 PASS AC=1;AF=0.643;AN=2;DP=2033;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,31:57:99:1087,0,1273:19,7,23,8 chr1 182509617 . C A 192.1 PASS AC=1;AF=0.643;AN=2;DP=729;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,14:27:99:453,0,442:1,12,2,12 chr1 182517238 . C A 103.54 PASS AC=1;AF=0.68;AN=2;DP=152;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant15-variant16-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:2,4:6:74:118,0,74:1,1,3,1 chr1 182517357 . G C 376.07 PASS AC=1;AF=0.643;AN=2;DP=1186;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,16:33:99:449,0,440:12,5,12,4 chr1 182529584 . T C 468.03 PASS AC=1;AF=0.5;AN=2;DP=276;FractionInformativeReads=1;MQ=60;set=variant13-variant20-variant21-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:41,32:73:99:659,0,850:19,22,17,15 chr1 182542826 . G A 9463.11 PASS AC=2;AF=0.989;AN=2;DP=9411;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:2,210:212:99:6411,585,0:1,1,127,83 chr1 182543175 . G A 7371.26 PASS AC=2;AF=0.989;AN=2;DP=8740;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,209:209:99:6900,626,0:0,0,82,127 chr1 182544220 . TA T 113.47 PASS AC=1;AF=0.5;AN=2;DP=35;FractionInformativeReads=1;MQ=60;set=variant20-variant35 GT:AD:DP:GQ:PL:SB 0/1:10,13:23:99:418,0,305:7,3,7,6 chr1 182544815 . T C 1151.44 PASS AC=1;AF=0.596;AN=2;DP=1000;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant18-variant19-variant22-variant24-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,18:34:99:573,0,416:5,11,4,14 chr1 182549019 . A G 2285.32 PASS AC=1;AF=0.886;AN=2;DP=6930;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:83,75:158:99:1815,0,2230:48,35,34,41 chr1 182558398 . T C 1050.25 PASS AC=2;AF=1;AN=2;DP=1323;FS=0;MQ=60;MQRankSum=0.545;ReadPosRankSum=-0.149;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1210,123,0:0,0,18,23 chr1 182568204 . G C 716.98 PASS AC=2;AF=0.943;AN=2;DP=2044;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1305,128,0:0,0,23,20 chr1 182568729 . C G 749.06 PASS AC=2;AF=0.736;AN=2;DP=2064;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:1726,162,0:0,0,28,26 chr1 182569626 . T C 486.88 PASS AC=2;AF=0.955;AN=2;DP=4087;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,102:102:99:3146,306,0:0,0,48,54 chr1 182571003 . C T 295.55 PASS AC=2;AF=0.743;AN=2;DP=682;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:813,66,0:0,0,17,5 chr1 182571277 . C T 999.16 PASS AC=1;AF=0.66;AN=2;DP=2622;MQ=60;set=variant2-variant3-variant4-variant7-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant22-variant25-variant26-variant28-variant30-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:64,48:112:99:1116,0,1666:32,32,23,25 chr1 182573227 . T C 1970.84 PASS AC=2;AF=0.955;AN=2;DP=6551;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,178:178:99:5520,533,0:0,0,113,65 chr1 182778094 . TAA TA,T,TAAA 45.51 PASS AC=1,0,0;AF=0.425,0.05,0.025;AN=2;DP=511;MQ=60;set=filterInvariant5-variant6-filterInvariant8-variant10-variant12-filterInvariant17-variant19-variant20-variant21-variant27-variant28-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant44 GT:DP:GQ:SB 0/1:34:99:12,6,11,5 chr1 182778367 . G A 2340.89 PASS AC=2;AF=0.989;AN=2;DP=3089;FractionInformativeReads=1;MQRankSum=1.175;ReadPosRankSum=-0.914;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,78:78:99:2227,233,0:0,0,35,43 chr1 182808646 . C G 1339.72 PASS AC=2;AF=0.966;AN=2;DP=2202;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:1884,165,0:0,0,15,40 chr1 182850727 . T C 2730.61 PASS AC=2;AF=0.977;AN=2;DP=2973;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,78:78:99:2667,234,0:0,0,36,42 chr1 182854017 . G A 402.69 PASS AC=2;AF=0.768;AN=2;DP=1570;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1154,107,0:0,0,9,27 chr1 182993025 . C T 4834.73 PASS AC=2;AF=0.645;AN=2;DP=12288;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:4,445:449:99:13018,1245,0:3,1,240,205 chr1 183072590 . T C 1534.32 PASS AC=2;AF=0.667;AN=2;DP=7222;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,224:226:99:7135,628,0:1,1,111,113 chr1 183072908 . T C 352.46 PASS AC=2;AF=0.667;AN=2;DP=1746;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:1939,174,0:0,0,20,38 chr1 183077296 . A AG 88.29 PASS AC=2;AF=0.686;AN=2;DP=467;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:727,54,0:0,0,16,2 chr1 183077615 . C T 79.68 PASS AC=2;AF=0.671;AN=2;DP=407;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:720,48,0:0,0,2,14 chr1 183077618 . C T 79.68 PASS AC=2;AF=0.671;AN=2;DP=392;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:720,48,0:0,0,2,14 chr1 183079509 . C T 547.58 PASS AC=2;AF=0.667;AN=2;DP=1061;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:1072,87,0:0,0,24,5 chr1 183079853 . T C 109.87 PASS AC=2;AF=0.667;AN=2;DP=825;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:669,51,0:0,0,5,12 chr1 183084607 . A G 1654.88 PASS AC=2;AF=0.667;AN=2;DP=2779;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,78:78:99:3480,235,0:0,0,47,31 chr1 183084608 . C A 1654.88 PASS AC=2;AF=0.667;AN=2;DP=2802;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,78:78:99:3480,235,0:0,0,47,31 chr1 183085568 . C T 322.67 PASS AC=2;AF=0.667;AN=2;DP=731;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:1013,81,0:0,0,23,4 chr1 183085611 . C CA,CAA 418.09 PASS AC=1,0;AF=0.5,0.086;AN=2;DP=1607;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:56:99:9,2,30,15 chr1 183085696 . A G 1498.44 PASS AC=2;AF=0.667;AN=2;DP=4289;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,112:113:99:3484,328,0:0,1,56,56 chr1 183085755 . A G 1351.87 PASS AC=2;AF=0.667;AN=2;DP=4697;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,113:113:99:3506,339,0:0,0,45,68 chr1 183086757 . A C 2462.35 PASS AC=2;AF=0.667;AN=2;DP=6734;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,186:186:99:5974,557,0:0,0,91,95 chr1 183090751 . A G 396.63 PASS AC=2;AF=0.667;AN=2;DP=1213;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1353,129,0:0,0,29,14 chr1 183093875 . T C 1414.16 PASS AC=2;AF=0.667;AN=2;DP=4662;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,121:121:99:4032,363,0:0,0,59,62 chr1 183094547 . T C 379.19 PASS AC=2;AF=0.667;AN=2;DP=2684;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,96:96:99:2901,288,0:0,0,56,40 chr1 183094802 . G A 91.65 PASS AC=2;AF=0.645;AN=2;DP=558;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:571,57,0:0,0,7,12 chr1 183095185 . TAA T,TA 530.44 PASS AC=2,0;AF=0.653,0.014;AN=2;DP=1095;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-filterInvariant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:29:87:0,0,20,9 chr1 183095234 . A G 189.72 PASS AC=2;AF=0.667;AN=2;DP=1740;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1764,168,0:0,0,35,21 chr1 183095477 . G A 235.9 PASS AC=2;AF=0.667;AN=2;DP=1386;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1041,102,0:0,0,11,23 chr1 183096253 . T TATA 313.55 PASS AC=2;AF=0.657;AN=2;DP=477;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:45:665,45,0:0,0,14,0 chr1 183096634 . G A 291.29 PASS AC=2;AF=0.667;AN=2;DP=912;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,29:30:80:996,80,0:0,1,7,22 chr1 183096668 . C T 136.72 PASS AC=2;AF=0.682;AN=2;DP=450;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant35-variant36-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:727,54,0:0,0,1,17 chr1 183097956 . G GTTA 681.05 PASS AC=2;AF=0.667;AN=2;DP=2028;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:2671,180,0:0,0,25,34 chr1 183098001 . A G 220.07 PASS AC=2;AF=0.667;AN=2;DP=1026;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1185,116,0:0,0,12,27 chr1 183099701 . G A 217.76 PASS AC=2;AF=0.667;AN=2;DP=1298;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:501,42,0:0,0,3,11 chr1 183100307 . CA CAAA,CAAAAAA,CAAAA,CAAAAA,C 83.67 PASS AC=0,0,0,2,0;AF=0.091,0.091,0.273,0.136,0.045;AN=2;DP=208;set=variant-variant2-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant18-variant20-variant22-variant25-variant26-variant29-variant30-variant35-variant36-variant42-variant43-variant44 GT:DP:GQ:SB 4/4:9:13:1,0,8,0 chr1 183100555 . T C 704.78 PASS AC=2;AF=0.667;AN=2;DP=1744;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:2075,146,0:0,0,16,32 chr1 183100562 . G GT 696.62 PASS AC=2;AF=0.672;AN=2;DP=1440;set=variant-filterInvariant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:2168,150,0:0,0,11,35 chr1 183100563 . GGT GTGTGTGTGT,GGTGT,GTGTGTGTGTGTGT,GTGTGTGTGTGT,GTGTGTGTGTGTGTGT,GTGTGTGT,GTGTGTGTGTGTGTGTGTGT,GTGTGTGTGTGTGTGTGT,GGTGTGT,G 649.43 PASS AC=0,0,2,0,0,0,0,0,0,0;AF=0.053,0.197,0.224,0.092,0.092,0.039,0.013,0.026,0.026,0.013;AN=2;DP=1674;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant7-variant10-variant11-variant12-variant13-variant16-variant14-variant18-variant19-variant15-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant17-variant37-variant38-variant20-variant40-variant41-variant23-variant42-variant43-variant44 GT:DP:GQ:SB 3/3:43:99:0,0,11,32 chr1 183100596 . A G 271.56 PASS AC=2;AF=0.671;AN=2;DP=678;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:720,48,0:0,0,2,14 chr1 183100598 . T G 271.56 PASS AC=2;AF=0.662;AN=2;DP=628;FractionInformativeReads=1;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:48:720,48,0:0,0,1,14 chr1 183101427 . AAAT A 97.73 PASS AC=2;AF=0.84;AN=2;DP=122;FS=0;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant18-variant19-variant21-variant24-variant25-variant27-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:18:270,18,0:0,0,5,0 chr1 183101444 . A C 106.77 PASS AC=2;AF=0.759;AN=2;DP=193;FS=0;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant18-variant19-variant21-variant24-variant25-variant27-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:39:585,39,0:0,0,11,1 chr1 183101451 . T G 214.55 PASS AC=2;AF=0.72;AN=2;DP=240;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant18-variant19-variant21-variant22-variant25-variant27-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:45:667,45,0:0,0,13,1 chr1 183101471 . G A 361.76 PASS AC=2;AF=0.677;AN=2;DP=497;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant18-variant19-variant21-variant22-variant24-variant25-variant27-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:843,63,0:0,0,17,4 chr1 183101686 . G A 750.87 PASS AC=2;AF=0.667;AN=2;DP=2763;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,69:69:99:2187,207,0:0,0,31,38 chr1 183104013 . G A 461.98 PASS AC=2;AF=0.636;AN=2;DP=1887;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,69:69:99:2208,207,0:0,0,34,35 chr1 183104340 . AT A 557.86 PASS AC=2;AF=0.667;AN=2;DP=3310;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:1919,205,0:0,0,25,43 chr1 183105324 . C T 139.94 PASS AC=2;AF=0.667;AN=2;DP=571;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:504,39,0:0,0,11,2 chr1 183105399 . C G 767.37 PASS AC=2;AF=0.681;AN=2;DP=2061;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:1755,171,0:0,0,37,20 chr1 183105534 . T C 1160.08 PASS AC=2;AF=0.667;AN=2;DP=3980;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,115:115:99:3421,343,0:0,0,58,57 chr1 183105705 . G A 491.02 PASS AC=2;AF=0.636;AN=2;DP=1321;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:1680,162,0:0,0,17,37 chr1 183106739 . G A 202.81 PASS AC=2;AF=0.667;AN=2;DP=893;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:829,78,0:0,0,18,8 chr1 183112041 . G C 406.39 PASS AC=2;AF=0.667;AN=2;DP=1972;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:1860,164,0:0,0,28,27 chr1 183112412 . A G 1559.09 PASS AC=2;AF=0.667;AN=2;DP=3467;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,103:103:99:3304,309,0:0,0,55,48 chr1 183112505 . T C 3125.01 PASS AC=2;AF=0.667;AN=2;DP=6756;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,181:181:99:5523,541,0:0,0,96,85 chr1 183112566 . T C 3607.03 PASS AC=2;AF=0.667;AN=2;DP=9338;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,269:269:99:8224,804,0:0,0,150,119 chr1 183112764 . A G 3881.27 PASS AC=2;AF=0.667;AN=2;DP=9622;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,251:252:99:7730,722,0:1,0,102,149 chr1 183113862 . C T 575.08 PASS AC=2;AF=0.667;AN=2;DP=1707;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1476,138,0:0,0,23,23 chr1 183113952 . A G 570.49 PASS AC=2;AF=0.667;AN=2;DP=1893;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1764,168,0:0,0,35,21 chr1 183114119 . C T 766.87 PASS AC=2;AF=0.667;AN=2;DP=2414;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:2206,203,0:0,0,34,34 chr1 183114146 . T C 727.08 PASS AC=2;AF=0.667;AN=2;DP=2435;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:2353,213,0:0,0,38,33 chr1 183114634 . G A 1868.18 PASS AC=2;AF=0.667;AN=2;DP=5020;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,138:138:99:4550,411,0:0,0,38,100 chr1 183114797 . A G 130.7 PASS AC=2;AF=0.724;AN=2;DP=228;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant11-variant12-variant15-variant16-variant19-variant20-variant21-variant22-variant24-variant25-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:345,27,0:0,0,1,8 chr1 183155482 . C A 1569.99 PASS AC=2;AF=0.65;AN=2;DP=2664;set=variant2-variant4-variant7-variant8-variant9-variant11-variant12-variant16-variant19-variant20-variant22-variant25-variant26-variant29-variant31-variant35-variant36-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,139:139:99:4287,414,0:0,0,77,62 chr1 183155700 . C A 1817.33 PASS AC=2;AF=0.65;AN=2;DP=2855;MQ=60;set=variant2-variant4-variant7-variant8-variant9-variant11-variant12-variant16-variant19-variant20-variant22-variant25-variant26-variant29-variant31-variant35-variant36-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,186:186:99:5395,554,0:0,0,75,111 chr1 183155715 . CT C 2077.74 PASS AC=2;AF=0.672;AN=2;DP=3526;MQ=60;set=variant2-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant29-variant31-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,166:166:99:7394,503,0:0,0,62,104 chr1 183155717 . C A 2086.73 PASS AC=2;AF=0.672;AN=2;DP=3480;MQ=60;set=variant2-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant29-variant31-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,167:167:99:7394,503,0:0,0,62,105 chr1 183155778 . A C 377.97 PASS AC=2;AF=0.672;AN=2;DP=1017;MQ=60;set=variant2-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant29-variant31-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:2083,162,0:0,0,8,46 chr1 183176970 . GT G,GTTT,GTT,GTTTT,GTTTTT 229.72 PASS AC=0,1,1,0,0;AF=0.09,0.231,0.244,0.013,0.026;AN=2;DP=3357;set=filterInvariant-variant2-variant3-variant4-filterInvariant5-filterInvariant6-variant7-variant8-variant9-filterInvariant10-variant12-variant13-filterInvariant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-filterInvariant28-variant29-variant31-filterInvariant32-variant33-filterInvariant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 3/2:86:99:8,3,43,32 chr1 183177218 . A G 471.52 PASS AC=2;AF=0.731;AN=2;DP=1064;MQ=60;set=variant2-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant15-variant16-variant17-variant19-variant20-variant22-variant25-variant26-variant29-variant31-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1636,132,0:0,0,10,34 chr1 183184663 . G A 2189.99 PASS AC=1;AF=0.5;AN=2;DP=285;FractionInformativeReads=1;MQ=60;set=variant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:69,57:126:99:1481,0,1894:40,29,35,22 chr1 183205523 . CAAAA CAA,CAAA,CA,C 115.33 PASS AC=2,0,0,0;AF=0.333,0.217,0.1,0.017;AN=2;DP=385;set=variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant20-variant22-variant24-variant25-variant26-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:DP:GQ:SB 1/1:12:27:0,1,10,1 chr1 183213281 . G T 3061.96 PASS AC=1;AF=0.5;AN=2;DP=1875;MQ=60;set=variant7-variant12-variant19-variant22-variant35-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:137,145:282:99:3280,0,3327:74,63,74,71 chr1 183217574 . G A 586.5 PASS AC=1;AF=0.5;AN=2;DP=64;FS=0.995;FractionInformativeReads=1;MQ=60;MQRankSum=0.308;QD=9.16;ReadPosRankSum=-0.504;SOR=0.657;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:41,23:64:99:615,0,1144:19,22,12,11 chr1 183218026 . AGTGTGTGT AGTGT,AGTGTGT,AGTGTGTGTGTGT,AGTGTGTGTGT,A,AGT 461.76 PASS AC=0,1,0,0,0,0;AF=0.052,0.414,0.034,0.034,0.034,0.017;AN=2;DP=698;set=variant-variant2-variant4-variant6-variant8-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant27-variant28-variant29-variant30-filterInvariant31-variant33-variant35-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:14:99:5,1,6,2 chr1 183218817 . CGTGTGTGTGTGTGT CGTGT,CGTGTGTGTGT,C,CGTGTGT,CGTGTGTGTGTGTGTGT,CGTGTGTGT,CGTGTGTGTGTGT,CGTGTGTGTGTGTGTGTGTGTGT 376.05 PASS AC=0,0,0,0,0,0,1,0;AF=0.054,0.071,0.054,0.071,0.179,0.071,0.125,0.036;AN=2;DP=867;set=variant2-variant3-variant4-variant6-variant8-variant9-variant10-filterInvariant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant25-variant26-variant29-variant30-filterInvariant32-variant33-filterInvariant35-variant37-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/7:10:71:1,5,1,3 chr1 183229954 . CAAAA CAAA,CAAAAA,CAA,CA,C 52.1 PASS AC=0,0,1,0,0;AF=0.2,0.04,0.22,0.12,0.02;AN=2;DP=347;set=variant-variant3-variant6-variant7-variant9-variant10-variant11-variant12-variant16-variant18-variant19-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant29-variant31-variant34-variant35-variant36-variant37-variant43 GT:DP:GQ:SB 0/3:12:23:1,1,10,0 chr1 183259603 . T G 89.17 PASS AC=1;AF=0.548;AN=2;DP=194;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant9-variant12-variant15-variant16-variant20-variant22-variant24-variant25-variant26-variant30-variant31-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:2,8:10:61:323,0,61:0,2,1,7 chr1 183261710 . A G 149.07 PASS AC=2;AF=0.647;AN=2;DP=1568;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant7-variant8-variant9-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,69:70:99:2185,164,0:1,0,47,22 chr1 183273751 . C T 530.75 PASS AC=1;AF=0.583;AN=2;DP=541;FractionInformativeReads=1;MQ=60;set=variant-variant7-variant12-variant14-variant19-variant22-variant24-variant27-variant31-variant33-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,28:40:99:850,0,374:11,1,21,7 chr1 183471295 . G T 412.66 PASS AC=1;AF=0.884;AN=2;DP=560;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,10:22:99:331,0,354:10,2,9,1 chr1 183481943 . CTTT CTT,CTTTT,CT,C 211.04 PASS AC=1,0,0,0;AF=0.333,0.13,0.037,0.019;AN=2;DP=1359;set=variant5-variant6-variant7-variant10-filterInvariant11-variant14-filterInvariant15-variant16-variant17-variant19-variant20-variant22-filterInvariant23-filterInvariant24-variant25-variant26-variant27-filterInvariant28-variant31-variant33-filterInvariant34-variant35-filterInvariant37-variant39-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:40:99:13,9,8,10 chr1 183486859 . G A 3569.45 PASS AC=1;AF=0.872;AN=2;DP=5932;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:81,75:156:99:1703,0,1832:44,37,42,33 chr1 183524855 . C A 9375.79 PASS AC=1;AF=0.884;AN=2;DP=11842;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:174,139:313:99:2955,0,4167:84,90,67,72 chr1 183525452 . T G 4670.67 PASS AC=1;AF=0.884;AN=2;DP=5384;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,84:144:99:2040,0,1551:26,34,38,46 chr1 183617266 . C G 2372.73 PASS AC=2;AF=0.643;AN=2;DP=2362;MQ=60;set=variant-variant4-variant8-variant11-variant15-variant16-variant21-variant22-variant24-variant25-variant27-variant35-variant37-variant38 GT:AD:DP:GQ:PL:SB 1/1:2,173:175:99:5342,475,0:1,1,93,80 chr1 183711483 . C T 2625.17 PASS AC=2;AF=0.717;AN=2;DP=2357;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant32-variant34-variant35-variant36-variant37-variant38-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,61:61:99:1848,182,0:0,0,24,37 chr1 183774241 . C T 453.31 PASS AC=1;AF=0.5;AN=2;DP=39;FS=5.217;FractionInformativeReads=1;MQ=60;MQRankSum=1.11;QD=11.62;ReadPosRankSum=0.66;SOR=0.185;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:19,20:39:99:482,0,587:15,4,12,8 chr1 183816683 . G T 162.12 PASS AC=1;AF=0.583;AN=2;DP=185;FractionInformativeReads=1;MQ=60;set=variant-variant7-variant9-variant12-variant13-variant16-variant27-variant28-variant29-variant31-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:12,10:22:99:246,0,337:10,2,6,4 chr1 183852914 . G C 3734.1 PASS AC=2;AF=0.661;AN=2;DP=3187;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant26-variant27-variant28-variant30-variant31-variant33-variant35-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,157:157:99:4605,470,0:0,0,86,71 chr1 183857394 . A G 279.58 PASS AC=2;AF=0.708;AN=2;DP=341;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:244,21,0:0,0,5,2 chr1 183861007 . G A 635.3 PASS AC=2;AF=0.625;AN=2;DP=375;FractionInformativeReads=1;MQ=60;set=variant-variant8-variant9-variant10-variant12-variant16-variant17-variant19-variant20-variant26-variant27-variant30-variant31-variant33-variant35-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:991,84,0:0,0,21,7 chr1 183866849 . G T 2097.1 PASS AC=2;AF=0.618;AN=2;DP=981;FractionInformativeReads=1;MQ=60;set=variant-variant8-variant9-variant10-variant11-variant12-variant16-variant17-variant19-variant20-variant26-variant27-variant30-variant31-variant33-variant35-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:1992,171,0:0,0,44,13 chr1 183871637 . G A 2621.69 PASS AC=2;AF=0.703;AN=2;DP=1832;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant26-variant27-variant28-variant30-variant31-variant33-variant35-variant36-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:1651,144,0:0,0,35,13 chr1 183876182 . C T 2386.1 PASS AC=2;AF=0.639;AN=2;DP=1953;MQ=60;set=variant-variant8-variant9-variant10-variant11-variant12-variant16-variant17-variant19-variant20-variant26-variant27-variant30-variant31-variant33-variant35-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,137:138:99:4296,403,0:0,1,75,62 chr1 183895178 . G A 1844.96 PASS AC=2;AF=0.7;AN=2;DP=1928;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:1961,174,0:0,0,42,16 chr1 183895721 . C A 3886.16 PASS AC=2;AF=0.7;AN=2;DP=4900;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,120:120:99:3807,360,0:0,0,47,73 chr1 183896961 . T C 9289.99 PASS AC=2;AF=0.729;AN=2;DP=8882;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,282:283:99:8253,835,0:1,0,125,157 chr1 183897297 . TA TAA,T 848.37 PASS AC=1,0;AF=0.479,0.063;AN=2;DP=1782;MQ=60;set=variant-filterInvariant6-filterInvariant7-variant8-variant9-variant10-variant11-variant12-variant16-variant17-variant18-variant19-variant20-filterInvariant23-variant26-variant27-variant30-variant31-variant33-variant35-variant39-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:86:99:7,11,35,33 chr1 183905132 . C CG 410.42 PASS AC=1;AF=0.5;AN=2;DP=817;MQ=60;set=variant6-variant9-variant12-variant15-variant21-variant22-variant25-variant29-variant30-variant33-variant34-variant35-variant36-variant40 GT:AD:DP:GQ:PL:SB 0/1:33,39:72:99:1054,0,842:15,18,21,18 chr1 183905477 . T C 2738.56 PASS AC=1;AF=0.594;AN=2;DP=1007;MQ=60;set=variant-variant8-variant9-variant10-variant12-variant16-variant17-variant19-variant20-variant27-variant30-variant31-variant33-variant35-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,31:56:99:1307,0,1834:15,10,19,12 chr1 183905484 . GAA G 2930.78 PASS AC=1;AF=0.594;AN=2;DP=1061;FractionInformativeReads=1;MQ=60;set=variant-variant8-variant9-variant10-variant12-variant16-variant17-variant19-variant20-variant27-variant30-variant31-variant33-variant35-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,33:60:99:1304,0,1875:17,10,20,13 chr1 183906009 . A G 1105.37 PASS AC=2;AF=0.8;AN=2;DP=1829;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1811,167,0:0,0,30,26 chr1 183906089 . A G 1094.87 PASS AC=1;AF=0.667;AN=2;DP=1892;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,29:74:99:762,0,1056:27,18,12,17 chr1 183906245 . C T 1760.59 PASS AC=1;AF=0.594;AN=2;DP=1211;MQ=60;set=variant-variant8-variant9-variant10-variant12-variant16-variant17-variant19-variant20-variant27-variant30-variant31-variant33-variant35-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,36:86:99:887,0,1329:24,26,23,13 chr1 183906371 . G A 1245.39 PASS AC=1;AF=0.708;AN=2;DP=1836;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,37:68:99:954,0,734:13,18,17,20 chr1 183906614 . G A 423.44 PASS AC=1;AF=0.5;AN=2;DP=427;FractionInformativeReads=1;MQ=60;set=variant6-variant9-variant12-variant15-variant21-variant22-variant25-variant29-variant30-variant33-variant34-variant35-variant36-variant40 GT:AD:DP:GQ:PL:SB 0/1:18,22:40:99:623,0,451:10,8,10,12 chr1 183906925 . T C 1278.13 PASS AC=1;AF=0.708;AN=2;DP=1860;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,30:57:99:708,0,532:13,14,13,17 chr1 183907252 . A G 3560.07 PASS AC=1;AF=0.708;AN=2;DP=3841;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,39:86:99:879,0,1064:25,22,22,17 chr1 183907291 . G A 2817.86 PASS AC=1;AF=0.708;AN=2;DP=3218;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,35:71:99:943,0,1007:15,21,21,14 chr1 183907331 . AT A 825.96 PASS AC=1;AF=0.5;AN=2;DP=1358;set=variant6-variant9-variant12-variant15-variant21-variant22-variant25-variant30-variant33-variant34-variant35-variant36-variant40 GT:AD:DP:GQ:PL:SB 0/1:53,41:94:99:854,0,2083:29,24,21,20 chr1 183907343 . TAAA T,TAA 1313.65 PASS AC=1,0;AF=0.479,0.021;AN=2;DP=2678;set=variant-filterInvariant5-variant8-variant9-variant10-filterInvariant11-variant12-variant13-variant16-variant17-variant19-variant20-variant21-variant26-variant27-filterInvariant28-variant29-variant30-variant31-variant33-variant35-filterInvariant38-variant43-variant44 GT:DP:GQ:SB 0/1:101:99:34,28,22,17 chr1 183907346 . A T,ATTTT,ATT 4020.25 PASS AC=0,1,0;AF=0.431,0.25,0.028;AN=2;DP=3865;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant13-variant26-variant27-variant28-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:104:99:27,22,31,24 chr1 183907415 . G GTGAT 4533.02 PASS AC=1;AF=0.5;AN=2;DP=2991;MQ=60;set=variant6-variant9-variant12-variant15-variant21-variant22-variant25-variant29-variant30-variant33-variant34-variant35-variant36-variant40 GT:AD:DP:GQ:PL:SB 0/1:114,97:211:99:3813,0,4489:60,54,55,42 chr1 183907670 . A G 8872.21 PASS AC=2;AF=0.813;AN=2;DP=10479;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,233:233:99:7103,698,0:0,0,114,119 chr1 183908222 . C T 956.98 PASS AC=1;AF=0.5;AN=2;DP=965;MQ=60;set=variant6-variant9-variant12-variant15-variant21-variant22-variant25-variant29-variant30-variant33-variant34-variant35-variant36-variant40 GT:AD:DP:GQ:PL:SB 0/1:31,42:73:99:1046,0,787:12,19,17,25 chr1 183909717 . G A 1549.87 PASS AC=1;AF=0.5;AN=2;DP=1757;MQ=60;set=variant6-variant9-variant12-variant15-variant21-variant22-variant25-variant29-variant30-variant33-variant34-variant35-variant36-variant40 GT:AD:DP:GQ:PL:SB 0/1:64,67:131:99:1632,0,1612:41,23,42,25 chr1 183909934 . G A 1383.7 PASS AC=1;AF=0.5;AN=2;DP=1239;FractionInformativeReads=1;MQ=60;set=variant6-variant9-variant12-variant15-variant21-variant22-variant25-variant29-variant30-variant33-variant34-variant35-variant36-variant40 GT:AD:DP:GQ:PL:SB 0/1:45,55:100:99:1400,0,1059:19,26,19,36 chr1 183913540 . C T 283.54 PASS AC=1;AF=0.6;AN=2;DP=227;FractionInformativeReads=1;MQ=60;set=variant-variant8-variant10-variant12-variant13-variant16-variant17-variant19-variant27-variant30-variant31-variant35-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,9:12:99:282,0,102:1,2,2,7 chr1 183942950 . C T 277.98 PASS AC=2;AF=0.784;AN=2;DP=460;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:579,51,0:0,0,4,13 chr1 183944089 . A C 417.67 PASS AC=2;AF=0.792;AN=2;DP=423;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:440,30,0:0,0,9,1 chr1 183944444 . C T 454.1 PASS AC=2;AF=0.792;AN=2;DP=467;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:900,84,0:0,0,8,20 chr1 183947757 . G GA 339.45 PASS AC=2;AF=0.806;AN=2;DP=519;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:290,30,0:0,0,1,9 chr1 184006888 . AGTGTGT AGTGTGTGTGTGT,AGTGTGTGT,AGT,AGTGT,AGTGTGTGTGTGTGTGTGTGT,AGTGTGTGTGTGTGTGT,AGTGTGTGTGT,AGTGTGTGTGTGTGTGTGT,AGTGTGTGTGTGTGT,AGTGAGTGTGTGT,A,AGTGTGTGTGTGTGTGTGTGTGTGTGTGT 704.4 PASS AC=0,1,0,0,0,0,0,0,0,0,0,0;AF=0.074,0.147,0.059,0.029,0.029,0.059,0.074,0.059,0.029,0.029,0.029,0.015;AN=2;DP=2351;set=variant-variant2-variant3-variant5-variant6-variant7-filterInvariant10-variant11-variant12-variant13-variant15-filterInvariant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant34-filterInvariant35-variant38-variant39-variant40-variant41-variant43-variant44 GT:DP:GQ:SB 0/2:23:99:1,14,1,7 chr1 184476621 . T C 178.51 PASS AC=1;AF=0.68;AN=2;DP=173;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant10-variant11-variant13-variant14-variant15-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:2,2:4:75:75,0,76:2,0,2,0 chr1 184537506 . ACTC A 955.46 PASS AC=1;AF=0.542;AN=2;DP=590;MQ=60;set=variant-variant4-variant11-variant14-variant19-variant22-variant24-variant29-variant33-variant35-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:25,43:68:99:1696,0,1106:18,7,32,11 chr1 184567463 . G T 885.7 PASS AC=1;AF=0.575;AN=2;DP=941;MQ=60;set=variant-variant4-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant22-variant24-variant27-variant29-variant31-variant32-variant33-variant35-variant37-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:24,39:63:99:930,0,544:14,10,22,17 chr1 184594874 . G A 1622.67 PASS AC=1;AF=0.5;AN=2;DP=113;FS=3.44;FractionInformativeReads=1;MQ=60;MQRankSum=-0.79;QD=14.36;ReadPosRankSum=0.416;SOR=1.039;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:55,58:113:99:1651,0,1594:27,28,24,34 chr1 184596584 . C A 737.31 PASS AC=2;AF=0.63;AN=2;DP=1378;FractionInformativeReads=1;MQ=60;set=variant4-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant30-variant31-variant33-variant35-variant37-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,67:67:99:2077,201,0:0,0,42,25 chr1 184597065 . A G 646.02 PASS AC=1;AF=0.583;AN=2;DP=843;MQ=60;set=variant5-variant6-variant7-variant8-variant11-variant13-variant14-variant15-variant19-variant20-variant21-variant22-variant23-variant25-variant30-variant35-variant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:29,17:46:99:343,0,681:14,15,8,9 chr1 184597866 . T C 1078.54 PASS AC=1;AF=0.522;AN=2;DP=1466;MQ=60;set=variant4-variant6-variant7-variant8-variant11-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant29-variant30-variant33-variant34-variant35-variant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:30,38:68:99:939,0,700:16,14,19,19 chr1 184597980 . G A 1407.13 PASS AC=1;AF=0.5;AN=2;DP=975;MQ=60;set=variant3-variant5-variant10-variant14-variant17-variant27-variant35-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:48,48:96:99:1050,0,1225:26,22,25,23 chr1 184597999 . T C 1829.72 PASS AC=1;AF=0.522;AN=2;DP=2517;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant7-variant8-variant11-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant29-variant30-variant33-variant34-variant35-variant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:49,53:102:99:1296,0,1154:27,22,28,25 chr1 184659254 . C T 284.98 PASS AC=1;AF=0.5;AN=2;DP=58;FractionInformativeReads=1;MQ=60;set=variant4-variant7-variant28-variant33-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:5,5:10:99:146,0,153:4,1,4,1 chr1 184659318 . T A 280.94 PASS AC=1;AF=0.647;AN=2;DP=1590;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,16:34:99:467,0,459:12,6,11,5 chr1 184659545 . T TA 413.56 PASS AC=1;AF=0.647;AN=2;DP=3003;MQ=60;set=variant2-variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,45:93:99:984,0,1035:21,27,18,27 chr1 184660110 . TA T 4901.27 PASS AC=1;AF=0.633;AN=2;DP=11548;MQ=60;set=variant2-variant4-variant7-variant8-variant9-variant10-variant11-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:171,212:383:99:5492,0,4241:70,101,86,126 chr1 184660205 . T A 2209.24 PASS AC=1;AF=0.647;AN=2;DP=4640;MQ=60;set=variant2-variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,66:126:99:1835,0,1630:21,39,21,45 chr1 184661642 . G A 5153.75 PASS AC=1;AF=0.676;AN=2;DP=16672;set=variant2-variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:252,235:487:99:5597,0,6185:125,127,102,133 chr1 184662181 . C T 3470.02 PASS AC=1;AF=0.633;AN=2;DP=8593;MQ=60;set=variant2-variant4-variant7-variant8-variant9-variant10-variant11-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:145,112:257:99:2631,0,3645:75,70,58,54 chr1 184663581 . T C 857.9 PASS AC=1;AF=0.638;AN=2;DP=1755;MQ=60;set=variant2-variant4-variant7-variant8-variant9-variant10-variant11-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,28:67:99:684,0,942:17,22,10,18 chr1 184663643 . TA T 223.13 PASS AC=1;AF=0.638;AN=2;DP=715;MQ=60;set=variant2-variant4-variant7-filterInvariant8-variant9-variant10-variant11-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,11:28:99:258,0,444:4,13,1,10 chr1 184671909 . C A 292.83 PASS AC=1;AF=0.5;AN=2;DP=138;FractionInformativeReads=1;MQ=60;set=variant4-variant7-variant25-variant28-variant33-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:8,14:22:99:354,0,283:8,0,10,4 chr1 184677464 . G A 941.87 PASS AC=1;AF=0.676;AN=2;DP=3085;MQ=60;set=variant2-variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,33:91:99:752,0,1456:22,36,11,22 chr1 184681081 . A G 76.45 PASS AC=1;AF=0.691;AN=2;DP=441;set=variant2-variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,7:18:99:177,0,377:1,10,2,5 chr1 184688237 . C T 481.26 PASS AC=1;AF=0.5;AN=2;DP=153;FractionInformativeReads=1;MQ=60;set=variant4-variant7-variant28-variant33-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:7,17:24:99:457,0,192:7,0,14,3 chr1 184692999 . TAA TAAA,TA,TAAAA,T 90.47 PASS AC=0,0,1,0;AF=0.391,0.094,0.047,0.016;AN=2;DP=1132;set=variant2-variant3-variant4-variant5-variant6-filterInvariant9-variant10-variant11-variant13-variant14-variant15-variant16-filterInvariant19-variant22-variant24-variant25-variant26-filterInvariant27-variant28-filterInvariant29-variant31-filterInvariant32-variant34-variant35-filterInvariant37-variant38-variant39-variant40-variant41-variant42-variant43-filterInvariant44 GT:DP:GQ:SB 0/3:22:99:4,8,5,5 chr1 184695571 . C T 477.41 PASS AC=1;AF=0.676;AN=2;DP=902;MQ=60;set=variant2-variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,15:26:99:464,0,357:2,9,3,12 chr1 184706212 . GT G 670.49 PASS AC=1;AF=0.676;AN=2;DP=2966;MQ=60;set=variant2-variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,37:76:99:1145,0,1215:15,24,14,23 chr1 184706306 . G A 554.59 PASS AC=1;AF=0.5;AN=2;DP=101;FractionInformativeReads=1;MQ=60;set=variant4-variant7-variant28-variant33-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:6,7:13:99:227,0,193:1,5,1,6 chr1 184718601 . G A 836.5 PASS AC=1;AF=0.5;AN=2;DP=425;MQ=60;set=variant4-variant7-variant28-variant33-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:37,41:78:99:791,0,772:20,17,22,19 chr1 184718750 . GAAAAA GAAAA,GAA,GAAAAAA,G,GAAA 34.92 PASS AC=0,1,0,0,0;AF=0.092,0.461,0.013,0.013,0.013;AN=2;DP=1195;set=filterInvariant-variant2-filterInvariant3-variant4-variant5-filterInvariant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-filterInvariant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-filterInvariant40-variant41-variant43-variant44 GT:DP:GQ:SB 0/2:14:99:3,3,3,5 chr1 184760001 . T C 2893.78 PASS AC=1;AF=0.671;AN=2;DP=7454;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:96,99:195:99:2524,0,2495:41,55,45,54 chr1 184760433 . C T 3336.63 PASS AC=1;AF=0.671;AN=2;DP=9524;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:158,152:310:99:3435,0,3885:89,69,81,71 chr1 184760624 . CTT CT,C,CTTT 429.46 PASS AC=1,0,0;AF=0.511,0.068,0.023;AN=2;DP=10111;set=filterInvariant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-filterInvariant11-filterInvariant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-filterInvariant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:156:99:32,39,44,41 chr1 184761093 . CTT CT,C 1348.28 PASS AC=1,1;AF=0.295,0.557;AN=2;DP=6722;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-filterInvariant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 2/1:125:99:2,3,35,85 chr1 184761365 . A G 87.23 PASS AC=1;AF=0.688;AN=2;DP=405;FractionInformativeReads=1;set=variant2-variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,7:12:99:263,0,147:2,3,5,2 chr1 184763525 . A G 1301.44 PASS AC=1;AF=0.671;AN=2;DP=2213;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,25:61:99:599,0,870:16,20,14,11 chr1 184763596 . C T 1610.69 PASS AC=1;AF=0.588;AN=2;DP=2564;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,44:76:99:1172,0,781:17,15,28,16 chr1 184764067 . C G 1366.95 PASS AC=1;AF=0.588;AN=2;DP=4193;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:75,80:155:99:2386,0,2085:41,34,43,37 chr1 184801065 . T C 885.83 PASS AC=2;AF=0.604;AN=2;DP=1869;MQ=60;set=variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant13-variant14-variant17-variant18-variant19-variant21-variant25-variant28-variant31-variant32-variant35-variant36-variant37-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,85:85:99:2433,253,0:0,0,39,46 chr1 184868251 . G A 2671.64 PASS AC=2;AF=0.588;AN=2;DP=1044;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant7-variant11-variant14-variant16-variant17-variant19-variant21-variant31-variant32-variant34-variant35-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:1858,165,0:0,0,42,13 chr1 185014506 . T TC 351.24 PASS AC=2;AF=1;AN=2;DP=1055;FS=0;MQ=60;MQRankSum=1.639;ReadPosRankSum=-0.421;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,28:28:99:1058,99,0:0,0,22,6 chr1 185069540 . A G 2808.8 PASS AC=1;AF=0.5;AN=2;DP=226;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.263;QD=12.43;ReadPosRankSum=3.681;SOR=0.695;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:117,109:226:99:2837,0,2995:43,74,40,69 chr1 185069675 . G GT 3546.91 PASS AC=1;AF=0.537;AN=2;DP=6725;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant22-variant24-variant25-variant30-variant31-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:129,103:232:99:1903,0,2717:71,58,61,42 chr1 185070964 . GTT GTTTTT,GT,G,GTTTTTTTT,GTTT,GTTTTTT,GTTTT 167.51 PASS AC=0,0,0,0,1,0,0;AF=0.214,0.179,0.071,0.018,0.054,0.018,0.018;AN=2;DP=1440;set=variant-filterInvariant2-variant3-filterInvariant4-variant6-variant9-variant11-variant12-filterInvariant13-variant14-variant16-filterInvariant17-variant19-variant20-variant21-filterInvariant23-variant24-variant25-variant27-variant28-filterInvariant29-variant30-variant31-variant32-variant35-variant37-filterInvariant38-filterInvariant39 GT:DP:GQ:SB 0/5:28:99:4,10,6,8 chr1 185087634 . A T 2899.06 PASS AC=1;AF=0.563;AN=2;DP=5024;MQ=60;set=variant-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant18-variant22-variant24-variant25-variant30-variant31-variant35-variant36-variant37-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:87,90:177:99:2329,0,2078:39,48,44,46 chr1 185088697 . T C 4539.46 PASS AC=1;AF=0.54;AN=2;DP=7200;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant22-variant24-variant25-variant30-variant31-variant35-variant36-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:163,144:307:99:3832,0,4263:92,71,88,56 chr1 185094277 . G T 485.22 PASS AC=1;AF=0.538;AN=2;DP=964;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant18-variant22-variant24-variant25-variant30-variant31-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:13,25:38:99:805,0,313:4,9,4,21 chr1 185119794 . C T 408.52 PASS AC=2;AF=1;AN=2;DP=565;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:324,27,0:0,0,3,6 chr1 185121070 . G GA 530.16 PASS AC=1;AF=0.5;AN=2;DP=210;MQ=60;set=variant9-variant12-variant22-variant35 GT:AD:DP:GQ:PL:SB 0/1:25,25:50:99:552,0,550:9,16,9,16 chr1 185135745 . A G 765.41 PASS AC=1;AF=0.558;AN=2;DP=1932;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant18-variant22-variant24-variant25-variant30-variant31-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:39,39:78:99:927,0,859:19,20,17,22 chr1 185137454 . T TAAATGATAGAC 2145.84 PASS AC=1;AF=0.558;AN=2;DP=2121;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant18-variant22-variant24-variant25-variant30-variant31-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:46,26:72:99:926,0,3184:21,25,9,17 chr1 185137461 . A T 2001.71 PASS AC=1;AF=0.558;AN=2;DP=1908;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant18-variant22-variant24-variant25-variant30-variant31-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:48,20:68:99:722,0,3455:19,29,6,14 chr1 185137464 . T TAA 1939.88 PASS AC=1;AF=0.558;AN=2;DP=1890;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant18-variant22-variant24-variant25-variant30-variant31-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:51,19:70:99:686,0,3374:20,31,6,13 chr1 185143721 . A G 1370.22 PASS AC=1;AF=0.563;AN=2;DP=1655;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant9-variant10-variant18-variant22-variant24-variant31-variant35-variant36-variant37-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:63,48:111:99:1319,0,1573:30,33,26,22 chr1 185144347 . T G 48.25 PASS AC=2;AF=0.682;AN=2;DP=61;FS=0;FractionInformativeReads=1;set=variant-variant5-variant7-variant10-variant18-variant22-variant24-variant31-variant35-variant40-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:229,18,0:0,0,1,5 chr1 185153545 . G GT 761.2 PASS AC=1;AF=0.563;AN=2;DP=753;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant9-variant10-variant18-variant22-variant24-variant31-variant35-variant36-variant37-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:26,27:53:99:944,0,890:10,16,10,17 chr1 185171869 . A G 1523.94 PASS AC=1;AF=0.533;AN=2;DP=1645;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant9-variant10-variant18-variant22-variant24-variant31-variant35-variant36-variant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:63,56:119:99:1306,0,1432:27,36,24,32 chr1 185176015 . A G 187.36 PASS AC=1;AF=0.536;AN=2;DP=114;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant9-variant10-variant22-variant24-variant31-variant35-variant36-variant37-variant42 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:99:117,0,115:0,3,0,3 chr1 185201061 . T C 655.86 PASS AC=1;AF=0.556;AN=2;DP=647;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant9-variant10-variant13-variant18-variant22-variant24-variant31-variant35-variant36-variant37-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:26,16:42:99:423,0,561:11,15,4,12 chr1 185240474 . A G 1509.88 PASS AC=1;AF=0.522;AN=2;DP=2558;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant16-variant22-variant24-variant25-variant31-variant32-variant35-variant36-variant37-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:60,56:116:99:1308,0,1340:24,36,23,33 chr1 185259731 . A G 78.47 PASS AC=1;AF=0.522;AN=2;DP=396;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant16-variant18-variant22-variant24-variant25-variant27-variant31-variant35-variant36-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,12:17:99:396,0,131:4,1,10,2 chr1 185265711 . T C 5655.07 PASS AC=1;AF=0.58;AN=2;DP=11418;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant16-variant18-variant22-variant24-variant25-variant27-variant31-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:237,214:451:99:5027,0,5459:108,129,98,116 chr1 185267114 . A G 3841.63 PASS AC=1;AF=0.58;AN=2;DP=6406;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant16-variant18-variant22-variant24-variant25-variant27-variant31-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:148,117:265:99:2917,0,3927:58,90,39,78 chr1 185269916 . T C 199.68 PASS AC=1;AF=0.577;AN=2;DP=316;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant18-variant22-variant24-variant25-variant27-variant31-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:7,4:11:99:135,0,265:7,0,4,0 chr1 185833565 . A C 278.15 PASS AC=1;AF=0.641;AN=2;DP=943;MQ=60;set=variant-variant5-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,11:32:99:318,0,693:16,5,9,2 chr1 185988567 . CT C 320.82 PASS AC=2;AF=0.731;AN=2;DP=243;MQ=60;set=variant2-variant6-variant9-variant11-variant15-variant17-variant18-variant19-variant20-variant21-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:254,27,0:0,0,8,1 chr1 186022032 . T G 365.74 PASS AC=2;AF=0.679;AN=2;DP=862;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:1054,96,0:0,0,23,9 chr1 186026474 . T C 1787.88 PASS AC=2;AF=0.645;AN=2;DP=5173;MQ=60;set=variant-variant2-variant5-variant6-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,133:133:99:3869,399,0:0,0,67,66 chr1 186030902 . G T 62.08 PASS AC=2;AF=0.667;AN=2;DP=968;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:539,42,0:0,0,12,2 chr1 186031041 . C T 752.68 PASS AC=2;AF=0.679;AN=2;DP=4450;MQ=60;set=variant-variant2-variant5-variant6-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,112:112:99:3097,335,0:0,0,55,57 chr1 186039006 . C T 367.2 PASS AC=1;AF=0.653;AN=2;DP=552;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant6-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,7:12:99:232,0,164:0,5,1,6 chr1 186050417 . A G 1033.75 PASS AC=1;AF=0.657;AN=2;DP=2855;MQ=60;set=variant-variant5-variant6-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,39:94:99:900,0,1355:30,25,19,20 chr1 186055371 . A G 1560.4 PASS AC=1;AF=0.671;AN=2;DP=2562;MQ=60;set=variant-variant5-variant6-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,48:76:99:1239,0,658:18,10,29,19 chr1 186057181 . T C 2306.83 PASS AC=1;AF=0.671;AN=2;DP=5063;set=variant-variant5-variant6-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:77,68:145:99:1691,0,1909:32,45,28,40 chr1 186077463 . A G 334.78 PASS AC=1;AF=0.657;AN=2;DP=765;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant6-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,8:25:99:276,0,681:17,0,8,0 chr1 186081918 . C T 1095 PASS AC=1;AF=0.671;AN=2;DP=3685;MQ=60;set=variant-variant5-variant6-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,61:122:99:1581,0,1374:32,29,39,22 chr1 186086578 . G A 1232.46 PASS AC=1;AF=0.657;AN=2;DP=4250;MQ=60;set=variant-variant5-variant6-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:72,50:122:99:1261,0,1727:42,30,37,13 chr1 186089072 . G A 2358.01 PASS AC=1;AF=0.563;AN=2;DP=3493;MQ=60;set=variant6-variant9-variant10-variant13-variant14-variant17-variant18-variant20-variant22-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:82,84:166:99:1947,0,1920:45,37,47,37 chr1 186089112 . T C 2351.44 PASS AC=1;AF=0.583;AN=2;DP=4249;MQ=60;set=variant6-variant9-variant10-variant13-variant14-variant17-variant18-variant20-variant22-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:115,89:204:99:1789,0,2483:57,58,48,41 chr1 186089363 . C A 229.07 PASS AC=1;AF=0.604;AN=2;DP=442;MQ=60;set=variant6-variant9-variant10-variant13-variant14-variant17-variant18-variant20-variant22-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,15:27:99:440,0,308:4,8,4,11 chr1 186092076 . A C 964.74 PASS AC=1;AF=0.635;AN=2;DP=1931;MQ=60;set=variant-variant6-variant9-variant10-variant13-variant14-variant17-variant18-variant20-variant22-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,42:76:99:1185,0,826:22,12,29,13 chr1 186101317 . G A 502.51 PASS AC=1;AF=0.625;AN=2;DP=53;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant9-variant23-variant35 GT:AD:DP:GQ:PL:SB 0/1:10,3:13:84:84,0,288:5,5,2,1 chr1 186101539 . A G 918.68 PASS AC=1;AF=0.614;AN=2;DP=1232;FractionInformativeReads=1;MQ=60;set=variant6-variant9-variant10-variant13-variant14-variant17-variant18-variant20-variant22-variant24-variant27-variant28-variant29-variant30-variant32-variant35-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,28:53:99:728,0,637:10,15,11,17 chr1 186113931 . T G 710.04 PASS AC=1;AF=0.587;AN=2;DP=1958;MQ=60;set=variant-variant6-variant9-variant10-variant14-variant17-variant18-variant22-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,31:86:99:734,0,1388:23,32,10,21 chr1 186115161 . GA GAA,G 260.27 PASS AC=0,1;AF=0.476,0.048;AN=2;DP=827;MQ=60;set=variant5-filterInvariant7-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant25-filterInvariant28-variant29-filterInvariant32-filterInvariant35-variant37-variant38-variant40-variant41-variant42-variant43 GT:DP:GQ:SB 0/2:47:99:13,22,5,7 chr1 186159684 . C T 4103.92 PASS AC=1;AF=0.5;AN=2;DP=4059;MQ=60;set=variant5-variant8-variant9-variant11-variant12-variant13-variant19-variant20-variant27-variant32-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:199,184:383:99:4609,0,4768:102,97,81,103 chr1 186159835 . A G 3507.39 PASS AC=2;AF=0.989;AN=2;DP=4769;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:2,114:116:99:3743,262,0:2,0,36,78 chr1 186277088 . G C 7257.11 PASS AC=2;AF=1;AN=2;DP=22715;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,570:570:99:17482,1709,0:0,0,283,287 chr1 186292720 . A T 303.15 PASS AC=1;AF=0.5;AN=2;DP=113;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant10-variant20-variant23-variant30-variant35-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:3,9:12:99:281,0,99:3,0,7,2 chr1 186292803 . C T 181.7 PASS AC=1;AF=0.6;AN=2;DP=178;MQ=60;set=variant2-variant11-variant20-variant21-variant35 GT:AD:DP:GQ:PL:SB 0/1:28,14:42:99:330,0,747:17,11,9,5 chr1 186304109 . C T 255.1 PASS AC=1;AF=0.571;AN=2;DP=54;FractionInformativeReads=1;MQ=60;set=variant3-variant10-variant20-variant30-variant35-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:4,2:6:69:69,0,98:3,1,2,0 chr1 186304298 . C T 1253.25 PASS AC=1;AF=0.5;AN=2;DP=667;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant10-variant20-variant23-variant30-variant35-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:44,57:101:99:1299,0,982:22,22,29,28 chr1 186313249 . A G 1097.06 PASS AC=2;AF=0.977;AN=2;DP=1594;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1142,99,0:0,0,9,24 chr1 186315474 . C A 932.74 PASS AC=1;AF=0.5;AN=2;DP=278;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant10-variant20-variant23-variant30-variant35-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:13,12:25:99:352,0,361:3,10,1,11 chr1 186319282 . C T 595.42 PASS AC=1;AF=0.5;AN=2;DP=179;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant10-variant20-variant23-variant30-variant35-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:10,5:15:99:160,0,318:8,2,5,0 chr1 186326757 . TA T 442.71 PASS AC=1;AF=0.5;AN=2;DP=269;MQ=60;set=variant3-variant6-variant10-variant20-variant23-variant30-variant35-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:13,16:29:99:434,0,335:3,10,3,13 chr1 186329869 . C G 3129.35 PASS AC=1;AF=0.686;AN=2;DP=3157;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,34:84:99:777,0,1186:28,22,20,14 chr1 186330643 . T C 587.79 PASS AC=1;AF=0.691;AN=2;DP=466;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,9:20:99:334,0,314:9,2,9,0 chr1 186330700 . A AG 913.98 PASS AC=1;AF=0.529;AN=2;DP=796;MQ=60;set=variant3-variant6-variant8-variant9-variant10-variant17-variant18-variant20-variant22-variant23-variant28-variant30-variant31-variant35-variant36-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:36,21:57:99:644,0,1158:23,13,16,5 chr1 186345125 . AGTGT AGTGTGTGTGTGT,AGTGTGTGTGTGTGTGT,AGTGTGTGT,AGTGTGTGTGT,AGTGTGTGTGTGTGT,AGTGTGT,A 316.69 PASS AC=1,0,1,0,0,0,0;AF=0.27,0.014,0.068,0.284,0.014,0.149,0.014;AN=2;DP=763;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant43-variant44 GT:DP:GQ:SB 3/1:15:99:0,0,5,10 chr1 186357523 . T C 929.35 PASS AC=2;AF=0.966;AN=2;DP=1142;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:792,69,0:0,0,17,6 chr1 186360814 . G A 1236.68 PASS AC=1;AF=0.5;AN=2;DP=669;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant10-variant20-variant23-variant30-variant35-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:49,27:76:99:501,0,1214:25,24,14,13 chr1 186363211 . T C 260.97 PASS AC=1;AF=0.5;AN=2;DP=176;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant10-variant20-variant23-variant35-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:9,8:17:99:251,0,220:2,7,2,6 chr1 186367619 . C T 484.58 PASS AC=1;AF=0.5;AN=2;DP=350;MQ=60;set=variant3-variant6-variant10-variant20-variant23-variant30-variant35-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:29,11:40:99:221,0,853:8,21,2,9 chr1 186368338 . AT A,ATT 32.69 PASS AC=1,0;AF=0.439,0.061;AN=2;DP=2230;set=filterInvariant-variant2-filterInvariant3-variant4-filterInvariant5-variant6-filterInvariant7-filterInvariant8-filterInvariant9-variant10-filterInvariant11-variant12-variant13-variant14-filterInvariant15-variant16-variant17-filterInvariant18-variant19-variant20-variant21-filterInvariant22-filterInvariant23-variant24-variant25-variant26-filterInvariant29-variant30-filterInvariant31-filterInvariant32-variant33-variant35-variant36-filterInvariant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:28:99:3,14,2,9 chr1 186370598 . T TTCTG 945.06 PASS AC=1;AF=0.671;AN=2;DP=1255;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,23:32:99:909,0,442:3,6,11,12 chr1 186390303 . A C 10458.4 PASS AC=1;AF=0.686;AN=2;DP=10957;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:119,161:280:99:3954,0,2761:56,63,71,90 chr1 186413714 . G C 83.3 PASS AC=1;AF=0.5;AN=2;DP=71;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant10-variant20-variant23-variant30-variant35 GT:AD:DP:GQ:PL:SB 0/1:4,12:16:99:379,0,126:0,4,2,10 chr1 186417697 . T C 4184.14 PASS AC=1;AF=0.522;AN=2;DP=7008;MQ=60;set=variant3-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant30-variant31-variant32-variant35-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:185,157:342:99:3575,0,4631:113,72,87,70 chr1 186641058 . G A 1604.25 PASS AC=1;AF=0.5;AN=2;DP=870;FractionInformativeReads=1;MQ=60;set=variant5-variant10-variant18-variant23-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:67,73:140:99:1679,0,1690:36,31,36,37 chr1 186641197 . C T 677.66 PASS AC=1;AF=0.5;AN=2;DP=192;FractionInformativeReads=1;MQ=60;set=variant5-variant10-variant23-variant35 GT:AD:DP:GQ:PL:SB 0/1:35,18:53:99:517,0,1076:8,27,3,15 chr1 186641265 . C T 332.6 PASS AC=1;AF=0.5;AN=2;DP=95;FractionInformativeReads=1;MQ=60;set=variant5-variant10-variant23-variant35 GT:AD:DP:GQ:PL:SB 0/1:19,10:29:99:279,0,578:6,13,3,7 chr1 186641626 . G A 3774.78 PASS AC=2;AF=1;AN=2;DP=5071;FS=0;MQ=60;MQRankSum=1.272;ReadPosRankSum=1.028;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,118:118:99:3749,354,0:0,0,62,56 chr1 186641682 . T C 1395.96 PASS AC=1;AF=0.5;AN=2;DP=396;FractionInformativeReads=1;MQ=60;set=variant5-variant10-variant23-variant35 GT:AD:DP:GQ:PL:SB 0/1:57,51:108:99:1231,0,1275:30,27,24,27 chr1 186642429 . A G 2852.11 PASS AC=2;AF=0.932;AN=2;DP=10479;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,226:226:99:7533,678,0:0,0,97,129 chr1 186643058 . A G 1980.98 PASS AC=1;AF=0.577;AN=2;DP=4417;MQ=60;set=variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant21-variant22-variant23-variant25-variant26-variant28-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:75,109:184:99:2732,0,1805:45,30,56,53 chr1 186644309 . G A 157.2 PASS AC=1;AF=0.5;AN=2;DP=64;FractionInformativeReads=1;MQ=60;set=variant5-variant10-variant23-variant35 GT:AD:DP:GQ:PL:SB 0/1:11,7:18:99:238,0,319:8,3,7,0 chr1 186649221 . A G 748.73 PASS AC=1;AF=0.814;AN=2;DP=2418;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,36:65:99:837,0,747:17,12,20,16 chr1 186862419 . A G 1176.76 PASS AC=1;AF=0.563;AN=2;DP=512;MQ=60;set=variant8-variant11-variant12-variant15-variant18-variant19-variant22-variant23-variant24-variant25-variant27-variant34-variant35-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:25,19:44:99:650,0,778:4,21,2,17 chr1 186863385 . TAA T 616.44 PASS AC=1;AF=0.63;AN=2;DP=970;MQ=60;set=variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant15-variant18-variant19-variant22-variant23-variant24-variant25-variant27-variant29-variant34-variant35-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:19,23:42:99:907,0,747:5,14,7,16 chr1 186908385 . C T 589.04 PASS AC=1;AF=0.639;AN=2;DP=385;MQ=60;set=variant-variant4-variant5-variant6-variant10-variant12-variant13-variant16-variant18-variant21-variant26-variant29-variant35-variant37-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:7,13:20:99:379,0,204:1,6,3,10 chr1 186919732 . A T 359.28 PASS AC=2;AF=0.965;AN=2;DP=847;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:847,75,0:0,0,19,6 chr1 186919993 . G A 1714.03 PASS AC=2;AF=0.965;AN=2;DP=2106;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1860,153,0:0,0,13,38 chr1 186925168 . A G 151.77 PASS AC=2;AF=0.965;AN=2;DP=514;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:591,42,0:0,0,9,5 chr1 186925169 . G T 234.21 PASS AC=1;AF=0.556;AN=2;DP=103;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant10-variant16-variant26-variant29-variant35-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:2,10:12:54:352,0,54:1,1,7,3 chr1 186925194 . T C 373.54 PASS AC=2;AF=0.965;AN=2;DP=795;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:704,51,0:0,0,14,3 chr1 186925552 . T C 1147.33 PASS AC=2;AF=0.965;AN=2;DP=1538;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:1060,90,0:0,0,6,24 chr1 186946912 . G A 2238.28 PASS AC=2;AF=0.977;AN=2;DP=3474;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,73:73:99:2290,218,0:0,0,24,49 chr1 187610538 . C G 954.36 PASS AC=2;AF=0.833;AN=2;DP=3902;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,92:92:99:2993,276,0:0,0,38,54 chr1 187610698 . C A 3224.98 PASS AC=1;AF=0.717;AN=2;DP=4150;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant30-variant31-variant34-variant35-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:74,80:154:99:1810,0,1856:37,37,41,39 chr1 187610777 . C G 1459.08 PASS AC=1;AF=0.659;AN=2;DP=3133;MQ=60;set=variant2-variant3-variant5-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant19-variant20-variant22-variant23-variant26-variant31-variant34-variant35-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:80,76:156:99:1750,0,2056:36,44,39,37 chr1 187610852 . A T,C 538.32 PASS AC=1,1;AF=0.321,0.512;AN=2;DP=5016;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 2/1:135:99:0,0,58,77 chr1 187611003 . A G 190.13 PASS AC=1;AF=0.542;AN=2;DP=173;MQ=60;set=variant12-variant13-variant19-variant25-variant27-variant30-variant32-variant33-variant35-variant37-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,4:17:99:126,0,447:2,11,1,3 chr1 190066742 . G A 1137.36 PASS AC=1;AF=0.677;AN=2;DP=2218;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant27-variant28-variant30-variant31-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,45:80:99:1234,0,963:24,11,32,13 chr1 190234239 . T A 219.93 PASS AC=1;AF=0.5;AN=2;DP=481;MQ=60;set=variant5-variant7-variant10-variant14-variant15-variant18-variant26-variant30-variant35-variant37-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:12,7:19:99:171,0,306:4,8,1,6 chr1 190707578 . C A 1567.26 PASS AC=1;AF=0.5;AN=2;DP=158;FractionInformativeReads=1;MQ=60;set=variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:40,41:81:99:1595,0,1987:26,14,28,13 chr1 190707587 . C T 1606.01 PASS AC=1;AF=0.5;AN=2;DP=173;FractionInformativeReads=1;MQ=60;set=variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:40,44:84:99:1634,0,2001:24,16,28,16 chr1 190707652 . C T 1614.85 PASS AC=1;AF=0.5;AN=2;DP=314;MQ=60;set=variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:78,70:148:99:1643,0,1923:40,38,44,26 chr1 190760498 . T C 369.74 PASS AC=2;AF=0.656;AN=2;DP=1454;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1307,126,0:0,0,26,16 chr1 190760787 . T C 89.43 PASS AC=1;AF=0.5;AN=2;DP=29;FS=0;FractionInformativeReads=1;MQ=60;set=variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:10,4:14:99:118,0,313:2,8,0,4 chr1 190768874 . G C 332.93 PASS AC=1;AF=0.5;AN=2;DP=113;FractionInformativeReads=1;MQ=60;set=variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:23,17:40:99:361,0,652:16,7,10,7 chr1 190768945 . C A 709.97 PASS AC=1;AF=0.5;AN=2;DP=194;FractionInformativeReads=1;MQ=60;set=variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:36,30:66:99:738,0,941:19,17,18,12 chr1 190769108 . GGTGTGTGT GGTGT,G,GGTGTGTGTGT,GGT 119.94 PASS AC=1,0,0,0;AF=0.583,0.021,0.063,0.021;AN=2;DP=344;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant10-variant12-variant14-variant17-variant19-variant21-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant42 GT:DP:GQ:SB 0/1:7:57:1,3,0,3 chr1 192127637 . T G 5764.38 PASS AC=1;AF=0.66;AN=2;DP=4163;MQ=60;set=variant-variant3-variant8-variant9-variant10-variant11-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:98,90:188:99:2180,0,2399:49,49,42,48 chr1 192128183 . G A 589.89 PASS AC=1;AF=0.756;AN=2;DP=788;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,11:22:99:307,0,344:9,2,7,4 chr1 192129370 . G A 332.99 PASS AC=1;AF=0.771;AN=2;DP=352;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,2:6:72:72,0,156:4,0,2,0 chr1 192335271 . C CTAAT 1879.74 PASS AC=1;AF=0.667;AN=2;DP=3349;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:50,31:81:99:1213,0,2444:32,18,16,15 chr1 192335792 . A G 3901.61 PASS AC=1;AF=0.667;AN=2;DP=11521;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:190,189:379:99:4408,0,4306:100,90,102,87 chr1 192336359 . T TAGACAAAATTTTGTCTTCC 910.31 PASS AC=1;AF=0.63;AN=2;DP=2554;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant29-variant30-variant31-variant34-variant35-variant36-variant37-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:32,25:57:99:1000,0,1933:10,22,7,18 chr1 192544754 . C CT 202.04 PASS AC=2;AF=0.762;AN=2;DP=696;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:626,72,0:0,0,18,6 chr1 192544795 . A G 595.17 PASS AC=2;AF=0.872;AN=2;DP=1381;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1250,117,0:0,0,25,14 chr1 192545099 . G A 1405.93 PASS AC=2;AF=0.845;AN=2;DP=1218;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1129,105,0:0,0,12,23 chr1 192547710 . A G 2981.26 PASS AC=1;AF=0.563;AN=2;DP=4352;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant20-variant21-variant22-variant24-variant27-variant30-variant31-variant32-variant34-variant35-variant36-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:83,111:194:99:2602,0,2004:45,38,55,56 chr1 192547847 . T A 2989.1 PASS AC=1;AF=0.5;AN=2;DP=1594;MQ=60;set=variant13-variant17-variant24-variant30-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:145,124:269:99:3333,0,4039:91,54,82,42 chr1 192548045 . T C 4356.18 PASS AC=1;AF=0.5;AN=2;DP=3547;MQ=60;set=variant13-variant16-variant17-variant24-variant30-variant34-variant35-variant36-variant41 GT:AD:DP:GQ:PL:SB 0/1:248,224:472:99:5547,0,6332:107,141,99,125 chr1 192548543 . T G 873.8 PASS AC=1;AF=0.5;AN=2;DP=496;MQ=60;set=variant13-variant16-variant24-variant30-variant34-variant35-variant36-variant41 GT:AD:DP:GQ:PL:SB 0/1:32,26:58:99:930,0,1574:12,20,10,16 chr1 192548559 . G C 835.52 PASS AC=1;AF=0.5;AN=2;DP=455;FractionInformativeReads=1;MQ=60;set=variant13-variant16-variant24-variant30-variant34-variant35-variant36-variant41 GT:AD:DP:GQ:PL:SB 0/1:27,22:49:99:747,0,1443:11,16,9,13 chr1 192605325 . C T 4213.87 PASS AC=1;AF=0.71;AN=2;DP=8999;MQ=60;set=variant-variant3-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:138,137:275:99:3108,0,2984:73,65,73,64 chr1 192605507 . C G 801.88 PASS AC=1;AF=0.655;AN=2;DP=1956;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant13-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:42,33:75:99:831,0,1187:11,31,9,24 chr1 192778255 . G C 2410.79 PASS AC=1;AF=0.5;AN=2;DP=208;FS=1.072;FractionInformativeReads=1;MQ=60;MQRankSum=-2.046;QD=11.59;ReadPosRankSum=2.454;SOR=0.788;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:108,100:208:99:2439,0,2555:58,50,56,44 chr1 193051685 . G A 1717.5 PASS AC=2;AF=0.845;AN=2;DP=1640;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:908,81,0:0,0,19,8 chr1 193054154 . G A 1900.18 PASS AC=2;AF=0.643;AN=2;DP=2342;MQ=60;set=variant3-variant4-variant5-variant8-variant9-variant10-variant12-variant13-variant19-variant22-variant23-variant24-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,96:96:99:2923,287,0:0,0,43,53 chr1 193054485 . T C 4661.28 PASS AC=2;AF=0.833;AN=2;DP=18220;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,441:441:99:13265,1320,0:0,0,265,176 chr1 193057207 . A G 1201.6 PASS AC=2;AF=0.845;AN=2;DP=1264;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1419,123,0:0,0,12,29 chr1 193057513 . A AT 2843.65 PASS AC=2;AF=0.854;AN=2;DP=3661;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,96:98:99:2616,240,0:1,1,51,45 chr1 193057971 . T A 5895.83 PASS AC=2;AF=0.845;AN=2;DP=5254;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,127:127:99:4375,378,0:0,0,69,58 chr1 193058937 . CT C,CTT 77.39 PASS AC=0,1;AF=0.385,0.115;AN=2;DP=548;set=variant-filterInvariant3-filterInvariant7-variant8-variant12-filterInvariant14-filterInvariant16-filterInvariant21-filterInvariant24-filterInvariant29-filterInvariant33-variant34-filterInvariant35 GT:DP:GQ:SB 0/2:23:91:2,12,4,5 chr1 193074371 . A G 133.63 PASS AC=2;AF=0.849;AN=2;DP=553;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:400,30,0:0,0,9,1 chr1 193074651 . T A 869.91 PASS AC=2;AF=0.849;AN=2;DP=3542;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,94:95:99:3010,240,0:0,1,48,46 chr1 193075108 . C T 4928.55 PASS AC=2;AF=0.849;AN=2;DP=11510;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,203:203:99:8954,643,0:0,0,113,90 chr1 193075118 . C CAA 5062.45 PASS AC=2;AF=0.849;AN=2;DP=12028;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,211:211:99:9103,685,0:0,0,112,99 chr1 193090865 . C A 1985.36 PASS AC=2;AF=0.81;AN=2;DP=9701;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,247:247:99:7239,738,0:0,0,125,122 chr1 193094375 . T C 463.8 PASS AC=2;AF=0.81;AN=2;DP=1798;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1597,147,0:0,0,14,35 chr1 193104827 . G A 46.49 PASS AC=2;AF=0.843;AN=2;DP=209;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:241,18,0:0,0,1,5 chr1 193202001 . C G 82.72 PASS AC=2;AF=0.861;AN=2;DP=275;FractionInformativeReads=1;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:251,21,0:0,0,6,1 chr1 193205272 . T A 1177.54 PASS AC=2;AF=0.821;AN=2;DP=3136;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,71:72:99:2154,174,0:0,1,47,24 chr1 193218843 . C G 308.51 PASS AC=1;AF=0.5;AN=2;DP=358;MQ=60;set=variant8-variant9-variant10-variant13-variant23-variant26-variant35-variant36-variant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:20,24:44:99:655,0,476:12,8,18,6 chr1 196227526 . A G 3027.56 PASS AC=2;AF=1;AN=2;DP=3780;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,119:119:99:3575,357,0:0,0,53,66 chr1 196242764 . T G 923.19 PASS AC=2;AF=0.942;AN=2;DP=1794;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:1564,140,0:0,0,12,35 chr1 196251522 . T C 171.18 PASS AC=1;AF=0.85;AN=2;DP=951;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,15:20:85:512,0,85:2,3,1,14 chr1 196254970 . C T 606.9 PASS AC=2;AF=1;AN=2;DP=1089;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:690,66,0:0,0,7,15 chr1 196303319 . G A 49.76 PASS AC=1;AF=0.5;AN=2;DP=26;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant10-variant15-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:3,2:5:70:75,0,70:1,2,0,2 chr1 196311513 . G A 206.42 PASS AC=1;AF=0.688;AN=2;DP=493;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant16-variant17-variant19-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,16:27:99:520,0,415:0,11,1,15 chr1 196342444 . A G 382.75 PASS AC=1;AF=0.5;AN=2;DP=282;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant10-variant15-variant22-variant35-variant36-variant41 GT:AD:DP:GQ:PL:SB 0/1:13,19:32:99:553,0,415:2,11,5,14 chr1 196398619 . T C 299.27 PASS AC=2;AF=0.662;AN=2;DP=1031;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:1273,90,0:0,0,29,1 chr1 196398974 . T A 146.83 PASS AC=2;AF=0.662;AN=2;DP=673;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:554,42,0:0,0,0,14 chr1 196461513 . C T 607.53 PASS AC=2;AF=0.989;AN=2;DP=654;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:683,54,0:0,0,2,16 chr1 196620917 . C T 563.71 PASS AC=2;AF=0.575;AN=2;DP=499;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant8-variant9-variant11-variant12-variant17-variant18-variant22-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:761,57,0:0,0,17,2 chr1 196654324 . A C 2151.96 PASS AC=2;AF=0.709;AN=2;DP=9927;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,203:204:99:5886,575,0:1,0,104,99 chr1 196658497 . G T 62.35 PASS AC=2;AF=0.705;AN=2;DP=517;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:518,51,0:0,0,8,9 chr1 196658905 . G A 280.9 PASS AC=2;AF=0.731;AN=2;DP=429;MQ=60;set=variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:395,27,0:0,0,0,9 chr1 196659237 . C T 527.58 PASS AC=2;AF=0.709;AN=2;DP=3046;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,64:64:99:1969,191,0:0,0,39,25 chr1 196670757 . C T 125.25 PASS AC=2;AF=0.725;AN=2;DP=322;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:128,9,0:0,0,1,2 chr1 196682947 . G A 500.71 PASS AC=1;AF=0.632;AN=2;DP=2715;FractionInformativeReads=1;set=variant2-variant3-variant4-variant6-variant7-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:46,32:78:99:704,0,1068:25,21,20,12 chr1 196684574 . C T 77.46 PASS AC=1;AF=0.556;AN=2;DP=148;FS=0;MQ=60;set=variant2-variant3-variant11-variant15-variant17-variant18-variant21-variant25-variant28-variant30-variant31-variant33-variant35-variant37-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,5:11:99:192,0,237:5,1,5,0 chr1 196684575 . A G 77.46 PASS AC=1;AF=0.556;AN=2;DP=154;FS=0;MQ=60;set=variant2-variant3-variant11-variant15-variant17-variant18-variant21-variant25-variant28-variant30-variant31-variant33-variant35-variant37-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,5:11:99:192,0,237:5,1,5,0 chr1 196684625 . G T 395.07 PASS AC=2;AF=0.707;AN=2;DP=1025;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:1036,87,0:0,0,23,6 chr1 196695742 . A G 963.27 PASS AC=1;AF=0.536;AN=2;DP=1311;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant6-variant8-variant9-variant13-variant20-variant26-variant27-variant30-variant31-variant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,37:92:99:917,0,1326:31,24,18,19 chr1 196709774 . G T 648.34 PASS AC=1;AF=0.533;AN=2;DP=736;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant6-variant8-variant9-variant13-variant20-variant26-variant27-variant29-variant30-variant31-variant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,26:51:99:683,0,717:19,6,17,9 chr1 196709869 . C T 1012.99 PASS AC=1;AF=0.5;AN=2;DP=97;FS=5.122;FractionInformativeReads=1;MQ=60;MQRankSum=-2.56;QD=10.44;ReadPosRankSum=-0.405;SOR=0.813;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:56,41:97:99:1041,0,1311:31,25,18,23 chr1 196710916 . T C 185.91 PASS AC=1;AF=0.548;AN=2;DP=278;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant6-variant11-variant15-variant17-variant18-variant21-variant22-variant25-variant28-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:7,7:14:99:270,0,274:7,0,7,0 chr1 196712577 . T C 330.22 PASS AC=1;AF=0.5;AN=2;DP=3444;FractionInformativeReads=1;set=variant-variant4-variant5-filterInvariant6-variant7-variant8-variant9-variant10-variant13-variant14-variant16-variant17-variant19-variant21-variant23-variant24-variant25-filterInvariant26-variant27-variant28-variant29-variant30-filterInvariant31-variant32-variant35-variant37-filterInvariant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:98,32:130:99:1055,0,6026:67,31,24,8 chr1 196712586 . C T 389.67 PASS AC=1;AF=0.5;AN=2;DP=3826;FractionInformativeReads=1;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant16-variant17-variant19-variant21-variant23-variant24-variant25-filterInvariant26-variant27-variant28-variant29-variant30-filterInvariant31-variant32-variant35-variant37-filterInvariant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:117,35:152:99:1057,0,6416:77,40,24,11 chr1 196743927 . A C 79.48 PASS AC=2;AF=0.676;AN=2;DP=199;FractionInformativeReads=1;set=variant-variant4-variant5-variant6-variant8-variant9-variant10-variant13-variant20-variant26-variant27-variant29-variant30-variant31-variant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:208,18,0:0,0,5,1 chr1 196743964 . C A 191.66 PASS AC=2;AF=0.647;AN=2;DP=380;FractionInformativeReads=1;set=variant-variant4-variant5-variant6-variant8-variant9-variant10-variant13-variant20-variant26-variant27-variant29-variant30-variant31-variant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:399,39,0:0,0,9,4 chr1 196757258 . C T 230.47 PASS AC=2;AF=0.833;AN=2;DP=184;FractionInformativeReads=1;set=variant-variant4-variant5-variant7-variant8-variant9-variant10-variant16-variant19-variant20-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:193,21,0:0,0,4,3 chr1 196757392 . C T 248.54 PASS AC=2;AF=0.796;AN=2;DP=365;set=variant-variant4-variant5-variant6-variant8-variant9-variant10-variant14-variant16-variant17-variant19-variant20-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:189,18,0:0,0,2,4 chr1 196757874 . G A 1473.85 PASS AC=2;AF=0.676;AN=2;DP=1343;FractionInformativeReads=1;set=variant-variant4-variant5-variant6-variant8-variant9-variant10-variant13-variant20-variant26-variant27-variant29-variant30-variant31-variant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1711,117,0:0,0,19,19 chr1 196757881 . G T 1473.85 PASS AC=2;AF=0.647;AN=2;DP=1382;FractionInformativeReads=1;set=variant-variant4-variant5-variant6-variant8-variant9-variant10-variant13-variant20-variant26-variant27-variant29-variant30-variant31-variant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1711,117,0:0,0,20,19 chr1 196758286 . T C 726.37 PASS AC=2;AF=0.676;AN=2;DP=654;FractionInformativeReads=1;set=variant-variant4-variant5-variant6-variant8-variant9-variant10-variant13-variant20-variant26-variant27-variant29-variant30-variant31-variant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:74:816,74,0:0,0,19,6 chr1 196758430 . A T 2452.89 PASS AC=2;AF=0.694;AN=2;DP=3225;MQ=60;set=variant-variant4-variant5-variant6-variant8-variant9-variant10-variant13-variant20-variant26-variant27-variant29-variant30-variant31-variant35-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,111:111:99:3138,331,0:0,0,53,58 chr1 196758541 . A C 733.34 PASS AC=2;AF=0.676;AN=2;DP=899;FractionInformativeReads=1;set=variant-variant4-variant5-variant6-variant8-variant9-variant10-variant13-variant20-variant26-variant27-variant29-variant30-variant31-variant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:893,78,0:0,0,6,20 chr1 196758778 . G A 269.99 PASS AC=2;AF=0.679;AN=2;DP=170;FractionInformativeReads=1;set=variant-variant4-variant5-variant6-variant8-variant10-variant13-variant26-variant27-variant29-variant31-variant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:91,9,0:0,0,2,1 chr1 196763707 . T C 90.04 PASS AC=2;AF=0.7;AN=2;DP=42;FractionInformativeReads=1;set=variant-variant5-variant10-variant31-variant35 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:87,6,0:0,0,2,0 chr1 196795844 . C T 583.43 PASS AC=2;AF=0.714;AN=2;DP=451;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant6-variant8-variant9-variant13-variant18-variant26-variant27-variant30-variant31-variant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:720,48,0:0,0,11,5 chr1 196795849 . A G 611.51 PASS AC=2;AF=0.781;AN=2;DP=1185;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:781,54,0:0,0,12,6 chr1 196796184 . G A 998.15 PASS AC=2;AF=0.774;AN=2;DP=2174;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant16-variant17-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1150,122,0:0,0,19,22 chr1 196796240 . T A 532.27 PASS AC=2;AF=0.774;AN=2;DP=1049;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant16-variant17-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:645,60,0:0,0,6,14 chr1 196797123 . C T 409.13 PASS AC=2;AF=0.774;AN=2;DP=831;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant16-variant17-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:84,6,0:0,0,1,1 chr1 196797238 . C T 366.36 PASS AC=2;AF=0.759;AN=2;DP=1104;set=variant-variant4-variant5-variant6-variant7-variant8-filterInvariant9-variant10-variant13-variant16-variant17-variant19-filterInvariant21-filterInvariant23-variant24-variant25-filterInvariant26-variant27-variant28-variant29-variant30-variant31-variant32-filterInvariant35-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:180,12,0:0,0,2,2 chr1 196797244 . C G 369.37 PASS AC=2;AF=0.759;AN=2;DP=1035;FractionInformativeReads=1;set=variant-variant4-filterInvariant5-variant6-variant7-variant8-filterInvariant9-variant10-variant13-variant16-variant17-variant19-filterInvariant21-variant24-variant25-filterInvariant26-variant27-variant28-variant29-variant31-variant32-filterInvariant35-variant37-variant40-variant41-variant42-filterInvariant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:180,12,0:0,0,2,2 chr1 196799691 . G A 642.85 PASS AC=2;AF=0.692;AN=2;DP=916;FractionInformativeReads=1;set=variant-variant4-variant6-variant8-variant9-variant13-variant26-variant27-variant30-variant31-variant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1451,129,0:0,0,30,13 chr1 196801042 . G T 1276.34 PASS AC=2;AF=0.774;AN=2;DP=4112;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant16-variant17-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,64:64:99:1954,192,0:0,0,31,33 chr1 196801078 . A T 1107.45 PASS AC=2;AF=0.75;AN=2;DP=4024;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant16-variant17-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant37-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,63:63:99:1897,189,0:0,0,26,37 chr1 196801190 . C A 319.26 PASS AC=2;AF=0.75;AN=2;DP=1319;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant16-variant17-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant37-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:575,45,0:0,0,2,13 chr1 196874192 . A G 194.18 PASS AC=1;AF=0.5;AN=2;DP=32;FractionInformativeReads=1;MQ=60;set=variant31-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:7,8:15:99:210,0,235:7,0,6,2 chr1 196874356 . G T 2988.99 PASS AC=2;AF=1;AN=2;DP=4392;FS=0;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,92:92:99:2688,275,0:0,0,45,47 chr1 196875957 . T C 1251.05 PASS AC=1;AF=0.5;AN=2;DP=306;FractionInformativeReads=1;set=variant6-variant30-variant35 GT:AD:DP:GQ:PL:SB 0/1:58,45:103:99:1177,0,1460:30,28,19,26 chr1 196883469 . T A 387.48 PASS AC=1;AF=0.545;AN=2;DP=365;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant6-variant8-variant9-variant26-variant27-variant30-variant31-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:13,17:30:99:473,0,276:7,6,12,5 chr1 196883940 . TA TAA,T 32.53 PASS AC=0,2;AF=0.273,0.5;AN=2;DP=55;FS=0;set=variant4-variant7-variant8-variant16-variant24-variant26-variant29-variant30-variant32-variant34-variant35 GT:DP:GQ:SB 2/2:4:12:0,0,4,0 chr1 196884074 . A AT 94.84 PASS AC=1;AF=0.5;AN=2;DP=603;set=variant-variant4-variant5-variant6-variant8-filterInvariant10-variant20-variant26-variant27-variant29-variant30-variant31-variant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,12:41:99:225,0,747:25,4,10,2 chr1 196884258 . A T 703.05 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=2069;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:93,27:120:99:396,0,2167:31,62,7,20 chr1 196884290 . T A 481.3 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=1160;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:62,17:79:99:236,0,1531:18,44,4,13 chr1 196887181 . T G 232.5 PASS AC=2;AF=0.676;AN=2;DP=116;FS=0;FractionInformativeReads=1;set=variant3-variant5-variant6-variant8-variant9-variant13-variant15-variant21-variant25-variant31-variant33-variant35-variant36-variant37-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:135,9,0:0,0,3,0 chr1 196887274 . G A 1028.51 PASS AC=2;AF=0.618;AN=2;DP=842;FractionInformativeReads=1;set=variant-variant4-variant6-variant8-variant9-variant11-variant13-variant14-variant15-variant26-variant27-variant30-variant31-variant33-variant34-variant35-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:1655,144,0:0,0,36,12 chr1 196920178 . C T 888.92 PASS AC=2;AF=0.607;AN=2;DP=1962;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant11-variant13-variant14-variant15-variant18-variant21-variant22-variant25-variant26-variant27-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:1508,141,0:0,0,16,31 chr1 196926973 . C A 418.2 PASS AC=2;AF=0.607;AN=2;DP=531;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant11-variant13-variant14-variant15-variant18-variant21-variant22-variant25-variant26-variant27-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:1244,90,0:0,0,28,2 chr1 196946869 . T A 3982 PASS AC=1;AF=0.575;AN=2;DP=7009;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant24-variant26-variant27-variant30-variant32-variant33-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:171,165:336:99:4162,0,4258:58,113,53,112 chr1 196951925 . A G 588.01 PASS AC=1;AF=0.5;AN=2;DP=139;FractionInformativeReads=1;MQ=60;set=variant8-variant31-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:17,13:30:99:358,0,419:12,5,10,3 chr1 196952268 . C T 1005.29 PASS AC=1;AF=0.575;AN=2;DP=2489;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant24-variant26-variant27-variant30-variant32-variant33-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:58,50:108:99:1111,0,1614:28,30,24,26 chr1 196978615 . T G 3088.78 PASS AC=1;AF=0.561;AN=2;DP=7560;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:108,132:240:99:3274,0,2458:54,54,63,69 chr1 197008365 . C T 500.22 PASS AC=1;AF=0.685;AN=2;DP=1384;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant22-variant24-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38 GT:AD:DP:GQ:PL:SB 0/1:27,14:41:99:408,0,805:19,8,9,5 chr1 197008597 . A C 1046.95 PASS AC=1;AF=0.621;AN=2;DP=2937;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant25-variant26-variant28-variant29-variant31-variant35-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,40:81:99:880,0,1041:19,22,19,21 chr1 197009798 . A G 865.92 PASS AC=1;AF=0.621;AN=2;DP=2190;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant25-variant26-variant28-variant29-variant31-variant35-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,24:71:99:502,0,1172:22,25,12,12 chr1 197026289 . A G 1307.66 PASS AC=1;AF=0.5;AN=2;DP=242;FractionInformativeReads=1;MQ=60;set=variant6-variant30-variant35 GT:AD:DP:GQ:PL:SB 0/1:38,51:89:99:1196,0,1011:26,12,26,25 chr1 197026672 . A G 53.48 PASS AC=2;AF=0.908;AN=2;DP=237;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:218,18,0:0,0,1,5 chr1 197029345 . G A 52.74 PASS AC=2;AF=0.7;AN=2;DP=36;FS=0;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant12-variant15-variant21-variant26-variant29-variant31-variant35-variant39 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:94,9,0:0,0,2,1 chr1 197030201 . T C 1010.39 PASS AC=2;AF=0.881;AN=2;DP=1244;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1440,124,0:0,0,9,33 chr1 197031021 . C T 1213.96 PASS AC=2;AF=0.881;AN=2;DP=3000;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,64:64:99:1963,192,0:0,0,31,33 chr1 197053296 . A G 364.44 PASS AC=1;AF=0.5;AN=2;DP=130;MQ=60;set=variant6-variant30-variant35 GT:AD:DP:GQ:PL:SB 0/1:22,22:44:99:564,0,566:13,9,14,8 chr1 197053373 . G A 2040.54 PASS AC=2;AF=0.881;AN=2;DP=3510;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,78:78:99:2393,234,0:0,0,46,32 chr1 197053561 . TA TAA,T 180.13 PASS AC=1,0;AF=0.534,0.034;AN=2;DP=1454;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant19-variant22-variant24-variant26-variant27-variant28-filterInvariant29-variant30-variant32-variant33-variant34-variant35-variant36-variant38-filterInvariant42 GT:DP:GQ:SB 0/1:27:99:3,9,6,9 chr1 197055925 . T C 3347.2 PASS AC=2;AF=0.881;AN=2;DP=3992;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,87:88:99:2629,217,0:1,0,52,35 chr1 197059878 . G A 657.38 PASS AC=2;AF=0.869;AN=2;DP=521;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:669,48,0:0,0,16,0 chr1 197059892 . A G 887.62 PASS AC=2;AF=0.881;AN=2;DP=709;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:784,54,0:0,0,18,0 chr1 197059928 . A G 1448.11 PASS AC=2;AF=0.881;AN=2;DP=1653;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1648,138,0:0,0,36,10 chr1 197063352 . C T 962.66 PASS AC=1;AF=0.685;AN=2;DP=1758;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant22-variant24-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38 GT:AD:DP:GQ:PL:SB 0/1:49,39:88:99:845,0,1092:23,26,15,24 chr1 197070442 . G T 1292.71 PASS AC=1;AF=0.685;AN=2;DP=2234;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant22-variant24-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38 GT:AD:DP:GQ:PL:SB 0/1:47,47:94:99:1131,0,1133:22,25,22,25 chr1 197070697 . T C 3436.45 PASS AC=1;AF=0.685;AN=2;DP=3144;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant22-variant24-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38 GT:AD:DP:GQ:PL:SB 0/1:64,45:109:99:1625,0,3935:42,22,26,19 chr1 197070707 . G A 3538.95 PASS AC=1;AF=0.685;AN=2;DP=3435;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant22-variant24-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38 GT:AD:DP:GQ:PL:SB 0/1:64,46:110:99:1662,0,3932:41,23,28,18 chr1 197070815 . T C 6470.92 PASS AC=2;AF=0.893;AN=2;DP=8108;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,177:178:99:5279,521,0:0,1,87,90 chr1 197070901 . A G 5425.37 PASS AC=2;AF=0.989;AN=2;DP=7339;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,154:154:99:4917,461,0:0,0,71,83 chr1 197072420 . T C 1604.92 PASS AC=1;AF=0.685;AN=2;DP=3009;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant22-variant24-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38 GT:AD:DP:GQ:PL:SB 0/1:46,50:96:99:1373,0,1183:24,22,25,25 chr1 197073932 . T C 1168.03 PASS AC=1;AF=0.685;AN=2;DP=2565;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant22-variant24-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38 GT:AD:DP:GQ:PL:SB 0/1:49,53:102:99:1391,0,1214:23,26,24,29 chr1 197091537 . A T 4296.68 PASS AC=2;AF=0.881;AN=2;DP=5208;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,102:104:99:3098,261,0:1,1,59,43 chr1 197091808 . T C 172.41 PASS AC=1;AF=0.685;AN=2;DP=444;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant22-variant24-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38 GT:AD:DP:GQ:PL:SB 0/1:10,10:20:99:300,0,277:2,8,3,7 chr1 197094030 . C T 681.26 PASS AC=1;AF=0.548;AN=2;DP=1010;MQ=60;set=variant-variant3-variant5-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant20-variant23-variant26-variant29-variant31-variant35-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,19:39:99:522,0,654:17,3,14,5 chr1 197097891 . AAAAT A 37.76 PASS AC=1;AF=0.844;AN=2;DP=86;FS=0;MQ=60;set=variant3-variant4-variant6-variant7-variant11-variant14-variant22-variant24-variant26-variant27-variant28-variant32-variant33-variant34-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:3,5:8:99:188,0,138:1,2,1,4 chr1 197101303 . C A 52.74 PASS AC=2;AF=0.8;AN=2;DP=67;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant7-variant9-variant11-variant12-variant14-variant16-variant24-variant27-variant28-variant32-variant33-variant35-variant36 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:139,12,0:0,0,3,1 chr1 197101621 . T C 136.65 PASS AC=1;AF=0.68;AN=2;DP=171;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant23-variant25-variant26-variant28-variant29-variant31-variant35-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,4:7:99:118,0,102:1,2,1,3 chr1 197102839 . A C 2894.17 PASS AC=2;AF=0.893;AN=2;DP=3710;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:2500,224,0:0,0,22,53 chr1 197104149 . TA T 57.87 PASS AC=2;AF=0.953;AN=2;DP=142;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:107,9,0:0,0,3,0 chr1 197109042 . C T 705.39 PASS AC=2;AF=0.881;AN=2;DP=869;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:1000,90,0:0,0,10,20 chr1 197112533 . G A 6641.83 PASS AC=2;AF=0.881;AN=2;DP=7959;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,222:222:99:6518,665,0:0,0,107,115 chr1 197113073 . G A 1241.31 PASS AC=2;AF=0.881;AN=2;DP=1495;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1367,117,0:0,0,23,16 chr1 197141243 . A C 420.09 PASS AC=2;AF=0.845;AN=2;DP=1196;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:672,66,0:0,0,15,7 chr1 197147471 . A C 66.25 PASS AC=1;AF=0.685;AN=2;DP=482;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-filterInvariant13-variant14-variant15-variant16-variant19-variant22-variant24-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38 GT:AD:DP:GQ:PL:SB 0/1:4,3:7:96:96,0,120:3,1,3,0 chr1 197297540 . A T 474.8 PASS AC=1;AF=0.576;AN=2;DP=958;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,12:27:99:289,0,422:9,6,8,4 chr1 197316435 . T C 4138.84 PASS AC=2;AF=0.814;AN=2;DP=4778;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,108:108:99:3321,322,0:0,0,71,37 chr1 197325908 . T G 3496.87 PASS AC=2;AF=0.837;AN=2;DP=4396;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,102:102:99:3176,306,0:0,0,60,42 chr1 197390368 . A G 3690.02 PASS AC=2;AF=0.966;AN=2;DP=5883;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,140:140:99:4546,419,0:0,0,80,60 chr1 197398086 . A G 1035.61 PASS AC=2;AF=0.632;AN=2;DP=2032;MQ=60;set=variant-variant5-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:1829,173,0:0,0,35,23 chr1 197407942 . A G 7790.81 PASS AC=2;AF=0.966;AN=2;DP=9351;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,213:213:99:6487,637,0:0,0,90,123 chr1 197408247 . G C 9055.11 PASS AC=2;AF=0.966;AN=2;DP=11771;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:2,298:300:99:8970,849,0:1,1,151,147 chr1 197408614 . G A 10555.6 PASS AC=2;AF=0.989;AN=2;DP=14414;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,311:311:99:9735,933,0:0,0,154,157 chr1 197409070 . C T 3264.07 PASS AC=2;AF=0.966;AN=2;DP=3737;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,81:81:99:3007,243,0:0,0,20,61 chr1 197410295 . C A 8698.85 PASS AC=2;AF=0.966;AN=2;DP=10437;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,201:201:99:6358,603,0:0,0,108,93 chr1 197410348 . T C 10142.1 PASS AC=2;AF=0.966;AN=2;DP=11851;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,271:271:99:8059,812,0:0,0,146,125 chr1 197410789 . CTTTTTT CTTTTTTT,CTTTTT,CTTTT,CTTTTTTTTTTTTTTTTTTTTTT,CTTTTTTTT,C 32.5 PASS AC=0,0,0,0,1,0;AF=0.25,0.1,0.075,0.025,0.05,0.025;AN=2;DP=785;set=filterInvariant2-filterInvariant3-variant4-filterInvariant5-filterInvariant8-variant11-filterInvariant16-variant17-variant18-variant19-filterInvariant20-variant23-filterInvariant27-variant31-filterInvariant32-variant35-filterInvariant36-variant40-filterInvariant41-variant44 GT:DP:GQ:SB 0/5:22:99:5,8,5,4 chr1 197412251 . TAA TA,T 127.49 PASS AC=1,0;AF=0.549,0.159;AN=2;DP=828;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:26:46:3,4,16,3 chr1 197412372 . A G 2058.94 PASS AC=1;AF=0.5;AN=2;DP=548;FractionInformativeReads=1;MQ=60;set=variant15-variant16-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:57,68:125:99:1596,0,1536:33,24,41,27 chr1 197413628 . C T 15332.1 PASS AC=2;AF=0.966;AN=2;DP=17758;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,389:389:99:12651,1165,0:0,0,220,169 chr1 197414036 . T TACAC,TAC,TACACAC 935.4 PASS AC=2,0,0;AF=0.886,0.057,0.023;AN=2;DP=1265;FS=0;set=Intersection GT:DP:GQ:SB 1/1:19:56:0,0,1,18 chr1 197446702 . G T 604.15 PASS AC=2;AF=0.648;AN=2;DP=1653;FractionInformativeReads=1;MQ=60;set=variant5-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant19-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:1845,177,0:0,0,38,21 chr1 197473969 . A T 4832.64 PASS AC=2;AF=0.977;AN=2;DP=7796;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,128:129:99:3469,356,0:1,0,58,70 chr1 197474565 . A G 6889.41 PASS AC=2;AF=0.977;AN=2;DP=7689;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,185:185:99:6044,554,0:0,0,84,101 chr1 197474817 . A G 7584.86 PASS AC=2;AF=0.989;AN=2;DP=8008;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,169:170:99:5492,482,0:1,0,78,91 chr1 197474845 . A ATTAAC 8364.44 PASS AC=2;AF=0.977;AN=2;DP=7322;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,136:136:99:6292,427,0:0,0,67,69 chr1 197475055 . CAATCT C 4967.96 PASS AC=2;AF=0.977;AN=2;DP=5619;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,111:111:99:4988,335,0:0,0,45,66 chr1 197475085 . T C 3400.05 PASS AC=2;AF=0.977;AN=2;DP=4691;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,102:102:99:3246,304,0:0,0,40,62 chr1 197475908 . C A 6865.16 PASS AC=2;AF=0.977;AN=2;DP=11090;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,226:226:99:7260,678,0:0,0,99,127 chr1 197476279 . CATTATTATTATTATT C,CATTATT,CATTATTATT,CATT 149.44 PASS AC=2,0,0,0;AF=0.939,0.012,0.012,0.037;AN=2;DP=846;FS=0;MQ=60;MQRankSum=0.751;ReadPosRankSum=0.751;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:4:14:0,0,3,1 chr1 197477237 . T C 13488.2 PASS AC=2;AF=0.977;AN=2;DP=17749;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,338:338:99:10588,1014,0:0,0,163,175 chr1 197477448 . C T 4626.98 PASS AC=2;AF=0.653;AN=2;DP=12225;MQ=60;set=variant-variant5-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,315:315:99:9234,945,0:0,0,134,181 chr1 197477498 . G A 2530.83 PASS AC=2;AF=0.575;AN=2;DP=4350;MQ=60;set=variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant23-variant26-variant28-variant32-variant33-variant34-variant35-variant37-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,193:193:99:5933,577,0:0,0,75,118 chr1 197477760 . G A 1191.87 PASS AC=1;AF=0.5;AN=2;DP=243;FractionInformativeReads=1;MQ=60;set=variant15-variant16-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:30,28:58:99:719,0,928:16,14,15,13 chr1 197478756 . ATT AT,A 371.25 PASS AC=1,0;AF=0.524,0.146;AN=2;DP=1849;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-filterInvariant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:DP:GQ:SB 0/1:47:99:8,5,24,10 chr1 197479378 . C A 9486.28 PASS AC=2;AF=0.977;AN=2;DP=12728;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,262:262:99:8160,781,0:0,0,106,156 chr1 197480927 . C T 1041.95 PASS AC=2;AF=0.571;AN=2;DP=2830;FractionInformativeReads=1;MQ=60;set=variant-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,95:95:99:2802,285,0:0,0,60,35 chr1 197482167 . C G 137.64 PASS AC=2;AF=0.966;AN=2;DP=509;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:608,51,0:0,0,4,13 chr1 197510025 . G T 903.22 PASS AC=2;AF=0.977;AN=2;DP=1166;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:1014,84,0:0,0,21,7 chr1 197510299 . G A 634.06 PASS AC=2;AF=1;AN=2;DP=593;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:411,33,0:0,0,2,9 chr1 197515253 . ATGTTCAG A 682.97 PASS AC=2;AF=1;AN=2;DP=531;FS=0;MQ=60;MQRankSum=0.474;ReadPosRankSum=1.107;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,16:16:49:721,49,0:0,0,3,13 chr1 197515715 . G A 317.08 PASS AC=2;AF=0.841;AN=2;DP=369;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:271,24,0:0,0,6,2 chr1 197515777 . A T 1676.77 PASS AC=2;AF=0.833;AN=2;DP=1795;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1195,114,0:0,0,24,14 chr1 197515981 . T C 567.57 PASS AC=2;AF=0.574;AN=2;DP=983;FractionInformativeReads=1;MQ=60;set=variant-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,31:31:93:1111,93,0:0,0,5,26 chr1 197521877 . T C 11904.3 PASS AC=2;AF=0.841;AN=2;DP=14901;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,341:341:99:10284,1019,0:0,0,178,163 chr1 197576307 . A AT 993.9 PASS AC=2;AF=0.989;AN=2;DP=1531;MQ=60;MQRankSum=0.655;ReadPosRankSum=-0.267;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1283,105,0:0,0,12,23 chr1 197704717 . C T 1443.03 PASS AC=2;AF=0.556;AN=2;DP=2331;MQ=60;set=variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant23-variant26-variant28-variant32-variant33-variant34-variant35-variant37-variant39-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,132:132:99:4123,396,0:0,0,81,51 chr1 197741951 . C A 1802.45 PASS AC=2;AF=0.989;AN=2;DP=3083;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:1862,212,0:0,0,45,26 chr1 197742171 . C T 621.07 PASS AC=2;AF=0.845;AN=2;DP=928;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:1215,96,0:0,0,4,28 chr1 197872019 . G T 2373.25 PASS AC=1;AF=0.625;AN=2;DP=2996;MQ=60;set=variant3-variant4-variant7-variant9-variant10-variant13-variant15-variant16-variant17-variant18-variant23-variant24-variant26-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,88:141:99:2520,0,1288:15,38,28,60 chr1 197874949 . T C 1284.52 PASS AC=1;AF=0.56;AN=2;DP=2695;MQ=60;set=variant5-variant6-variant8-variant9-variant10-variant12-variant14-variant15-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant35-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:69,58:127:99:1248,0,1476:38,31,30,28 chr1 197876533 . C A 6356.34 PASS AC=2;AF=0.977;AN=2;DP=8310;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,185:186:99:5553,512,0:1,0,96,89 chr1 197885301 . G A 495.03 PASS AC=1;AF=0.5;AN=2;DP=207;FractionInformativeReads=1;MQ=60;set=variant14-variant23-variant29-variant35 GT:AD:DP:GQ:PL:SB 0/1:22,31:53:99:798,0,611:16,6,20,11 chr1 197887584 . A G 1218.72 PASS AC=1;AF=0.5;AN=2;DP=441;FractionInformativeReads=1;MQ=60;set=variant13-variant14-variant23-variant29-variant35 GT:AD:DP:GQ:PL:SB 0/1:42,56:98:99:1518,0,1129:20,22,26,30 chr1 197890422 . C G 1010.75 PASS AC=1;AF=0.943;AN=2;DP=2510;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:30,33:63:99:858,0,876:23,7,23,10 chr1 197898072 . G A 164.79 PASS AC=1;AF=0.5;AN=2;DP=75;FractionInformativeReads=1;MQ=60;set=variant14-variant23-variant29-variant35 GT:AD:DP:GQ:PL:SB 0/1:17,4:21:99:109,0,427:10,7,3,1 chr1 197900023 . C T 11924.6 PASS AC=2;AF=1;AN=2;DP=14356;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,320:320:99:9748,959,0:0,0,156,164 chr1 197900589 . A C 8045.38 PASS AC=1;AF=0.943;AN=2;DP=9781;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:121,96:217:99:2591,0,3151:46,75,33,63 chr1 197901727 . A G 3126.33 PASS AC=1;AF=0.5;AN=2;DP=923;FractionInformativeReads=1;MQ=60;set=variant14-variant23-variant29-variant35 GT:AD:DP:GQ:PL:SB 0/1:134,127:261:99:3467,0,3454:50,84,47,80 chr1 197902508 . G A 2923.22 PASS AC=1;AF=0.5;AN=2;DP=1188;MQ=60;set=variant14-variant23-variant29-variant35 GT:AD:DP:GQ:PL:SB 0/1:121,145:266:99:3788,0,3048:78,43,88,57 chr1 197902814 . T C 1397.85 PASS AC=1;AF=0.65;AN=2;DP=2530;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,30:75:99:755,0,1391:18,27,14,16 chr1 197902871 . CAAA CA,C,CAA,CAAAAA 110.71 PASS AC=2,0,0,0;AF=0.693,0.08,0.068,0.011;AN=2;DP=1778;set=Intersection GT:DP:GQ:SB 1/1:30:42:1,3,11,15 chr1 197903352 . T G 6885.96 PASS AC=1;AF=0.943;AN=2;DP=8617;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:86,93:179:99:2326,0,2238:46,40,54,39 chr1 197903389 . GT G 7066.62 PASS AC=1;AF=0.667;AN=2;DP=5572;MQ=60;set=variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant19-variant21-variant23-variant24-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:90,105:195:99:2670,0,2221:47,43,57,48 chr1 197903975 . GT G 718.24 PASS AC=1;AF=0.5;AN=2;DP=302;MQ=60;set=variant14-variant23-variant29-variant35 GT:AD:DP:GQ:PL:SB 0/1:29,35:64:99:859,0,639:8,21,9,26 chr1 197904639 . C T 505.21 PASS AC=1;AF=0.5;AN=2;DP=160;FractionInformativeReads=1;MQ=60;set=variant14-variant23-variant29-variant35 GT:AD:DP:GQ:PL:SB 0/1:19,24:43:99:728,0,475:6,13,7,17 chr1 198126017 . A C 257.57 PASS AC=1;AF=0.5;AN=2;DP=76;FS=0;FractionInformativeReads=1;MQ=60;set=variant19-variant29-variant33-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:2,8:10:19:283,0,19:1,1,7,1 chr1 198126053 . A T 352.56 PASS AC=1;AF=0.5;AN=2;DP=108;MQ=60;set=variant19-variant29-variant33-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:3,13:16:47:404,0,47:2,1,11,2 chr1 198225478 . G A 2916.62 PASS AC=1;AF=0.5;AN=2;DP=1028;FractionInformativeReads=1;MQ=60;set=variant19-variant29-variant33-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:96,100:196:99:2285,0,2305:53,43,53,47 chr1 198225658 . T C 1722.93 PASS AC=1;AF=0.5;AN=2;DP=1246;MQ=60;set=variant10-variant19-variant25-variant29-variant33-variant35-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:63,39:102:99:950,0,1796:21,42,12,27 chr1 198288709 . A G 2896.93 PASS AC=1;AF=0.615;AN=2;DP=7288;MQ=60;set=variant2-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant16-variant17-variant19-variant21-variant22-variant25-variant26-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:149,133:282:99:3564,0,4117:86,63,84,49 chr1 198290806 . A G 1516.26 PASS AC=1;AF=0.5;AN=2;DP=536;MQ=60;set=variant19-variant29-variant33-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:54,55:109:99:1465,0,1519:23,31,24,31 chr1 198663661 . G A 5217.92 PASS AC=1;AF=0.5;AN=2;DP=5800;MQ=60;set=variant10-variant13-variant15-variant16-variant17-variant18-variant22-variant24-variant31-variant32-variant35-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:226,229:455:99:5264,0,5475:129,97,128,101 chr1 198677420 . T A 344.87 PASS AC=1;AF=0.5;AN=2;DP=220;MQ=60;set=variant13-variant15-variant16-variant18-variant22-variant24-variant32-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:11,9:20:99:241,0,351:2,9,2,7 chr1 198701289 . T C 106.77 PASS AC=1;AF=0.804;AN=2;DP=196;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant15-variant17-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,3:9:99:108,0,234:6,0,3,0 chr1 198717218 . GTT GTTT,G,GTTTT,GT 210.43 PASS AC=1,0,0,0;AF=0.368,0.074,0.029,0.103;AN=2;DP=1478;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant20-filterInvariant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant43-variant44 GT:DP:GQ:SB 0/1:45:99:11,12,12,10 chr1 200080463 . C T 217.78 PASS AC=1;AF=0.5;AN=2;DP=666;set=variant4-filterInvariant5-variant11-variant12-filterInvariant14-filterInvariant16-variant17-variant21-variant23-variant25-variant31-filterInvariant35-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:26,7:33:60:60,0,694:9,17,2,5 chr1 200089872 . C T 434.79 PASS AC=1;AF=0.629;AN=2;DP=1959;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant14-variant15-variant16-variant17-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,37:72:99:1111,0,1082:27,8,29,8 chr1 200090120 . G A 659.77 PASS AC=1;AF=0.604;AN=2;DP=1931;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant14-variant16-variant18-variant22-variant23-variant24-variant25-variant28-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,36:80:99:1002,0,1155:15,29,9,27 chr1 200143064 . CTTTTT CTTTT,CT,CTTT,C 107.95 PASS AC=0,1,0,0;AF=0.175,0.375,0.025,0.013;AN=2;DP=1044;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-filterInvariant38-variant39-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:17:99:4,3,7,3 chr1 200143442 . T C 729.36 PASS AC=1;AF=0.736;AN=2;DP=2040;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant17-variant18-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,21:49:99:604,0,668:16,12,14,7 chr1 200143844 . C G 1126.97 PASS AC=2;AF=0.78;AN=2;DP=3990;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,108:108:99:3769,324,0:0,0,60,48 chr1 200144089 . T G 5914.98 PASS AC=2;AF=0.78;AN=2;DP=16411;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,388:389:99:11822,1122,0:1,0,194,194 chr1 200145506 . G A 1285.4 PASS AC=1;AF=0.591;AN=2;DP=879;FractionInformativeReads=1;MQ=60;set=variant9-variant10-variant16-variant19-variant21-variant27-variant30-variant32-variant34-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:48,40:88:99:1082,0,1256:23,25,19,21 chr1 200145509 . G A 1285.84 PASS AC=2;AF=0.744;AN=2;DP=3356;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,84:86:99:3147,215,0:1,1,40,44 chr1 200145533 . G A 1275.52 PASS AC=2;AF=0.744;AN=2;DP=3343;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,79:81:99:2521,193,0:1,1,42,37 chr1 200145662 . G T 1740.43 PASS AC=2;AF=0.744;AN=2;DP=6228;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,188:188:99:5273,563,0:0,0,98,90 chr1 200145893 . A G 722.85 PASS AC=2;AF=0.78;AN=2;DP=2572;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:2152,215,0:0,0,44,28 chr1 200146493 . GA G 2495.85 PASS AC=2;AF=0.716;AN=2;DP=8992;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,268:268:99:9535,806,0:0,0,102,166 chr1 200182654 . T C 1613.59 PASS AC=2;AF=0.932;AN=2;DP=1979;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:1992,165,0:0,0,32,22 chr1 200182664 . C T 402.72 PASS AC=1;AF=0.661;AN=2;DP=1348;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant20-variant21-variant23-variant25-variant26-variant29-variant31-variant32-variant35-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:32,26:58:99:607,0,739:17,15,15,11 chr1 200182721 . G C 672.2 PASS AC=1;AF=0.5;AN=2;DP=584;MQ=60;set=variant-variant6-variant15-variant21-variant25-variant26-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:48,27:75:99:953,0,1958:26,22,15,12 chr1 200182725 . G A 666.42 PASS AC=1;AF=0.5;AN=2;DP=601;MQ=60;set=variant-variant6-variant15-variant21-variant25-variant26-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:48,27:75:99:956,0,1936:25,23,15,12 chr1 200182732 . A G 663.41 PASS AC=1;AF=0.5;AN=2;DP=610;MQ=60;set=variant-variant6-variant15-variant21-variant25-variant26-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:46,27:73:99:956,0,1897:24,22,15,12 chr1 200182733 . C T,G 746.91 PASS AC=1,0;AF=0.5,0.063;AN=2;DP=612;MQ=60;set=variant-variant6-variant15-variant21-variant25-variant26-variant35-variant41 GT:DP:GQ:SB 0/1:79:99:25,23,16,15 chr1 200182834 . A G 538.45 PASS AC=1;AF=0.643;AN=2;DP=3144;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant20-variant21-variant23-variant25-variant26-variant29-variant31-variant32-variant35-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:62,42:104:99:1055,0,1569:35,27,24,18 chr1 200183398 . C A 460.73 PASS AC=1;AF=0.661;AN=2;DP=2351;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant20-variant21-variant23-variant25-variant26-variant29-variant31-variant32-variant35-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:49,50:99:99:1145,0,1312:22,27,22,28 chr1 200183460 . C T 175.33 PASS AC=1;AF=0.604;AN=2;DP=985;set=variant-variant2-variant6-variant7-variant8-variant9-variant10-variant13-variant15-variant16-variant20-variant21-variant23-variant25-variant26-variant29-variant32-variant35-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:23,19:42:99:517,0,754:10,13,7,12 chr1 200311868 . C G 1136.92 PASS AC=1;AF=0.767;AN=2;DP=4604;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:80,53:133:99:1308,0,2016:35,45,26,27 chr1 200312546 . CAA CA,C 254 PASS AC=1,0;AF=0.81,0.071;AN=2;DP=782;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:DP:GQ:SB 0/1:16:3:0,2,3,11 chr1 200342046 . A C 1292.39 PASS AC=1;AF=0.64;AN=2;DP=760;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant13-variant14-variant18-variant19-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:28,11:39:99:294,0,790:20,8,9,2 chr1 200342825 . C A 443.99 PASS AC=1;AF=0.767;AN=2;DP=2346;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,23:80:99:467,0,1511:32,25,14,9 chr1 200521131 . T C 4147.85 PASS AC=2;AF=0.875;AN=2;DP=12887;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,277:277:99:8419,830,0:0,0,154,123 chr1 200521291 . TTTC T 2272.78 PASS AC=1;AF=0.606;AN=2;DP=5203;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant11-variant13-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:80,64:144:99:2319,0,3490:31,49,25,39 chr1 200521412 . G A 1512.57 PASS AC=1;AF=0.718;AN=2;DP=5039;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:74,45:119:99:1160,0,1905:40,34,23,22 chr1 200522039 . T G 245.29 PASS AC=2;AF=0.767;AN=2;DP=816;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,19:19:59:812,59,0:0,0,1,18 chr1 200522043 . TTTTATTTATTTATTTATTTA TTTTA,T,TTTTATTTA,TTTTATTTATTTA 193.63 PASS AC=2,0,0,0;AF=0.5,0.147,0.074,0.029;AN=2;DP=583;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:13:51:0,0,0,13 chr1 200522351 . A T 676.11 PASS AC=2;AF=0.782;AN=2;DP=2294;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,61:61:99:1840,183,0:0,0,39,22 chr1 200522566 . G C 1447.42 PASS AC=1;AF=0.606;AN=2;DP=3701;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant11-variant13-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:80,61:141:99:1357,0,1896:43,37,29,32 chr1 200523514 . A G 233.9 PASS AC=2;AF=0.803;AN=2;DP=401;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:664,45,0:0,0,13,2 chr1 200523518 . C CA 116.27 PASS AC=1;AF=0.5;AN=2;DP=98;set=variant3-variant5-variant8-variant18-variant19-variant24-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,6:15:99:115,0,205:9,0,4,2 chr1 200534248 . C T 1701.58 PASS AC=2;AF=0.782;AN=2;DP=4466;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,116:116:99:4051,348,0:0,0,66,50 chr1 200534255 . T A 1927.88 PASS AC=1;AF=0.5;AN=2;DP=278;FractionInformativeReads=1;MQ=60;set=variant3-variant35 GT:AD:DP:GQ:PL:SB 0/1:72,45:117:99:842,0,1742:40,32,25,20 chr1 200538885 . C T 319.54 PASS AC=2;AF=0.884;AN=2;DP=774;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:322,30,0:0,0,7,3 chr1 200549590 . T C 34.7 PASS AC=2;AF=0.797;AN=2;DP=329;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:598,48,0:0,0,3,13 chr1 200555482 . C T 80.65 PASS AC=1;AF=0.606;AN=2;DP=488;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant11-variant13-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,7:15:99:223,0,243:2,6,1,6 chr1 200558286 . GA G 638.65 PASS AC=1;AF=0.5;AN=2;DP=474;MQ=60;set=variant3-variant5-variant8-variant18-variant19-variant24-variant35-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,25:51:99:563,0,587:16,10,14,11 chr1 200558363 . T C 829.21 PASS AC=2;AF=0.875;AN=2;DP=4249;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,85:85:99:2483,254,0:0,0,41,44 chr1 200569392 . C A 1141.94 PASS AC=2;AF=0.977;AN=2;DP=2799;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1445,131,0:0,0,23,21 chr1 200576045 . G GA 39.71 PASS AC=1;AF=0.5;AN=2;DP=140;MQ=60;set=variant3-variant4-variant8-variant18-variant19-variant24-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:9,11:20:99:234,0,186:1,8,3,8 chr1 200578093 . G A 831.74 PASS AC=2;AF=0.977;AN=2;DP=1748;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1438,147,0:0,0,18,31 chr1 200589810 . C T 1165.47 PASS AC=1;AF=0.563;AN=2;DP=511;FractionInformativeReads=1;MQ=60;set=variant5-variant8-variant12-variant19-variant24-variant35-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,27:59:99:626,0,1221:17,15,12,15 chr1 200589813 . C A 383.39 PASS AC=1;AF=0.613;AN=2;DP=1857;MQ=60;set=variant-variant2-variant4-variant6-variant8-variant10-variant11-variant13-variant15-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,31:56:99:645,0,1014:12,13,17,14 chr1 200593174 . A G 61.77 PASS AC=1;AF=0.9;AN=2;DP=39;FS=0;FractionInformativeReads=1;MQ=60;set=variant5-variant9-variant12-variant18-variant21-variant25-variant27-variant35-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:2,4:6:94:159,0,94:1,1,3,1 chr1 200593193 . T C 61.77 PASS AC=1;AF=0.882;AN=2;DP=70;FractionInformativeReads=1;MQ=60;set=variant5-variant6-variant7-variant9-variant12-variant14-variant16-variant17-variant18-variant20-variant21-variant26-variant32-variant34-variant35-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:4,5:9:99:198,0,112:2,2,4,1 chr1 200593274 . G C 291.22 PASS AC=1;AF=0.596;AN=2;DP=326;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant7-variant8-variant9-variant11-variant16-variant17-variant18-variant19-variant21-variant24-variant25-variant27-variant28-variant30-variant31-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,10:16:99:272,0,216:4,2,7,3 chr1 200593325 . C T 103.26 PASS AC=1;AF=0.617;AN=2;DP=642;MQ=60;set=variant-variant3-variant5-variant7-variant8-variant9-variant11-filterInvariant12-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant24-variant25-variant27-variant28-variant30-variant31-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,18:28:99:482,0,282:8,2,11,7 chr1 200593418 . T TG 507.99 PASS AC=1;AF=0.617;AN=2;DP=1177;MQ=60;set=variant-variant3-variant5-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant24-variant25-variant27-variant28-variant30-variant31-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,25:51:99:848,0,844:13,13,13,12 chr1 200593468 . T A 604.65 PASS AC=1;AF=0.617;AN=2;DP=1080;MQ=60;set=variant-variant3-variant5-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant24-variant25-variant27-variant28-variant30-variant31-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,19:44:99:495,0,547:11,14,9,10 chr1 200593535 . CTAT C,CTATTATTATTATTAT,CTATTATTATTATTATTAT 485.55 PASS AC=1,0,0;AF=0.638,0.034,0.017;AN=2;DP=490;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant24-variant25-variant27-variant28-variant30-variant31-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:DP:GQ:SB 0/1:10:64:1,1,2,6 chr1 200593551 . T C 494.4 PASS AC=1;AF=0.661;AN=2;DP=332;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant12-variant14-variant15-variant16-variant18-variant19-variant21-variant24-variant25-variant27-variant28-variant30-variant31-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,8:10:64:289,0,64:1,1,2,6 chr1 200593562 . A T 472.64 PASS AC=1;AF=0.679;AN=2;DP=251;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant12-variant14-variant15-variant16-variant18-variant19-variant21-variant24-variant25-variant27-variant28-variant30-variant31-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,5:6:27:207,0,27:0,1,1,4 chr1 200594240 . G A 1679.22 PASS AC=2;AF=1;AN=2;DP=1673;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:1031,81,0:0,0,5,22 chr1 200610525 . TA T 128.3 PASS AC=2;AF=0.923;AN=2;DP=450;FS=0;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:157,18,0:0,0,1,5 chr1 200618238 . T C 822.66 PASS AC=2;AF=0.943;AN=2;DP=2846;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,54:55:99:1457,118,0:1,0,28,26 chr1 200619478 . C A 187.9 PASS AC=2;AF=1;AN=2;DP=541;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:1077,81,0:0,0,24,3 chr1 200619530 . T C 1234.47 PASS AC=2;AF=1;AN=2;DP=1617;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1836,150,0:0,0,42,8 chr1 200638847 . A G 334.7 PASS AC=1;AF=0.667;AN=2;DP=1056;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant10-variant11-variant13-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,8:30:99:147,0,538:13,9,5,3 chr1 200639023 . TGCGGA T,TGCGGGGCGGAGCGGA,TGCGGGGCGGAGCGGAGCGGA,TGCGGGGCGGAGCGGAGCGGAGCGGAGCGGA,TGCGGGGCGGA 1395.66 PASS AC=0,1,0,0,0;AF=0.086,0.414,0.017,0.017,0.017;AN=2;DP=2417;set=variant-variant3-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant24-variant25-variant27-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:DP:GQ:SB 0/2:72:99:16,19,20,17 chr1 200639040 . CGGAGCGTAGA C 355.37 PASS AC=1;AF=0.667;AN=2;DP=2467;set=variant-variant2-variant4-variant6-variant7-variant8-variant10-variant11-variant13-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,31:70:99:1184,0,1433:21,18,16,15 chr1 200639047 . T G 3381.86 PASS AC=1;AF=0.571;AN=2;DP=2202;MQ=60;set=variant3-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant16-variant17-variant18-variant19-variant21-variant24-variant25-variant27-variant28-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,34:65:99:1324,0,1200:16,15,18,16 chr1 200639050 . A C 3381.48 PASS AC=1;AF=0.571;AN=2;DP=2174;MQ=60;set=variant3-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant16-variant17-variant18-variant19-variant21-variant24-variant25-variant27-variant28-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,34:65:99:1323,0,1201:16,15,18,16 chr1 200639156 . G A 96.25 PASS AC=1;AF=0.677;AN=2;DP=496;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant10-variant11-variant13-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:99:121,0,134:1,3,2,2 chr1 200816521 . G T 631.52 PASS AC=2;AF=0.778;AN=2;DP=914;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,31:31:93:1104,93,0:0,0,7,24 chr1 200816658 . T C 623.01 PASS AC=2;AF=1;AN=2;DP=592;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:664,48,0:0,0,13,3 chr1 200819424 . AT A 956.91 PASS AC=1;AF=0.5;AN=2;DP=822;MQ=60;set=variant3-variant7-variant14-variant16-variant21-variant23-variant28-variant33-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:37,38:75:99:857,0,864:9,28,14,24 chr1 200824978 . C T 130.7 PASS AC=1;AF=0.661;AN=2;DP=263;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant6-variant8-variant10-variant11-variant13-variant14-variant15-variant20-variant21-variant22-variant23-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,3:10:99:105,0,738:5,2,2,1 chr1 200824980 . C T 130.7 PASS AC=1;AF=0.643;AN=2;DP=263;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant6-variant8-variant10-variant11-variant13-variant14-variant15-variant20-variant21-variant22-variant23-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,3:10:99:105,0,738:5,2,2,1 chr1 200824981 . C T 130.7 PASS AC=1;AF=0.643;AN=2;DP=269;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant6-variant8-variant10-variant11-variant13-variant14-variant15-variant20-variant21-variant22-variant23-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,3:10:99:105,0,738:5,2,2,1 chr1 200842005 . T A 2900.7 PASS AC=1;AF=0.661;AN=2;DP=1581;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant20-variant21-variant22-variant23-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,31:51:99:1181,0,1114:14,6,24,7 chr1 200842006 . C G 2900.7 PASS AC=1;AF=0.661;AN=2;DP=1631;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant20-variant21-variant22-variant23-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,30:51:99:1181,0,1114:14,7,23,7 chr1 200843305 . G T 3143.46 PASS AC=1;AF=0.685;AN=2;DP=3142;MQ=60;set=variant-variant2-variant4-variant6-variant8-variant10-variant11-variant13-variant14-variant15-variant20-variant21-variant22-variant23-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:63,60:123:99:1592,0,1745:20,43,17,43 chr1 200864267 . T C 773.09 PASS AC=1;AF=0.735;AN=2;DP=222;MQ=60;set=variant3-variant7-variant11-variant12-variant14-variant16-variant22-variant23-variant25-variant28-variant29-variant31-variant32-variant33-variant35-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,11:23:99:302,0,356:7,5,5,6 chr1 200868493 . GTGTGTGTGCA G 631.85 PASS AC=1;AF=0.619;AN=2;DP=836;MQ=60;set=variant2-variant3-variant7-variant11-variant12-variant14-variant16-variant20-variant22-variant23-variant25-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,19:36:99:607,0,1608:10,7,11,8 chr1 200877850 . T G 249.53 PASS AC=1;AF=0.605;AN=2;DP=719;MQ=60;set=variant2-variant5-variant7-variant11-variant12-variant14-variant16-variant20-variant22-variant23-variant28-variant29-variant32-variant33-variant34-variant35-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,13:27:99:331,0,373:9,5,8,5 chr1 200878727 . G A 368.9 PASS AC=1;AF=0.605;AN=2;DP=237;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant7-variant11-variant12-variant14-variant16-variant20-variant22-variant23-variant28-variant29-variant32-variant33-variant34-variant35-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,14:22:99:461,0,182:2,6,2,12 chr1 200880978 . C T 1054.2 PASS AC=1;AF=0.808;AN=2;DP=1789;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,21:64:99:489,0,1209:21,22,8,13 chr1 200881172 . C A 995.71 PASS AC=1;AF=0.694;AN=2;DP=3968;set=variant-variant2-variant3-variant4-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,58:114:99:1393,0,1389:33,23,36,22 chr1 200881392 . C T 581.77 PASS AC=1;AF=0.591;AN=2;DP=1381;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant7-variant10-variant11-variant12-variant14-variant16-variant19-variant20-variant22-variant23-variant28-variant29-variant32-variant33-variant34-variant35-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,40:87:99:1001,0,1279:17,30,14,26 chr1 200881480 . CCATGTCTAGCT C 1597.05 PASS AC=1;AF=0.538;AN=2;DP=287;MQ=60;set=variant3-variant4-variant11-variant16-variant18-variant19-variant25-variant26-variant29-variant31-variant32-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:14,12:26:99:462,0,552:3,11,2,10 chr1 200938474 . G T 73.27 PASS AC=1;AF=0.63;AN=2;DP=169;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant6-variant8-variant9-variant10-variant11-variant13-variant15-variant18-variant20-variant21-variant24-variant28-variant30-variant31-variant34-variant35-variant36-variant37-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,5:9:99:117,0,114:2,2,2,3 chr1 200939642 . C T 897.13 PASS AC=1;AF=0.583;AN=2;DP=1173;MQ=60;set=variant2-variant5-variant7-variant11-variant14-variant16-variant20-variant22-variant23-variant28-variant29-variant32-variant33-variant34-variant35-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,28:68:99:817,0,986:19,21,12,16 chr1 200940180 . G A 458.17 PASS AC=1;AF=0.597;AN=2;DP=1797;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant24-variant25-variant28-variant30-variant31-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,34:76:99:723,0,1063:23,19,15,19 chr1 200941549 . T C 2295.06 PASS AC=2;AF=1;AN=2;DP=3775;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,106:106:99:3349,318,0:0,0,56,50 chr1 200941716 . G A 1087.02 PASS AC=1;AF=0.6;AN=2;DP=2958;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant24-variant25-variant28-variant30-variant31-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,52:106:99:1142,0,1196:23,31,22,30 chr1 200943793 . CAGGA C 907.85 PASS AC=2;AF=1;AN=2;DP=3107;FS=0;MQ=60;MQRankSum=0.976;ReadPosRankSum=0.682;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,73:73:99:3278,220,0:0,0,51,22 chr1 200944840 . T G 337.45 PASS AC=1;AF=0.825;AN=2;DP=710;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,16:28:99:425,0,404:4,8,6,10 chr1 200957697 . A G 329.79 PASS AC=1;AF=0.583;AN=2;DP=408;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant7-variant11-variant14-variant16-variant20-variant22-variant23-variant28-variant29-variant32-variant33-variant34-variant35-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,14:30:99:387,0,505:15,1,12,2 chr1 200960307 . G A 368.41 PASS AC=1;AF=0.588;AN=2;DP=410;MQ=60;set=variant2-variant5-variant7-variant11-variant14-variant16-variant20-variant22-variant23-variant28-variant29-variant32-variant33-variant34-variant35-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,18:29:99:541,0,348:1,10,4,14 chr1 200965601 . G A 830.74 PASS AC=1;AF=0.6;AN=2;DP=1568;MQ=60;set=variant-variant2-variant5-variant7-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,24:53:99:622,0,770:13,16,10,14 chr1 200967490 . A G 117.84 PASS AC=1;AF=0.617;AN=2;DP=908;MQ=60;set=variant-variant2-variant5-variant7-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,32:49:99:763,0,406:13,4,20,12 chr1 200967778 . G T 254.02 PASS AC=1;AF=0.529;AN=2;DP=935;MQ=60;set=variant-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant20-variant21-variant24-variant28-variant35-variant36-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,37:67:99:989,0,854:9,21,12,25 chr1 201008582 . T TG 151.64 PASS AC=1;AF=0.679;AN=2;DP=486;MQ=60;set=variant-variant2-variant5-variant7-variant11-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,14:24:99:382,0,254:9,1,12,2 chr1 201008898 . G A 2333.93 PASS AC=1;AF=0.5;AN=2;DP=166;FS=3.611;FractionInformativeReads=1;MQ=60;MQRankSum=-1.742;QD=14.06;ReadPosRankSum=3.628;SOR=0.462;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:75,91:166:99:2362,0,1943:32,43,45,46 chr1 201009556 . A G 1496.24 PASS AC=1;AF=0.614;AN=2;DP=1416;MQ=60;set=variant2-variant5-variant7-variant11-variant14-variant16-variant20-variant22-variant23-variant25-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,33:62:99:732,0,709:13,16,16,17 chr1 201009897 . T C 828.78 PASS AC=2;AF=1;AN=2;DP=1696;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1288,123,0:0,0,16,25 chr1 201010862 . T C 337.64 PASS AC=1;AF=0.667;AN=2;DP=794;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant7-variant10-variant11-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,21:38:99:581,0,516:3,14,6,15 chr1 201012597 . G A 1605.04 PASS AC=1;AF=0.5;AN=2;DP=1918;MQ=60;set=variant5-variant7-variant11-variant14-variant20-variant22-variant28-variant32-variant33-variant34-variant35-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:76,81:157:99:1957,0,1982:28,48,32,49 chr1 201020105 . A G 1678.17 PASS AC=1;AF=0.768;AN=2;DP=3544;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,50:105:99:1174,0,1362:31,24,28,22 chr1 201020360 . G A 871.98 PASS AC=1;AF=0.5;AN=2;DP=1105;MQ=60;set=variant5-variant7-variant11-variant14-variant20-variant22-variant28-variant32-variant33-variant34-variant35-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,36:69:99:1018,0,891:13,20,12,24 chr1 201020574 . T G 222.72 PASS AC=1;AF=0.789;AN=2;DP=384;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,10:14:99:246,0,99:1,3,4,6 chr1 201031307 . A C 152.85 PASS AC=1;AF=0.686;AN=2;DP=780;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant28-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,12:22:99:338,0,317:1,9,2,10 chr1 201044577 . A C 197.79 PASS AC=1;AF=0.5;AN=2;DP=1396;MQ=60;set=variant-variant2-filterInvariant3-filterInvariant4-filterInvariant5-variant6-filterInvariant7-variant8-filterInvariant9-filterInvariant11-variant13-variant16-filterInvariant17-filterInvariant18-variant19-variant20-variant21-filterInvariant22-filterInvariant24-filterInvariant25-variant26-filterInvariant27-variant28-variant29-variant30-filterInvariant32-variant33-filterInvariant35-filterInvariant36-filterInvariant37-variant38-variant40-filterInvariant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,11:37:67:67,0,364:12,14,9,2 chr1 201044583 . T C 58.98 PASS AC=1;AF=0.5;AN=2;DP=1848;MQ=60;set=filterInvariant-variant2-filterInvariant3-filterInvariant4-filterInvariant5-variant6-filterInvariant7-variant8-filterInvariant9-variant11-variant13-variant14-filterInvariant15-variant16-variant17-filterInvariant18-filterInvariant19-variant20-filterInvariant21-variant22-variant23-variant24-filterInvariant25-variant26-variant27-variant28-variant29-variant30-filterInvariant31-variant32-variant33-variant34-variant35-filterInvariant36-filterInvariant37-variant38-variant39-variant40-variant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:28,16:44:99:267,0,1189:9,19,16,0 chr1 201044587 . T C 194.3 PASS AC=1;AF=0.5;AN=2;DP=1602;MQ=60;set=variant2-variant3-filterInvariant4-filterInvariant5-variant6-variant7-filterInvariant8-variant9-variant11-variant13-variant14-filterInvariant15-variant16-variant17-variant18-variant19-variant20-filterInvariant24-filterInvariant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-filterInvariant34-variant35-filterInvariant36-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,8:41:99:261,0,1246:14,19,8,0 chr1 201047062 . G A 833.62 PASS AC=1;AF=0.568;AN=2;DP=1773;MQ=60;set=variant-variant3-variant5-variant8-variant10-variant11-variant12-variant14-variant15-variant21-variant23-variant25-variant26-variant30-variant32-variant35-variant36-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,41:91:99:1002,0,1277:28,22,26,15 chr1 201047075 . A G 830.63 PASS AC=1;AF=0.713;AN=2;DP=3651;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,45:97:99:1182,0,1280:29,23,27,18 chr1 201052199 . T C 826.67 PASS AC=1;AF=0.568;AN=2;DP=1152;MQ=60;set=variant-variant3-variant5-variant8-variant10-variant11-variant12-variant14-variant15-variant21-variant23-variant25-variant26-variant30-variant32-variant35-variant36-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,30:66:99:873,0,1063:27,9,23,7 chr1 201054197 . G T 603.4 PASS AC=1;AF=0.571;AN=2;DP=524;MQ=60;set=variant-variant3-variant8-variant10-variant11-variant12-variant16-variant21-variant35-variant36-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,19:40:99:582,0,546:8,13,4,15 chr1 201079235 . C T 546.98 PASS AC=1;AF=0.605;AN=2;DP=888;MQ=60;set=variant2-variant3-variant6-variant9-variant10-variant11-variant13-variant16-variant22-variant26-variant27-variant28-variant34-variant35-variant37-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:24,27:51:99:732,0,750:19,5,19,8 chr1 201079458 . T A 347.27 PASS AC=1;AF=0.606;AN=2;DP=2798;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant9-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:48,44:92:99:1124,0,1212:19,29,16,28 chr1 201081698 . T C 463.57 PASS AC=1;AF=0.588;AN=2;DP=614;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant6-variant9-variant10-variant11-variant13-variant16-variant27-variant28-variant29-variant34-variant35-variant37-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:28,13:41:99:294,0,718:16,12,4,9 chr1 201081777 . C G 54.22 PASS AC=1;AF=0.6;AN=2;DP=221;MQ=60;set=variant2-variant3-variant9-variant10-variant11-variant13-variant16-variant27-variant29-variant34-variant35-variant37-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:14,4:18:72:72,0,334:4,10,3,1 chr1 201083343 . A G 754.73 PASS AC=1;AF=0.6;AN=2;DP=2066;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant9-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant23-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:35,36:71:99:1029,0,1014:11,24,15,21 chr1 201083506 . A G 1267.92 PASS AC=1;AF=0.6;AN=2;DP=4021;set=variant-variant2-variant3-variant4-variant6-variant7-variant9-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant23-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:58,79:137:99:2068,0,1182:31,27,45,34 chr1 201096101 . AGCCCT A 460.6 PASS AC=1;AF=0.594;AN=2;DP=520;MQ=60;set=variant2-variant3-variant6-variant10-variant11-variant13-variant16-variant27-variant28-variant29-variant34-variant35-variant37-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:26,11:37:99:384,0,1886:19,7,7,4 chr1 201096383 . A G 565.45 PASS AC=1;AF=0.6;AN=2;DP=983;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant9-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant23-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:28,18:46:99:531,0,853:11,17,7,11 chr1 201104341 . T TA 1181.31 PASS AC=1;AF=0.603;AN=2;DP=2843;set=variant5-variant6-variant7-variant8-variant9-variant12-variant14-variant15-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:71,62:133:99:1806,0,2121:32,39,30,32 chr1 201104556 . C A 181.19 PASS AC=1;AF=0.531;AN=2;DP=628;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant15-variant16-variant17-variant18-variant20-variant21-variant23-variant33-variant35-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:26,21:47:99:482,0,704:14,12,11,10 chr1 201104589 . A G 508.47 PASS AC=1;AF=0.603;AN=2;DP=1192;FractionInformativeReads=1;MQ=60;set=variant5-variant6-variant7-variant8-variant9-variant12-variant14-variant15-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,25:50:99:754,0,595:13,12,12,13 chr1 201112981 . A G 2086.61 PASS AC=2;AF=0.714;AN=2;DP=5063;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,162:162:99:4994,486,0:0,0,93,69 chr1 201113118 . A G 1724.33 PASS AC=2;AF=0.932;AN=2;DP=4962;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,111:111:99:3475,331,0:0,0,41,70 chr1 201115822 . A G 1175.3 PASS AC=1;AF=0.543;AN=2;DP=3714;MQ=60;set=variant-variant3-variant6-variant7-variant9-variant10-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant31-variant35-variant37-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:72,69:141:99:1657,0,1524:35,37,37,32 chr1 201116018 . C G 1234.79 PASS AC=2;AF=0.932;AN=2;DP=2556;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,67:67:99:2012,201,0:0,0,26,41 chr1 201120730 . C A 326.88 PASS AC=1;AF=0.565;AN=2;DP=488;MQ=60;set=variant-variant2-variant6-variant10-variant11-variant12-variant13-variant14-variant19-variant24-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,15:26:99:402,0,404:10,1,10,5 chr1 201122784 . C T 441.42 PASS AC=2;AF=0.714;AN=2;DP=1831;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1608,150,0:0,0,34,16 chr1 201122947 . T G 1564.58 PASS AC=2;AF=0.932;AN=2;DP=4504;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,106:106:99:3333,318,0:0,0,52,54 chr1 201140516 . G A 186.65 PASS AC=1;AF=0.536;AN=2;DP=351;MQ=60;set=variant-variant6-variant7-variant15-variant16-variant18-variant21-variant22-variant24-variant25-variant30-variant35-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:9,7:16:99:110,0,261:7,2,4,3 chr1 201140614 . G T 272.17 PASS AC=1;AF=0.536;AN=2;DP=792;MQ=60;set=variant-variant6-variant7-variant15-variant16-variant18-variant21-variant22-variant24-variant25-variant30-variant35-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:27,22:49:99:483,0,633:15,12,12,10 chr1 201162411 . G A 1636.75 PASS AC=2;AF=0.596;AN=2;DP=1385;MQ=60;set=variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant15-variant18-variant19-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1583,167,0:0,0,29,27 chr1 201162643 . G A 40.75 PASS AC=2;AF=0.786;AN=2;DP=33;FS=0;FractionInformativeReads=1;MQ=60;set=variant15-variant21-variant22-variant28-variant34-variant35-variant36 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:128,12,0:0,0,2,2 chr1 201164764 . T C 544.18 PASS AC=2;AF=0.609;AN=2;DP=343;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant15-variant18-variant19-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant33-variant35-variant36-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:452,42,0:0,0,7,7 chr1 201166435 . T C 1630.72 PASS AC=2;AF=0.93;AN=2;DP=4439;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,90:90:99:3148,269,0:0,0,38,52 chr1 201166598 . C T 539.79 PASS AC=2;AF=0.596;AN=2;DP=500;MQ=60;set=variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant15-variant18-variant19-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:788,69,0:0,0,6,17 chr1 201169601 . C T 2819.12 PASS AC=2;AF=0.609;AN=2;DP=1111;MQ=60;set=variant3-variant6-variant7-variant8-variant9-variant10-variant15-variant18-variant19-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant35-variant36-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,61:61:99:2191,182,0:0,0,10,51 chr1 201170772 . A G 2088.19 PASS AC=2;AF=0.943;AN=2;DP=2168;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:1933,174,0:0,0,41,17 chr1 201170824 . C G 3259.2 PASS AC=2;AF=0.943;AN=2;DP=4657;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,117:117:99:3436,351,0:0,0,64,53 chr1 201171007 . T G 503.79 PASS AC=2;AF=0.788;AN=2;DP=1671;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1525,135,0:0,0,13,32 chr1 201173104 . C T 321.22 PASS AC=2;AF=0.726;AN=2;DP=2318;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,64:64:99:2031,192,0:0,0,20,44 chr1 201174204 . C T 391.57 PASS AC=1;AF=0.553;AN=2;DP=1435;MQ=60;set=variant2-variant3-variant7-variant8-variant9-variant10-variant19-variant20-variant22-variant27-variant28-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,41:94:99:968,0,1401:28,25,21,20 chr1 201174215 . C A 1123.63 PASS AC=1;AF=0.571;AN=2;DP=639;FractionInformativeReads=1;MQ=60;set=variant4-variant18-variant24-variant25-variant30-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:41,49:90:99:1286,0,1007:20,21,26,23 chr1 201175227 . C A 3948.19 PASS AC=2;AF=0.744;AN=2;DP=7586;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,190:192:99:5633,553,0:0,2,109,81 chr1 201175274 . A G 2284.46 PASS AC=1;AF=0.621;AN=2;DP=6023;MQ=60;set=variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:113,85:198:99:1885,0,2979:62,51,44,41 chr1 201175715 . G T 2284.79 PASS AC=2;AF=0.744;AN=2;DP=3975;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,92:92:99:2967,275,0:0,0,51,41 chr1 201176018 . A G 947.96 PASS AC=2;AF=0.756;AN=2;DP=2465;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:1814,165,0:0,0,23,32 chr1 201179050 . A G 2418.73 PASS AC=1;AF=0.5;AN=2;DP=22480;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:371,134:505:99:4119,0,11501:178,193,49,85 chr1 201179068 . G A 1628.99 PASS AC=1;AF=0.5;AN=2;DP=21916;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-filterInvariant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-filterInvariant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:377,118:495:99:3142,0,17644:185,192,44,74 chr1 201179082 . G A 1349.97 PASS AC=1;AF=0.5;AN=2;DP=20395;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-filterInvariant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:372,93:465:99:2770,0,17020:174,198,32,61 chr1 201179089 . G A 4204.23 PASS AC=1;AF=0.5;AN=2;DP=3163;set=variant4-variant18-variant24-variant25-variant30-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:248,181:429:99:3969,0,7747:108,140,82,99 chr1 201180145 . G A 3658.49 PASS AC=1;AF=0.5;AN=2;DP=10897;set=filterInvariant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-filterInvariant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-filterInvariant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-filterInvariant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:133,135:268:99:5067,0,5390:79,54,47,88 chr1 201180148 . A G 3645.8 PASS AC=1;AF=0.5;AN=2;DP=10844;set=filterInvariant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-filterInvariant11-variant12-variant13-variant14-filterInvariant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-filterInvariant26-variant27-filterInvariant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-filterInvariant41-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:140,123:263:99:4867,0,5786:85,55,42,81 chr1 201180153 . A G 3351.98 PASS AC=1;AF=0.5;AN=2;DP=11055;set=variant-variant2-variant3-filterInvariant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-filterInvariant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-filterInvariant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-filterInvariant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:153,106:259:99:4016,0,6353:89,64,35,71 chr1 201180162 . A C 3126.83 PASS AC=1;AF=0.5;AN=2;DP=10482;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-filterInvariant15-variant17-variant18-variant19-variant20-variant22-variant23-variant25-filterInvariant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-filterInvariant40-filterInvariant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:179,91:270:99:3356,0,7403:106,73,27,64 chr1 201180172 . G A 2232.85 PASS AC=1;AF=0.5;AN=2;DP=10477;set=variant-variant2-variant3-filterInvariant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-filterInvariant15-variant17-variant18-variant19-variant20-variant22-filterInvariant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant40-filterInvariant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:212,87:299:99:3051,0,8721:124,88,28,59 chr1 201180193 . A G 642.65 PASS AC=1;AF=0.5;AN=2;DP=10514;set=variant-variant2-filterInvariant3-filterInvariant4-variant8-filterInvariant9-variant10-variant11-variant12-filterInvariant13-filterInvariant14-filterInvariant15-filterInvariant17-variant18-variant19-variant20-variant22-variant26-filterInvariant27-filterInvariant28-filterInvariant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant40-filterInvariant41-filterInvariant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:266,46:312:99:1423,0,11132:148,118,11,35 chr1 201180200 . T G 378.54 PASS AC=1;AF=0.5;AN=2;DP=7241;set=filterInvariant-variant2-filterInvariant4-variant8-variant10-filterInvariant11-filterInvariant12-variant18-variant19-filterInvariant20-filterInvariant22-variant26-filterInvariant28-filterInvariant31-filterInvariant33-variant34-filterInvariant35-variant37-variant38-variant41-filterInvariant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:284,34:318:99:665,0,12073:158,126,10,24 chr1 201181223 . A G 5963.39 PASS AC=2;AF=1;AN=2;DP=9965;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,279:279:99:8365,836,0:0,0,138,141 chr1 201183424 . G A 2339.55 PASS AC=1;AF=0.571;AN=2;DP=1375;MQ=60;set=variant4-variant18-variant24-variant25-variant30-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:98,85:183:99:1930,0,2561:48,50,35,50 chr1 201184878 . C A 2534.9 PASS AC=1;AF=0.571;AN=2;DP=1403;MQ=60;set=variant4-variant18-variant24-variant25-variant30-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:110,102:212:99:2465,0,2662:58,52,54,48 chr1 201187764 . T C 1381.83 PASS AC=2;AF=0.864;AN=2;DP=6566;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,136:136:99:4289,408,0:0,0,64,72 chr1 201187828 . T C 872.32 PASS AC=2;AF=0.864;AN=2;DP=4629;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,93:93:99:2912,279,0:0,0,38,55 chr1 201187954 . C T 207.96 PASS AC=2;AF=0.864;AN=2;DP=726;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:452,39,0:0,0,2,11 chr1 201193668 . G T 1317.73 PASS AC=2;AF=0.898;AN=2;DP=3935;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,104:104:99:3234,312,0:0,0,58,46 chr1 201195119 . C T 1994.67 PASS AC=1;AF=0.694;AN=2;DP=8034;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:134,123:257:99:2990,0,3127:72,62,66,57 chr1 201197331 . G A 197.88 PASS AC=1;AF=0.676;AN=2;DP=904;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,7:18:99:233,0,336:9,2,7,0 chr1 201197358 . G C 511.19 PASS AC=1;AF=0.558;AN=2;DP=1029;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant32-variant35-variant36-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,19:46:99:574,0,852:21,6,16,3 chr1 201197471 . T C 1562.13 PASS AC=1;AF=0.558;AN=2;DP=3567;MQ=60;set=variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant32-variant35-variant36-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:100,84:184:99:1932,0,2338:57,43,46,38 chr1 201197781 . C T 628.54 PASS AC=1;AF=0.558;AN=2;DP=1906;MQ=60;set=variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant32-variant35-variant36-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,47:92:99:1026,0,1113:28,17,22,25 chr1 201197808 . T A 1207.13 PASS AC=1;AF=0.667;AN=2;DP=1940;MQ=60;set=variant3-variant4-variant5-variant6-variant9-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:44,47:91:99:1187,0,1052:20,24,27,20 chr1 201198183 . A G 70.66 PASS AC=2;AF=0.927;AN=2;DP=250;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:292,27,0:0,0,2,7 chr1 201252701 . A T 2922.89 PASS AC=2;AF=0.825;AN=2;DP=3754;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,85:85:99:2610,253,0:0,0,49,36 chr1 201263330 . C G 1008.07 PASS AC=1;AF=0.5;AN=2;DP=747;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant7-variant8-variant10-variant11-variant16-variant17-variant20-variant21-variant35-variant36-variant39 GT:AD:DP:GQ:PL:SB 0/1:35,27:62:99:658,0,982:13,22,10,17 chr1 201282167 . C G 241.77 PASS AC=1;AF=0.75;AN=2;DP=779;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,11:20:99:351,0,287:8,1,9,2 chr1 201285759 . A G 1540.25 PASS AC=2;AF=0.989;AN=2;DP=2887;MQ=60;MQRankSum=-0.525;ReadPosRankSum=0.673;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,61:61:99:1887,182,0:0,0,31,30 chr1 201285909 . A G 322.85 PASS AC=1;AF=0.814;AN=2;DP=729;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,10:20:99:293,0,319:3,7,2,8 chr1 201286614 . GA G 457.73 PASS AC=2;AF=0.907;AN=2;DP=1399;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:93:1375,93,0:0,0,19,11 chr1 201286628 . C G 553.59 PASS AC=2;AF=0.907;AN=2;DP=1676;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1564,111,0:0,0,24,13 chr1 201286678 . C T 823.55 PASS AC=1;AF=0.533;AN=2;DP=942;MQ=60;set=variant3-variant5-variant7-variant8-variant10-variant11-variant16-variant17-variant20-variant21-variant24-variant28-variant35-variant36-variant39 GT:AD:DP:GQ:PL:SB 0/1:33,36:69:99:956,0,735:17,16,24,12 chr1 201286771 . C T 1691.97 PASS AC=1;AF=0.533;AN=2;DP=1463;MQ=60;set=variant3-variant5-variant7-variant8-variant10-variant11-variant16-variant17-variant20-variant21-variant24-variant28-variant35-variant36-variant39 GT:AD:DP:GQ:PL:SB 0/1:49,69:118:99:1530,0,1074:28,21,35,34 chr1 201288007 . G A 613.12 PASS AC=2;AF=0.917;AN=2;DP=947;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:83:789,83,0:0,0,10,18 chr1 201288898 . A C 571.36 PASS AC=2;AF=1;AN=2;DP=3035;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,75:76:99:2260,218,0:0,1,42,33 chr1 201288955 . G A 2210.81 PASS AC=1;AF=0.533;AN=2;DP=1597;MQ=60;set=variant3-variant5-variant7-variant8-variant10-variant11-variant16-variant17-variant20-variant21-variant24-variant28-variant35-variant36-variant39 GT:AD:DP:GQ:PL:SB 0/1:45,67:112:99:1915,0,1136:28,17,42,25 chr1 201289175 . G A 981.91 PASS AC=1;AF=0.533;AN=2;DP=949;set=variant3-variant5-variant7-variant8-variant10-variant11-variant16-variant17-variant20-variant21-variant24-variant28-variant35-variant36-variant39 GT:AD:DP:GQ:PL:SB 0/1:39,29:68:99:821,0,983:15,24,11,18 chr1 201290968 . T G 752.17 PASS AC=2;AF=1;AN=2;DP=1632;FS=0;MQ=60;MQRankSum=1.238;ReadPosRankSum=0.413;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:1157,90,0:0,0,26,4 chr1 201291066 . C T 3618.84 PASS AC=1;AF=0.756;AN=2;DP=6448;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:85,97:182:99:2401,0,2061:53,32,65,32 chr1 201291283 . C T 1737 PASS AC=1;AF=0.533;AN=2;DP=1230;MQ=60;set=variant3-variant5-variant7-variant8-variant10-variant11-variant16-variant17-variant20-variant21-variant24-variant28-variant35-variant36-variant39 GT:AD:DP:GQ:PL:SB 0/1:42,44:86:99:1257,0,1357:7,35,11,33 chr1 201292036 . T C 570.6 PASS AC=1;AF=0.536;AN=2;DP=329;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant8-variant10-variant11-variant16-variant17-variant20-variant21-variant24-variant28-variant35-variant36-variant39 GT:AD:DP:GQ:PL:SB 0/1:16,7:23:99:205,0,482:12,4,5,2 chr1 201292110 . T C 915.68 PASS AC=2;AF=1;AN=2;DP=2851;FS=0;MQ=60;MQRankSum=1.606;ReadPosRankSum=0.472;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:1955,171,0:0,0,39,18 chr1 201293512 . TG T 2618.6 PASS AC=1;AF=0.764;AN=2;DP=3373;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,45:100:99:1303,0,1646:33,22,27,18 chr1 201293970 . C T 366.99 PASS AC=2;AF=0.989;AN=2;DP=515;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.58;ReadPosRankSum=-0.731;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:508,42,0:0,0,11,3 chr1 201293985 . G A 415.31 PASS AC=1;AF=0.829;AN=2;DP=562;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,10:15:99:311,0,99:3,2,8,2 chr1 201299263 . A G 511.33 PASS AC=2;AF=1;AN=2;DP=595;FS=0;MQ=60;MQRankSum=1.542;ReadPosRankSum=-0.964;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:410,36,0:0,0,9,3 chr1 201299393 . T G 709.57 PASS AC=2;AF=0.977;AN=2;DP=777;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:662,63,0:0,0,12,9 chr1 201299470 . A C 1130.08 PASS AC=2;AF=0.854;AN=2;DP=1299;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1283,130,0:0,0,26,18 chr1 201299748 . G A 2607.3 PASS AC=2;AF=0.8;AN=2;DP=2963;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:2294,223,0:0,0,36,39 chr1 201299785 . A C 2031.13 PASS AC=2;AF=0.86;AN=2;DP=2926;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,63:63:99:2318,189,0:0,0,34,29 chr1 201299852 . A G 1523.27 PASS AC=2;AF=0.775;AN=2;DP=3217;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:2453,228,0:0,0,38,38 chr1 201299900 . G A 1853.56 PASS AC=2;AF=0.775;AN=2;DP=3464;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,73:73:99:2212,217,0:0,0,36,37 chr1 201300842 . T C 2029.79 PASS AC=2;AF=0.92;AN=2;DP=3459;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,100:100:99:3092,300,0:0,0,47,53 chr1 201300858 . C A 2123.53 PASS AC=2;AF=0.989;AN=2;DP=3319;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,87:87:99:2746,261,0:0,0,39,48 chr1 201301873 . A G 1760.62 PASS AC=1;AF=0.849;AN=2;DP=4047;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:73,59:132:99:1570,0,1987:43,30,29,30 chr1 201301906 . C G 2392.59 PASS AC=1;AF=0.852;AN=2;DP=4417;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:85,62:147:99:1584,0,2152:47,38,27,35 chr1 201331554 . T G 2300.46 PASS AC=2;AF=0.841;AN=2;DP=5684;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,137:137:99:4098,410,0:0,0,79,58 chr1 201331664 . C A 1793.77 PASS AC=2;AF=0.736;AN=2;DP=3356;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,89:89:99:2726,267,0:0,0,31,58 chr1 201334382 . G A 5598.03 PASS AC=2;AF=0.841;AN=2;DP=7627;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,187:188:99:5662,552,0:0,1,81,106 chr1 201334795 . C T 1618.55 PASS AC=1;AF=0.5;AN=2;DP=982;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant20-variant22-variant30-variant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,52:113:99:1211,0,1581:33,28,26,26 chr1 201335899 . C T 747.99 PASS AC=2;AF=0.989;AN=2;DP=1572;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1325,111,0:0,0,20,17 chr1 201336984 . C T 1048.34 PASS AC=1;AF=0.629;AN=2;DP=2438;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant12-variant13-variant15-variant16-variant17-variant18-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,46:99:99:967,0,1150:22,31,21,25 chr1 201337170 . A G 546.6 PASS AC=2;AF=0.852;AN=2;DP=1449;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:1721,165,0:0,0,34,21 chr1 201338553 . T C 1068.41 PASS AC=2;AF=0.841;AN=2;DP=1878;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:2230,186,0:0,0,11,51 chr1 201338586 . A G 609.24 PASS AC=2;AF=0.736;AN=2;DP=983;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1666,138,0:0,0,8,38 chr1 201338896 . T C 1425.84 PASS AC=2;AF=0.73;AN=2;DP=3281;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,104:106:99:2962,268,0:1,1,56,48 chr1 201339043 . C T 953.7 PASS AC=2;AF=0.737;AN=2;DP=1800;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,69:69:99:2042,206,0:0,0,28,41 chr1 201341175 . CAGAAG C 3385.05 PASS AC=2;AF=0.736;AN=2;DP=4000;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,101:101:99:4522,305,0:0,0,67,34 chr1 201341341 . C T 2441.19 PASS AC=2;AF=0.841;AN=2;DP=3769;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,99:99:99:3077,294,0:0,0,33,66 chr1 201347048 . G A 70.68 PASS AC=1;AF=0.75;AN=2;DP=14;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.633;ReadPosRankSum=-0.365;SOR=0.693;set=variant7-variant35 GT:AD:DP:GQ:PL:SB 0/1:4,6:10:69:118,0,69:2,2,3,3 chr1 201350082 . C T 220.02 PASS AC=1;AF=0.5;AN=2;DP=165;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant20-variant22-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,9:30:99:216,0,692:13,8,7,2 chr1 201352080 . G A 300.53 PASS AC=1;AF=0.5;AN=2;DP=318;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant20-variant22-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,35:67:99:996,0,900:20,12,16,19 chr1 201353827 . G C 575.81 PASS AC=1;AF=0.724;AN=2;DP=1110;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,15:35:99:354,0,470:12,8,9,6 chr1 201354102 . C G 577.37 PASS AC=1;AF=0.525;AN=2;DP=921;MQ=60;set=variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant16-variant17-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant35-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,25:53:99:502,0,816:9,19,11,14 chr1 201354292 . C T 179.74 PASS AC=1;AF=0.625;AN=2;DP=37;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant20-variant35 GT:AD:DP:GQ:PL:SB 0/1:5,3:8:67:67,0,142:2,3,1,2 chr1 201355522 . T C 1277.44 PASS AC=1;AF=0.688;AN=2;DP=3282;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant35-variant36-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:66,50:116:99:1228,0,1828:35,31,26,24 chr1 201355669 . T C 854.39 PASS AC=1;AF=0.5;AN=2;DP=899;MQ=60;set=variant2-variant7-variant20-variant22-variant23-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,66:122:99:1691,0,1415:26,30,34,32 chr1 201355943 . C T 1858.57 PASS AC=1;AF=0.672;AN=2;DP=4959;MQ=60;set=variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant35-variant36-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:77,88:165:99:2157,0,2028:35,42,38,50 chr1 201356428 . C A 1519.09 PASS AC=1;AF=0.688;AN=2;DP=1564;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,22:47:99:600,0,615:10,15,8,14 chr1 201368463 . G GT 2463.31 PASS AC=2;AF=0.579;AN=2;DP=2129;MQ=60;set=variant5-variant6-variant7-variant10-variant11-variant12-variant13-variant14-variant20-variant21-variant23-variant24-variant27-variant29-variant33-variant35-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,136:136:99:5358,415,0:0,0,86,50 chr1 201373844 . G A 2176.14 PASS AC=1;AF=0.6;AN=2;DP=3208;MQ=60;set=variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:96,100:196:99:2695,0,2397:45,51,34,66 chr1 201374653 . C T 424.04 PASS AC=1;AF=0.661;AN=2;DP=1754;MQ=60;set=variant-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,38:75:99:955,0,960:16,21,17,21 chr1 201374677 . A C 506.11 PASS AC=1;AF=0.672;AN=2;DP=1840;MQ=60;set=variant-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,37:75:99:1051,0,847:17,21,14,23 chr1 201375370 . TCCTCATCTGTAAATTTG T 422.19 PASS AC=1;AF=0.656;AN=2;DP=2190;MQ=60;set=variant-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,21:49:99:744,0,4464:11,17,13,8 chr1 201375658 . A G 745.27 PASS AC=1;AF=0.672;AN=2;DP=1479;MQ=60;set=variant-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,18:38:99:521,0,551:8,12,6,12 chr1 201375751 . T C 650.45 PASS AC=1;AF=0.672;AN=2;DP=1233;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,24:34:99:860,0,254:6,4,16,8 chr1 201375813 . A G 965.67 PASS AC=1;AF=0.672;AN=2;DP=1968;MQ=60;set=variant-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,35:54:99:978,0,472:13,6,20,15 chr1 201376007 . G C 894.03 PASS AC=1;AF=0.643;AN=2;DP=2593;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant26-variant27-variant28-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,42:102:99:1009,0,1671:29,31,21,21 chr1 201376261 . A G 492.97 PASS AC=1;AF=0.672;AN=2;DP=1874;set=variant-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,33:68:99:806,0,903:22,13,19,14 chr1 201377438 . A G 588.95 PASS AC=2;AF=0.898;AN=2;DP=2535;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:1866,174,0:0,0,33,25 chr1 201377885 . G A 1490.81 PASS AC=1;AF=0.716;AN=2;DP=1878;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,28:56:99:1082,0,2353:12,16,12,16 chr1 201377891 . C A 787.33 PASS AC=1;AF=0.673;AN=2;DP=1280;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant26-variant27-variant28-variant33-variant34-variant35-variant36-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,27:55:99:1048,0,2397:13,15,12,15 chr1 201377894 . A T 1524.62 PASS AC=1;AF=0.716;AN=2;DP=1766;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,26:53:99:1051,0,2329:13,14,11,15 chr1 201383616 . A G 255.29 PASS AC=2;AF=0.898;AN=2;DP=1987;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:2046,179,0:0,0,40,20 chr1 201383643 . A C 586.49 PASS AC=2;AF=0.898;AN=2;DP=3015;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,88:88:99:2810,263,0:0,0,57,31 chr1 201390969 . TCACACACACACACA TCACACACACACACACA,TCACACACACA,TCACACACACACACACACA,T,TCACACACACACACACACACA,TCACACACACACACACACACACA,TCACACACACACA,TCACACACACACACACACACACACACA 37.9 PASS AC=0,0,0,0,0,0,1,0;AF=0.235,0.118,0.235,0.029,0.088,0.029,0.059,0.059;AN=2;DP=212;FS=0;set=variant-variant3-variant6-variant9-variant10-variant12-variant13-variant15-variant16-variant18-variant20-variant27-variant31-variant35-variant36-variant37-variant43 GT:DP:GQ:SB 0/7:7:69:1,1,1,4 chr1 201391213 . A G 86.95 PASS AC=1;AF=0.5;AN=2;DP=284;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant10-variant15-variant21-variant23-variant24-variant26-variant29-variant34-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:17,14:31:99:331,0,400:6,11,5,9 chr1 201398228 . C T 406.01 PASS AC=1;AF=0.718;AN=2;DP=2135;FractionInformativeReads=1;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,25:53:99:551,0,798:16,12,11,14 chr1 201434740 . G A 1412.29 PASS AC=2;AF=0.771;AN=2;DP=2415;MQ=60;set=variant4-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2371,209,0:0,0,45,25 chr1 201437477 . A T 1109.5 PASS AC=1;AF=0.5;AN=2;DP=2385;MQ=60;set=variant-variant3-variant5-variant8-variant15-variant18-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant34-variant35-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:74,78:152:99:1839,0,1858:49,25,45,33 chr1 201438087 . G GGA 1081.53 PASS AC=1;AF=0.718;AN=2;DP=1848;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,23:42:99:873,0,746:8,11,14,9 chr1 201438449 . G A 393.76 PASS AC=1;AF=0.718;AN=2;DP=1000;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,13:25:99:405,0,302:5,7,1,12 chr1 201453289 . T C 1131.55 PASS AC=2;AF=0.898;AN=2;DP=1702;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1284,114,0:0,0,15,23 chr1 201457639 . GA G 137.95 PASS AC=2;AF=0.703;AN=2;DP=530;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:322,27,0:0,0,8,1 chr1 201475727 . A C 2884.05 PASS AC=2;AF=0.86;AN=2;DP=4842;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,104:104:99:3360,312,0:0,0,64,40 chr1 201489286 . C G 443.83 PASS AC=1;AF=0.611;AN=2;DP=1335;FractionInformativeReads=1;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant12-variant14-variant16-variant17-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,25:44:99:569,0,534:15,4,15,10 chr1 201687451 . A G 699.96 PASS AC=2;AF=0.737;AN=2;DP=3534;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,107:107:99:3453,321,0:0,0,71,36 chr1 201754410 . CTT CT,C 66.77 PASS AC=1,0;AF=0.5,0.237;AN=2;DP=1700;set=variant-variant2-filterInvariant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-filterInvariant35-variant36-variant37-variant38-filterInvariant40-variant41-variant43 GT:DP:GQ:SB 0/1:38:99:16,11,6,5 chr1 201754411 . T TC 136.96 PASS AC=1;AF=0.5;AN=2;DP=606;set=variant4-variant5-variant13-filterInvariant16-filterInvariant21-filterInvariant24-filterInvariant25-variant35-filterInvariant36-variant39-filterInvariant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,11:38:99:149,0,701:14,13,8,3 chr1 201754720 . G A 197.89 PASS AC=1;AF=0.55;AN=2;DP=505;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant12-variant13-variant16-variant17-variant21-variant23-variant24-variant25-variant33-variant35-variant36-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,16:26:99:529,0,325:3,7,2,14 chr1 201763184 . T C 1627.21 PASS AC=1;AF=0.743;AN=2;DP=6703;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:133,118:251:99:2606,0,2977:71,62,69,49 chr1 201763499 . C T 211.59 PASS AC=1;AF=0.721;AN=2;DP=687;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,11:31:99:296,0,566:11,9,7,4 chr1 201763912 . T C 248.86 PASS AC=1;AF=0.757;AN=2;DP=539;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,8:15:99:253,0,262:0,7,1,7 chr1 201772863 . T TG 1655.53 PASS AC=2;AF=1;AN=2;DP=2972;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:2539,228,0:0,0,18,58 chr1 201773013 . A G 615.58 PASS AC=1;AF=0.5;AN=2;DP=38;FS=5.711;FractionInformativeReads=1;MQ=60;MQRankSum=1.074;QD=16.2;ReadPosRankSum=-1.437;SOR=0.174;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:14,24:38:99:644,0,416:12,2,16,8 chr1 201773729 . AAT A 50.18 DRAGENHardINDEL AC=1;AF=0.5;AN=2;DP=60;FS=5.799;FractionInformativeReads=0.783;MQ=60;MQRankSum=0.392;QD=0.84;ReadPosRankSum=0.987;SOR=1.255;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:38,9:47:87:87,0,1203:15,23,6,3 chr1 201788804 . G A 357.89 PASS AC=1;AF=0.5;AN=2;DP=371;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant9-variant12-variant13-variant15-variant16-variant17-variant18-variant21-variant24-variant25-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,4:20:99:113,0,576:14,2,4,0 chr1 201789944 . C CT 1666.56 PASS AC=1;AF=0.559;AN=2;DP=1282;MQ=60;set=variant-variant2-variant4-variant10-variant12-variant20-variant21-variant24-variant25-variant27-variant29-variant33-variant34-variant35-variant36-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,37:78:99:766,0,896:17,24,16,21 chr1 201790239 . A G 553.12 PASS AC=1;AF=0.5;AN=2;DP=1635;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant9-variant12-variant13-variant15-variant16-variant17-variant18-variant21-variant23-variant24-variant25-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,47:88:99:1151,0,949:18,23,22,25 chr1 201790270 . A G 556.77 PASS AC=1;AF=0.518;AN=2;DP=1596;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant12-variant13-variant15-variant16-variant17-variant18-variant21-variant23-variant24-variant25-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,39:73:99:1007,0,778:15,19,18,21 chr1 201790633 . GACACACACACACACACACAC GAC,GACACACACACACACACACACAC,GACACACACACACACACAC,GACACACACACACACAC,G,GACACACACACACACACACACACAC,GACACAC 241.33 PASS AC=1,1,0,0,0,0,0;AF=0.274,0.095,0.214,0.048,0.202,0.012,0.024;AN=2;DP=821;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/2:21:99:0,1,8,12 chr1 201790826 . T C 233.89 PASS AC=1;AF=0.652;AN=2;DP=944;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant30-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,19:30:99:556,0,288:8,3,9,10 chr1 201791200 . G A 307.33 PASS AC=1;AF=0.605;AN=2;DP=831;MQ=60;set=variant2-variant3-variant6-variant7-variant10-variant11-variant12-variant13-variant16-variant19-variant22-variant26-variant27-variant28-variant32-variant34-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:31,28:59:99:835,0,771:15,16,13,15 chr1 201792306 . T C 399.06 PASS AC=1;AF=0.5;AN=2;DP=1185;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant9-variant12-variant13-variant15-variant16-variant17-variant18-variant21-variant23-variant24-variant25-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,21:53:99:600,0,735:14,18,11,10 chr1 201792491 . CGT C,CGTGT 104.86 PASS AC=1,0;AF=0.405,0.143;AN=2;DP=455;set=variant-variant4-variant5-variant9-variant12-variant16-variant20-variant21-variant23-variant24-variant25-variant27-variant29-variant31-variant33-variant34-variant35-variant36-variant39-variant40-variant44 GT:DP:GQ:SB 0/1:27:99:6,6,8,7 chr1 201792498 . G GTA 379.7 PASS AC=1;AF=0.618;AN=2;DP=789;set=variant2-variant3-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-filterInvariant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,10:30:99:241,0,740:10,10,5,5 chr1 201793440 . C G 438.36 PASS AC=1;AF=0.636;AN=2;DP=965;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant30-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,17:31:99:450,0,382:9,5,7,10 chr1 201793764 . G A 431.36 PASS AC=2;AF=1;AN=2;DP=1284;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:857,75,0:0,0,10,15 chr1 201794455 . TAA TA,T,TAAA 80.79 PASS AC=1,0,0;AF=0.321,0.013,0.167;AN=2;DP=2502;set=filterInvariant-variant2-variant3-variant4-filterInvariant5-filterInvariant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-filterInvariant17-variant19-filterInvariant21-variant22-filterInvariant23-variant24-variant25-variant27-filterInvariant28-variant29-variant30-variant31-variant32-variant33-filterInvariant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:50:99:15,19,10,6 chr1 201816943 . C T 172.78 PASS AC=1;AF=0.579;AN=2;DP=521;MQ=60;set=variant2-variant3-variant6-variant7-variant10-variant11-variant12-variant13-variant16-variant19-variant22-variant26-variant27-variant28-variant32-variant34-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:14,9:23:99:288,0,441:5,9,0,9 chr1 201821216 . A G 305.36 PASS AC=1;AF=0.5;AN=2;DP=40;FS=3.151;FractionInformativeReads=1;MQ=60;MQRankSum=0.462;QD=7.63;ReadPosRankSum=1.444;SOR=1.341;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:27,13:40:99:334,0,756:17,10,10,3 chr1 201824390 . G A 1397.91 PASS AC=1;AF=0.534;AN=2;DP=1805;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant9-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant27-variant29-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,44:94:99:968,0,1131:23,27,21,23 chr1 201832451 . T G 914.82 PASS AC=2;AF=1;AN=2;DP=1298;FS=0;FractionInformativeReads=1;MQRankSum=1.639;ReadPosRankSum=1.264;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1262,111,0:0,0,27,10 chr1 201837934 . CGT C 1370.41 PASS AC=2;AF=0.942;AN=2;DP=5570;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,119:120:99:4016,325,0:1,0,62,57 chr1 201840059 . GTTATT G 1518.88 PASS AC=2;AF=0.989;AN=2;DP=2377;FS=0;MQ=60;MQRankSum=1.89;ReadPosRankSum=-0.095;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:2413,163,0:0,0,20,34 chr1 201840464 . T C 2592.57 PASS AC=2;AF=1;AN=2;DP=3209;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:2501,216,0:0,0,25,47 chr1 201840537 . G A 250.12 PASS AC=1;AF=0.722;AN=2;DP=91;FS=0;set=variant2-variant3-variant7-variant10-variant22-variant26-variant28-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,6:15:99:217,0,285:0,9,0,6 chr1 201841734 . AAACAACAAC AAACAACAACAAC,A 315.22 PASS AC=1,0;AF=0.55,0.025;AN=2;DP=371;MQ=60;set=variant2-variant3-variant6-variant7-variant10-variant11-variant12-variant13-variant16-variant19-variant22-variant26-variant27-variant28-variant32-variant34-variant35-variant41-variant42-variant43 GT:DP:GQ:SB 0/1:12:99:6,0,6,0 chr1 201844128 . G A 1707.15 PASS AC=2;AF=1;AN=2;DP=2606;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:1863,185,0:0,0,27,35 chr1 201845882 . GA GAA,GAAA,G 1242.12 PASS AC=1,0,0;AF=0.535,0.035,0.012;AN=2;DP=3072;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-filterInvariant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-filterInvariant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:63:99:6,8,24,25 chr1 201846615 . TCACACACACACA T,TCACACACACACACA,TCACACACACACACACA,TCACACACACA 2734.61 PASS AC=1,0,0,0;AF=0.622,0.024,0.122,0.024;AN=2;DP=1838;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:43:99:11,2,21,9 chr1 201846689 . G T 784.67 PASS AC=1;AF=0.605;AN=2;DP=1391;MQ=60;set=variant2-variant3-variant6-variant7-variant10-variant11-variant12-variant13-variant16-variant19-variant22-variant26-variant27-variant28-variant32-variant34-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:41,21:62:99:352,0,983:20,21,11,10 chr1 201849926 . A G 545.49 PASS AC=1;AF=0.5;AN=2;DP=753;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant9-variant12-variant13-variant15-variant16-variant17-variant18-variant21-variant23-variant24-variant25-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,23:35:99:816,0,311:5,7,16,7 chr1 201850391 . C CACTT 2265.52 PASS AC=2;AF=0.81;AN=2;DP=1944;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,53:54:99:2388,124,0:1,0,25,28 chr1 201852299 . TC TCCC,TCC,T 1327.23 PASS AC=1,1,0;AF=0.238,0.536,0.012;AN=2;DP=3542;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 2/1:68:99:2,2,17,47 chr1 201853165 . G T 875.62 PASS AC=1;AF=0.534;AN=2;DP=1299;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant9-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant27-variant29-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,22:41:99:610,0,436:9,10,11,11 chr1 201858887 . C T 231.44 PASS AC=1;AF=0.575;AN=2;DP=417;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant6-variant7-variant10-variant11-variant12-variant13-variant16-variant19-variant22-variant26-variant27-variant28-variant32-variant34-variant35-variant37-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,8:17:99:257,0,333:0,9,0,8 chr1 201860626 . A G 1008.71 PASS AC=2;AF=0.821;AN=2;DP=3138;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,61:61:99:1818,183,0:0,0,29,32 chr1 201861016 . C G 3670.11 PASS AC=1;AF=0.532;AN=2;DP=6274;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant27-variant29-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:136,121:257:99:3052,0,3285:66,70,55,66 chr1 201865763 . A G 3384.55 PASS AC=2;AF=0.821;AN=2;DP=5323;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,142:142:99:4291,425,0:0,0,60,82 chr1 201868333 . C T 653.01 PASS AC=1;AF=0.6;AN=2;DP=618;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant6-variant7-variant10-variant11-variant12-variant13-variant16-variant19-variant22-variant26-variant27-variant28-variant32-variant34-variant35-variant37-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:16,20:36:99:571,0,374:11,5,13,7 chr1 201915658 . A C 1525.98 PASS AC=2;AF=1;AN=2;DP=2089;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.073;ReadPosRankSum=1.098;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:1630,144,0:0,0,18,30 chr1 201915718 . C G 998.97 PASS AC=2;AF=1;AN=2;DP=1429;FS=0;MQ=60;MQRankSum=-0.788;ReadPosRankSum=-0.788;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:1087,96,0:0,0,11,21 chr1 201938482 . C T 79.91 PASS AC=2;AF=0.717;AN=2;DP=138;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant7-variant8-variant9-variant15-variant17-variant18-variant21-variant23-variant24-variant26-variant27-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:132,9,0:0,0,3,0 chr1 201938995 . C T 6504.36 PASS AC=2;AF=0.621;AN=2;DP=12348;MQ=60;set=variant-variant3-variant5-variant7-variant8-variant9-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant26-variant27-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,395:396:99:12082,1141,0:1,0,203,192 chr1 201939752 . C T 2573.25 PASS AC=1;AF=0.586;AN=2;DP=5054;MQ=60;set=variant-variant3-variant5-variant7-variant8-variant9-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant26-variant27-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:87,96:183:99:2465,0,2216:33,54,42,54 chr1 201939785 . A T 1910.31 PASS AC=1;AF=0.586;AN=2;DP=3209;MQ=60;set=variant-variant3-variant5-variant7-variant8-variant9-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant26-variant27-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,68:120:99:1791,0,1394:18,34,26,42 chr1 201952294 . C G 679.27 PASS AC=2;AF=0.6;AN=2;DP=1240;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,31:31:93:1327,93,0:0,0,10,21 chr1 201952310 . T G 559.49 PASS AC=2;AF=0.6;AN=2;DP=1080;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:75:1058,75,0:0,0,8,16 chr1 201952440 . C CCTT 727.34 PASS AC=2;AF=0.6;AN=2;DP=1928;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:3233,219,0:0,0,45,27 chr1 201952574 . T C 1917.18 PASS AC=2;AF=0.629;AN=2;DP=5050;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,152:152:99:4678,456,0:0,0,82,70 chr1 201952598 . G A 1450.81 PASS AC=1;AF=0.531;AN=2;DP=2335;MQ=60;set=variant5-variant7-variant9-variant10-variant11-variant20-variant21-variant26-variant27-variant31-variant35-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,97:161:99:2195,0,1614:34,30,50,47 chr1 201952755 . T A 697.79 PASS AC=2;AF=0.6;AN=2;DP=2524;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,73:73:99:2312,218,0:0,0,24,49 chr1 201958268 . C T 703.15 PASS AC=1;AF=0.5;AN=2;DP=125;FractionInformativeReads=1;MQ=60;set=variant27-variant35 GT:AD:DP:GQ:PL:SB 0/1:38,28:66:99:812,0,1153:11,27,6,22 chr1 201969082 . G A 659.53 PASS AC=1;AF=0.7;AN=2;DP=2275;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant8-variant10-variant14-variant15-variant16-variant17-variant18-variant19-variant23-variant24-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,31:84:99:855,0,1348:32,21,21,10 chr1 201970562 . T C 8545.54 PASS AC=2;AF=1;AN=2;DP=12138;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,325:325:99:9704,972,0:0,0,143,182 chr1 201970748 . G A 848.72 PASS AC=1;AF=0.717;AN=2;DP=2520;set=variant-variant2-variant3-variant4-variant7-variant8-variant10-variant14-variant15-variant16-variant17-variant18-variant19-variant23-variant24-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,42:86:99:1172,0,1237:24,20,20,22 chr1 201972167 . G A 525.55 PASS AC=1;AF=0.5;AN=2;DP=311;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant10-variant20-variant26-variant27-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:19,23:42:99:610,0,585:14,5,16,7 chr1 201977028 . T C 275.32 PASS AC=1;AF=0.5;AN=2;DP=172;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant20-variant26-variant27-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:10,9:19:99:293,0,302:8,2,6,3 chr1 201977254 . T C 1016.87 PASS AC=1;AF=0.717;AN=2;DP=2687;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:58,45:103:99:1084,0,1375:35,23,24,21 chr1 201977827 . G T 810.37 PASS AC=1;AF=0.714;AN=2;DP=561;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant31-variant33-variant35-variant36-variant37-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:3,16:19:71:443,0,71:1,2,5,11 chr1 201977860 . GT G 279.49 PASS AC=2;AF=0.732;AN=2;DP=407;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant31-variant33-variant35-variant36-variant37-variant42 GT:AD:DP:GQ:PL:SB 1/1:1,9:10:19:374,19,0:1,0,2,7 chr1 201977867 . T G 277.59 PASS AC=2;AF=0.639;AN=2;DP=238;MQ=60;set=variant3-variant4-variant5-variant6-variant9-variant11-variant12-variant13-variant14-variant15-variant21-variant22-variant24-variant25-variant33-variant35-variant36-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,9:10:19:374,19,0:1,0,2,7 chr1 201978323 . T C 1074.83 PASS AC=1;AF=0.594;AN=2;DP=1344;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,21:42:99:496,0,445:14,7,13,8 chr1 201978396 . A G 468.83 PASS AC=1;AF=0.5;AN=2;DP=147;FractionInformativeReads=1;MQ=60;set=variant5-variant27-variant35 GT:AD:DP:GQ:PL:SB 0/1:29,27:56:99:621,0,748:14,15,12,15 chr1 201980095 . AT A 3158.2 PASS AC=1;AF=0.553;AN=2;DP=1849;MQ=60;set=variant2-variant5-variant11-variant18-variant19-variant20-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant35-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,58:116:99:1991,0,1960:29,29,29,29 chr1 201980119 . C G 1571.12 PASS AC=1;AF=0.7;AN=2;DP=4140;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,56:115:99:1550,0,1539:28,31,30,26 chr1 201981005 . CAA CA,CAAA,C 89.72 PASS AC=1,0,0;AF=0.346,0.135,0.019;AN=2;DP=452;set=variant2-filterInvariant4-variant5-variant8-filterInvariant10-variant12-variant13-filterInvariant15-variant16-filterInvariant17-variant18-variant19-variant20-variant22-variant23-variant24-variant29-variant30-variant32-variant34-variant35-variant37-variant38-variant39-variant41-variant43 GT:DP:GQ:SB 0/1:19:86:10,2,6,1 chr1 201981218 . C G 2720.94 PASS AC=1;AF=0.583;AN=2;DP=2481;MQ=60;set=variant2-variant3-variant5-variant10-variant11-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant35-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,49:91:99:1188,0,972:17,25,19,30 chr1 201981354 . T C 1096.77 PASS AC=1;AF=0.583;AN=2;DP=731;MQ=60;set=variant2-variant3-variant5-variant10-variant11-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant35-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,12:24:99:486,0,713:6,6,8,4 chr1 201981355 . G C 1096.77 PASS AC=1;AF=0.583;AN=2;DP=740;MQ=60;set=variant2-variant3-variant5-variant10-variant11-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant35-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,13:26:99:486,0,713:7,6,8,5 chr1 201981862 . T C 567.15 PASS AC=1;AF=0.632;AN=2;DP=2270;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,48:84:99:1298,0,858:13,23,16,32 chr1 201983242 . C T 61.77 PASS AC=1;AF=0.596;AN=2;DP=639;MQ=60;set=variant-variant3-variant4-variant8-variant14-variant15-variant17-variant18-variant19-variant21-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,5:25:99:109,0,591:7,13,1,4 chr1 201985648 . GAA GA,G,GAAA 3965.58 PASS AC=1,1,0;AF=0.841,0.091,0.011;AN=2;DP=12542;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-filterInvariant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 2/1:253:99:11,11,127,104 chr1 201985731 . G A 2872.3 PASS AC=2;AF=0.786;AN=2;DP=12185;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,300:301:99:8938,887,0:0,1,131,169 chr1 202092046 . C T 2472.31 PASS AC=2;AF=0.833;AN=2;DP=3176;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,97:97:99:3220,290,0:0,0,63,34 chr1 202092360 . G A 3144.42 PASS AC=2;AF=0.866;AN=2;DP=5532;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,133:133:99:4184,396,0:0,0,70,63 chr1 202092415 . A G 3381.3 PASS AC=2;AF=0.866;AN=2;DP=6672;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,174:174:99:5447,522,0:0,0,91,83 chr1 202092580 . T C 4095.49 PASS AC=2;AF=0.866;AN=2;DP=7361;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,205:205:99:6432,614,0:0,0,102,103 chr1 202096815 . G A 2209.63 PASS AC=2;AF=0.808;AN=2;DP=4240;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,96:97:99:2857,258,0:1,0,55,41 chr1 202098078 . C T 867.38 PASS AC=2;AF=0.614;AN=2;DP=1203;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant15-variant16-variant18-variant22-variant23-variant24-variant27-variant30-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1379,129,0:0,0,15,28 chr1 202103802 . G A 1544.95 PASS AC=2;AF=0.646;AN=2;DP=581;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant15-variant16-variant18-variant20-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant34-variant35-variant36-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:1173,90,0:0,0,4,26 chr1 202107422 . AACACACAC AAC,AACAC,AACACACACAC,AACACAC,A,AACACACACACACAC 961.24 PASS AC=1,0,0,0,1,0;AF=0.59,0.077,0.013,0.064,0.051,0.013;AN=2;DP=1135;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 5/1:43:99:0,0,28,15 chr1 202113781 . C A 2473.65 PASS AC=1;AF=0.5;AN=2;DP=222;FS=7.014;FractionInformativeReads=1;MQ=60;MQRankSum=-1.888;QD=11.14;ReadPosRankSum=4.02;SOR=1.153;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:110,112:222:99:2502,0,2578:41,69,32,80 chr1 202113835 . T G 2382.38 PASS AC=2;AF=0.792;AN=2;DP=2476;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,85:85:99:3189,255,0:0,0,13,72 chr1 202116238 . G A 2088.91 PASS AC=2;AF=0.643;AN=2;DP=1696;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant15-variant16-variant18-variant20-variant22-variant23-variant25-variant30-variant31-variant32-variant34-variant35-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,90:92:99:2723,219,0:1,1,47,43 chr1 202116957 . T A 1515.98 PASS AC=2;AF=0.636;AN=2;DP=1797;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant15-variant16-variant18-variant20-variant22-variant23-variant25-variant30-variant31-variant32-variant34-variant35-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,83:83:99:2680,249,0:0,0,38,45 chr1 202119205 . C A 307.36 PASS AC=2;AF=0.675;AN=2;DP=219;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant15-variant16-variant18-variant20-variant22-variant23-variant25-variant30-variant31-variant32-variant34-variant35-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:32:314,32,0:0,0,8,3 chr1 202122783 . C A 550.99 PASS AC=2;AF=0.65;AN=2;DP=372;FractionInformativeReads=1;set=variant-variant2-variant4-variant5-variant7-variant9-variant15-variant18-variant20-variant22-variant23-variant25-variant30-variant31-variant32-variant34-variant35-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:643,48,0:0,0,14,2 chr1 202129196 . T C 149.21 PASS AC=2;AF=0.567;AN=2;DP=208;MQ=60;set=variant-variant2-variant5-variant13-variant22-variant24-variant29-variant30-variant32-variant33-variant35-variant38-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:479,39,0:0,0,4,9 chr1 202129826 . T C 2355.42 PASS AC=1;AF=0.65;AN=2;DP=3246;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant11-variant12-variant15-variant16-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:82,65:147:99:1620,0,2001:43,39,35,30 chr1 202130166 . G A 852.84 PASS AC=1;AF=0.725;AN=2;DP=2341;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,23:42:99:585,0,531:8,11,12,11 chr1 202130754 . T C 1289.39 PASS AC=1;AF=0.738;AN=2;DP=2816;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,26:78:99:639,0,1253:24,28,13,13 chr1 202155331 . CTGCCCCCTTGCCCCCT C,CTGCCCCCT 325.33 PASS AC=2,0;AF=0.5,0.188;AN=2;DP=205;set=variant4-variant10-variant12-variant14-variant32-variant35-variant36-variant40 GT:DP:GQ:SB 1/1:20:63:0,0,4,16 chr1 202155543 . A C 5684.56 PASS AC=2;AF=0.909;AN=2;DP=9324;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,256:257:99:7756,726,0:1,0,126,130 chr1 202156135 . C CCCTCGCTCCTCGCTCCTCGCTCCTCGCT,CCCTCGCT,CCCTCGCTCCTCGCTCCTCGCT,CCCTCGCTCCTCGCT,CCCTCGCTCCTCGCTCCTCGCTCCTCGCTCCTCGCT 785.79 PASS AC=0,1,1,0,0;AF=0.159,0.511,0.125,0.057,0.023;AN=2;DP=2824;set=Intersection GT:DP:GQ:SB 2/3:43:99:0,0,22,21 chr1 202156482 . G A 2307.92 PASS AC=2;AF=0.886;AN=2;DP=4825;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,147:147:99:4282,438,0:0,0,91,56 chr1 202156628 . A C 2701.97 PASS AC=2;AF=0.898;AN=2;DP=4743;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,115:115:99:3794,344,0:0,0,38,77 chr1 202163063 . T C 2031.84 PASS AC=2;AF=0.886;AN=2;DP=3121;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,87:87:99:2896,261,0:0,0,34,53 chr1 202163364 . C G 276.52 PASS AC=2;AF=0.875;AN=2;DP=1101;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1240,102,0:0,0,16,18 chr1 202163516 . C A 4017.32 PASS AC=2;AF=0.886;AN=2;DP=5241;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,137:137:99:4179,408,0:0,0,88,49 chr1 202163621 . G A 1947.27 PASS AC=1;AF=0.636;AN=2;DP=7068;set=variant2-variant4-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:136,115:251:99:2573,0,3661:63,73,59,56 chr1 202172769 . T G 433.68 PASS AC=1;AF=0.571;AN=2;DP=597;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant12-variant14-variant16-variant19-variant20-variant25-variant26-variant29-variant31-variant33-variant34-variant35-variant36-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,12:22:99:328,0,350:7,3,9,3 chr1 202183308 . C T 1661.26 PASS AC=1;AF=0.719;AN=2;DP=4854;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:93,77:170:99:1869,0,2383:43,50,36,41 chr1 202194441 . G C 271.37 PASS AC=1;AF=0.673;AN=2;DP=796;MQ=60;set=variant-variant3-variant6-variant8-variant11-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant30-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,9:26:99:228,0,557:13,4,7,2 chr1 202194838 . TTCC T 140.21 PASS AC=1;AF=0.696;AN=2;DP=167;MQ=60;set=variant3-variant5-variant7-variant9-variant10-variant11-variant17-variant18-variant19-variant21-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,4:10:99:150,0,289:3,3,3,1 chr1 202196931 . G A 2053.34 PASS AC=2;AF=0.83;AN=2;DP=2683;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:2,57:59:99:1661,127,0:1,1,35,22 chr1 202197011 . C T 1569.94 PASS AC=1;AF=0.5;AN=2;DP=119;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.94;QD=13.19;ReadPosRankSum=-1.158;SOR=0.641;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:56,63:119:99:1598,0,1269:31,25,34,29 chr1 202197161 . C T 578.85 PASS AC=1;AF=0.613;AN=2;DP=1654;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant13-variant16-variant17-variant18-variant19-variant21-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:30,20:50:99:498,0,876:8,22,6,14 chr1 202266547 . C T 3287.08 PASS AC=1;AF=0.718;AN=2;DP=5766;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:95,92:187:99:2168,0,2407:58,37,53,39 chr1 202266607 . C T 4279.39 PASS AC=1;AF=0.672;AN=2;DP=6040;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:127,119:246:99:2757,0,3014:64,63,57,62 chr1 202274936 . T C 4854.85 PASS AC=1;AF=0.672;AN=2;DP=5400;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:100,86:186:99:1846,0,2145:52,48,44,42 chr1 202276494 . C T 947.45 PASS AC=1;AF=0.672;AN=2;DP=2399;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:51,52:103:99:1248,0,1274:22,29,22,30 chr1 202278054 . C T 416.44 PASS AC=1;AF=0.5;AN=2;DP=58;FractionInformativeReads=1;MQ=60;set=variant32-variant35 GT:AD:DP:GQ:PL:SB 0/1:18,21:39:99:740,0,574:15,3,19,2 chr1 202283667 . A G 984.11 PASS AC=1;AF=0.641;AN=2;DP=1266;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:26,22:48:99:522,0,659:17,9,14,8 chr1 202287206 . T C 4106.87 PASS AC=1;AF=0.705;AN=2;DP=7427;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:157,98:255:99:2335,0,3906:76,81,49,49 chr1 202287537 . G A 5534.84 PASS AC=1;AF=0.641;AN=2;DP=5787;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:125,115:240:99:2641,0,3529:77,48,61,54 chr1 202287813 . T C 7469.02 PASS AC=1;AF=0.705;AN=2;DP=10725;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:156,137:293:99:3420,0,4341:85,71,66,71 chr1 202288462 . C A 2219.92 PASS AC=1;AF=0.705;AN=2;DP=2927;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,44:96:99:1094,0,1387:23,29,23,21 chr1 202303815 . T C 49.73 PASS AC=1;AF=0.583;AN=2;DP=30;FS=0;FractionInformativeReads=1;MQ=60;set=variant10-variant14-variant27-variant32-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:99:114,0,115:3,0,3,0 chr1 202304868 . T C 1650.67 PASS AC=1;AF=0.592;AN=2;DP=4581;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:71,53:124:99:1349,0,1880:36,35,30,23 chr1 202318316 . A C 1008.46 PASS AC=1;AF=0.574;AN=2;DP=3898;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:70,55:125:99:1384,0,1658:26,44,16,39 chr1 202386075 . T C 1783.26 PASS AC=2;AF=0.989;AN=2;DP=3673;MQRankSum=-1.183;ReadPosRankSum=-0.055;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,81:81:99:2600,243,0:0,0,32,49 chr1 202457784 . T A 466.49 PASS AC=1;AF=0.574;AN=2;DP=1534;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:21,16:37:99:423,0,619:6,15,5,11 chr1 202464280 . G A 407.15 PASS AC=1;AF=0.571;AN=2;DP=511;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,9:14:99:338,0,170:5,0,9,0 chr1 202531741 . C T 239.91 PASS AC=1;AF=0.571;AN=2;DP=793;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:10,10:20:99:245,0,225:5,5,6,4 chr1 202536848 . C T 1117.12 PASS AC=1;AF=0.574;AN=2;DP=2494;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:26,45:71:99:1175,0,589:13,13,26,19 chr1 202550272 . G A 754.51 PASS AC=1;AF=0.7;AN=2;DP=2931;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,33:62:99:954,0,853:12,17,17,16 chr1 202550547 . G A 465.78 PASS AC=1;AF=0.679;AN=2;DP=2085;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,26:55:99:677,0,767:13,16,14,12 chr1 202551071 . A G 1337.61 PASS AC=1;AF=0.697;AN=2;DP=3400;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,49:98:99:1303,0,1304:16,33,17,32 chr1 202552100 . G A 2624.05 PASS AC=1;AF=0.679;AN=2;DP=6429;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:69,69:138:99:1785,0,2012:52,17,48,21 chr1 202552302 . T C 8258.28 PASS AC=2;AF=1;AN=2;DP=9611;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,210:210:99:6718,628,0:0,0,75,135 chr1 202552839 . T C 674.71 PASS AC=1;AF=0.692;AN=2;DP=2081;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,24:47:99:620,0,698:10,13,11,13 chr1 202556632 . C CTGTT 628.22 PASS AC=1;AF=0.689;AN=2;DP=1902;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,28:54:99:1113,0,1454:15,11,17,11 chr1 202557017 . C T 667.91 PASS AC=1;AF=0.689;AN=2;DP=2581;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,48:105:99:1156,0,1480:33,24,24,24 chr1 202560412 . T C 1233.11 PASS AC=1;AF=0.688;AN=2;DP=4566;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:77,49:126:99:1089,0,2010:34,43,21,28 chr1 202560658 . A G 1422.49 PASS AC=1;AF=0.692;AN=2;DP=5192;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:85,63:148:99:1442,0,2072:49,36,36,27 chr1 202560681 . T G 1611.18 PASS AC=1;AF=0.692;AN=2;DP=6135;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:109,71:180:99:1472,0,2738:61,48,39,32 chr1 202562427 . G A 1291.05 PASS AC=1;AF=0.652;AN=2;DP=2934;MQ=60;set=variant3-variant4-variant5-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,42:92:99:1194,0,1202:24,26,22,20 chr1 202563829 . TAC TACAC,TACACACACACACACACAC,TACACACACACACAC,TACACACACACACACACACACAC,T,TACACACACACACACACACAC,TACACACACAC,TACACACACACACACACACACACACACAC,TACACACACACACACAC,TACACACACACAC,TACACACACACACACACACACACAC,TACACACAC 498.81 PASS AC=1,0,0,0,0,0,0,0,0,0,0,0;AF=0.192,0.244,0.064,0.064,0.013,0.128,0.026,0.013,0.051,0.026,0.013,0.026;AN=2;DP=1042;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:27:73:2,3,11,11 chr1 202565436 . T C,TACACACACAC 489.76 PASS AC=2,0;AF=0.594,0.125;AN=2;DP=288;set=variant13-variant15-filterInvariant19-variant20-variant21-variant22-variant23-variant25-variant26-variant29-variant30-variant3-variant31-variant34-variant35-variant37 GT:DP:GQ:SB 1/1:14:26:0,1,9,4 chr1 202565948 . G A 960.36 PASS AC=2;AF=0.589;AN=2;DP=4235;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant21-variant22-variant24-variant26-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,176:176:99:5132,527,0:0,0,89,87 chr1 202703053 . G A 1764.81 PASS AC=1;AF=0.83;AN=2;DP=3060;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:35,36:71:99:845,0,917:11,24,15,21 chr1 202705455 . G C 2324.42 PASS AC=1;AF=0.798;AN=2;DP=3676;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,30:79:99:646,0,1255:26,23,15,15 chr1 202715244 . G GA 1197.03 PASS AC=1;AF=0.798;AN=2;DP=1894;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,20:43:99:451,0,555:9,14,13,7 chr1 202715284 . G A 1665.83 PASS AC=1;AF=0.798;AN=2;DP=2870;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,37:65:99:910,0,678:13,15,23,14 chr1 202718028 . A G 1038.73 PASS AC=1;AF=0.788;AN=2;DP=785;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,13:26:99:461,0,458:12,1,13,0 chr1 202718202 . G A 4302.04 PASS AC=1;AF=0.788;AN=2;DP=6174;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,90:155:99:2096,0,1719:29,36,42,48 chr1 202722277 . G A 922.32 PASS AC=1;AF=0.788;AN=2;DP=1365;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,15:31:99:417,0,391:5,11,4,11 chr1 202722348 . A G 201.22 PASS AC=1;AF=0.857;AN=2;DP=451;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,8:12:99:202,0,115:0,4,3,5 chr1 202731986 . C CCTCAA 491.94 PASS AC=1;AF=0.825;AN=2;DP=504;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,13:19:99:517,0,361:1,5,1,12 chr1 202733238 . C T 2893.82 PASS AC=1;AF=0.798;AN=2;DP=4445;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,39:93:99:1003,0,1222:26,28,21,18 chr1 202735751 . T C 6914.51 PASS AC=1;AF=0.788;AN=2;DP=8789;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:123,145:268:99:3328,0,2795:60,63,76,69 chr1 202778261 . G A 1866.25 PASS AC=1;AF=0.852;AN=2;DP=2474;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:40,28:68:99:731,0,1157:18,22,11,17 chr1 202794787 . T C 2558.44 PASS AC=1;AF=0.548;AN=2;DP=3480;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant12-variant13-variant14-variant17-variant21-variant23-variant26-variant30-variant32-variant34-variant35-variant37-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:92,106:198:99:2655,0,2288:51,41,60,46 chr1 202795849 . G A 421.07 PASS AC=1;AF=0.548;AN=2;DP=784;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant12-variant13-variant14-variant17-variant21-variant23-variant26-variant30-variant32-variant34-variant35-variant37-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,20:43:99:547,0,627:12,11,7,13 chr1 202827191 . G A 1015.24 PASS AC=1;AF=0.635;AN=2;DP=1394;set=variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant26-variant28-variant29-variant31-variant35-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,36:58:99:857,0,569:11,11,24,12 chr1 202827398 . A G 912.31 PASS AC=1;AF=0.635;AN=2;DP=1149;FractionInformativeReads=1;set=variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant26-variant28-variant29-variant31-variant35-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,24:51:99:672,0,717:9,18,5,19 chr1 202848587 . G A 207.7 PASS AC=1;AF=0.769;AN=2;DP=1423;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,15:34:99:393,0,545:14,5,9,6 chr1 202849606 . C T 6007.8 PASS AC=2;AF=0.989;AN=2;DP=7549;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,185:185:99:5648,554,0:0,0,95,90 chr1 202849723 . G A 1277.54 PASS AC=1;AF=0.769;AN=2;DP=3635;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,55:120:99:1400,0,1668:25,40,19,36 chr1 202849770 . T C 935.06 PASS AC=1;AF=0.769;AN=2;DP=2008;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,23:61:99:645,0,1016:15,23,8,15 chr1 202861211 . G GAA,GA 547.4 PASS AC=1,0;AF=0.727,0.159;AN=2;DP=1235;set=Intersection GT:DP:GQ:SB 0/1:15:99:2,4,4,5 chr1 202878454 . T A 391.47 PASS AC=1;AF=0.75;AN=2;DP=519;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant25-variant26-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,7:17:99:201,0,309:1,9,0,7 chr1 202887295 . G A 1205.95 PASS AC=1;AF=0.75;AN=2;DP=3157;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,22:68:99:452,0,1228:23,23,10,12 chr1 202889207 . T C 90.3 PASS AC=2;AF=1;AN=2;DP=300;FS=0;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:311,24,0:0,0,2,6 chr1 202897431 . A G 729.62 PASS AC=1;AF=0.75;AN=2;DP=463;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,11:22:99:358,0,227:8,3,9,2 chr1 202915940 . TA T 64.88 PASS AC=1;AF=0.5;AN=2;DP=166;MQ=60;set=variant4-variant6-variant9-variant12-variant25-variant28-variant29-variant30-variant31-variant35-variant36-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,5:9:57:97,0,57:1,3,1,4 chr1 202917724 . G A 419.42 PASS AC=1;AF=0.5;AN=2;DP=78;FractionInformativeReads=1;MQ=60;set=variant12-variant32-variant35 GT:AD:DP:GQ:PL:SB 0/1:16,11:27:99:281,0,464:4,12,3,8 chr1 202920300 . A C 1186.77 PASS AC=1;AF=0.622;AN=2;DP=1648;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,25:51:99:964,0,1397:11,15,8,17 chr1 202920304 . T C 1186.77 PASS AC=1;AF=0.618;AN=2;DP=1629;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,24:50:99:964,0,1397:11,15,8,16 chr1 202927501 . T C 599.14 PASS AC=2;AF=0.92;AN=2;DP=1137;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1473,131,0:0,0,22,22 chr1 202927507 . C T 160.64 PASS AC=1;AF=0.581;AN=2;DP=800;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant9-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,20:45:99:433,0,536:13,12,9,11 chr1 202931839 . G A 1547.38 PASS AC=1;AF=0.583;AN=2;DP=3533;set=variant-variant2-variant6-variant8-variant9-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:73,56:129:99:1271,0,1917:32,41,22,34 chr1 202931958 . G A 470.94 PASS AC=1;AF=0.6;AN=2;DP=1168;MQ=60;set=variant-variant6-variant8-variant9-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant28-variant29-variant31-variant35-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,21:55:99:467,0,1017:18,16,10,11 chr1 202931998 . C A 635.33 PASS AC=1;AF=0.578;AN=2;DP=2175;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant9-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,24:65:99:482,0,1303:25,16,13,11 chr1 202933657 . T A 550.67 PASS AC=1;AF=0.589;AN=2;DP=1619;MQ=60;set=variant-variant2-variant6-variant8-variant9-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,35:70:99:900,0,887:21,14,21,14 chr1 202933992 . G C 690.92 PASS AC=1;AF=0.578;AN=2;DP=1344;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant9-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,13:27:99:390,0,463:2,12,3,10 chr1 202934764 . TC T 242.69 PASS AC=1;AF=0.515;AN=2;DP=1053;set=variant-variant2-filterInvariant5-variant7-variant8-variant9-variant10-filterInvariant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant39-variant40-variant41-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:17,9:26:99:134,0,468:8,9,2,7 chr1 202934765 . C T 122.34 PASS AC=1;AF=0.583;AN=2;DP=882;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant12-variant13-variant14-variant15-variant16-variant18-variant20-filterInvariant21-variant23-variant25-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,13:26:99:365,0,381:3,10,7,6 chr1 202936456 . G C 192.99 PASS AC=1;AF=0.639;AN=2;DP=197;MQ=60;set=variant-variant6-variant8-variant9-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant28-variant29-variant31-variant35-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,3:8:99:111,0,154:1,4,0,3 chr1 202956340 . T G 2858.66 PASS AC=1;AF=0.646;AN=2;DP=2170;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant12-variant13-variant15-variant18-variant20-variant23-variant24-variant25-variant27-variant30-variant32-variant33-variant35-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,54:94:99:1524,0,1088:13,27,21,33 chr1 202978032 . C G 490.39 PASS AC=2;AF=0.672;AN=2;DP=1057;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant17-variant18-variant20-variant21-variant22-variant25-variant26-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1165,114,0:0,0,16,22 chr1 202987770 . T C 933.83 PASS AC=2;AF=0.62;AN=2;DP=1976;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant7-variant8-variant9-variant10-variant12-variant14-variant17-variant18-variant22-variant25-variant26-variant27-variant29-variant30-variant32-variant35-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,81:81:99:2536,243,0:0,0,30,51 chr1 202987796 . G A 795.44 PASS AC=2;AF=0.62;AN=2;DP=1690;MQ=60;set=variant-variant3-variant4-variant7-variant8-variant9-variant10-variant12-variant14-variant17-variant18-variant22-variant25-variant26-variant27-variant29-variant30-variant32-variant35-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:2172,213,0:0,0,25,46 chr1 202990110 . CTTTT CTTT,CT,CTTTTT,C,CTT 51.61 PASS AC=0,1,0,0,1;AF=0.195,0.341,0.037,0.012,0.012;AN=2;DP=3048;set=filterInvariant2-variant3-variant4-filterInvariant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-filterInvariant15-filterInvariant16-variant17-variant18-variant20-filterInvariant21-variant22-variant23-filterInvariant24-variant25-variant26-variant27-filterInvariant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-filterInvariant37-variant38-variant39-variant40-variant41-variant42-filterInvariant43-variant44 GT:DP:GQ:SB 2/5:67:77:0,0,16,51 chr1 202990155 . CT CTT,C 43.74 PASS AC=1,0;AF=0.333,0.2;AN=2;DP=425;set=filterInvariant3-variant6-variant8-filterInvariant9-variant10-filterInvariant15-variant19-filterInvariant22-variant30-filterInvariant31-variant35-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:17:43:0,5,1,11 chr1 202993198 . C A 1747.83 PASS AC=2;AF=0.62;AN=2;DP=3250;MQ=60;set=variant-variant3-variant4-variant7-variant8-variant9-variant10-variant12-variant14-variant17-variant18-variant22-variant25-variant26-variant27-variant29-variant30-variant32-variant35-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,154:154:99:4631,461,0:0,0,84,70 chr1 202993608 . A AT,ATT,ATTT 694.3 PASS AC=1,0,0;AF=0.406,0.063,0.031;AN=2;DP=2184;set=variant7-variant8-filterInvariant9-filterInvariant12-variant13-variant17-variant18-variant22-variant25-filterInvariant27-filterInvariant29-variant35-filterInvariant40-variant41-filterInvariant42-variant44 GT:DP:GQ:SB 0/1:83:99:22,24,18,19 chr1 202993614 . G T 715.89 PASS AC=1;AF=0.522;AN=2;DP=3214;set=variant-variant2-variant4-variant7-variant8-variant9-variant10-variant12-variant13-variant17-variant18-variant22-variant25-variant27-variant29-variant32-variant33-variant35-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,73:95:99:1680,0,264:10,12,33,40 chr1 202993848 . G A 616.69 PASS AC=2;AF=0.62;AN=2;DP=1140;MQ=60;set=variant-variant3-variant4-variant7-variant8-variant9-variant10-variant12-variant14-variant17-variant18-variant22-variant25-variant26-variant27-variant29-variant30-variant32-variant35-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1452,158,0:0,0,25,28 chr1 202995581 . CG CGG,CGGG,C 39.65 PASS AC=2,0,0;AF=0.569,0.017,0.017;AN=2;DP=369;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant8-variant12-variant13-variant14-variant17-variant18-variant20-variant21-variant22-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:DP:GQ:SB 1/1:4:12:0,0,2,2 chr1 202995887 . C T 485.59 PASS AC=2;AF=0.652;AN=2;DP=492;MQ=60;set=variant3-variant4-variant7-variant8-variant9-variant10-variant12-variant14-variant17-variant18-variant22-variant25-variant26-variant27-variant29-variant30-variant32-variant35-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:735,66,0:0,0,6,16 chr1 203003870 . G A 5210.81 PASS AC=1;AF=0.797;AN=2;DP=4422;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:72,69:141:99:1990,0,1902:33,39,29,40 chr1 203004627 . A AC 1450.99 PASS AC=2;AF=1;AN=2;DP=2819;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,74:74:99:2451,234,0:0,0,28,46 chr1 203004930 . T TAGC 116.46 PASS AC=1;AF=0.577;AN=2;DP=813;set=variant-variant2-variant5-variant6-variant8-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant24-variant26-variant27-variant28-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,10:33:99:350,0,909:8,15,1,9 chr1 203004980 . CT C 225.09 PASS AC=2;AF=0.989;AN=2;DP=534;FS=0;MQ=60;MQRankSum=-0.053;ReadPosRankSum=1.107;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:562,45,0:0,0,0,15 chr1 203006098 . A G 330.12 PASS AC=1;AF=0.56;AN=2;DP=554;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant10-variant13-variant15-variant16-variant17-variant18-variant20-variant24-variant26-variant27-variant28-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,13:23:99:473,0,369:10,0,12,1 chr1 203006179 . G A 1542.52 PASS AC=1;AF=0.565;AN=2;DP=2472;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant10-variant15-variant16-variant18-variant20-variant24-variant26-variant27-variant28-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:62,55:117:99:1500,0,1821:46,16,37,18 chr1 203006243 . A G 7004.81 PASS AC=2;AF=0.989;AN=2;DP=8799;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,203:203:99:5953,607,0:0,0,105,98 chr1 203008174 . G C 2136.06 PASS AC=2;AF=1;AN=2;DP=5182;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,103:103:99:3198,309,0:0,0,47,56 chr1 203008286 . C G 270.6 PASS AC=1;AF=0.725;AN=2;DP=2327;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,28:68:99:732,0,1006:18,22,12,16 chr1 203012705 . C G 748.7 PASS AC=1;AF=0.639;AN=2;DP=3741;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:78,47:125:99:1276,0,1859:34,44,13,34 chr1 203012906 . G A 498.49 PASS AC=1;AF=0.791;AN=2;DP=2424;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,26:75:99:704,0,1280:28,21,15,11 chr1 203014196 . T C 259.59 PASS AC=1;AF=0.703;AN=2;DP=359;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant35-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,8:9:10:252,0,10:1,0,5,3 chr1 203022659 . TCAAAAAACAAACAAACCAAAAACCAAAAAC T 232.73 PASS AC=1;AF=0.727;AN=2;DP=61;MQ=60;set=variant7-variant8-variant16-variant19-variant20-variant22-variant25-variant29-variant35-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,3:7:99:115,0,1069:3,1,2,1 chr1 203024767 . C T 1393.86 PASS AC=1;AF=0.625;AN=2;DP=1875;MQ=60;set=variant-variant3-variant7-variant8-variant9-variant16-variant19-variant20-variant22-variant25-variant28-variant29-variant31-variant35-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:68,75:143:99:1839,0,1747:23,45,27,48 chr1 203025428 . G A 246.84 PASS AC=1;AF=0.625;AN=2;DP=544;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant7-variant8-variant9-variant16-variant19-variant20-variant22-variant25-variant28-variant29-variant31-variant35-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:23,15:38:99:392,0,744:11,12,8,7 chr1 203025583 . G A 1738.89 PASS AC=1;AF=0.5;AN=2;DP=510;MQ=60;set=variant3-variant19-variant22-variant35 GT:AD:DP:GQ:PL:SB 0/1:51,67:118:99:1599,0,1109:22,29,36,31 chr1 203028711 . C G 148.92 PASS AC=1;AF=0.736;AN=2;DP=883;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,19:32:99:652,0,420:12,1,16,3 chr1 203029017 . A C 1175.82 PASS AC=1;AF=0.652;AN=2;DP=1860;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant11-variant16-variant19-variant20-variant22-variant25-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:38,40:78:99:1099,0,925:13,25,11,29 chr1 203030071 . C T 1244.32 PASS AC=1;AF=0.594;AN=2;DP=1520;MQ=60;set=variant-variant3-variant7-variant8-variant9-variant16-variant19-variant20-variant22-variant25-variant28-variant29-variant31-variant35-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:56,46:102:99:1053,0,1445:36,20,29,17 chr1 203030685 . T C 963.7 PASS AC=1;AF=0.75;AN=2;DP=2312;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:30,49:79:99:1374,0,778:18,12,30,19 chr1 203032922 . C T 865.31 PASS AC=1;AF=0.677;AN=2;DP=3176;set=variant-variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:73,69:142:99:1415,0,1599:38,35,36,33 chr1 203036757 . T C 1004.72 PASS AC=1;AF=0.743;AN=2;DP=3296;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:65,46:111:99:1106,0,1667:41,24,29,17 chr1 203040673 . A G 1028.4 PASS AC=2;AF=1;AN=2;DP=1097;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1356,114,0:0,0,30,8 chr1 203040740 . T C 615.58 PASS AC=1;AF=0.725;AN=2;DP=2838;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,31:85:99:759,0,1416:33,21,22,9 chr1 203040816 . G C 1110.68 PASS AC=1;AF=0.725;AN=2;DP=6121;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:85,60:145:99:1328,0,2269:45,40,34,26 chr1 203040922 . G T 1194.53 PASS AC=1;AF=0.6;AN=2;DP=3148;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant11-variant16-variant19-variant20-variant22-variant25-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:66,44:110:99:1089,0,1692:29,37,17,27 chr1 203045413 . G T 1642.2 PASS AC=1;AF=0.615;AN=2;DP=5962;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant11-variant15-variant16-variant18-variant19-variant20-variant22-variant25-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:114,131:245:99:3288,0,2832:69,45,81,50 chr1 203045583 . T C 2495.01 PASS AC=1;AF=0.615;AN=2;DP=5634;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant11-variant15-variant16-variant18-variant19-variant20-variant22-variant25-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:127,140:267:99:3659,0,3037:48,79,49,91 chr1 203045901 . G A,T 709.99 PASS AC=1,0;AF=0.564,0.141;AN=2;DP=2609;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:77:99:18,15,25,19 chr1 203046029 . C T 1012.75 PASS AC=1;AF=0.588;AN=2;DP=1776;MQ=60;set=variant-variant3-variant7-variant8-variant9-variant15-variant16-variant18-variant19-variant20-variant22-variant25-variant29-variant31-variant35-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:34,45:79:99:1136,0,880:19,15,21,24 chr1 203046195 . A G 323.89 PASS AC=1;AF=0.705;AN=2;DP=1733;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,17:44:99:443,0,691:9,18,8,9 chr1 203046340 . G A 590.24 PASS AC=1;AF=0.588;AN=2;DP=725;MQ=60;set=variant-variant3-variant7-variant8-variant9-variant15-variant16-variant18-variant19-variant20-variant22-variant25-variant29-variant31-variant35-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:18,17:35:99:452,0,395:10,8,8,9 chr1 203047621 . C A 531.66 PASS AC=1;AF=0.791;AN=2;DP=2416;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,30:50:99:754,0,509:11,9,14,16 chr1 203047880 . CTTTTTTTTTTTTTT CTTTTTTTTTTTTTTTT,C,CTTTTTT,CTTTTTTTTT,CTTTTTTTTTTTT,CTTTTT,CTTTTTTT 77.01 PASS AC=0,0,0,0,0,0,1;AF=0.059,0.265,0.118,0.059,0.118,0.059,0.088;AN=2;DP=262;MQ=60;set=variant2-variant5-variant7-variant8-variant11-variant16-variant18-variant22-variant25-variant26-variant28-variant31-variant33-variant34-variant35-variant36-variant37 GT:DP:GQ:SB 0/7:17:99:4,5,2,6 chr1 203052360 . A G 247.45 PASS AC=2;AF=1;AN=2;DP=682;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:239,21,0:0,0,3,4 chr1 203053768 . T C 1986.45 PASS AC=2;AF=0.977;AN=2;DP=3787;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,94:94:99:2812,281,0:0,0,49,45 chr1 203059728 . T C 760.95 PASS AC=1;AF=0.763;AN=2;DP=1643;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,30:56:99:768,0,601:17,9,20,10 chr1 203098275 . T G 2038.36 PASS AC=1;AF=0.609;AN=2;DP=4075;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant11-variant15-variant16-variant18-variant20-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant33-variant35-variant36-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:95,112:207:99:3151,0,2285:33,62,34,78 chr1 203098455 . T C 122.82 PASS AC=1;AF=0.609;AN=2;DP=443;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant11-variant15-variant16-variant18-variant20-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant33-variant35-variant36-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,8:15:99:234,0,233:2,5,3,5 chr1 203119928 . CTCTGTCCTCCCCCTA C 615.79 PASS AC=1;AF=0.5;AN=2;DP=224;MQ=60;set=variant10-variant23-variant28-variant35 GT:AD:DP:GQ:PL:SB 0/1:45,25:70:99:822,0,6204:16,29,13,12 chr1 203134135 . A AT 278.85 PASS AC=1;AF=0.525;AN=2;DP=661;MQ=60;set=variant2-variant4-variant5-variant10-variant11-variant13-variant14-variant17-variant20-variant27-variant30-variant32-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,10:25:99:250,0,415:13,2,6,4 chr1 203135325 . A C 1317.37 PASS AC=2;AF=0.966;AN=2;DP=3325;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,74:74:99:2279,222,0:0,0,40,34 chr1 203135375 . C T 927.05 PASS AC=1;AF=0.5;AN=2;DP=315;MQ=60;set=variant10-variant23-variant28-variant35 GT:AD:DP:GQ:PL:SB 0/1:49,41:90:99:1084,0,1213:26,23,22,19 chr1 203135840 . CT C 2090.39 PASS AC=2;AF=0.966;AN=2;DP=3179;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,78:78:99:2860,234,0:0,0,43,35 chr1 203136983 . A T 812.82 PASS AC=2;AF=0.764;AN=2;DP=2465;MQ=60;set=variant2-variant4-variant5-variant6-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,95:96:99:2816,241,0:1,0,59,36 chr1 203137784 . A ACT 2292.17 PASS AC=1;AF=0.917;AN=2;DP=3314;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,50:93:99:1970,0,1658:26,17,32,18 chr1 203140671 . G A 732.94 PASS AC=1;AF=0.571;AN=2;DP=538;FractionInformativeReads=1;MQ=60;set=variant6-variant10-variant21-variant23-variant28-variant30-variant35 GT:AD:DP:GQ:PL:SB 0/1:34,60:94:99:1608,0,800:17,17,26,34 chr1 203141240 . G T 550.7 PASS AC=1;AF=0.5;AN=2;DP=101;FractionInformativeReads=1;MQ=60;set=variant10-variant23-variant28-variant35 GT:AD:DP:GQ:PL:SB 0/1:15,14:29:99:389,0,523:2,13,3,11 chr1 203143725 . G C 372.24 PASS AC=1;AF=0.528;AN=2;DP=1168;MQ=60;set=variant2-variant4-variant5-variant10-variant11-variant13-variant14-variant17-variant27-variant32-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,42:82:99:1006,0,924:17,23,18,24 chr1 203143823 . C T 284.37 PASS AC=1;AF=0.5;AN=2;DP=81;FractionInformativeReads=1;MQ=60;set=variant10-variant23-variant28-variant35 GT:AD:DP:GQ:PL:SB 0/1:17,12:29:99:310,0,510:4,13,2,10 chr1 203148360 . G A 1602.67 PASS AC=1;AF=0.5;AN=2;DP=435;FractionInformativeReads=1;set=variant10-variant23-variant35 GT:AD:DP:GQ:PL:SB 0/1:81,77:158:99:1764,0,2052:44,37,38,39 chr1 203148633 . A G 1941.93 PASS AC=2;AF=1;AN=2;DP=4278;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,100:100:99:3083,300,0:0,0,47,53 chr1 203149906 . C T 314.32 PASS AC=1;AF=0.5;AN=2;DP=84;MQ=60;set=variant10-variant23-variant35 GT:AD:DP:GQ:PL:SB 0/1:14,26:40:99:577,0,352:7,7,13,13 chr1 203150208 . G A 847.61 PASS AC=2;AF=0.563;AN=2;DP=443;MQ=60;set=variant4-variant5-variant9-variant10-variant11-variant13-variant14-variant17-variant23-variant27-variant35-variant37-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1263,108,0:0,0,26,10 chr1 203151794 . G C 669.33 PASS AC=1;AF=0.5;AN=2;DP=210;FractionInformativeReads=1;MQ=60;set=variant10-variant23-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:34,44:78:99:1284,0,750:20,14,29,15 chr1 203154532 . A G 1722.99 PASS AC=1;AF=0.743;AN=2;DP=1740;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,38:55:99:1151,0,436:3,14,9,29 chr1 203155412 . G A 1127.64 PASS AC=1;AF=0.5;AN=2;DP=635;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant35-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,72:133:99:1693,0,1367:29,32,35,37 chr1 203155703 . A T 2481.55 PASS AC=1;AF=0.531;AN=2;DP=2811;MQ=60;set=variant4-variant5-variant7-variant9-variant10-variant11-variant13-variant14-variant17-variant27-variant35-variant37-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:91,114:205:99:2530,0,2145:56,35,62,52 chr1 203155882 . G C 2134.7 PASS AC=2;AF=0.81;AN=2;DP=4309;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,128:128:99:3909,384,0:0,0,50,78 chr1 203155998 . G A 470.71 PASS AC=1;AF=0.538;AN=2;DP=252;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant7-variant10-variant11-variant14-variant17-variant27-variant35-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,11:22:99:380,0,427:0,11,2,9 chr1 203174864 . T C 551.46 PASS AC=1;AF=0.5;AN=2;DP=640;MQ=60;set=variant4-variant6-variant8-variant9-variant12-variant14-variant21-variant23-variant25-variant28-variant29-variant32-variant34-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,24:48:99:531,0,632:17,7,14,10 chr1 203174921 . A G 1190.22 PASS AC=1;AF=0.5;AN=2;DP=1379;MQ=60;set=variant4-variant6-variant8-variant9-variant12-variant14-variant21-variant23-variant25-variant28-variant29-variant32-variant34-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,34:80:99:833,0,1137:28,18,19,15 chr1 203175107 . A C 435.88 PASS AC=1;AF=0.672;AN=2;DP=1426;MQ=60;set=variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,26:46:99:762,0,592:6,14,9,17 chr1 203186950 . C CAGACCATGGCCCCGCCCAGTCCCT 538.24 PASS AC=1;AF=0.5;AN=2;DP=788;MQ=60;set=variant4-variant6-variant8-variant12-variant14-variant21-variant23-variant25-variant28-variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,26:63:99:871,0,8599:15,22,9,17 chr1 203187341 . T TGGTCAA 4267.03 PASS AC=1;AF=0.604;AN=2;DP=5746;MQ=60;set=variant2-variant4-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant16-variant21-variant22-variant23-variant25-variant27-variant29-variant32-variant34-variant35-variant36-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:122,117:239:99:4631,0,8521:55,67,58,59 chr1 203188692 . A C 645.75 PASS AC=1;AF=0.656;AN=2;DP=2119;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant16-variant17-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,28:61:99:747,0,835:21,12,21,7 chr1 203191262 . C G 577.89 PASS AC=1;AF=0.5;AN=2;DP=425;MQ=60;set=variant4-variant5-variant6-variant12-variant14-variant21-variant23-variant25-variant28-variant29-variant32-variant34-variant35-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,17:29:99:606,0,389:11,1,16,1 chr1 203192448 . GC G 401.35 PASS AC=1;AF=0.5;AN=2;DP=381;MQ=60;set=variant4-variant5-variant12-variant14-variant21-variant23-variant25-variant29-variant32-variant34-variant35-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,28:37:99:853,0,191:2,7,7,21 chr1 203277244 . AG A 636.23 PASS AC=2;AF=1;AN=2;DP=1701;FS=0;MQ=60;MQRankSum=1.141;ReadPosRankSum=0.465;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1032,102,0:0,0,20,14 chr1 203278585 . AAAT A 3562.74 PASS AC=1;AF=0.5;AN=2;DP=178;FS=2.65;FractionInformativeReads=0.978;MQ=60;MQRankSum=0.428;QD=20.02;ReadPosRankSum=4.818;SOR=0.923;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:81,93:174:99:3600,0,3333:40,41,41,52 chr1 203278596 . GTATGTTTGTAAGC G 3363.99 PASS AC=1;AF=0.5;AN=2;DP=173;FS=0;FractionInformativeReads=0.965;MQ=60;MQRankSum=1.872;QD=19.45;ReadPosRankSum=5.214;SOR=0.704;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:80,87:167:99:3401,0,3859:37,43,40,47 chr1 203309752 . T C 77.28 PASS AC=1;AF=0.636;AN=2;DP=96;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant14-variant23-variant25-variant27-variant29-variant32-variant35-variant36-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:2,9:11:59:210,0,59:2,0,5,4 chr1 203309880 . G A 147.66 PASS AC=1;AF=0.583;AN=2;DP=269;FractionInformativeReads=1;MQ=60;set=variant2-variant12-variant14-variant23-variant25-variant27-variant29-variant32-variant35-variant36-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:23,15:38:99:333,0,631:14,9,10,5 chr1 203309966 . G C 798.26 PASS AC=2;AF=0.681;AN=2;DP=1183;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1610,153,0:0,0,25,26 chr1 203311216 . T C 957 PASS AC=1;AF=0.583;AN=2;DP=723;MQ=60;set=variant2-variant12-variant14-variant23-variant25-variant27-variant29-variant32-variant35-variant36-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:31,29:60:99:745,0,913:20,11,15,14 chr1 203311736 . T C 476.9 PASS AC=1;AF=0.7;AN=2;DP=850;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant16-variant17-variant18-variant19-variant20-variant21-variant28-variant30-variant33-variant34-variant35-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:23,17:40:99:607,0,685:6,17,1,16 chr1 203317162 . C T 4701.78 PASS AC=2;AF=0.857;AN=2;DP=6656;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,173:173:99:5424,516,0:0,0,90,83 chr1 203320408 . G C 1806.64 PASS AC=2;AF=0.915;AN=2;DP=2600;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,82:82:99:2542,246,0:0,0,43,39 chr1 203596318 . A G 991.72 PASS AC=1;AF=0.866;AN=2;DP=1648;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,21:43:99:611,0,483:9,13,10,11 chr1 203651824 . C T 649.9 PASS AC=2;AF=0.919;AN=2;DP=1036;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:680,63,0:0,0,14,7 chr1 203651927 . T C 1688.98 PASS AC=2;AF=0.919;AN=2;DP=2525;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:1619,165,0:0,0,30,25 chr1 203652040 . T C 1363.09 PASS AC=2;AF=0.919;AN=2;DP=2593;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:1757,174,0:0,0,29,29 chr1 203652140 . C G 1212.27 PASS AC=2;AF=0.919;AN=2;DP=2137;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:2138,144,0:0,0,24,24 chr1 203652141 . G A 1212.27 PASS AC=2;AF=0.919;AN=2;DP=2125;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:2138,144,0:0,0,24,24 chr1 203652444 . A G 3234.51 PASS AC=2;AF=0.919;AN=2;DP=5550;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,128:128:99:3899,384,0:0,0,62,66 chr1 203667409 . T C 3987.4 PASS AC=2;AF=0.919;AN=2;DP=7625;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,174:174:99:5276,521,0:0,0,87,87 chr1 203667577 . TA T 605.55 PASS AC=1;AF=0.643;AN=2;DP=726;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant14-variant19-variant20-variant25-variant30-variant32-variant35-variant36-variant38 GT:AD:DP:GQ:PL:SB 0/1:18,24:42:99:674,0,467:5,13,5,19 chr1 203677250 . G A 1628.2 PASS AC=1;AF=0.654;AN=2;DP=1174;MQ=60;set=variant-variant3-variant6-variant7-variant14-variant19-variant20-variant25-variant30-variant32-variant35-variant36-variant38 GT:AD:DP:GQ:PL:SB 0/1:41,52:93:99:1341,0,1040:14,27,23,29 chr1 203679934 . A G 1491.09 PASS AC=2;AF=0.733;AN=2;DP=3678;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant22-variant24-variant25-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,119:119:99:4034,357,0:0,0,76,43 chr1 203689936 . C G 715.14 PASS AC=1;AF=0.625;AN=2;DP=1067;set=variant-variant3-variant6-variant7-variant14-variant19-variant20-variant22-variant25-variant26-variant30-variant32-variant35-variant36-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:26,29:55:99:723,0,928:10,16,12,17 chr1 203698627 . C T 58.97 PASS AC=1;AF=0.643;AN=2;DP=220;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant6-variant7-variant14-variant19-variant20-variant22-variant25-variant30-variant32-variant35-variant36-variant38 GT:AD:DP:GQ:PL:SB 0/1:10,7:17:99:190,0,339:9,1,6,1 chr1 203698672 . CAA CA,CAAA,C 226.51 PASS AC=0,0,1;AF=0.449,0.064,0.064;AN=2;DP=1533;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-filterInvariant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-filterInvariant34-variant35-variant36-variant37-variant38-variant39-variant41-variant43 GT:DP:GQ:SB 0/3:38:99:18,7,8,5 chr1 203709034 . A G 353.12 PASS AC=2;AF=0.722;AN=2;DP=1826;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:1993,179,0:0,0,27,33 chr1 203709068 . T C 450.79 PASS AC=2;AF=0.722;AN=2;DP=1828;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,69:69:99:2289,207,0:0,0,29,40 chr1 203709569 . CTTT CT,CTT,CTTTT,C 863.68 PASS AC=1,1,0,0;AF=0.349,0.244,0.035,0.012;AN=2;DP=3762;set=variant-filterInvariant2-variant3-variant4-variant5-variant6-variant7-variant8-filterInvariant9-variant10-filterInvariant12-variant13-variant14-variant15-filterInvariant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-filterInvariant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-filterInvariant37-variant38-variant39-variant40-variant41-variant42-variant43-filterInvariant44 GT:DP:GQ:SB 1/2:72:99:7,0,44,21 chr1 203710919 . C CT 3699.58 PASS AC=1;AF=0.579;AN=2;DP=4876;MQ=60;set=variant3-variant4-variant7-variant8-variant12-variant13-variant17-variant18-variant22-variant24-variant25-variant28-variant31-variant32-variant33-variant35-variant36-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:137,139:276:99:3459,0,3439:74,63,71,68 chr1 203712996 . T C 5739.76 PASS AC=1;AF=0.553;AN=2;DP=6654;MQ=60;set=variant3-variant4-variant7-variant8-variant12-variant13-variant17-variant18-variant22-variant24-variant25-variant28-variant31-variant32-variant33-variant35-variant36-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:183,200:383:99:5016,0,4712:77,106,97,103 chr1 203713133 . G A 4713.64 PASS AC=1;AF=0.553;AN=2;DP=5695;MQ=60;set=variant3-variant4-variant7-variant8-variant12-variant13-variant17-variant18-variant22-variant24-variant25-variant28-variant31-variant32-variant33-variant35-variant36-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:166,158:324:99:3753,0,3958:85,81,69,89 chr1 203734231 . T G 589.73 PASS AC=1;AF=0.611;AN=2;DP=1006;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant7-variant12-variant13-variant17-variant24-variant25-variant28-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,21:51:99:505,0,761:19,11,14,7 chr1 203742915 . G A 450.54 PASS AC=2;AF=0.591;AN=2;DP=669;set=variant4-variant5-variant7-variant11-variant12-variant13-variant16-variant21-variant24-variant25-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:998,81,0:0,0,19,8 chr1 203743122 . G A 2634.75 PASS AC=2;AF=0.614;AN=2;DP=4622;MQ=60;set=variant4-variant5-variant7-variant11-variant12-variant13-variant16-variant21-variant24-variant25-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,240:240:99:7533,719,0:0,0,113,127 chr1 203743653 . C T 2855.2 PASS AC=2;AF=0.614;AN=2;DP=3763;MQ=60;set=variant4-variant5-variant7-variant11-variant12-variant13-variant16-variant21-variant24-variant25-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,178:178:99:5436,532,0:0,0,88,90 chr1 203743798 . C T 1028.56 PASS AC=1;AF=0.5;AN=2;DP=297;FractionInformativeReads=1;MQ=60;set=variant11-variant35-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:42,37:79:99:1006,0,1187:15,27,14,23 chr1 203744001 . ATTC A 550.54 PASS AC=1;AF=0.5;AN=2;DP=303;MQ=60;set=variant11-variant16-variant21-variant31-variant34-variant35-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:21,17:38:99:651,0,1004:10,11,5,12 chr1 203744457 . G A 115.65 PASS AC=2;AF=0.632;AN=2;DP=193;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant7-variant11-variant12-variant13-variant16-variant21-variant24-variant25-variant28-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:605,48,0:0,0,13,3 chr1 203744527 . A AC 505.82 PASS AC=2;AF=0.625;AN=2;DP=902;MQ=60;set=variant4-variant5-variant7-variant11-variant12-variant13-variant16-variant18-variant21-variant24-variant25-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1663,132,0:0,0,30,14 chr1 203744707 . G C 8045.78 PASS AC=2;AF=0.989;AN=2;DP=9634;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,208:208:99:6575,622,0:0,0,124,84 chr1 203745184 . A G 198.93 PASS AC=2;AF=0.619;AN=2;DP=279;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant7-variant11-variant12-variant13-variant16-variant21-variant24-variant25-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:375,36,0:0,0,4,8 chr1 203764803 . C T 639.5 PASS AC=1;AF=0.5;AN=2;DP=368;FractionInformativeReads=1;set=variant10-variant11-variant16-variant21-variant31-variant34-variant35-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:31,22:53:99:600,0,704:16,15,17,5 chr1 203765864 . A C 2219.24 PASS AC=1;AF=0.5;AN=2;DP=1607;MQ=60;set=variant10-variant11-variant16-variant21-variant31-variant34-variant35-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:79,65:144:99:1690,0,2126:45,34,35,30 chr1 203766395 . T C 3564.59 PASS AC=1;AF=0.808;AN=2;DP=4005;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,54:109:99:1421,0,1426:19,36,16,38 chr1 203767822 . T G 1873.97 PASS AC=1;AF=0.5;AN=2;DP=1389;MQ=60;set=variant10-variant11-variant16-variant21-variant31-variant34-variant35-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:82,69:151:99:1756,0,2304:32,50,31,38 chr1 203770116 . A T 1996.77 PASS AC=1;AF=0.5;AN=2;DP=1549;MQ=60;set=variant10-variant11-variant16-variant21-variant31-variant34-variant35-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:77,84:161:99:1985,0,1859:33,44,37,47 chr1 203770210 . T G 911.19 PASS AC=1;AF=0.5;AN=2;DP=698;FractionInformativeReads=1;MQ=60;set=variant10-variant11-variant16-variant21-variant31-variant34-variant35-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:29,28:57:99:870,0,877:11,18,13,15 chr1 203770448 . T A 7784.16 PASS AC=1;AF=0.588;AN=2;DP=8346;set=variant3-variant5-variant10-variant11-variant12-variant13-variant16-variant17-variant18-variant21-variant27-variant31-variant34-variant35-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:275,217:492:99:5488,0,6763:149,126,119,98 chr1 203770945 . ATT AT,A,ATTT 940.64 PASS AC=0,1,0;AF=0.58,0.307,0.011;AN=2;DP=2312;MQ=60;set=Intersection GT:DP:GQ:SB 0/2:30:99:6,6,9,9 chr1 203771007 . C CA 1218.24 PASS AC=1;AF=0.5;AN=2;DP=545;MQ=60;set=variant10-variant11-variant16-variant21-variant31-variant34-variant35-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:35,22:57:99:545,0,972:20,15,15,7 chr1 203771794 . G T 1080.4 PASS AC=2;AF=1;AN=2;DP=1671;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1061,101,0:0,0,15,19 chr1 203786152 . A C 500.62 PASS AC=1;AF=0.55;AN=2;DP=235;FractionInformativeReads=1;set=variant10-variant11-variant16-variant21-variant31-variant34-variant35-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:14,12:26:99:381,0,478:11,3,10,2 chr1 203787700 . T C 1303.51 PASS AC=2;AF=1;AN=2;DP=1567;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1100,99,0:0,0,22,11 chr1 203799343 . C T 1070.93 PASS AC=1;AF=0.5;AN=2;DP=688;MQ=60;set=variant10-variant11-variant16-variant21-variant31-variant34-variant35-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:55,32:87:99:644,0,1432:34,21,17,15 chr1 203803016 . A G 3020.8 PASS AC=2;AF=1;AN=2;DP=3611;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,80:80:99:2473,240,0:0,0,31,49 chr1 203807233 . T C 1796.82 PASS AC=1;AF=0.5;AN=2;DP=1509;MQ=60;set=variant10-variant11-variant16-variant21-variant31-variant34-variant35-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:68,73:141:99:1822,0,1782:25,43,29,44 chr1 203807273 . A G 1168.66 PASS AC=1;AF=0.5;AN=2;DP=935;MQ=60;set=variant10-variant11-variant16-variant21-variant31-variant34-variant35-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:52,48:100:99:1319,0,1187:21,31,16,32 chr1 203809380 . G A 161.13 PASS AC=1;AF=0.5;AN=2;DP=149;MQ=60;set=variant10-variant11-variant16-variant21-variant31-variant35-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:13,3:16:84:84,0,421:10,3,3,0 chr1 203817549 . T C 660.78 PASS AC=1;AF=0.5;AN=2;DP=493;FractionInformativeReads=1;MQ=60;set=variant10-variant11-variant16-variant21-variant31-variant34-variant35-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:29,28:57:99:724,0,722:13,16,12,16 chr1 203817608 . A G 392.41 PASS AC=1;AF=0.5;AN=2;DP=261;MQ=60;set=variant10-variant11-variant16-variant21-variant31-variant34-variant35-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:18,18:36:99:455,0,503:5,13,7,11 chr1 203817620 . G C 374.98 PASS AC=1;AF=0.5;AN=2;DP=193;FractionInformativeReads=1;MQ=60;set=variant10-variant11-variant16-variant21-variant31-variant34-variant35-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:15,18:33:99:456,0,378:4,11,7,11 chr1 203818654 . A C 211.45 PASS AC=1;AF=0.5;AN=2;DP=81;FractionInformativeReads=1;MQ=60;set=variant10-variant11-variant16-variant21-variant31-variant35-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:9,3:12:91:91,0,315:9,0,3,0 chr1 203818973 . C A 2224.8 PASS AC=1;AF=0.607;AN=2;DP=2450;FractionInformativeReads=1;set=variant4-variant7-variant13-variant24-variant25-variant26-variant28-variant32-variant33-variant35-variant36-variant37-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:103,88:191:99:2353,0,2755:53,50,45,43 chr1 203819177 . T C 1914.96 PASS AC=1;AF=0.607;AN=2;DP=1791;MQ=60;set=variant4-variant7-variant13-variant24-variant25-variant26-variant28-variant32-variant33-variant35-variant36-variant37-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:65,69:134:99:1641,0,1467:26,39,30,39 chr1 203819203 . A G 1048.92 PASS AC=1;AF=0.5;AN=2;DP=882;FractionInformativeReads=1;MQ=60;set=variant10-variant11-variant16-variant21-variant31-variant34-variant35-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:63,46:109:99:1184,0,1436:27,36,15,31 chr1 203821200 . G A 2008.86 PASS AC=2;AF=1;AN=2;DP=3191;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:2255,224,0:0,0,47,28 chr1 203821314 . G A 2409.28 PASS AC=1;AF=0.607;AN=2;DP=2112;set=variant4-variant7-variant13-variant24-variant25-variant26-variant28-variant32-variant33-variant35-variant36-variant37-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:72,83:155:99:2139,0,1813:40,32,42,41 chr1 203830556 . C A 112.59 PASS AC=1;AF=0.5;AN=2;DP=107;FractionInformativeReads=1;MQ=60;set=variant6-variant10-variant11-variant16-variant21-variant34-variant35-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:9,4:13:99:134,0,233:6,3,4,0 chr1 203831261 . G A 871.16 PASS AC=1;AF=0.55;AN=2;DP=914;FractionInformativeReads=1;MQ=60;set=variant6-variant10-variant11-variant16-variant21-variant34-variant35-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:53,28:81:99:640,0,1304:27,26,13,15 chr1 203832964 . A G 418.16 PASS AC=1;AF=0.5;AN=2;DP=489;FractionInformativeReads=1;MQ=60;set=variant6-variant10-variant11-variant16-variant21-variant34-variant35-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:32,27:59:99:736,0,764:13,19,7,20 chr1 203839273 . C T 780.9 PASS AC=1;AF=0.854;AN=2;DP=828;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,9:28:99:199,0,604:13,6,5,4 chr1 203839427 . T TA 1092.12 PASS AC=1;AF=0.5;AN=2;DP=913;MQ=60;set=variant6-variant10-variant11-variant16-variant21-variant34-variant35-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:39,50:89:99:1543,0,1117:23,16,35,15 chr1 203839505 . T C 9146.91 PASS AC=2;AF=1;AN=2;DP=10805;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,219:219:99:6346,655,0:0,0,116,103 chr1 204006538 . T C 482.13 PASS AC=2;AF=0.898;AN=2;DP=2165;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1721,168,0:0,0,33,23 chr1 204006597 . G A 917.88 PASS AC=2;AF=0.864;AN=2;DP=4198;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,107:107:99:3140,320,0:0,0,62,45 chr1 204010389 . G T 697.94 PASS AC=2;AF=0.898;AN=2;DP=2069;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1455,146,0:0,0,20,29 chr1 204081655 . A ACACACT,ACACACACACT,ACACT,ACACACACT,ACACACACACACT,ACACACACACACACACACT,ACACACACACACACACT 1397.54 PASS AC=0,1,0,1,0,0,0;AF=0.19,0.431,0.103,0.121,0.103,0.017,0.017;AN=2;DP=1136;set=variant-variant7-variant8-variant11-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant12-variant26-variant28-variant30-variant31-variant32-variant35-variant24-variant36-variant37-variant38-variant39-variant41-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 4/2:35:99:0,0,31,4 chr1 204082002 . C T 1309.73 PASS AC=2;AF=0.661;AN=2;DP=3139;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant9-variant11-variant12-variant14-variant15-variant16-variant19-variant20-variant22-variant23-variant24-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,122:122:99:4046,366,0:0,0,65,57 chr1 204082323 . C T 332.79 PASS AC=2;AF=0.689;AN=2;DP=1335;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:1481,143,0:0,0,19,29 chr1 204095426 . C T 584.48 PASS AC=1;AF=0.5;AN=2;DP=316;FractionInformativeReads=1;MQ=60;set=variant14-variant19-variant35-variant36-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:38,24:62:99:590,0,1180:16,22,6,18 chr1 204096472 . CACCCAGCCCTG C 110.85 PASS AC=1;AF=0.5;AN=2;DP=44;FS=40.36;FractionInformativeReads=0.909;MQ=60;MQRankSum=0.712;QD=2.52;ReadPosRankSum=0.854;SOR=4.16;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:33,7:40:99:148,0,1766:6,27,7,0 chr1 204096487 . CT C 115.54 PASS AC=1;AF=0.5;AN=2;DP=43;FS=36.514;FractionInformativeReads=0.907;MQ=60;MQRankSum=-0.714;QD=2.69;ReadPosRankSum=-0.421;SOR=4.16;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:32,7:39:99:153,0,1728:7,25,7,0 chr1 204096506 . CT C 37.27 DRAGENHardINDEL AC=1;AF=0.5;AN=2;DP=39;FS=29.747;FractionInformativeReads=0.949;MQ=60;MQRankSum=-1.355;QD=0.96;ReadPosRankSum=-2.466;SOR=3.585;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:32,5:37:75:75,0,1814:6,26,5,0 chr1 204096630 . T C 916.54 PASS AC=2;AF=0.92;AN=2;DP=2028;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,63:63:99:1836,189,0:0,0,29,34 chr1 204103618 . G A 722.58 PASS AC=2;AF=0.75;AN=2;DP=1376;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1156,108,0:0,0,22,14 chr1 204110334 . A G 3004.95 PASS AC=2;AF=0.966;AN=2;DP=7143;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,173:173:99:5177,517,0:0,0,98,75 chr1 204116452 . G A 917.46 PASS AC=1;AF=0.5;AN=2;DP=648;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant9-variant10-variant12-variant17-variant20-variant22-variant35-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:40,36:76:99:1015,0,1273:33,7,28,8 chr1 204121237 . T C 96.21 PASS AC=1;AF=0.5;AN=2;DP=65;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant9-variant11-variant21-variant28-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:76:76,0,96:0,3,1,2 chr1 204129671 . A C 996.96 PASS AC=1;AF=0.559;AN=2;DP=1725;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant9-variant13-variant14-variant18-variant19-variant21-variant25-variant27-variant28-variant35-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:57,49:106:99:1346,0,1447:34,23,34,15 chr1 204130376 . G C 157.49 PASS AC=1;AF=0.63;AN=2;DP=1136;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant20-variant22-variant23-variant25-variant31-variant33-variant34-variant35-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,28:58:99:627,0,696:18,12,15,13 chr1 204159611 . CT C 892.21 PASS AC=1;AF=0.567;AN=2;DP=814;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant9-variant13-variant14-variant18-variant21-variant25-variant27-variant35-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:35,23:58:99:733,0,1155:23,12,16,7 chr1 204159787 . G C 1669.63 PASS AC=1;AF=0.559;AN=2;DP=2282;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant13-variant14-variant18-variant21-variant25-variant27-variant35-variant36-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:66,74:140:99:1771,0,1782:30,36,37,37 chr1 204165609 . CA C 196.28 PASS AC=1;AF=0.571;AN=2;DP=580;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant21-variant26-variant27-variant32-variant34-variant35-variant36-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:18,14:32:99:428,0,574:7,11,6,8 chr1 204190412 . C G 286.77 PASS AC=1;AF=0.661;AN=2;DP=1248;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant17-variant19-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:28,32:60:99:815,0,733:16,12,19,13 chr1 204190508 . C T 383.57 PASS AC=1;AF=0.596;AN=2;DP=1381;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant7-variant8-variant10-variant11-variant14-variant17-variant19-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:35,33:68:99:784,0,870:18,17,17,16 chr1 204190576 . C T 332.45 PASS AC=1;AF=0.596;AN=2;DP=1617;MQ=60;set=variant-variant3-variant7-variant8-variant10-variant11-variant14-variant17-variant19-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:24,23:47:99:672,0,693:14,10,9,14 chr1 204190873 . A G 590.18 PASS AC=1;AF=0.661;AN=2;DP=3245;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant17-variant19-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:74,49:123:99:1195,0,1863:39,35,26,23 chr1 204191148 . ATCTC ATC,ATCTCTCTCTCTCTC,ATCTCTC,ATCTCTCTCTCTCTCTCTC,ATCTCTCTCTCTCTCTCTCTCTC,A,ATCTCTCTCTCTCTCTCTCTC,ATCTCTCTC,ATCTCTCTCTCTCTCTC 369.01 PASS AC=1,0,0,0,0,0,1,0,0;AF=0.64,0.012,0.012,0.198,0.023,0.012,0.023,0.023,0.035;AN=2;DP=2429;FS=0;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 1/7:35:99:1,0,13,21 chr1 204191409 . T C 566.88 PASS AC=1;AF=0.661;AN=2;DP=2321;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant17-variant19-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:60,48:108:99:1182,0,1564:29,31,23,25 chr1 204197007 . T A 521.77 PASS AC=1;AF=0.7;AN=2;DP=287;MQ=60;set=variant3-variant4-variant5-variant8-variant10-variant14-variant17-variant19-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,4:12:95:95,0,284:7,1,2,2 chr1 204197048 . C T 156.3 PASS AC=1;AF=0.672;AN=2;DP=582;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant13-variant14-variant17-variant19-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:15,7:22:99:147,0,352:8,7,4,3 chr1 204198209 . A G 551.74 PASS AC=1;AF=0.667;AN=2;DP=1469;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant13-variant14-variant17-variant19-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:30,24:54:99:755,0,730:9,21,4,20 chr1 204199614 . C T 1086.83 PASS AC=1;AF=0.667;AN=2;DP=3305;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant13-variant14-variant17-variant19-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:78,55:133:99:1310,0,1878:44,34,36,19 chr1 204210750 . C A 109.86 PASS AC=1;AF=0.583;AN=2;DP=786;MQ=60;set=variant-variant3-variant7-variant8-variant10-variant14-variant17-variant19-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:20,23:43:99:635,0,600:8,12,12,11 chr1 204210791 . G A 378.17 PASS AC=1;AF=0.583;AN=2;DP=1030;MQ=60;set=variant-variant3-variant7-variant8-variant10-variant14-variant17-variant19-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:17,31:48:99:931,0,488:11,6,19,12 chr1 204214975 . TACACACAC TAC,TACACAC,T,TACAC 1010.66 PASS AC=2,0,0,0;AF=0.684,0.013,0.013,0.013;AN=2;DP=1952;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:54:99:0,0,13,41 chr1 204216410 . C T 5956.25 PASS AC=2;AF=0.736;AN=2;DP=6588;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,188:188:99:5464,564,0:0,0,105,83 chr1 204216468 . C T 5271.6 PASS AC=2;AF=0.722;AN=2;DP=6580;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,205:205:99:5973,614,0:0,0,97,108 chr1 204216601 . G A 1528.13 PASS AC=2;AF=0.722;AN=2;DP=2558;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1883,167,0:0,0,19,37 chr1 204216762 . C T 403.45 PASS AC=2;AF=0.722;AN=2;DP=860;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:558,54,0:0,0,6,12 chr1 204218633 . G C 800.96 PASS AC=2;AF=0.73;AN=2;DP=1237;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1353,126,0:0,0,16,26 chr1 204218714 . T C 286.77 PASS AC=2;AF=1;AN=2;DP=564;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:761,63,0:0,0,5,16 chr1 204219850 . G A 1527.06 PASS AC=2;AF=0.73;AN=2;DP=2436;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,91:91:99:2996,273,0:0,0,30,61 chr1 204230581 . G A 1323.58 PASS AC=2;AF=0.688;AN=2;DP=2343;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant10-variant11-variant14-variant16-variant17-variant18-variant19-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,89:89:99:2860,267,0:0,0,33,56 chr1 204234196 . GGT G,GGTGT,GGTGTGT 2004.54 PASS AC=1,1,0;AF=0.21,0.435,0.016;AN=2;DP=2520;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant10-variant11-variant14-variant16-variant17-variant18-variant19-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 1/2:96:99:2,2,36,56 chr1 204234222 . T C 2812.67 PASS AC=2;AF=0.743;AN=2;DP=2469;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,92:92:99:4153,283,0:0,0,35,57 chr1 204234225 . G A 943.96 PASS AC=1;AF=0.661;AN=2;DP=1975;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant17-variant19-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:52,43:95:99:962,0,1496:19,33,16,27 chr1 204237113 . TC T 1023.55 PASS AC=2;AF=0.722;AN=2;DP=1024;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:1052,78,0:0,0,20,6 chr1 204237416 . C T 2816.02 PASS AC=2;AF=0.716;AN=2;DP=5506;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,161:161:99:4941,482,0:0,0,66,95 chr1 204242731 . C A 398.22 PASS AC=1;AF=0.65;AN=2;DP=392;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant7-variant16-variant18-variant31-variant35-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,27:50:99:624,0,717:19,4,17,10 chr1 204242838 . A C 1271.11 PASS AC=1;AF=0.636;AN=2;DP=1216;MQ=60;set=variant-variant2-variant6-variant7-variant16-variant18-variant31-variant34-variant35-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:66,59:125:99:1428,0,1485:33,33,33,26 chr1 204243732 . C G 301.96 PASS AC=2;AF=0.75;AN=2;DP=414;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:229,18,0:0,0,5,1 chr1 204379617 . T C 4944.53 PASS AC=2;AF=0.989;AN=2;DP=7006;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:2,169:171:99:5206,462,0:1,1,88,81 chr1 204392575 . CA C,CAA,CAAA 57.53 PASS AC=1,0,0;AF=0.25,0.167,0.083;AN=2;DP=148;set=variant3-variant7-variant8-variant11-variant24-variant27-variant28-variant29-variant31-variant35-filterInvariant36-variant41 GT:DP:GQ:SB 0/1:7:47:2,1,2,2 chr1 204393072 . G A 625.86 PASS AC=1;AF=0.5;AN=2;DP=59;FS=2.208;FractionInformativeReads=1;MQ=60;MQRankSum=-0.19;QD=10.61;ReadPosRankSum=-0.373;SOR=1.101;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:32,27:59:99:654,0,728:16,16,11,16 chr1 204409281 . C G 794.88 PASS AC=2;AF=0.977;AN=2;DP=2015;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:1888,162,0:0,0,42,12 chr1 204413297 . C T 5482.42 PASS AC=2;AF=0.869;AN=2;DP=6429;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,154:154:99:6879,467,0:0,0,69,85 chr1 204413299 . G A 5482.42 PASS AC=2;AF=0.869;AN=2;DP=6357;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,151:151:99:6879,467,0:0,0,69,82 chr1 204418198 . T C 1232.67 PASS AC=2;AF=0.884;AN=2;DP=1726;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1484,132,0:0,0,24,20 chr1 204418889 . C T 559.86 PASS AC=2;AF=0.869;AN=2;DP=913;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1097,101,0:0,0,25,9 chr1 204418939 . C T 1190.47 PASS AC=2;AF=0.869;AN=2;DP=2037;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,52:52:99:1612,156,0:0,0,29,23 chr1 204426052 . A C 328.94 PASS AC=2;AF=0.85;AN=2;DP=377;set=variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:38:552,38,0:0,0,10,3 chr1 204429212 . A T 2305.51 PASS AC=2;AF=0.989;AN=2;DP=2409;MQ=60;MQRankSum=1.266;ReadPosRankSum=-0.789;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,63:63:99:2732,190,0:0,0,19,44 chr1 204429213 . T G 2305.51 PASS AC=2;AF=0.989;AN=2;DP=2309;FS=0;MQ=60;MQRankSum=0.031;ReadPosRankSum=-0.123;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:2732,190,0:0,0,15,43 chr1 204429215 . T A 2221.77 PASS AC=2;AF=0.989;AN=2;DP=2256;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.831;ReadPosRankSum=0.277;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:2599,175,0:0,0,14,41 chr1 204429216 . A G 2176.77 PASS AC=2;AF=0.989;AN=2;DP=2224;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.054;ReadPosRankSum=-0.081;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:2565,172,0:0,0,14,39 chr1 204429285 . A G 773.1 PASS AC=2;AF=0.989;AN=2;DP=861;FractionInformativeReads=1;MQ=60;MQRankSum=0.318;ReadPosRankSum=-1.059;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:505,42,0:0,0,5,9 chr1 204429838 . C G 3127.64 PASS AC=2;AF=0.977;AN=2;DP=7026;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,166:167:99:5090,455,0:1,0,80,86 chr1 204433093 . A C 1309.59 PASS AC=2;AF=0.881;AN=2;DP=2002;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1739,150,0:0,0,36,14 chr1 204433511 . T TC 1136.72 PASS AC=2;AF=0.989;AN=2;DP=1807;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1392,114,0:0,0,23,13 chr1 204434277 . T C 1451.6 PASS AC=2;AF=0.989;AN=2;DP=1349;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:913,87,0:0,0,19,10 chr1 204436520 . G C 61.77 PASS AC=2;AF=0.97;AN=2;DP=144;FS=0;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:180,12,0:0,0,2,2 chr1 204438334 . C T 4814.17 PASS AC=2;AF=0.953;AN=2;DP=7265;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,193:193:99:6111,577,0:0,0,92,101 chr1 204438643 . G T 1387.37 PASS AC=2;AF=0.953;AN=2;DP=3844;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,86:87:99:2497,248,0:1,0,42,44 chr1 204494436 . C T 955.99 PASS AC=2;AF=0.656;AN=2;DP=1763;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:1916,177,0:0,0,44,15 chr1 204494756 . G GT 136.23 PASS AC=1;AF=0.5;AN=2;DP=918;MQ=60;set=variant4-filterInvariant8-filterInvariant10-filterInvariant11-variant12-filterInvariant15-variant25-filterInvariant29-filterInvariant32-variant35-variant36-variant37-filterInvariant38-filterInvariant39-variant40-filterInvariant42 GT:AD:DP:GQ:PL:SB 0/1:23,11:34:99:128,0,479:4,19,4,7 chr1 204495595 . GTT GTTT,GTTTT,G 514.13 PASS AC=2,0,0;AF=0.605,0.013,0.053;AN=2;DP=1789;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-filterInvariant42-variant43-variant44 GT:DP:GQ:SB 1/1:30:63:0,1,9,20 chr1 204505976 . GA G 335.63 PASS AC=2;AF=0.656;AN=2;DP=562;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:405,39,0:0,0,10,3 chr1 204506107 . C T 1194.34 PASS AC=2;AF=0.73;AN=2;DP=2295;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:1675,171,0:0,0,29,28 chr1 204512100 . T C 625.1 PASS AC=2;AF=0.73;AN=2;DP=1135;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,36:38:51:908,51,0:1,1,10,26 chr1 204515863 . C T 444.37 PASS AC=2;AF=0.736;AN=2;DP=566;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:691,60,0:0,0,15,5 chr1 204516025 . A G 2592.95 PASS AC=2;AF=0.73;AN=2;DP=4394;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,134:134:99:3801,401,0:0,0,67,67 chr1 204518842 . C A 5770.27 PASS AC=2;AF=0.833;AN=2;DP=7923;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,213:213:99:7030,638,0:0,0,122,91 chr1 204519187 . C G 6734.33 PASS AC=2;AF=0.656;AN=2;DP=7631;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,220:220:99:6949,659,0:0,0,93,127 chr1 204519258 . G GT 2002.13 PASS AC=2;AF=0.641;AN=2;DP=3807;set=variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant12-filterInvariant13-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:4,78:82:99:1726,143,0:1,3,22,56 chr1 204519692 . GT G 279.59 PASS AC=2;AF=0.764;AN=2;DP=574;MQ=60;set=variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:334,39,0:0,0,5,8 chr1 204520044 . A T 2203.82 PASS AC=2;AF=0.75;AN=2;DP=386;MQ=60;MQRankSum=-2.462;ReadPosRankSum=-0.545;set=variant4-variant35 GT:AD:DP:GQ:PL:SB 1/1:0,179:179:99:5273,535,0:0,0,97,82 chr1 204520209 . C T 2994.87 PASS AC=2;AF=0.716;AN=2;DP=2415;set=variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,69:69:99:2337,207,0:0,0,20,49 chr1 204520589 . CTTTTTTTTTTT CTT,CT,CTTTTTT,CTTTTTTTTTT,CTTTTT,CTTTT,C,CTTT,CTTTTTTTT 242.23 PASS AC=0,0,0,0,0,0,0,2,0;AF=0.026,0.026,0.079,0.026,0.132,0.132,0.026,0.105,0.026;AN=2;DP=449;set=variant2-variant3-variant8-filterInvariant9-variant13-variant16-variant22-variant23-variant25-variant27-variant28-variant30-variant31-variant35-variant36-variant37-variant38-variant43-variant44 GT:DP:GQ:SB 8/8:23:5:4,0,4,15 chr1 204522457 . T C 1764.91 PASS AC=2;AF=0.73;AN=2;DP=3054;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,91:91:99:2987,272,0:0,0,40,51 chr1 204522489 . C T 1733.74 PASS AC=2;AF=0.716;AN=2;DP=2683;set=variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,69:69:99:2467,206,0:0,0,37,32 chr1 204524474 . G T 496.69 PASS AC=2;AF=0.716;AN=2;DP=882;set=variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:988,78,0:0,0,23,3 chr1 204525054 . GT G 8077.97 PASS AC=2;AF=0.73;AN=2;DP=11469;set=variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:3,328:331:99:9020,907,0:2,1,165,163 chr1 204525568 . G T 157.45 PASS AC=2;AF=0.685;AN=2;DP=276;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant7-variant8-variant10-variant12-variant13-variant14-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant33-variant34-variant35-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:53:570,53,0:0,0,5,13 chr1 204526721 . G A 1060.73 PASS AC=2;AF=0.656;AN=2;DP=1216;set=variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:1184,90,0:0,0,27,3 chr1 204527057 . TAAC T 3174.27 PASS AC=2;AF=0.662;AN=2;DP=2819;set=variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,81:82:99:3517,241,0:0,1,31,50 chr1 204586805 . G A 1917.24 PASS AC=2;AF=0.625;AN=2;DP=1943;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1629,158,0:0,0,28,25 chr1 204587240 . G A 3282 PASS AC=2;AF=0.625;AN=2;DP=3134;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,101:101:99:2979,300,0:0,0,52,49 chr1 204590044 . G A 1264.54 PASS AC=2;AF=0.778;AN=2;DP=1069;MQ=60;set=variant2-variant4-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:983,90,0:0,0,13,17 chr1 204591237 . A G 620.32 PASS AC=2;AF=0.779;AN=2;DP=2437;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:1831,180,0:0,0,27,33 chr1 204889909 . G A 401.02 PASS AC=1;AF=0.5;AN=2;DP=111;FractionInformativeReads=1;MQ=60;set=variant29-variant30-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:15,26:41:99:673,0,422:5,10,7,19 chr1 204913592 . A G 68.02 PASS AC=1;AF=0.5;AN=2;DP=67;MQ=60;set=filterInvariant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,11:36:96:96,0,449:13,12,0,11 chr1 204913652 . A G 91.72 PASS AC=1;AF=0.869;AN=2;DP=678;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,13:26:99:409,0,341:5,8,3,10 chr1 204915393 . A G 1140.01 PASS AC=1;AF=0.869;AN=2;DP=4901;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:76,34:110:99:754,0,1909:44,32,19,15 chr1 204915757 . G A 3314.8 PASS AC=1;AF=0.5;AN=2;DP=2678;MQ=60;set=variant13-variant20-variant25-variant27-variant29-variant30-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:184,191:375:99:4446,0,4198:84,100,89,102 chr1 204917708 . AAAAAC A 952.88 PASS AC=1;AF=0.5;AN=2;DP=842;MQ=60;set=variant13-variant20-variant25-variant27-variant28-variant29-variant30-variant35-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:54,43:97:99:1609,0,3244:31,23,33,10 chr1 204917909 . T C 761.26 PASS AC=1;AF=0.55;AN=2;DP=492;FractionInformativeReads=1;MQ=60;set=variant13-variant20-variant25-variant27-variant28-variant29-variant30-variant35-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:26,27:53:99:709,0,762:7,19,8,19 chr1 204919494 . C T 329.02 PASS AC=1;AF=0.5;AN=2;DP=224;FractionInformativeReads=1;MQ=60;set=variant13-variant20-variant25-variant27-variant28-variant29-variant30-variant35-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:15,15:30:99:538,0,550:14,1,15,0 chr1 204943285 . A T 3938.45 PASS AC=2;AF=0.989;AN=2;DP=5921;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,172:173:99:4629,504,0:0,1,94,78 chr1 204943947 . C A 1078.68 PASS AC=1;AF=0.583;AN=2;DP=3100;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant22-variant32-variant34-variant35-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:75,70:145:99:1714,0,2038:35,40,30,40 chr1 204943991 . C T 947.13 PASS AC=1;AF=0.583;AN=2;DP=2646;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant22-variant32-variant34-variant35-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,57:124:99:1427,0,1685:32,35,22,35 chr1 204943992 . A G 3809.19 PASS AC=2;AF=0.989;AN=2;DP=4911;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,126:126:99:4768,379,0:0,0,56,70 chr1 204945618 . G A 1427.28 PASS AC=1;AF=0.54;AN=2;DP=3043;MQ=60;set=variant2-variant5-variant6-variant7-variant9-variant11-variant13-variant14-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant29-variant31-variant32-variant35-variant36-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:72,72:144:99:1696,0,1822:35,37,38,34 chr1 204951209 . C T 603.73 PASS AC=1;AF=0.56;AN=2;DP=1788;MQ=60;set=variant2-variant5-variant6-variant7-variant9-variant11-variant13-variant14-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant29-variant31-variant32-variant35-variant36-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,44:84:99:1093,0,1027:17,23,20,24 chr1 204953459 . A ATG 238.79 PASS AC=1;AF=0.8;AN=2;DP=228;FS=0;set=variant2-variant3-variant4-variant5-variant11-variant14-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant29-variant33-variant35-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:6,3:9:82:82,0,198:1,5,0,3 chr1 204954993 . A G 118.4 PASS AC=1;AF=0.617;AN=2;DP=394;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant6-variant7-variant9-variant11-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,7:13:99:192,0,128:4,2,5,2 chr1 204955319 . G A 530.54 PASS AC=1;AF=0.586;AN=2;DP=980;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant6-variant7-variant9-variant11-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant35-variant36-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,19:35:99:732,0,1035:4,12,3,16 chr1 204955329 . A G 487.31 PASS AC=1;AF=0.586;AN=2;DP=825;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant6-variant7-variant9-variant11-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant35-variant36-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,17:32:99:669,0,998:4,11,3,14 chr1 204966170 . T C 271.39 PASS AC=1;AF=0.591;AN=2;DP=323;FractionInformativeReads=1;MQ=60;set=variant5-variant6-variant8-variant9-variant11-variant13-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant26-variant31-variant32-variant35-variant36-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,9:15:99:353,0,187:5,1,9,0 chr1 204966428 . C G 867.28 PASS AC=1;AF=0.536;AN=2;DP=1559;set=variant-variant2-variant6-variant12-variant13-variant20-variant23-variant28-variant31-variant35-variant37-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:34,64:98:99:1741,0,865:19,15,36,28 chr1 204966690 . G A 2831.92 PASS AC=2;AF=0.932;AN=2;DP=4475;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,126:126:99:3792,375,0:0,0,47,79 chr1 204966749 . A G 597.28 PASS AC=2;AF=0.779;AN=2;DP=2122;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:1936,186,0:0,0,21,41 chr1 204970148 . TC T 175.24 PASS AC=1;AF=0.55;AN=2;DP=428;MQ=60;set=variant2-variant5-variant6-variant9-variant10-variant11-variant17-variant18-variant19-variant21-variant22-variant23-variant26-variant31-variant32-variant35-variant37-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,18:28:99:536,0,251:8,2,14,4 chr1 204970243 . A G 509.96 PASS AC=1;AF=0.55;AN=2;DP=1786;MQ=60;set=variant2-variant5-variant6-variant9-variant10-variant11-variant17-variant18-variant19-variant21-variant22-variant23-variant26-variant31-variant32-variant35-variant37-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,52:98:99:1414,0,1098:27,19,31,21 chr1 204970302 . T C 1019.2 PASS AC=1;AF=0.55;AN=2;DP=2666;MQ=60;set=variant2-variant5-variant6-variant9-variant10-variant11-variant17-variant18-variant19-variant21-variant22-variant23-variant26-variant31-variant32-variant35-variant37-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:75,72:147:99:1837,0,1682:41,34,40,32 chr1 204970495 . C A 510.24 PASS AC=1;AF=0.55;AN=2;DP=728;MQ=60;set=variant2-variant5-variant6-variant9-variant10-variant11-variant17-variant18-variant19-variant21-variant22-variant23-variant26-variant31-variant32-variant35-variant37-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,27:37:99:733,0,244:2,8,8,19 chr1 204978533 . A G 4174.58 PASS AC=1;AF=0.786;AN=2;DP=4663;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,62:129:99:1531,0,1652:32,35,30,32 chr1 204978643 . C A 2424.86 PASS AC=1;AF=0.672;AN=2;DP=4120;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant28-variant30-variant31-variant32-variant35-variant36-variant37-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,94:159:99:2205,0,1659:35,30,47,47 chr1 204986586 . T C 1026.16 PASS AC=2;AF=0.943;AN=2;DP=1850;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1050,114,0:0,0,19,19 chr1 204988183 . C A 1363.89 PASS AC=2;AF=0.737;AN=2;DP=2624;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:2252,213,0:0,0,41,30 chr1 204988535 . T C 715.17 PASS AC=2;AF=0.736;AN=2;DP=2444;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:2064,186,0:0,0,24,38 chr1 204988603 . C CCATTCATT,CCATTCATTCATT,CCATTCATTCATTCATT,CCATT 727.14 PASS AC=2,0,0,0;AF=0.625,0.273,0.011,0.034;AN=2;DP=2091;set=Intersection GT:DP:GQ:SB 1/1:37:99:0,0,14,23 chr1 204989163 . T G 2241.75 PASS AC=2;AF=0.73;AN=2;DP=3370;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,96:96:99:3043,288,0:0,0,47,49 chr1 204990860 . G C 2528.43 PASS AC=2;AF=0.943;AN=2;DP=3598;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,89:89:99:2675,265,0:0,0,43,46 chr1 204991511 . G C 103.89 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=1404;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:54,21:75:99:264,0,1246:12,42,21,0 chr1 205028883 . CAG C 160.66 PASS AC=1;AF=0.643;AN=2;DP=680;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,10:16:99:401,0,225:1,5,2,8 chr1 205034852 . A ATGGCCTGCTGCACTGGTCAGGGCCGGTGGTC 1168.67 PASS AC=1;AF=0.657;AN=2;DP=1652;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,14:42:99:1008,0,7251:16,12,12,2 chr1 205038731 . C T 2522.09 PASS AC=1;AF=0.775;AN=2;DP=2787;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,49:79:99:1530,0,637:12,18,11,38 chr1 205039288 . T C 2408.9 PASS AC=1;AF=0.588;AN=2;DP=2857;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,45:94:99:1182,0,1278:14,35,15,30 chr1 205040835 . A G 156.22 PASS AC=1;AF=0.915;AN=2;DP=527;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,7:16:99:186,0,238:5,4,3,4 chr1 205040943 . C G 728.99 PASS AC=1;AF=0.639;AN=2;DP=1351;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,15:35:99:476,0,563:11,9,11,4 chr1 205041015 . G A 1535.02 PASS AC=1;AF=0.588;AN=2;DP=2520;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,35:75:99:923,0,1090:26,14,24,11 chr1 205043250 . G C 1286.91 PASS AC=1;AF=0.588;AN=2;DP=1974;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,22:59:99:514,0,949:20,17,9,13 chr1 205044354 . G A 1548.25 PASS AC=1;AF=0.886;AN=2;DP=2819;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:35,32:67:99:833,0,832:20,15,20,12 chr1 205044416 . C A 1344.87 PASS AC=1;AF=0.909;AN=2;DP=3003;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:41,43:84:99:1115,0,1030:18,23,20,23 chr1 205044866 . G C 863.29 PASS AC=1;AF=0.886;AN=2;DP=1146;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:19,14:33:99:394,0,660:8,11,6,8 chr1 205052939 . G A 2932.65 PASS AC=1;AF=0.875;AN=2;DP=4143;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:61,42:103:99:978,0,1763:24,37,19,23 chr1 205053219 . C T 2401.77 PASS AC=1;AF=0.886;AN=2;DP=5392;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:88,75:163:99:1967,0,2419:51,37,43,32 chr1 205053759 . A ACT 1168.21 PASS AC=1;AF=0.898;AN=2;DP=965;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:14,8:22:99:285,0,562:0,14,0,8 chr1 205055949 . G A 2296.37 PASS AC=1;AF=0.886;AN=2;DP=2960;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:39,21:60:99:581,0,958:19,20,11,10 chr1 205056326 . ATT A,AT,ATTT 253.97 PASS AC=1,0,0;AF=0.032,0.452,0.161;AN=2;DP=662;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant23-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:13:99:0,5,1,7 chr1 205056844 . T TTA 2262.45 PASS AC=1;AF=0.886;AN=2;DP=2903;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:41,45:86:99:1582,0,1453:20,21,20,25 chr1 205065733 . G T 2310.56 PASS AC=1;AF=0.588;AN=2;DP=2334;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,23:55:99:545,0,863:19,13,17,6 chr1 205067972 . CAA CA,C,CAAAA 67.31 PASS AC=1,0,0;AF=0.467,0.2,0.067;AN=2;DP=127;FS=0;set=variant4-variant6-variant7-variant12-variant15-variant16-variant17-variant22-variant23-variant26-variant35-variant37-variant39-variant40-variant41 GT:DP:GQ:SB 0/1:8:18:2,0,6,0 chr1 205074424 . C T 406.1 PASS AC=1;AF=0.597;AN=2;DP=371;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant20-variant22-variant24-variant25-variant26-variant27-variant29-variant31-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,4:10:99:150,0,205:0,6,0,4 chr1 205083865 . T C 386.88 PASS AC=1;AF=0.594;AN=2;DP=524;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant20-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,12:27:99:262,0,396:10,5,8,4 chr1 205084120 . G A 890.03 PASS AC=1;AF=0.614;AN=2;DP=967;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,17:37:99:406,0,538:6,14,8,9 chr1 205090885 . C G 634.79 PASS AC=1;AF=0.588;AN=2;DP=3288;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,53:100:99:1287,0,1211:27,20,29,24 chr1 205111761 . A C 1990.57 PASS AC=1;AF=0.588;AN=2;DP=2105;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,29:56:99:780,0,741:9,18,11,18 chr1 205114665 . G T 1828.61 PASS AC=1;AF=0.515;AN=2;DP=3120;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant35-variant37-filterInvariant39-variant40-variant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:59,19:78:99:330,0,1532:24,35,8,11 chr1 205115099 . G A 902.9 PASS AC=1;AF=0.588;AN=2;DP=1717;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,33:52:99:865,0,404:10,9,21,12 chr1 205130413 . A G 2290.47 PASS AC=1;AF=0.955;AN=2;DP=3669;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:39,42:81:99:1011,0,1029:23,16,21,21 chr1 205131059 . G GAC 1018.58 PASS AC=1;AF=0.886;AN=2;DP=1545;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:17,20:37:99:655,0,549:12,5,14,6 chr1 205225285 . G A 800.89 PASS AC=1;AF=0.594;AN=2;DP=982;MQ=60;set=variant2-variant3-variant7-variant12-variant19-variant21-variant24-variant25-variant28-variant30-variant32-variant33-variant35-variant36-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:53,36:89:99:692,0,1325:32,21,20,16 chr1 205240913 . A G 765.82 PASS AC=1;AF=0.955;AN=2;DP=1735;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:15,22:37:99:613,0,496:13,2,14,8 chr1 205241659 . T C 1478.75 PASS AC=1;AF=0.955;AN=2;DP=2692;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:31,34:65:99:968,0,785:16,15,18,16 chr1 205272292 . C T 624.82 PASS AC=1;AF=0.5;AN=2;DP=1262;MQ=60;set=variant-variant5-variant13-variant14-variant18-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,35:78:99:908,0,1105:22,21,19,16 chr1 205273784 . A G 283.4 PASS AC=1;AF=0.5;AN=2;DP=329;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant14-variant18-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,10:17:99:234,0,166:3,4,4,6 chr1 205274174 . A G 577.28 PASS AC=1;AF=0.762;AN=2;DP=1314;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,24:48:99:702,0,753:19,5,19,5 chr1 205275061 . C T 368.2 PASS AC=1;AF=0.679;AN=2;DP=325;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant8-variant10-variant12-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant27-variant28-variant30-variant31-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,4:9:99:153,0,198:5,0,4,0 chr1 205275206 . A T 6847.12 PASS AC=2;AF=0.989;AN=2;DP=6006;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,148:148:99:6625,452,0:0,0,87,61 chr1 205275207 . G T 6847.12 PASS AC=2;AF=0.989;AN=2;DP=6043;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,150:150:99:6625,452,0:0,0,89,61 chr1 205275421 . A G 2916.31 PASS AC=2;AF=0.989;AN=2;DP=5077;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,142:143:99:4419,389,0:1,0,57,85 chr1 205290794 . G A 2978.42 PASS AC=1;AF=0.56;AN=2;DP=4655;MQ=60;set=variant-variant5-variant6-variant9-variant12-variant13-variant14-variant16-variant17-variant18-variant20-variant22-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:109,78:187:99:1925,0,3004:53,56,35,43 chr1 205290965 . C T 768.21 PASS AC=1;AF=0.545;AN=2;DP=1082;MQ=60;set=variant-variant5-variant6-variant9-variant12-variant13-variant14-variant16-variant17-variant18-variant22-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:28,30:58:99:690,0,797:7,21,8,22 chr1 205305449 . C T 400.41 PASS AC=1;AF=0.55;AN=2;DP=1256;MQ=60;set=variant-variant5-variant6-variant9-variant12-variant13-variant14-variant16-variant18-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:42,33:75:99:705,0,1111:20,22,16,17 chr1 205305925 . G A 794.92 PASS AC=1;AF=0.55;AN=2;DP=1954;MQ=60;set=variant-variant5-variant6-variant9-variant12-variant13-variant14-variant16-variant18-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:54,48:102:99:1147,0,1242:24,30,25,23 chr1 205306102 . C T 434.99 PASS AC=1;AF=0.55;AN=2;DP=840;MQ=60;set=variant-variant5-variant6-variant9-variant12-variant13-variant14-variant16-variant18-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:18,30:48:99:815,0,501:11,7,11,19 chr1 205306445 . C T 472.43 PASS AC=1;AF=0.55;AN=2;DP=930;MQ=60;set=variant-variant5-variant6-variant9-variant12-variant13-variant14-variant16-variant18-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:29,33:62:99:811,0,707:16,13,17,16 chr1 205306590 . G A 548.07 PASS AC=1;AF=0.563;AN=2;DP=827;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant8-variant10-variant15-variant16-variant17-variant27-variant29-variant30-variant33-variant35-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,30:67:99:754,0,1037:22,15,16,14 chr1 205307789 . G A 719.26 PASS AC=1;AF=0.55;AN=2;DP=1774;MQ=60;set=variant-variant5-variant6-variant9-variant12-variant13-variant14-variant16-variant18-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:43,36:79:99:1042,0,1150:20,23,12,24 chr1 205308335 . G A 278.42 PASS AC=1;AF=0.545;AN=2;DP=1056;MQ=60;set=variant-variant5-variant6-variant9-variant12-variant13-variant14-variant16-variant18-variant20-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:21,30:51:99:859,0,622:17,4,23,7 chr1 205308368 . C T 524.62 PASS AC=1;AF=0.545;AN=2;DP=1907;MQ=60;set=variant-variant5-variant6-variant9-variant12-variant13-variant14-variant16-variant18-variant20-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:44,59:103:99:1340,0,1153:31,13,39,20 chr1 205308591 . C T 416.95 PASS AC=1;AF=0.545;AN=2;DP=1432;MQ=60;set=variant-variant5-variant6-variant9-variant12-variant13-variant14-variant16-variant18-variant20-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:40,32:72:99:948,0,1188:14,26,10,22 chr1 205312280 . C G 224.78 PASS AC=1;AF=0.714;AN=2;DP=1558;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:27,25:52:99:833,0,933:24,3,23,2 chr1 205312767 . G T 1668.07 PASS AC=1;AF=0.603;AN=2;DP=3458;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant20-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant35-variant36-variant37-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:73,71:144:99:1700,0,2076:24,49,26,45 chr1 205313647 . G T 735.57 PASS AC=2;AF=0.966;AN=2;DP=1849;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1492,149,0:0,0,18,32 chr1 205317503 . C T 365.28 PASS AC=1;AF=0.5;AN=2;DP=617;MQ=60;set=variant2-variant5-variant12-variant14-variant15-variant17-variant18-variant21-variant23-variant28-variant31-variant32-variant33-variant34-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:29,23:52:99:678,0,723:18,11,16,7 chr1 205317676 . T C 327.23 PASS AC=1;AF=0.821;AN=2;DP=1620;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,20:35:99:546,0,354:6,9,5,15 chr1 205317684 . C A 1055.34 PASS AC=2;AF=1;AN=2;DP=1567;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:1256,96,0:0,0,10,22 chr1 205325609 . C A 3856.55 PASS AC=1;AF=0.697;AN=2;DP=3920;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:72,71:143:99:1837,0,1689:40,32,43,28 chr1 205353492 . A C 844.6 PASS AC=1;AF=0.5;AN=2;DP=957;MQ=60;set=variant5-variant12-variant15-variant17-variant22-variant28-variant29-variant31-variant32-variant35 GT:AD:DP:GQ:PL:SB 0/1:46,50:96:99:1251,0,1179:17,29,23,27 chr1 205385498 . C T 5266.32 PASS AC=2;AF=0.905;AN=2;DP=7481;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,170:170:99:4912,507,0:0,0,78,92 chr1 205388175 . A G 501.25 PASS AC=1;AF=0.5;AN=2;DP=309;FractionInformativeReads=1;MQ=60;set=variant5-variant12-variant15-variant17-variant22-variant29-variant31-variant32-variant35 GT:AD:DP:GQ:PL:SB 0/1:18,14:32:99:413,0,442:12,6,11,3 chr1 205389460 . T C 520.13 PASS AC=1;AF=0.542;AN=2;DP=308;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant12-variant15-variant17-variant22-variant28-variant29-variant31-variant32-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:12,11:23:99:376,0,337:10,2,11,0 chr1 205473728 . T TTCC 204.75 PASS AC=2;AF=0.682;AN=2;DP=1313;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,31:33:12:1282,12,0:1,1,19,12 chr1 205473772 . T C 838.27 PASS AC=1;AF=0.614;AN=2;DP=1015;MQ=60;set=variant3-variant4-variant8-variant9-variant14-variant15-variant16-variant17-variant22-variant23-variant24-variant25-variant27-variant31-variant34-variant35-variant36-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,21:41:99:464,0,504:13,7,10,11 chr1 205473974 . C G 3321.11 PASS AC=2;AF=1;AN=2;DP=4284;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,113:113:99:3302,336,0:0,0,58,55 chr1 205492756 . A G 4330.39 PASS AC=2;AF=0.943;AN=2;DP=6122;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,181:181:99:5741,542,0:0,0,82,99 chr1 205495392 . A G 6232.06 PASS AC=2;AF=0.943;AN=2;DP=9265;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,256:256:99:8131,768,0:0,0,128,128 chr1 205495976 . A G 2150.69 PASS AC=2;AF=1;AN=2;DP=5877;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,120:120:99:3576,359,0:0,0,51,69 chr1 205498021 . T C 116.87 PASS AC=1;AF=0.708;AN=2;DP=775;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:2,14:16:34:515,0,34:2,0,12,2 chr1 205499577 . C G 678.8 PASS AC=1;AF=0.597;AN=2;DP=1248;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant13-variant14-variant15-variant16-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:24,25:49:99:632,0,562:11,13,12,13 chr1 205499660 . C T 549.14 PASS AC=1;AF=0.528;AN=2;DP=779;MQ=60;set=variant3-variant6-variant13-variant14-variant15-variant16-variant19-variant22-variant24-variant25-variant27-variant30-variant35-variant36-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:25,29:54:99:778,0,790:17,8,18,11 chr1 205500543 . T C 2370.29 PASS AC=1;AF=0.526;AN=2;DP=2778;MQ=60;set=variant3-variant6-variant13-variant14-variant15-variant16-variant19-variant22-variant24-variant25-variant27-variant28-variant30-variant35-variant36-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:94,82:176:99:1910,0,2408:50,44,45,37 chr1 205501469 . A G 927.16 PASS AC=1;AF=0.563;AN=2;DP=2160;MQ=60;set=variant4-variant5-variant7-variant9-variant11-variant15-variant16-variant18-variant19-variant20-variant21-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant35-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,40:88:99:1003,0,1299:25,23,20,20 chr1 205501521 . A G 1281.29 PASS AC=1;AF=0.563;AN=2;DP=2768;set=variant4-variant5-variant7-variant9-variant11-variant15-variant16-variant18-variant19-variant20-variant21-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant35-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,60:118:99:1468,0,1357:36,22,32,28 chr1 205501843 . A G 522.47 PASS AC=1;AF=0.563;AN=2;DP=674;MQ=60;set=variant4-variant5-variant7-variant9-variant11-variant15-variant16-variant18-variant19-variant20-variant21-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant35-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,23:36:99:733,0,304:3,10,6,17 chr1 205501985 . T G 269.66 PASS AC=1;AF=0.595;AN=2;DP=175;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant9-variant11-variant15-variant16-variant19-variant20-variant21-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant35-variant37-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:1,5:6:9:204,0,9:0,1,1,4 chr1 205548956 . G A 2940.06 PASS AC=1;AF=0.5;AN=2;DP=779;MQ=60;set=variant5-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:149,124:273:99:2728,0,3880:74,75,54,70 chr1 205549757 . A C 232.08 PASS AC=1;AF=0.5;AN=2;DP=1148;set=variant2-filterInvariant3-filterInvariant5-variant6-filterInvariant7-variant8-filterInvariant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-filterInvariant19-variant20-variant21-filterInvariant24-variant26-variant27-variant29-variant33-variant34-variant35-variant36-filterInvariant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,18:42:99:554,0,406:7,17,17,1 chr1 205549763 . A C 252.24 PASS AC=1;AF=0.5;AN=2;DP=1388;set=variant2-filterInvariant3-variant4-variant5-variant6-variant7-variant8-filterInvariant9-variant10-variant11-filterInvariant12-variant13-variant14-variant16-variant17-filterInvariant18-filterInvariant19-variant20-variant21-variant24-variant26-variant27-variant28-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,19:48:99:583,0,478:11,18,19,0 chr1 205549767 . G C 249.23 PASS AC=1;AF=0.5;AN=2;DP=1537;set=variant2-filterInvariant3-variant5-variant6-variant7-filterInvariant8-filterInvariant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant26-filterInvariant27-variant28-variant29-variant32-filterInvariant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,16:52:99:428,0,1676:16,20,16,0 chr1 205549770 . A C 188.98 PASS AC=1;AF=0.5;AN=2;DP=1644;set=variant2-filterInvariant3-variant5-variant6-variant7-filterInvariant8-variant9-variant10-filterInvariant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-filterInvariant20-variant21-filterInvariant24-variant26-filterInvariant27-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,15:51:99:419,0,1751:16,20,15,0 chr1 205549773 . T C 176.93 PASS AC=1;AF=0.5;AN=2;DP=1638;set=variant2-filterInvariant3-variant5-variant6-variant7-filterInvariant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant24-variant26-variant27-variant28-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,15:54:99:412,0,1771:18,21,15,0 chr1 205549775 . T C 176.88 PASS AC=1;AF=0.5;AN=2;DP=1387;set=variant2-filterInvariant3-variant5-variant6-variant7-variant9-variant12-variant13-variant14-variant17-filterInvariant18-filterInvariant19-filterInvariant21-filterInvariant24-variant27-variant28-variant33-variant34-filterInvariant35-variant36-variant37-variant39-variant40-variant41-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,11:54:99:104,0,2190:22,21,11,0 chr1 205549778 . T C 106.31 PASS AC=1;AF=0.5;AN=2;DP=1246;set=variant2-variant5-variant6-variant7-variant9-filterInvariant11-variant12-variant13-variant14-filterInvariant16-variant17-filterInvariant18-filterInvariant21-variant26-variant28-variant34-filterInvariant35-variant36-variant37-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:47,10:57:99:104,0,2190:25,22,10,0 chr1 205553346 . ATTT ATT,ATTTT,ATTTTT,ATTTTTT,A 115.16 PASS AC=0,0,0,0,1;AF=0.28,0.14,0.06,0.04,0.02;AN=2;DP=1044;set=variant-variant2-variant3-filterInvariant4-variant6-variant7-filterInvariant9-variant12-variant13-variant15-variant17-variant19-variant22-variant23-variant26-filterInvariant28-filterInvariant31-variant32-variant35-filterInvariant37-filterInvariant38-variant39-variant40-variant43-variant44 GT:DP:GQ:SB 0/5:23:99:3,14,1,5 chr1 205554085 . G C 185.23 PASS AC=1;AF=0.661;AN=2;DP=2767;MQ=60;set=variant-variant3-variant6-variant7-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,45:90:99:1724,0,2186:20,25,20,25 chr1 205554095 . A C 182.24 PASS AC=1;AF=0.667;AN=2;DP=2495;MQ=60;set=variant-variant3-variant7-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,44:86:99:1707,0,2131:19,23,20,24 chr1 205555145 . G A 91.5 PASS AC=2;AF=0.672;AN=2;DP=338;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant13-variant14-variant15-variant16-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:244,21,0:0,0,6,1 chr1 205561372 . C T 3868.99 PASS AC=1;AF=0.588;AN=2;DP=1844;MQ=60;set=variant3-variant7-variant9-variant14-variant16-variant22-variant23-variant25-variant27-variant34-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,65:102:99:1591,0,869:12,25,25,40 chr1 205568147 . G A 347.18 PASS AC=1;AF=0.5;AN=2;DP=21;FS=1.999;FractionInformativeReads=1;MQ=60;MQRankSum=0.616;QD=16.53;ReadPosRankSum=-0.905;SOR=1.473;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:8,13:21:99:375,0,219:5,3,10,3 chr1 205582201 . TA T 2618.62 PASS AC=1;AF=0.65;AN=2;DP=9113;MQ=60;set=variant-variant2-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:137,166:303:99:3381,0,2661:57,80,73,93 chr1 205582799 . A C 278.66 PASS AC=1;AF=0.538;AN=2;DP=128;set=variant3-variant9-variant13-variant21-variant22-variant25-variant27-variant29-variant31-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,6:16:99:170,0,1092:1,9,6,0 chr1 205582805 . A C 275.55 PASS AC=1;AF=0.538;AN=2;DP=133;set=variant3-variant9-variant13-variant21-variant22-variant25-variant27-variant29-variant31-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,6:15:99:164,0,1379:1,8,6,0 chr1 205582809 . CAGAGAT C 251.46 PASS AC=1;AF=0.5;AN=2;DP=90;MQ=60;set=variant3-variant9-variant21-variant27-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:14,6:20:99:158,0,1562:5,9,6,0 chr1 205584518 . CAAA CA,CAA,CAAAA,C,CAAAAA 113.22 PASS AC=0,1,0,0,0;AF=0.143,0.167,0.119,0.048,0.024;AN=2;DP=648;set=variant-variant4-variant6-variant7-filterInvariant9-filterInvariant10-variant14-filterInvariant19-variant21-variant25-variant28-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42 GT:DP:GQ:SB 0/2:26:99:6,7,12,1 chr1 205600653 . C T 168.94 PASS AC=2;AF=0.879;AN=2;DP=295;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:57:468,57,0:0,0,11,9 chr1 205601199 . G A 1856.74 PASS AC=1;AF=0.675;AN=2;DP=1002;MQ=60;set=variant3-variant4-variant7-variant8-variant9-variant14-variant16-variant21-variant22-variant23-variant27-variant31-variant34-variant35-variant36-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,36:61:99:914,0,545:9,16,13,23 chr1 205615791 . A G 3736.5 PASS AC=1;AF=0.6;AN=2;DP=2697;MQ=60;set=variant3-variant4-variant8-variant9-variant11-variant14-variant16-variant21-variant22-variant23-variant24-variant26-variant28-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,51:109:99:1041,0,1364:36,22,28,23 chr1 205615947 . C A 1175.41 PASS AC=2;AF=0.909;AN=2;DP=1470;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,39:40:99:1126,115,0:0,1,11,28 chr1 205632932 . A G 798.79 PASS AC=2;AF=0.718;AN=2;DP=1294;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1276,114,0:0,0,11,27 chr1 205649327 . C T 381.74 PASS AC=2;AF=0.846;AN=2;DP=236;FS=0;MQ=60;set=variant3-variant4-variant8-variant9-variant13-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:526,48,0:0,0,10,6 chr1 205683280 . T C 11730.1 PASS AC=2;AF=1;AN=2;DP=16825;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,357:357:99:11390,1070,0:0,0,169,188 chr1 205683355 . T G 3775.53 PASS AC=1;AF=0.533;AN=2;DP=3476;MQ=60;set=variant5-variant10-variant11-variant12-variant18-variant19-variant20-variant21-variant25-variant26-variant27-variant28-variant29-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:105,118:223:99:2950,0,2639:45,60,50,68 chr1 205686523 . G GT,GTT 1161.96 PASS AC=1,0;AF=0.632,0.015;AN=2;DP=4108;set=variant-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-filterInvariant26-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:100:99:29,27,19,25 chr1 205687213 . TA T,TAA 911.53 PASS AC=0,1;AF=0.307,0.193;AN=2;DP=13087;set=variant-filterInvariant2-filterInvariant3-filterInvariant4-variant5-variant6-filterInvariant7-variant8-filterInvariant9-variant10-variant11-variant12-variant13-filterInvariant14-filterInvariant15-filterInvariant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-filterInvariant24-filterInvariant25-variant26-variant27-variant28-filterInvariant29-filterInvariant30-filterInvariant31-variant32-variant33-variant34-variant35-filterInvariant36-variant37-filterInvariant38-filterInvariant39-filterInvariant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:210:99:75,54,42,39 chr1 205687348 . CTTTTTTCTTT C 2291.46 PASS AC=1;AF=0.652;AN=2;DP=10985;set=variant-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:111,146:257:99:3272,0,4686:52,59,62,84 chr1 205689807 . T G 1089.07 PASS AC=1;AF=0.641;AN=2;DP=2065;set=variant-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,43:83:99:1085,0,975:14,26,15,28 chr1 205696671 . G A 146.45 PASS AC=2;AF=0.966;AN=2;DP=448;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:387,30,0:0,0,9,1 chr1 205737450 . T C 908.22 PASS AC=2;AF=0.955;AN=2;DP=2592;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:2012,168,0:0,0,15,41 chr1 205737665 . G GT,GTT 282.32 PASS AC=2,0;AF=0.866,0.037;AN=2;DP=578;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:10:4:0,1,4,5 chr1 205737739 . G A 103.46 PASS AC=1;AF=0.875;AN=2;DP=35;FS=0;MQ=60;set=variant5-variant19-variant20-variant21-variant26-variant28-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:1,4:5:27:165,0,27:0,1,1,3 chr1 205737956 . G C 464.01 PASS AC=2;AF=0.955;AN=2;DP=1420;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,44:45:99:1502,103,0:1,0,33,11 chr1 205738166 . T C 2846.14 PASS AC=2;AF=0.955;AN=2;DP=10183;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,249:249:99:7712,744,0:0,0,127,122 chr1 205738251 . C A 1628.01 PASS AC=2;AF=0.955;AN=2;DP=8923;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,226:226:99:6351,670,0:0,0,98,128 chr1 205738302 . G A 985.64 PASS AC=1;AF=0.652;AN=2;DP=4421;MQ=60;set=variant-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:78,61:139:99:1447,0,2140:28,50,21,40 chr1 205738975 . AC A 477.94 PASS AC=2;AF=0.955;AN=2;DP=1851;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1468,135,0:0,0,31,14 chr1 205739192 . T C 1583.98 PASS AC=2;AF=0.955;AN=2;DP=4195;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,80:80:99:2448,240,0:0,0,41,39 chr1 205739266 . C T 1200.02 PASS AC=2;AF=0.756;AN=2;DP=2517;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:2460,224,0:0,0,39,36 chr1 205739396 . T G 1081.37 PASS AC=2;AF=0.893;AN=2;DP=4049;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,102:102:99:2967,306,0:0,0,50,52 chr1 205740403 . A G 88.49 PASS AC=2;AF=0.94;AN=2;DP=333;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:181,15,0:0,0,4,1 chr1 205743932 . T C 398.31 PASS AC=1;AF=0.5;AN=2;DP=262;set=filterInvariant3-filterInvariant12-variant19-variant31-variant33-variant34-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:23,11:34:99:208,0,1378:9,14,11,0 chr1 205743938 . T C 385.78 PASS AC=1;AF=0.5;AN=2;DP=334;set=filterInvariant3-variant5-filterInvariant19-variant31-variant32-filterInvariant34-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:32,11:43:99:178,0,1798:16,16,11,0 chr1 205743943 . A C 380.23 PASS AC=1;AF=0.5;AN=2;DP=388;set=filterInvariant3-variant5-variant31-filterInvariant32-variant33-filterInvariant34-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:40,13:53:99:272,0,895:22,18,13,0 chr1 205744138 . G T 1462.29 PASS AC=2;AF=0.682;AN=2;DP=6389;MQ=60;set=variant-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,196:197:99:5640,574,0:1,0,94,102 chr1 205744546 . C A 551.67 PASS AC=2;AF=0.837;AN=2;DP=3948;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,84:85:99:2353,243,0:0,1,36,48 chr1 205759195 . G A 282.92 PASS AC=2;AF=0.667;AN=2;DP=1207;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant21-variant22-variant23-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1306,120,0:0,0,15,25 chr1 205759876 . T C 674.71 PASS AC=2;AF=0.895;AN=2;DP=2822;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2041,209,0:0,0,33,37 chr1 205764640 . G A 871.41 PASS AC=2;AF=0.846;AN=2;DP=4832;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,112:112:99:3281,334,0:0,0,49,63 chr1 205765795 . T A 43.71 PASS AC=2;AF=0.89;AN=2;DP=431;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:225,15,0:0,0,5,0 chr1 205765980 . C T 1293.38 PASS AC=1;AF=0.5;AN=2;DP=403;FractionInformativeReads=1;MQ=60;set=variant15-variant16-variant21-variant22-variant35 GT:AD:DP:GQ:PL:SB 0/1:46,38:84:99:922,0,1206:25,21,23,15 chr1 205766159 . CA C 1114.04 PASS AC=2;AF=0.89;AN=2;DP=5462;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,131:131:99:4644,393,0:0,0,67,64 chr1 205767885 . G A 934.23 PASS AC=2;AF=0.661;AN=2;DP=3704;MQ=60;set=variant-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant20-variant21-variant22-variant23-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,158:158:99:4753,471,0:0,0,84,74 chr1 205797413 . G T 63.64 PASS AC=2;AF=0.763;AN=2;DP=1313;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1099,111,0:0,0,20,17 chr1 205801872 . A G 1237.15 PASS AC=2;AF=0.743;AN=2;DP=4899;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,124:124:99:3722,372,0:0,0,55,69 chr1 205809642 . G C 1494.17 PASS AC=2;AF=0.806;AN=2;DP=2978;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,98:98:99:3020,294,0:0,0,36,62 chr1 205812614 . C T 226.57 PASS AC=2;AF=0.759;AN=2;DP=246;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant13-variant14-variant15-variant20-variant22-variant23-variant24-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:322,30,0:0,0,5,5 chr1 205813672 . T C 414.07 PASS AC=2;AF=0.629;AN=2;DP=441;MQ=60;set=variant-variant3-variant4-variant6-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:39:565,39,0:0,0,8,4 chr1 205813677 . T C 414.07 PASS AC=2;AF=0.955;AN=2;DP=670;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:565,39,0:0,0,8,5 chr1 205814497 . T C 1429.96 PASS AC=2;AF=0.943;AN=2;DP=5189;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,91:91:99:2873,273,0:0,0,52,39 chr1 205884646 . CTGTGTG CTG,CTGTGTGTG,C,CTGTGTGTGTGTGTGTG,CTGTGTGTGTGTGTG 339.76 PASS AC=0,2,0,0,0;AF=0.426,0.222,0.093,0.019,0.019;AN=2;DP=548;MQ=60;set=variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant19-variant20-variant-variant21-variant22-variant23-variant26-variant28-variant25-variant30-variant31-variant35-variant36-variant39-variant41-variant42 GT:DP:GQ:SB 2/2:5:18:0,0,1,4 chr1 205886647 . C T 495.23 PASS AC=1;AF=0.5;AN=2;DP=281;FractionInformativeReads=1;MQ=60;set=variant8-variant15-variant19-variant22-variant35 GT:AD:DP:GQ:PL:SB 0/1:38,20:58:99:439,0,926:19,19,11,9 chr1 205890679 . T C 3228.27 PASS AC=1;AF=0.919;AN=2;DP=6842;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:71,93:164:99:2224,0,1569:38,33,54,39 chr1 205896475 . C T 2237.1 PASS AC=2;AF=0.919;AN=2;DP=3466;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,95:95:99:3197,284,0:0,0,48,47 chr1 205896948 . A G 293.1 PASS AC=2;AF=0.75;AN=2;DP=765;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:1063,81,0:0,0,19,8 chr1 206224635 . G C 2833.79 PASS AC=1;AF=0.5;AN=2;DP=1653;MQ=60;set=variant3-variant4-variant5-variant13-variant29-variant32-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:132,141:273:99:3680,0,3215:69,63,62,79 chr1 206230958 . G A 2316.11 PASS AC=1;AF=0.5;AN=2;DP=1693;MQ=60;set=variant3-variant4-variant5-variant13-variant14-variant29-variant32-variant34-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:67,122:189:99:2983,0,1476:33,34,61,61 chr1 206230986 . G A 2031.02 PASS AC=1;AF=0.5;AN=2;DP=1576;MQ=60;set=variant3-variant4-variant5-variant13-variant14-variant29-variant32-variant34-variant35-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:63,93:156:99:2399,0,1405:32,31,41,52 chr1 206231152 . G A 1688.09 PASS AC=1;AF=0.5;AN=2;DP=1224;MQ=60;set=variant3-variant4-variant5-variant13-variant14-variant29-variant32-variant34-variant35-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:64,67:131:99:1711,0,1532:34,30,31,36 chr1 206231203 . G A 1177.13 PASS AC=1;AF=0.5;AN=2;DP=879;MQ=60;set=variant3-variant4-variant5-variant13-variant14-variant29-variant32-variant34-variant35-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:44,57:101:99:1415,0,1100:19,25,27,30 chr1 206231259 . A G 426.92 PASS AC=1;AF=0.531;AN=2;DP=975;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant13-variant14-variant15-variant29-variant31-variant32-variant34-variant35-variant36-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:30,41:71:99:1611,0,1117:12,18,17,24 chr1 206231264 . G A 1288.59 PASS AC=1;AF=0.5;AN=2;DP=674;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant13-variant14-variant29-variant32-variant34-variant35-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:26,42:68:99:1649,0,1068:10,16,19,23 chr1 206231429 . T A 1170.76 PASS AC=1;AF=0.5;AN=2;DP=590;MQ=60;set=variant3-variant4-variant5-variant13-variant14-variant29-variant32-variant34-variant35-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:34,30:64:99:740,0,796:18,16,12,18 chr1 206231608 . T TTTG 390.94 PASS AC=1;AF=0.5;AN=2;DP=256;MQ=60;set=variant3-variant4-variant5-variant13-variant14-variant29-variant32-variant34-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:10,11:21:99:431,0,400:5,5,4,7 chr1 206243599 . C T 1303.05 PASS AC=1;AF=0.5;AN=2;DP=99;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.345;QD=13.16;ReadPosRankSum=1.723;SOR=0.648;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:41,58:99:99:1331,0,997:20,21,29,29 chr1 206327510 . T C 649.19 PASS AC=1;AF=0.567;AN=2;DP=1197;MQ=60;set=variant5-variant6-variant7-variant9-variant10-variant11-variant14-variant17-variant25-variant30-variant33-variant34-variant35-variant37-variant42 GT:AD:DP:GQ:PL:SB 0/1:43,57:100:99:1536,0,1069:26,17,36,21 chr1 206327801 . A G 295.66 PASS AC=1;AF=0.588;AN=2;DP=336;FractionInformativeReads=1;MQ=60;set=variant5-variant6-variant7-variant9-variant10-variant11-variant14-variant17-variant25-variant30-variant33-variant34-variant35-variant37-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:5,12:17:99:318,0,174:0,5,4,8 chr1 206328647 . G C 514.53 PASS AC=1;AF=0.6;AN=2;DP=336;FractionInformativeReads=1;MQ=60;set=variant5-variant6-variant7-variant9-variant10-variant11-variant14-variant17-variant25-variant30-variant33-variant34-variant35-variant37-variant42 GT:AD:DP:GQ:PL:SB 0/1:13,7:20:99:238,0,391:10,3,7,0 chr1 206328803 . T C 2374.25 PASS AC=1;AF=0.567;AN=2;DP=3293;MQ=60;set=variant5-variant6-variant7-variant9-variant10-variant11-variant14-variant17-variant25-variant30-variant33-variant34-variant35-variant37-variant42 GT:AD:DP:GQ:PL:SB 0/1:110,128:238:99:3189,0,2627:65,45,74,54 chr1 206516159 . C T 385 PASS AC=1;AF=0.5;AN=2;DP=890;FS=0;FractionInformativeReads=1;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant4-variant5-filterInvariant6-filterInvariant7-filterInvariant8-variant9-filterInvariant10-variant11-filterInvariant12-filterInvariant13-filterInvariant14-filterInvariant15-filterInvariant16-variant17-filterInvariant18-filterInvariant19-filterInvariant20-variant21-filterInvariant22-filterInvariant23-variant24-filterInvariant25-filterInvariant26-filterInvariant27-variant28-filterInvariant29-filterInvariant31-filterInvariant32-filterInvariant33-filterInvariant34-filterInvariant35-variant36-filterInvariant37-filterInvariant38-filterInvariant39-filterInvariant40-filterInvariant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,8:22:99:187,0,392:14,0,8,0 chr1 206516261 . C T 1383.04 PASS AC=1;AF=0.5;AN=2;DP=7344;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:112,99:211:99:2221,0,2675:78,34,67,32 chr1 206566195 . C T 600.54 PASS AC=1;AF=0.5;AN=2;DP=3835;FractionInformativeReads=1;set=filterInvariant2-filterInvariant4-filterInvariant6-filterInvariant7-filterInvariant9-filterInvariant10-filterInvariant12-filterInvariant16-filterInvariant22-filterInvariant24-filterInvariant25-variant26-filterInvariant29-filterInvariant30-filterInvariant32-filterInvariant33-filterInvariant35-filterInvariant40-filterInvariant41-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:178,46:224:99:467,0,4071:80,98,22,24 chr1 206566860 . TA T,TAA 1207.73 PASS AC=1,0;AF=0.489,0.011;AN=2;DP=7735;set=variant-filterInvariant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-filterInvariant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:154:99:72,45,35,2 chr1 206566904 . T C 4778.55 PASS AC=1;AF=0.5;AN=2;DP=13435;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:165,110:275:99:2840,0,4219:93,72,83,27 chr1 206567100 . C T 3891.5 PASS AC=1;AF=0.5;AN=2;DP=13887;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-filterInvariant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:245,125:370:99:2639,0,6634:81,164,43,82 chr1 206567165 . T A 1278.33 PASS AC=1;AF=0.5;AN=2;DP=3453;set=variant-variant2-variant3-filterInvariant4-filterInvariant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant17-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:89,17:106:99:297,0,3100:12,77,3,14 chr1 206579936 . A G 105.89 PASS AC=1;AF=0.5;AN=2;DP=508;set=filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant10-filterInvariant11-filterInvariant14-variant15-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant30-filterInvariant32-filterInvariant33-filterInvariant35-filterInvariant36-filterInvariant40-variant42-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:14,6:20:99:105,0,296:8,6,4,2 chr1 206603535 . G A 4862.55 PASS AC=1;AF=0.7;AN=2;DP=4405;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:77,86:163:99:2003,0,1949:41,36,42,44 chr1 206623685 . G T 4103.51 PASS AC=1;AF=0.744;AN=2;DP=6638;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:90,82:172:99:1893,0,2226:53,37,50,32 chr1 206623866 . C T 356.53 PASS AC=1;AF=0.638;AN=2;DP=1235;MQ=60;set=variant2-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:12,18:30:99:572,0,387:2,10,3,15 chr1 206626607 . G A 1649.55 PASS AC=1;AF=0.633;AN=2;DP=4415;MQ=60;set=variant2-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:75,86:161:99:2230,0,1950:32,43,36,50 chr1 206626779 . A G 476.74 PASS AC=2;AF=0.795;AN=2;DP=1445;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1266,114,0:0,0,11,27 chr1 206626828 . C G 200.76 PASS AC=2;AF=0.653;AN=2;DP=567;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:660,54,0:0,0,4,14 chr1 206631518 . G T 513.17 PASS AC=2;AF=0.833;AN=2;DP=281;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:90,6,0:0,0,2,0 chr1 206631532 . T A 132.63 PASS AC=1;AF=0.68;AN=2;DP=231;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant8-variant10-variant11-variant14-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant35-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:2,4:6:32:115,0,32:1,1,4,0 chr1 206634174 . G GA 60.24 PASS AC=1;AF=0.5;AN=2;DP=16;FS=0;FractionInformativeReads=1;MQ=60;set=variant3-variant35 GT:AD:DP:GQ:PL:SB 0/1:5,6:11:99:135,0,107:4,1,4,2 chr1 206635380 . T C 526.47 PASS AC=1;AF=0.5;AN=2;DP=241;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant13-variant32-variant34-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,11:23:99:223,0,312:8,4,6,5 chr1 206636489 . A AT 1297.2 PASS AC=1;AF=0.577;AN=2;DP=1909;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant13-variant14-variant15-variant20-variant21-variant23-variant27-variant28-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,25:63:99:436,0,816:12,26,4,21 chr1 206636715 . G A 598.96 PASS AC=1;AF=0.5;AN=2;DP=417;MQ=60;set=variant3-variant4-variant5-variant13-variant32-variant34-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:53,20:73:99:428,0,1301:29,24,10,10 chr1 206636879 . T C 896.1 PASS AC=1;AF=0.648;AN=2;DP=2635;MQ=60;set=variant2-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant33-variant35-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:60,56:116:99:1475,0,1668:36,24,30,26 chr1 206637395 . C T 544.51 PASS AC=2;AF=0.629;AN=2;DP=2260;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:1848,170,0:0,0,33,24 chr1 206637799 . C G 1219.77 PASS AC=1;AF=0.625;AN=2;DP=3034;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant35-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:83,70:153:99:1785,0,2186:27,56,20,50 chr1 206643795 . C T 341.6 PASS AC=1;AF=0.5;AN=2;DP=124;FS=0;FractionInformativeReads=1;MQ=60;set=variant8-variant19-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:15,26:41:99:578,0,340:8,7,15,11 chr1 206644058 . C T 371.14 PASS AC=1;AF=0.821;AN=2;DP=970;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,13:17:21:250,0,21:2,2,10,3 chr1 206646427 . C A 387.62 PASS AC=1;AF=0.655;AN=2;DP=921;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:22,17:39:99:488,0,698:17,5,13,4 chr1 206647742 . A G 3223.55 PASS AC=2;AF=1;AN=2;DP=7149;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,199:199:99:5737,596,0:0,0,110,89 chr1 206647787 . T C 3973.81 PASS AC=1;AF=0.841;AN=2;DP=8262;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:111,116:227:99:2651,0,2619:57,54,61,55 chr1 206648378 . G A 507.11 PASS AC=1;AF=0.731;AN=2;DP=1118;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,12:25:99:408,0,412:3,10,2,10 chr1 206664396 . A T 997.06 PASS AC=1;AF=0.841;AN=2;DP=1378;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:19,19:38:99:514,0,482:10,9,11,8 chr1 206664407 . T G 403.02 PASS AC=1;AF=0.818;AN=2;DP=1488;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:20,19:39:99:509,0,530:10,10,11,8 chr1 206665896 . C G 2006.69 PASS AC=1;AF=0.818;AN=2;DP=6417;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:94,81:175:99:2220,0,2625:46,48,43,38 chr1 206667441 . G C,A 336.04 PASS AC=0,1;AF=0.054,0.607;AN=2;DP=1698;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant19-variant22-variant23-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41 GT:DP:GQ:SB 0/2:53:99:9,22,6,16 chr1 206669958 . G A 960.85 PASS AC=1;AF=0.638;AN=2;DP=2417;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant19-variant22-variant23-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:46,44:90:99:1075,0,1207:17,29,16,28 chr1 206670169 . G C 453.58 PASS AC=1;AF=0.638;AN=2;DP=1426;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant19-variant22-variant23-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:38,21:59:99:377,0,854:16,22,10,11 chr1 206670258 . G GGGAA 364.45 PASS AC=1;AF=0.636;AN=2;DP=741;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant19-variant21-variant22-variant23-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:10,13:23:99:516,0,582:3,7,6,7 chr1 206670827 . G T 905.91 PASS AC=1;AF=0.655;AN=2;DP=3566;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant19-variant22-variant23-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:65,84:149:99:1969,0,1698:35,30,49,35 chr1 206680983 . A C 648 PASS AC=1;AF=0.795;AN=2;DP=3864;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:73,57:130:99:1255,0,1756:39,34,31,26 chr1 206758077 . T A 2076.98 PASS AC=2;AF=0.907;AN=2;DP=5030;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,151:151:99:4625,451,0:0,0,61,90 chr1 206760474 . T C 2081 PASS AC=1;AF=0.898;AN=2;DP=3933;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:44,38:82:99:1079,0,1071:24,20,24,14 chr1 206760686 . T A 1918.59 PASS AC=1;AF=0.714;AN=2;DP=2865;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:42,34:76:99:781,0,1033:20,22,16,18 chr1 206766825 . CGA C 213.51 PASS AC=1;AF=0.658;AN=2;DP=418;set=variant3-variant4-variant6-variant7-variant8-variant11-variant12-variant14-variant18-variant21-variant24-variant25-variant31-variant33-variant35-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,6:11:99:142,0,161:4,1,4,2 chr1 206770283 . AC A 367.94 PASS AC=1;AF=0.727;AN=2;DP=514;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:7,7:14:99:176,0,171:5,2,6,1 chr1 206772194 . ACT A 592.73 PASS AC=1;AF=0.721;AN=2;DP=521;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant9-variant10-variant11-filterInvariant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:10,5:15:99:180,0,369:8,2,5,0 chr1 206772753 . A G 1142.34 PASS AC=1;AF=0.898;AN=2;DP=1460;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:18,24:42:99:595,0,400:12,6,16,8 chr1 206773659 . A G 3390.6 PASS AC=2;AF=0.989;AN=2;DP=4048;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,99:99:99:3137,297,0:0,0,46,53 chr1 206776097 . G A 521.9 PASS AC=1;AF=0.721;AN=2;DP=641;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,13:17:99:440,0,123:2,2,7,6 chr1 206776200 . C T 2086.86 PASS AC=1;AF=0.898;AN=2;DP=2432;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:15,29:44:99:780,0,422:12,3,19,10 chr1 206776203 . T C 2168.48 PASS AC=2;AF=1;AN=2;DP=2586;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1981,150,0:0,0,35,15 chr1 206786004 . T A 153.05 PASS AC=1;AF=0.62;AN=2;DP=251;MQ=60;set=variant2-variant3-filterInvariant4-variant6-variant7-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant29-variant31-variant32-variant34-variant35-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,6:9:99:178,0,111:1,2,1,5 chr1 206902471 . G A 1167.4 PASS AC=1;AF=0.577;AN=2;DP=1132;set=variant-variant12-variant13-variant16-variant20-variant24-variant26-variant27-variant29-variant30-variant32-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:65,54:119:99:1361,0,1552:26,39,20,34 chr1 206905618 . G T 646.72 PASS AC=1;AF=0.5;AN=2;DP=360;FractionInformativeReads=1;MQ=60;set=variant7-variant33-variant34-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:45,36:81:99:916,0,1271:24,21,17,19 chr1 206906625 . ATGTGTGTG A,ATGTGTG,ATGTG 1004.43 PASS AC=0,1,0;AF=0.026,0.303,0.382;AN=2;DP=2416;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-filterInvariant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-filterInvariant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:56:99:19,28,5,4 chr1 206940831 . A G 1100.13 PASS AC=1;AF=0.6;AN=2;DP=1178;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant31-variant32-variant34-variant35-variant36-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,28:49:99:810,0,630:18,3,22,6 chr1 206941529 . T C 513.76 PASS AC=1;AF=0.594;AN=2;DP=536;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant12-variant13-variant16-variant20-variant21-variant24-variant26-variant27-variant29-variant32-variant34-variant35-variant36-variant39 GT:AD:DP:GQ:PL:SB 0/1:13,15:28:99:407,0,338:6,7,10,5 chr1 206941864 . A G 1917.54 PASS AC=1;AF=0.6;AN=2;DP=4794;MQ=60;set=variant-variant2-variant4-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant31-variant32-variant34-variant35-variant36-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:78,61:139:99:1435,0,1880:41,37,35,26 chr1 206943351 . T C 676.08 PASS AC=2;AF=1;AN=2;DP=1548;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.141;ReadPosRankSum=1.648;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1407,123,0:0,0,10,31 chr1 206944112 . T A 715.32 PASS AC=1;AF=0.6;AN=2;DP=1121;MQ=60;set=variant-variant2-variant12-variant13-variant16-variant20-variant21-variant24-variant26-variant27-variant29-variant32-variant34-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:41,45:86:99:1194,0,1064:22,19,27,18 chr1 206944233 . A G 1944.46 PASS AC=2;AF=0.881;AN=2;DP=4630;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,113:113:99:3688,339,0:0,0,62,51 chr1 206944645 . T C 1490.29 PASS AC=2;AF=0.805;AN=2;DP=1738;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:2039,158,0:0,0,46,7 chr1 206944861 . A C 3110.69 PASS AC=2;AF=0.805;AN=2;DP=3412;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,90:90:99:2657,268,0:0,0,32,58 chr1 206972072 . C T 302.52 PASS AC=1;AF=0.694;AN=2;DP=915;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant28-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,9:17:99:273,0,279:6,2,5,4 chr1 207002356 . CTT CTTT,C,CT,CTTTT 142.41 PASS AC=1,0,0,0;AF=0.206,0.044,0.25,0.029;AN=2;DP=1159;set=variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-filterInvariant19-variant20-variant22-variant23-variant24-variant25-filterInvariant26-filterInvariant27-filterInvariant28-variant29-variant30-variant33-variant35-variant37-variant38-variant39-variant40-filterInvariant41-variant42-variant44 GT:DP:GQ:SB 0/1:21:99:3,7,2,9 chr1 207007641 . C G 386.36 PASS AC=2;AF=0.893;AN=2;DP=1151;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:873,87,0:0,0,17,12 chr1 207009910 . T C 680.3 PASS AC=2;AF=0.884;AN=2;DP=664;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:554,42,0:0,0,13,1 chr1 207014472 . A C 3339.06 PASS AC=2;AF=0.817;AN=2;DP=4418;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,101:102:99:3141,264,0:1,0,46,55 chr1 207014776 . C T 449.91 PASS AC=2;AF=0.884;AN=2;DP=649;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:600,48,0:0,0,2,14 chr1 207015957 . T C 2765.85 PASS AC=2;AF=0.78;AN=2;DP=4199;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,127:127:99:3619,380,0:0,0,68,59 chr1 207016225 . A G 364.32 PASS AC=2;AF=0.813;AN=2;DP=1134;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:985,104,0:0,0,15,20 chr1 207038686 . C T 538.2 PASS AC=1;AF=0.5;AN=2;DP=236;MQ=60;set=variant3-variant4-variant6-variant17-variant19-variant28-variant35-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:20,22:42:99:626,0,600:16,4,17,5 chr1 207040577 . G A 428.05 PASS AC=2;AF=0.793;AN=2;DP=673;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:673,57,0:0,0,15,4 chr1 207040659 . G A 1999.12 PASS AC=2;AF=0.793;AN=2;DP=3019;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,76:77:99:2418,204,0:1,0,50,26 chr1 207072959 . C T 1191.83 PASS AC=1;AF=0.694;AN=2;DP=1374;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant31-variant32-variant34-variant35-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,19:42:99:463,0,629:10,13,7,12 chr1 207074905 . T C 5731.19 PASS AC=1;AF=0.694;AN=2;DP=5798;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant31-variant32-variant34-variant35-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:94,90:184:99:2212,0,2263:50,44,51,39 chr1 207075171 . T C 863.28 PASS AC=1;AF=0.671;AN=2;DP=716;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,9:15:99:360,0,216:2,4,4,5 chr1 207077645 . T C 528.73 PASS AC=1;AF=0.661;AN=2;DP=636;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant31-variant32-variant34-variant35-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,13:20:99:413,0,202:7,0,13,0 chr1 207086969 . A G 2125.93 PASS AC=1;AF=0.688;AN=2;DP=2508;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant31-variant32-variant34-variant35-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,42:86:99:1208,0,1218:30,14,28,14 chr1 207087435 . C T 3535.7 PASS AC=1;AF=0.688;AN=2;DP=3240;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant31-variant32-variant34-variant35-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,48:104:99:1380,0,1502:17,39,11,37 chr1 207091138 . AT A 134.76 PASS AC=1;AF=0.5;AN=2;DP=1168;MQ=60;set=variant-filterInvariant2-filterInvariant3-filterInvariant4-variant6-filterInvariant7-variant8-filterInvariant9-variant11-variant12-variant13-variant14-filterInvariant16-variant17-variant18-variant19-filterInvariant22-variant23-variant24-filterInvariant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:23,13:36:99:215,0,376:10,13,6,7 chr1 207102008 . G A 514.74 PASS AC=1;AF=0.5;AN=2;DP=152;FractionInformativeReads=1;MQ=60;set=variant20-variant21-variant26-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:17,9:26:99:205,0,565:13,4,4,5 chr1 207102293 . A T 434.81 PASS AC=1;AF=0.694;AN=2;DP=456;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant31-variant32-variant34-variant35-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,16:21:99:460,0,162:1,4,4,12 chr1 207108191 . CAT C 685.74 PASS AC=1;AF=0.671;AN=2;DP=1697;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,19:29:99:621,0,278:2,8,5,14 chr1 207109116 . C T 2486.17 PASS AC=1;AF=0.677;AN=2;DP=3943;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant31-variant32-variant34-variant35-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:79,66:145:99:1458,0,1842:34,45,29,37 chr1 207109167 . G A 1747.03 PASS AC=1;AF=0.677;AN=2;DP=2167;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant31-variant32-variant34-variant35-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,42:86:99:1132,0,1226:14,30,11,31 chr1 207110363 . A G 51.19 PASS AC=1;AF=0.633;AN=2;DP=816;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant31-variant32-variant34-variant35-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,9:15:99:311,0,136:4,2,5,4 chr1 207110936 . T C 1798.54 PASS AC=1;AF=0.618;AN=2;DP=4250;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:75,68:143:99:1846,0,1915:40,35,35,33 chr1 207111257 . G T 708.03 PASS AC=1;AF=0.7;AN=2;DP=3394;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,36:88:99:880,0,1260:23,29,15,21 chr1 207113679 . T C 290.8 PASS AC=1;AF=0.618;AN=2;DP=1105;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,14:35:99:354,0,628:11,10,8,6 chr1 207113755 . G C 402.8 PASS AC=1;AF=0.633;AN=2;DP=1476;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant31-variant32-variant34-variant35-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,24:50:99:618,0,653:12,14,13,11 chr1 207119853 . C A 153.64 PASS AC=1;AF=0.607;AN=2;DP=878;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant14-variant17-variant19-variant20-variant21-variant22-variant24-variant26-variant28-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,22:28:99:572,0,169:2,4,7,15 chr1 207131571 . T G 340.67 PASS AC=1;AF=0.625;AN=2;DP=1013;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant14-variant17-variant19-variant20-variant21-variant22-variant24-variant26-variant28-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,17:38:99:432,0,520:10,11,9,8 chr1 207132345 . A G 673.23 PASS AC=1;AF=0.632;AN=2;DP=2598;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,35:70:99:951,0,870:12,23,12,23 chr1 207135389 . C T 233.16 PASS AC=1;AF=0.64;AN=2;DP=315;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant11-variant13-variant14-variant17-variant19-variant20-variant21-variant22-variant24-variant26-variant28-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,10:17:99:309,0,252:7,0,8,2 chr1 207135546 . G A 1055.07 PASS AC=1;AF=0.625;AN=2;DP=2767;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant14-variant17-variant19-variant20-variant21-variant22-variant24-variant26-variant28-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,57:124:99:1352,0,1653:33,34,30,27 chr1 207135991 . C T 378.23 PASS AC=1;AF=0.625;AN=2;DP=1346;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant14-variant17-variant19-variant20-variant21-variant22-variant24-variant26-variant28-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,28:57:99:762,0,679:13,16,11,17 chr1 207143422 . A G 346.11 PASS AC=1;AF=0.632;AN=2;DP=1703;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,31:60:99:797,0,712:17,12,20,11 chr1 207193177 . G A 678.7 PASS AC=1;AF=0.594;AN=2;DP=1888;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant18-variant19-variant20-variant21-variant22-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,32:69:99:739,0,981:17,20,17,15 chr1 207195779 . A G 1803.47 PASS AC=2;AF=0.989;AN=2;DP=4691;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,119:119:99:3710,357,0:0,0,56,63 chr1 207217359 . T C 684.44 PASS AC=1;AF=0.679;AN=2;DP=1220;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,14:32:99:487,0,663:0,18,1,13 chr1 207218942 . CA C,CAA 1036.56 PASS AC=1,0;AF=0.489,0.011;AN=2;DP=16172;set=variant-filterInvariant2-variant3-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant7-variant8-variant9-variant10-filterInvariant11-filterInvariant12-filterInvariant13-filterInvariant14-filterInvariant15-filterInvariant16-variant17-filterInvariant18-variant19-filterInvariant20-variant21-variant22-variant23-filterInvariant24-filterInvariant25-filterInvariant26-variant27-variant28-variant29-variant30-variant31-variant32-filterInvariant33-filterInvariant34-filterInvariant35-variant36-variant37-variant38-variant39-variant40-variant41-filterInvariant42-variant43-variant44 GT:DP:GQ:SB 0/1:368:99:156,130,48,34 chr1 207219603 . T C 3408.35 PASS AC=1;AF=0.609;AN=2;DP=8384;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:128,125:253:99:3138,0,3228:61,67,57,68 chr1 207220282 . G A 4268.85 PASS AC=1;AF=0.609;AN=2;DP=11229;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:198,170:368:99:3908,0,4758:100,98,84,86 chr1 207220800 . C A 4200.45 PASS AC=1;AF=0.603;AN=2;DP=8827;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:148,114:262:99:2953,0,3808:73,75,53,61 chr1 207221409 . T C 11015.5 PASS AC=2;AF=0.989;AN=2;DP=14304;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,304:304:99:8990,908,0:0,0,148,156 chr1 207221929 . T G 2282.09 PASS AC=1;AF=0.606;AN=2;DP=5329;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:86,84:170:99:2178,0,2042:44,42,39,45 chr1 207226083 . TGA T 176.64 PASS AC=1;AF=0.692;AN=2;DP=65;FS=0;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant10-variant13-variant14-variant22-variant27-variant29-variant32-variant35-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,5:10:99:192,0,190:4,1,5,0 chr1 207235954 . G A 1962.36 PASS AC=1;AF=0.609;AN=2;DP=5427;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:115,93:208:99:2342,0,2934:59,56,50,43 chr1 207237233 . GGT GGGGTGTGTGTGTGTGT,GGGGTGTGTGTGTGTGTGT,GGGGTGTGTGTGTGTGTGTGT,G,GGTGTGTGTGTGTGTGT,GGGGTGTGTGTGTGTGTGTGTGTGT,GGTGT,GGTGTGT,GGGGGGTGTGTGTGTGT 2834.86 PASS AC=0,0,1,0,0,0,0,0,0;AF=0.025,0.263,0.125,0.075,0.013,0.025,0.038,0.013,0.013;AN=2;DP=3264;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-filterInvariant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-filterInvariant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/3:89:99:12,28,17,32 chr1 207238419 . C T 1811.33 PASS AC=1;AF=0.625;AN=2;DP=1815;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant11-variant13-variant14-variant19-variant21-variant22-variant27-variant28-variant29-variant30-variant33-variant35-variant36-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,51:115:99:1098,0,1667:36,28,26,25 chr1 207241440 . AGT AGTGTGTGTGTGT,AGTGTGTGTGT,AGTGTGTGTGTGTGT,A,AGTGTGTGT,AGTGTGTGTGTGTGTGT,AGTGT 256.57 PASS AC=1,0,0,0,0,0,0;AF=0.5,0.031,0.016,0.016,0.016,0.016,0.016;AN=2;DP=767;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant27-variant28-variant29-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:30:99:11,6,10,3 chr1 207243851 . A G 383.6 PASS AC=1;AF=0.782;AN=2;DP=1229;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,20:45:99:513,0,607:10,15,9,11 chr1 207245045 . T C 778.2 PASS AC=1;AF=0.586;AN=2;DP=1218;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant18-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,15:43:99:393,0,835:6,22,3,12 chr1 207246004 . A G 412.7 PASS AC=1;AF=0.586;AN=2;DP=1128;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant18-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,24:44:99:669,0,420:11,9,12,12 chr1 207247476 . TTC T 613.95 PASS AC=1;AF=0.586;AN=2;DP=1081;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant18-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,22:39:99:873,0,738:7,10,12,10 chr1 207249855 . G A 1388.04 PASS AC=1;AF=0.586;AN=2;DP=3113;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant18-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,54:102:99:1412,0,1355:22,26,20,34 chr1 207249974 . A ACTGACTGACAGACAGACTTTAGTGTCTGTGTG 784.89 PASS AC=1;AF=0.586;AN=2;DP=3460;set=variant-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant18-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,46:102:99:1694,0,13751:26,30,25,21 chr1 207250300 . G A 4848.65 PASS AC=1;AF=0.653;AN=2;DP=11947;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:177,165:342:99:4219,0,4312:76,101,63,102 chr1 207250456 . C T 1481.43 PASS AC=1;AF=0.586;AN=2;DP=2229;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant18-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,29:87:99:749,0,1531:28,30,15,14 chr1 207250570 . A G 1408.97 PASS AC=1;AF=0.586;AN=2;DP=2937;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant18-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,51:96:99:1598,0,1289:23,22,37,14 chr1 207250631 . A G 2765.03 PASS AC=1;AF=0.586;AN=2;DP=6010;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant18-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:75,110:185:99:2896,0,2033:48,27,67,43 chr1 207253031 . C T 1387.12 PASS AC=1;AF=0.671;AN=2;DP=2611;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,36:64:99:979,0,686:11,17,16,20 chr1 207253165 . A G 1656.89 PASS AC=1;AF=0.703;AN=2;DP=1719;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,24:49:99:525,0,591:13,12,10,14 chr1 207253575 . A AT 7022.52 PASS AC=2;AF=1;AN=2;DP=8224;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,183:183:99:5666,550,0:0,0,85,98 chr1 207262980 . T G 3268.09 PASS AC=1;AF=0.636;AN=2;DP=3647;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:37,59:96:99:1631,0,921:17,20,22,37 chr1 207263829 . A G 2177.9 PASS AC=1;AF=0.633;AN=2;DP=2338;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:41,56:97:99:1344,0,937:19,22,24,32 chr1 207268779 . A G 3267.57 PASS AC=1;AF=0.613;AN=2;DP=2252;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:34,33:67:99:1095,0,1099:5,29,4,29 chr1 207273399 . ATGTGTGTG A,ATGTGTG,ATGTG,ATG 96.34 PASS AC=0,0,1,0;AF=0.04,0.1,0.38,0.02;AN=2;DP=1133;set=variant-filterInvariant2-variant3-variant4-variant6-variant7-variant11-variant12-filterInvariant14-variant16-variant17-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant34-filterInvariant35-variant36-variant44 GT:DP:GQ:SB 0/3:14:99:1,8,1,4 chr1 207288897 . T C 1256.91 PASS AC=2;AF=0.711;AN=2;DP=1401;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:878,72,0:0,0,4,20 chr1 207297484 . G C 692.6 PASS AC=1;AF=0.673;AN=2;DP=1101;MQ=60;set=variant-variant2-variant4-variant6-variant9-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant22-variant24-variant25-variant26-variant29-variant31-variant33-variant34-variant35-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:28,17:45:99:500,0,821:13,15,8,9 chr1 207297680 . T C 2071.17 PASS AC=1;AF=0.857;AN=2;DP=3864;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,49:91:99:1179,0,890:21,21,21,28 chr1 207500293 . C T 335.87 PASS AC=2;AF=0.792;AN=2;DP=635;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:726,60,0:0,0,4,16 chr1 207504669 . G A 263.04 PASS AC=2;AF=0.778;AN=2;DP=1209;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1295,108,0:0,0,7,29 chr1 207510289 . T C 1804.7 PASS AC=2;AF=1;AN=2;DP=3402;FS=0;MQ=60;MQRankSum=-0.763;ReadPosRankSum=0.47;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,83:83:99:2607,249,0:0,0,30,53 chr1 207510548 . A G 240.08 PASS AC=2;AF=0.778;AN=2;DP=672;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:906,69,0:0,0,19,4 chr1 207510596 . G A 554.66 PASS AC=2;AF=0.778;AN=2;DP=1972;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:2538,216,0:0,0,56,16 chr1 207520376 . T C 887.04 PASS AC=1;AF=0.5;AN=2;DP=790;MQ=60;set=variant4-variant6-variant8-variant9-variant11-variant13-variant17-variant21-variant22-variant27-variant29-variant30-variant31-variant32-variant35-variant37-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,20:40:99:522,0,586:13,7,8,12 chr1 207527285 . G A 446.46 PASS AC=1;AF=0.5;AN=2;DP=875;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant8-variant9-variant11-variant13-variant17-variant21-variant22-variant27-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,17:46:99:482,0,779:20,9,14,3 chr1 207627693 . T C 1539.83 PASS AC=1;AF=0.571;AN=2;DP=1687;FractionInformativeReads=1;MQ=60;set=variant6-variant7-variant11-variant12-variant14-variant23-variant25-variant28-variant30-variant32-variant34-variant35-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:74,80:154:99:2001,0,1952:44,30,48,32 chr1 207641840 . C T 313.33 PASS AC=1;AF=0.571;AN=2;DP=263;FractionInformativeReads=1;MQ=60;set=variant6-variant7-variant11-variant12-variant14-variant23-variant25-variant28-variant30-variant32-variant34-variant35-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,10:24:99:259,0,441:10,4,8,2 chr1 207642295 . G A 848.23 PASS AC=1;AF=0.571;AN=2;DP=572;MQ=60;set=variant6-variant7-variant11-variant12-variant14-variant23-variant25-variant28-variant30-variant32-variant34-variant35-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,20:43:99:566,0,542:8,15,6,14 chr1 207646322 . G A 1253 PASS AC=1;AF=0.596;AN=2;DP=2484;MQ=60;set=variant2-variant6-variant7-variant8-variant11-variant12-variant14-variant17-variant18-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,51:95:99:1282,0,1137:24,20,25,26 chr1 207646462 . G A 571.52 PASS AC=1;AF=0.6;AN=2;DP=1231;MQ=60;set=variant6-variant7-variant8-variant11-variant12-variant14-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,35:88:99:891,0,1442:25,28,20,15 chr1 207646898 . T C 1068.4 PASS AC=1;AF=0.6;AN=2;DP=1748;MQ=60;set=variant6-variant7-variant8-variant11-variant12-variant14-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,34:88:99:895,0,1378:26,28,21,13 chr1 207646923 . G A 1311.11 PASS AC=1;AF=0.6;AN=2;DP=2045;MQ=60;set=variant6-variant7-variant8-variant11-variant12-variant14-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,44:102:99:1056,0,1565:30,28,26,18 chr1 207653178 . C G 1114.45 PASS AC=1;AF=0.672;AN=2;DP=1223;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,15:31:99:449,0,429:11,5,11,4 chr1 207653395 . C A 3076.73 PASS AC=2;AF=0.826;AN=2;DP=3613;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:2385,215,0:0,0,29,43 chr1 207653444 . T A 751.34 PASS AC=1;AF=0.571;AN=2;DP=891;FractionInformativeReads=1;MQ=60;set=variant6-variant7-variant11-variant12-variant14-variant23-variant25-variant28-variant30-variant32-variant34-variant35-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,24:53:99:666,0,900:12,17,10,14 chr1 207662912 . T C 11102.8 PASS AC=1;AF=0.909;AN=2;DP=12807;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:163,149:312:99:3908,0,4411:88,75,89,60 chr1 207663256 . G GT,GTT 971.36 PASS AC=1,0;AF=0.886,0.011;AN=2;DP=1813;MQ=60;set=Intersection GT:DP:GQ:SB 0/1:47:99:1,22,4,20 chr1 207669924 . C G 61.77 PASS AC=1;AF=0.839;AN=2;DP=194;FS=0;FractionInformativeReads=1;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant28-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:1,2:3:37:81,0,37:0,1,0,2 chr1 207679307 . A G 5772.17 PASS AC=1;AF=0.826;AN=2;DP=7129;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:77,87:164:99:2451,0,1974:46,31,54,33 chr1 207753345 . C T 487.83 PASS AC=1;AF=0.667;AN=2;DP=706;MQ=60;set=variant3-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:7,11:18:99:382,0,254:7,0,10,1 chr1 207753831 . CT C,CTT 88.59 PASS AC=1,0;AF=0.429,0.071;AN=2;DP=832;MQ=60;set=filterInvariant-filterInvariant11-filterInvariant19-variant30-filterInvariant31-filterInvariant35-filterInvariant40 GT:DP:GQ:SB 0/1:127:92:58,49,9,11 chr1 207782916 . A T 3033.78 PASS AC=2;AF=0.989;AN=2;DP=5205;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,126:126:99:3907,378,0:0,0,56,70 chr1 207784968 . A G 4058.84 PASS AC=1;AF=0.802;AN=2;DP=4787;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,56:120:99:1451,0,1482:30,34,30,26 chr1 207795320 . A G 2790.75 PASS AC=2;AF=0.814;AN=2;DP=3931;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,102:102:99:3041,306,0:0,0,56,46 chr1 207812791 . A G 293.02 PASS AC=1;AF=0.5;AN=2;DP=206;FractionInformativeReads=1;set=variant2-variant12-variant14-variant24-variant25-variant30-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,14:19:99:448,0,121:1,4,3,11 chr1 207813726 . T C 40.97 PASS AC=1;AF=0.75;AN=2;DP=118;set=variant2-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant19-variant23-variant24-variant26-variant27-variant28-variant32-variant35-variant36-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:1,4:5:31:84,0,31:1,0,2,2 chr1 207818422 . G A 997.71 PASS AC=1;AF=0.5;AN=2;DP=636;MQ=60;set=variant2-variant12-variant14-variant24-variant25-variant30-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,39:78:99:1102,0,1199:29,10,31,8 chr1 207850717 . G A 758.12 PASS AC=1;AF=0.5;AN=2;DP=533;MQ=60;set=variant2-variant12-variant14-variant24-variant25-variant30-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,36:70:99:1008,0,1020:23,11,27,9 chr1 207851487 . T TA 871.66 PASS AC=1;AF=0.5;AN=2;DP=782;set=variant2-variant12-variant14-variant24-variant25-variant30-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,45:88:99:987,0,962:25,18,28,17 chr1 207851611 . A G 1860.34 PASS AC=1;AF=0.606;AN=2;DP=5221;set=variant2-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:85,88:173:99:2187,0,2040:41,44,41,47 chr1 207857254 . A G 1997.35 PASS AC=1;AF=0.5;AN=2;DP=1712;FractionInformativeReads=1;set=variant2-variant12-variant14-variant24-variant25-variant30-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:90,76:166:99:1768,0,1960:49,41,35,41 chr1 207872507 . G A 967.72 PASS AC=1;AF=0.5;AN=2;DP=556;FractionInformativeReads=1;set=variant2-variant12-variant14-variant24-variant25-variant30-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,47:72:99:1530,0,776:22,3,39,8 chr1 207875116 . GAGA G 2536.83 PASS AC=1;AF=0.5;AN=2;DP=934;set=variant2-variant12-variant14-variant24-variant25-variant30-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,57:94:99:2239,0,1615:10,27,12,45 chr1 207881485 . TA T 2664.26 PASS AC=2;AF=0.694;AN=2;DP=5682;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,160:161:99:7133,448,0:1,0,78,82 chr1 207881489 . T G 2719.32 PASS AC=2;AF=0.694;AN=2;DP=5635;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,156:156:99:7207,488,0:0,0,76,80 chr1 207881491 . C A 2722.35 PASS AC=2;AF=0.694;AN=2;DP=5633;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,155:155:99:7054,473,0:0,0,77,78 chr1 207881557 . A G 1424.17 PASS AC=2;AF=0.694;AN=2;DP=4056;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,111:111:99:3556,331,0:0,0,43,68 chr1 207888739 . G T 1542.91 PASS AC=2;AF=0.686;AN=2;DP=3752;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,113:113:99:3413,339,0:0,0,52,61 chr1 207941191 . G T 915.7 PASS AC=2;AF=0.826;AN=2;DP=956;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:653,60,0:0,0,6,14 chr1 207959122 . CTTTT C,CT,CTTT 763.59 PASS AC=1,0,1;AF=0.511,0.375,0.114;AN=2;DP=1566;FS=0;MQ=60;set=Intersection GT:DP:GQ:SB 1/3:21:99:0,0,8,13 chr1 207959136 . T TAAA,TAA 763.34 PASS AC=0,1;AF=0.405,0.5;AN=2;DP=1236;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant2-variant30-variant31-variant32-variant34-variant35-variant5-variant38-variant33-variant40-variant36-variant42-variant39-variant43-variant41-variant44 GT:DP:GQ:SB 0/2:21:99:4,7,4,6 chr1 208060806 . G A 1247.78 PASS AC=1;AF=0.63;AN=2;DP=1718;FractionInformativeReads=1;set=variant-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant34-variant35-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,38:61:99:1495,0,1181:14,9,20,18 chr1 208060807 . A G 1247.78 PASS AC=1;AF=0.63;AN=2;DP=1714;FractionInformativeReads=1;set=variant-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant34-variant35-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,38:61:99:1495,0,1181:14,9,20,18 chr1 208062260 . T C 906.75 PASS AC=1;AF=0.716;AN=2;DP=2033;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,33:47:99:848,0,346:4,10,12,21 chr1 208062471 . A C 648.22 PASS AC=1;AF=0.565;AN=2;DP=1259;MQ=60;set=variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant14-variant17-variant20-variant21-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,21:50:99:531,0,708:19,10,13,8 chr1 208062973 . A T 389.7 PASS AC=1;AF=0.583;AN=2;DP=1759;MQ=60;set=variant-variant4-variant5-variant7-variant9-variant11-variant12-variant16-variant18-variant19-variant20-variant21-variant23-variant26-variant28-variant30-variant31-variant34-variant35-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,35:91:99:806,0,1497:29,27,16,19 chr1 208063067 . G A 1144.4 PASS AC=1;AF=0.577;AN=2;DP=1951;MQ=60;set=variant-variant4-variant5-variant7-variant9-variant10-variant11-variant12-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant26-variant28-variant30-variant31-variant34-variant35-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,30:65:99:912,0,982:15,20,17,13 chr1 208063100 . G GA 503.26 PASS AC=1;AF=0.653;AN=2;DP=2874;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,25:57:99:451,0,676:20,12,14,11 chr1 208063466 . A T 852.56 PASS AC=1;AF=0.705;AN=2;DP=2583;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,33:71:99:879,0,929:14,24,11,22 chr1 208063505 . G A 393.34 PASS AC=1;AF=0.524;AN=2;DP=845;MQ=60;set=variant4-variant6-variant7-variant8-variant9-variant10-variant14-variant17-variant19-variant20-variant21-variant24-variant25-variant26-variant29-variant30-variant31-variant33-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,14:37:99:435,0,637:7,16,3,11 chr1 208063808 . G A 173.01 PASS AC=1;AF=0.607;AN=2;DP=1232;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant7-variant9-variant10-variant11-variant12-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant26-variant27-variant28-variant30-variant31-variant34-variant35-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,27:50:99:660,0,579:10,13,11,16 chr1 208195516 . A C 427.45 PASS AC=2;AF=0.988;AN=2;DP=358;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.747;ReadPosRankSum=0.747;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:181,15,0:0,0,3,2 chr1 208195981 . C T 203.17 PASS AC=2;AF=0.724;AN=2;DP=1765;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1375,145,0:0,0,28,21 chr1 208196081 . T C 777.75 PASS AC=2;AF=0.989;AN=2;DP=2001;MQ=60;MQRankSum=-1.275;ReadPosRankSum=-0.481;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1274,123,0:0,0,21,20 chr1 208197882 . G C 2425.26 PASS AC=2;AF=1;AN=2;DP=4057;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,109:109:99:3358,327,0:0,0,55,54 chr1 208198161 . C T 138.93 PASS AC=2;AF=0.711;AN=2;DP=1762;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1327,120,0:0,0,15,25 chr1 208199100 . T A 414.32 PASS AC=2;AF=0.724;AN=2;DP=2926;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2184,210,0:0,0,35,35 chr1 208199998 . T TC,TCTC 1400.58 PASS AC=2,0;AF=0.6,0.014;AN=2;DP=2326;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-filterInvariant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:52:85:1,3,36,12 chr1 208199999 . T TC 429.07 PASS AC=1;AF=0.5;AN=2;DP=2164;set=variant-variant2-variant3-variant4-variant6-variant7-filterInvariant8-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant30-variant31-variant33-variant34-variant35-variant36-filterInvariant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,38:53:99:753,0,144:10,5,26,12 chr1 208200127 . T A 5012.99 PASS AC=2;AF=1;AN=2;DP=5475;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,147:147:99:4222,439,0:0,0,70,77 chr1 208206946 . C G 266.86 PASS AC=2;AF=0.621;AN=2;DP=700;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,23:23:68:733,68,0:0,0,8,15 chr1 208207045 . T C 103.54 PASS AC=2;AF=1;AN=2;DP=216;FS=0;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:234,21,0:0,0,2,5 chr1 208207839 . G A 445.23 PASS AC=2;AF=0.737;AN=2;DP=2862;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:2419,224,0:0,0,44,31 chr1 208208034 . G C 624.35 PASS AC=2;AF=0.636;AN=2;DP=1922;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,63:63:99:2162,189,0:0,0,14,49 chr1 208208124 . C A 160.2 PASS AC=2;AF=0.743;AN=2;DP=407;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:302,21,0:0,0,1,6 chr1 208211887 . T C 506.52 PASS AC=2;AF=0.977;AN=2;DP=1357;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:739,63,0:0,0,7,14 chr1 208213125 . A G 1985.41 PASS AC=2;AF=1;AN=2;DP=5111;FS=0;MQ=60;MQRankSum=1.254;ReadPosRankSum=1.692;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,133:133:99:4033,399,0:0,0,74,59 chr1 208219164 . A C 1027.16 PASS AC=2;AF=0.86;AN=2;DP=2027;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1710,132,0:0,0,38,6 chr1 208224955 . G C 118.69 PASS AC=2;AF=0.689;AN=2;DP=654;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:981,66,0:0,0,7,15 chr1 208224957 . C T 414.54 PASS AC=2;AF=1;AN=2;DP=720;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,21:21:66:981,66,0:0,0,7,14 chr1 208252489 . T C 1690.36 PASS AC=2;AF=0.686;AN=2;DP=3655;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,120:120:99:3636,359,0:0,0,65,55 chr1 208255877 . T C 1130.69 PASS AC=2;AF=0.797;AN=2;DP=4054;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,102:104:99:3200,262,0:1,1,36,66 chr1 208276399 . C CCTCT 3892.76 PASS AC=2;AF=1;AN=2;DP=3778;FS=0;MQ=60;MQRankSum=-1.123;ReadPosRankSum=-0.961;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,103:103:99:4750,319,0:0,0,67,36 chr1 208390469 . C T 1834.23 PASS AC=1;AF=0.528;AN=2;DP=5489;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant14-variant15-variant16-variant20-variant22-variant35-variant36-variant37-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:177,153:330:99:3939,0,4502:91,86,81,72 chr1 208417649 . TGGCGGC T 772.06 PASS AC=2;AF=0.989;AN=2;DP=1523;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,30:30:92:1312,92,0:0,0,8,22 chr1 209603996 . A G 377.92 PASS AC=1;AF=0.679;AN=2;DP=1987;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,26:41:99:794,0,393:6,9,7,19 chr1 209605636 . TAGCAGCAGCAGCAGCAGC TAGCAGC,T 1080.09 PASS AC=1,0;AF=0.667,0.013;AN=2;DP=3470;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:70:99:14,23,14,19 chr1 209781417 . TACAC T,TACACAC,TAC,TACACACAC 277.97 PASS AC=1,0,0,0;AF=0.455,0.136,0.015,0.015;AN=2;DP=658;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:25:99:3,7,4,11 chr1 209782343 . A G 2134.61 PASS AC=1;AF=0.569;AN=2;DP=2345;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant35-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:59,26:85:99:587,0,1605:36,23,17,9 chr1 209784663 . A C 46.72 PASS AC=1;AF=0.703;AN=2;DP=761;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,16:25:99:520,0,272:8,1,11,5 chr1 209784927 . G T 781.3 PASS AC=1;AF=0.58;AN=2;DP=2103;set=variant-variant2-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant16-variant19-variant20-variant23-variant24-variant25-variant27-variant28-variant33-variant35-variant36-variant37-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,46:88:99:1192,0,1180:14,28,14,32 chr1 209785011 . G C 355.7 PASS AC=1;AF=0.571;AN=2;DP=952;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant16-variant19-variant20-variant23-variant24-variant25-variant27-variant28-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,17:34:99:452,0,558:8,9,8,9 chr1 209785957 . T G 406.24 PASS AC=1;AF=0.703;AN=2;DP=1378;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,10:30:99:299,0,570:15,5,7,3 chr1 209786078 . G A 1315.01 PASS AC=1;AF=0.689;AN=2;DP=5313;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:84,63:147:99:1460,0,2048:44,40,39,24 chr1 209786883 . C T 297.05 PASS AC=1;AF=0.583;AN=2;DP=909;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant16-variant19-variant20-variant23-variant24-variant25-variant27-variant28-variant33-variant35-variant36-variant37-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:31,24:55:99:587,0,811:13,18,9,15 chr1 209788213 . T C 242.87 PASS AC=1;AF=0.729;AN=2;DP=415;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,8:10:61:241,0,61:2,0,5,3 chr1 209788703 . T C 353.07 PASS AC=1;AF=0.569;AN=2;DP=2153;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant19-variant20-variant23-variant24-variant25-variant27-variant28-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,44:89:99:1099,0,1026:20,25,17,27 chr1 209792015 . A AC 2956.09 PASS AC=2;AF=0.966;AN=2;DP=5500;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,151:151:99:5647,457,0:0,0,66,85 chr1 209795909 . T C 408.43 PASS AC=1;AF=0.533;AN=2;DP=552;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant10-variant11-variant12-variant16-variant20-variant25-variant27-variant33-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:22,6:28:99:122,0,612:14,8,4,2 chr1 209796329 . T A 152.04 PASS AC=1;AF=0.533;AN=2;DP=561;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant10-variant11-variant12-variant16-variant20-variant25-variant27-variant33-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:30,28:58:99:619,0,812:18,12,17,11 chr1 209798771 . G A 337.35 PASS AC=1;AF=0.636;AN=2;DP=941;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,28:49:99:693,0,573:15,6,18,10 chr1 209798824 . A G 409.56 PASS AC=1;AF=0.575;AN=2;DP=1124;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant16-variant20-variant25-variant27-variant33-variant35-variant36-variant37-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:39,43:82:99:1021,0,875:21,18,25,18 chr1 209799253 . A G 4514.61 PASS AC=2;AF=0.833;AN=2;DP=5487;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,145:145:99:4487,434,0:0,0,64,81 chr1 209804095 . G A 1464.18 PASS AC=2;AF=0.909;AN=2;DP=2463;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1796,168,0:0,0,19,37 chr1 209807972 . G A 854.45 PASS AC=1;AF=0.636;AN=2;DP=4592;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant13-variant14-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:66,66:132:99:1590,0,1642:29,37,25,41 chr1 209811829 . A T 597.05 PASS AC=1;AF=0.525;AN=2;DP=1339;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant20-variant25-variant27-variant31-variant32-variant33-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:32,31:63:99:796,0,757:20,12,19,12 chr1 209811886 . T G 1415.23 PASS AC=1;AF=0.725;AN=2;DP=4171;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,48:93:99:1190,0,1179:24,21,26,22 chr1 209812063 . T C 1441.66 PASS AC=2;AF=0.854;AN=2;DP=2041;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,61:61:99:1959,182,0:0,0,22,39 chr1 209823354 . G A 310.98 PASS AC=1;AF=0.526;AN=2;DP=1534;MQ=60;set=variant-variant2-variant5-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant20-variant25-variant26-variant27-variant33-variant34-variant35-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:54,38:92:99:921,0,1358:25,29,17,21 chr1 209824099 . G C 56.69 PASS AC=1;AF=0.528;AN=2;DP=229;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant20-variant25-variant26-variant27-variant33-variant34-variant35-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:6,10:16:99:318,0,170:5,1,7,3 chr1 209848696 . G C 464.08 PASS AC=2;AF=0.977;AN=2;DP=1161;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1116,99,0:0,0,14,19 chr1 209849002 . T C 1070.58 PASS AC=2;AF=0.782;AN=2;DP=6004;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,167:167:99:5323,499,0:0,0,88,79 chr1 209849399 . AG A 1022.88 PASS AC=2;AF=0.782;AN=2;DP=3552;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:3550,241,0:0,0,40,39 chr1 209849406 . T G 3029.64 PASS AC=2;AF=0.977;AN=2;DP=3978;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:3420,232,0:0,0,38,38 chr1 209849714 . TA T 1022.09 PASS AC=2;AF=0.977;AN=2;DP=1925;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,31:31:93:964,93,0:0,0,16,15 chr1 209929299 . G A 61.77 PASS AC=2;AF=0.851;AN=2;DP=299;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:511,42,0:0,0,12,2 chr1 209950681 . T C 1061.93 PASS AC=2;AF=0.727;AN=2;DP=1353;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant9-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1668,150,0:0,0,27,23 chr1 209950760 . C G 1307.48 PASS AC=2;AF=0.915;AN=2;DP=2969;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,89:89:99:2776,266,0:0,0,53,36 chr1 209951400 . C G 784.39 PASS AC=1;AF=0.5;AN=2;DP=465;FractionInformativeReads=1;MQ=60;set=variant5-variant21-variant29-variant35-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:56,39:95:99:1009,0,1349:35,21,27,12 chr1 209951432 . T A 1668.76 PASS AC=1;AF=0.5;AN=2;DP=126;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.494;QD=13.24;ReadPosRankSum=0.741;SOR=0.733;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:53,73:126:99:1697,0,1331:30,23,42,31 chr1 209952865 . C G 10352.5 PASS AC=1;AF=0.654;AN=2;DP=6677;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant26-variant27-variant29-variant32-variant33-variant34-variant35-variant37-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:148,126:274:99:3043,0,3527:79,69,73,53 chr1 209953706 . C T 97.67 PASS AC=1;AF=0.714;AN=2;DP=48;FractionInformativeReads=1;MQ=60;set=variant9-variant15-variant20-variant25-variant30-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:99:114,0,119:2,1,3,0 chr1 209955848 . A C 1427.36 PASS AC=1;AF=0.648;AN=2;DP=1318;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant29-variant32-variant33-variant34-variant35-variant37-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:35,31:66:99:755,0,930:15,20,13,18 chr1 209959872 . G A 201.22 PASS AC=2;AF=0.934;AN=2;DP=309;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:328,30,0:0,0,4,6 chr1 209960922 . A C 761.44 PASS AC=1;AF=0.648;AN=2;DP=859;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant26-variant27-variant29-variant32-variant33-variant34-variant35-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,17:28:99:535,0,320:5,6,12,5 chr1 209965587 . G C,A 1695.01 PASS AC=1,0;AF=0.629,0.016;AN=2;DP=3801;MQ=60;set=variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant32-variant35-variant36-variant38-variant39-variant40-variant41-variant44 GT:DP:GQ:SB 0/1:136:99:36,28,41,31 chr1 209968319 . A C 637.11 PASS AC=1;AF=0.733;AN=2;DP=285;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant12-variant13-variant14-variant15-variant16-variant19-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,6:11:99:156,0,145:4,1,4,2 chr1 209968411 . C T 360.92 PASS AC=1;AF=0.6;AN=2;DP=435;set=variant9-variant15-variant20-variant22-variant25-variant29-variant30-variant32-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:21,14:35:99:346,0,548:14,7,10,4 chr1 209968684 . C A 2514.88 PASS AC=1;AF=0.65;AN=2;DP=4482;MQ=60;set=variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant32-variant35-variant36-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:80,72:152:99:1660,0,2111:35,45,32,40 chr1 209969902 . G C 256.35 PASS AC=1;AF=0.65;AN=2;DP=829;MQ=60;set=variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant32-variant35-variant36-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,14:30:99:399,0,528:3,13,2,12 chr1 209975386 . A G 951.79 PASS AC=1;AF=0.648;AN=2;DP=993;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant26-variant27-variant29-variant32-variant33-variant34-variant35-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:36,16:52:99:314,0,882:19,17,10,6 chr1 210001233 . C T 280.3 PASS AC=2;AF=0.893;AN=2;DP=532;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:419,33,0:0,0,10,1 chr1 210001543 . A T 2029.75 PASS AC=1;AF=0.545;AN=2;DP=1534;MQ=60;set=variant9-variant15-variant20-variant22-variant24-variant25-variant29-variant30-variant32-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:75,78:153:99:1922,0,1875:29,46,26,52 chr1 210001586 . A G 2547.29 PASS AC=1;AF=0.806;AN=2;DP=2732;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,42:81:99:1116,0,1001:12,27,15,27 chr1 210003388 . A C 1999.96 PASS AC=1;AF=0.635;AN=2;DP=1354;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant26-variant27-variant29-variant32-variant33-variant34-variant35-variant37-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:33,17:50:99:466,0,890:21,12,13,4 chr1 210003402 . T C 2230.48 PASS AC=2;AF=0.875;AN=2;DP=2486;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:1913,174,0:0,0,38,20 chr1 210004199 . C G 3113.15 PASS AC=2;AF=0.875;AN=2;DP=4499;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,104:104:99:3161,312,0:0,0,61,43 chr1 210006437 . G A 196.77 PASS AC=2;AF=0.895;AN=2;DP=374;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:675,45,0:0,0,12,3 chr1 210006438 . C T 196.77 PASS AC=2;AF=0.895;AN=2;DP=381;FS=0;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:675,45,0:0,0,12,3 chr1 210006603 . C T 5033.01 PASS AC=2;AF=0.875;AN=2;DP=5600;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,152:152:99:4621,456,0:0,0,91,61 chr1 210008367 . C G 1595.66 PASS AC=2;AF=0.875;AN=2;DP=2335;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:2185,162,0:0,0,33,21 chr1 210008374 . C T 1122.91 PASS AC=1;AF=0.545;AN=2;DP=720;MQ=60;set=variant9-variant15-variant20-variant22-variant24-variant25-variant29-variant30-variant32-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:20,37:57:99:1069,0,398:10,10,24,13 chr1 210008673 . T G 874.71 PASS AC=2;AF=0.875;AN=2;DP=991;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:989,84,0:0,0,5,23 chr1 210012102 . A G 2630.04 PASS AC=2;AF=0.875;AN=2;DP=3097;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,72:73:99:2405,183,0:1,0,50,22 chr1 210015568 . GCT G 2874.4 PASS AC=2;AF=0.893;AN=2;DP=2748;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,63:63:99:2788,190,0:0,0,37,26 chr1 210026097 . CT C 1184 PASS AC=1;AF=0.545;AN=2;DP=1070;MQ=60;set=variant9-variant15-variant20-variant22-variant24-variant25-variant29-variant30-variant32-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:59,54:113:99:1848,0,2033:29,30,28,26 chr1 210026596 . C T 4246.21 PASS AC=1;AF=0.635;AN=2;DP=3768;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant26-variant27-variant29-variant32-variant33-variant34-variant35-variant37-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:76,76:152:99:1909,0,1863:31,45,27,49 chr1 210027026 . G A 331.77 PASS AC=2;AF=0.694;AN=2;DP=816;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:65:603,65,0:0,0,14,8 chr1 210027965 . G A 684.04 PASS AC=1;AF=0.591;AN=2;DP=472;FractionInformativeReads=1;MQ=60;set=variant9-variant15-variant20-variant22-variant24-variant25-variant29-variant30-variant32-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:27,24:51:99:651,0,683:13,14,11,13 chr1 210126264 . CTTA C 166.66 PASS AC=1;AF=0.5;AN=2;DP=23;FS=0;MQ=60;set=variant5-variant35-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:99:117,0,122:1,2,1,2 chr1 210334665 . GTTAATT G 1135.73 PASS AC=1;AF=0.583;AN=2;DP=1428;set=variant2-variant6-variant7-variant10-variant11-variant16-variant26-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:41,40:81:99:1533,0,3014:9,32,13,27 chr1 210335028 . T C 1853.9 PASS AC=1;AF=0.583;AN=2;DP=2679;MQ=60;set=variant2-variant6-variant7-variant10-variant11-variant16-variant26-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:71,79:150:99:2162,0,1818:28,43,34,45 chr1 210335066 . G A 1712.61 PASS AC=1;AF=0.583;AN=2;DP=2416;MQ=60;set=variant2-variant6-variant7-variant10-variant11-variant16-variant26-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:68,67:135:99:2006,0,1930:35,33,32,35 chr1 210337043 . A G 3081.29 PASS AC=1;AF=0.845;AN=2;DP=11327;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:152,151:303:99:3718,0,3642:76,76,80,71 chr1 210407339 . T TAA,A 454.88 PASS AC=0,1;AF=0.096,0.558;AN=2;DP=811;MQ=60;set=variant13-variant16-variant19-variant2-variant7-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:26:99:4,9,6,7 chr1 210411266 . GT G,GTT 313.24 PASS AC=1,0;AF=0.447,0.079;AN=2;DP=1161;set=variant-variant2-variant3-filterInvariant5-variant7-filterInvariant10-variant11-variant16-filterInvariant18-filterInvariant20-variant21-variant25-variant27-variant29-variant31-variant32-variant33-variant35-variant36 GT:DP:GQ:SB 0/1:48:99:13,7,17,11 chr1 210416438 . CA CAA,CAAA,CAAAA,C,CAAAAA,CAAAAAAAAAA 281 PASS AC=1,0,0,0,0,0;AF=0.2,0.183,0.083,0.033,0.017,0.017;AN=2;DP=4359;set=filterInvariant-filterInvariant3-filterInvariant4-variant6-variant7-variant8-variant10-variant11-variant14-filterInvariant15-filterInvariant16-variant17-filterInvariant19-variant21-filterInvariant22-variant24-filterInvariant25-variant26-variant30-variant31-variant33-variant34-filterInvariant35-filterInvariant36-variant37-filterInvariant38-variant39-variant41-variant43-variant44 GT:DP:GQ:SB 0/1:97:99:40,20,23,14 chr1 210418825 . C T 1645.8 PASS AC=1;AF=0.5;AN=2;DP=646;FractionInformativeReads=1;MQ=60;set=variant5-variant29-variant35-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:72,73:145:99:1725,0,1614:34,38,36,37 chr1 210522080 . CGT CGTGTGTGT,CGTGTGTGTGTGT,CGTGTGT,C,CGTGT,CGTGTGTGTGTGTGT,CGTGTGTGTGT 361.23 PASS AC=0,0,0,1,0,0,0;AF=0.244,0.116,0.209,0.035,0.035,0.035,0.081;AN=2;DP=888;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/4:19:99:11,2,5,1 chr1 210577873 . G C 867.29 PASS AC=1;AF=0.802;AN=2;DP=3655;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,50:98:99:1145,0,1321:27,21,27,23 chr1 210577884 . G A 849.68 PASS AC=1;AF=0.55;AN=2;DP=887;MQ=60;set=variant3-variant4-variant13-variant18-variant19-variant20-variant23-variant32-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:52,47:99:99:1050,0,1355:29,23,25,22 chr1 210591742 . TG T 1102.63 PASS AC=1;AF=0.689;AN=2;DP=3812;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,51:109:99:1296,0,1503:12,46,15,36 chr1 210686570 . A G 1091.1 PASS AC=2;AF=0.793;AN=2;DP=3085;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:2183,224,0:0,0,31,44 chr1 210686614 . A G 420.19 PASS AC=1;AF=0.5;AN=2;DP=760;MQ=60;set=variant2-variant4-variant11-variant13-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant27-variant32-variant34-variant35-variant36-variant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:29,24:53:99:637,0,809:8,21,7,17 chr1 210761462 . G C 857.13 PASS AC=2;AF=1;AN=2;DP=1528;FS=0;MQ=60;MQRankSum=1.22;ReadPosRankSum=0.835;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1253,104,0:0,0,6,29 chr1 210847371 . T C 332.83 PASS AC=1;AF=0.55;AN=2;DP=139;set=variant-variant3-variant7-variant13-variant17-variant22-variant31-variant33-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:2,5:7:61:163,0,61:2,0,4,1 chr1 210847514 . A T 945.18 PASS AC=1;AF=0.718;AN=2;DP=2940;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,49:79:99:1252,0,759:17,13,30,19 chr1 210848224 . A G 1093.12 PASS AC=2;AF=0.86;AN=2;DP=1825;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1333,126,0:0,0,21,21 chr1 210848807 . AT A,ATTT,ATT 2119.3 PASS AC=1,0,0;AF=0.619,0.048,0.083;AN=2;DP=11151;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-filterInvariant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:213:99:48,58,46,61 chr1 210856585 . G T 3012.75 PASS AC=2;AF=0.86;AN=2;DP=3428;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,83:83:99:2480,249,0:0,0,42,41 chr1 210856604 . T G 1214.17 PASS AC=1;AF=0.5;AN=2;DP=920;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant7-variant13-variant17-variant22-variant31-variant33-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:38,50:88:99:1389,0,952:21,17,28,22 chr1 210857457 . A G 1782.09 PASS AC=2;AF=0.833;AN=2;DP=2499;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:2081,204,0:0,0,24,44 chr1 210970823 . T TG 1444.89 PASS AC=1;AF=0.563;AN=2;DP=2567;MQ=60;set=variant-variant2-variant3-variant5-variant11-variant17-variant20-variant21-variant22-variant26-variant29-variant30-variant33-variant35-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:69,76:145:99:2487,0,2109:44,25,48,28 chr1 211263836 . T A 458.31 PASS AC=1;AF=0.5;AN=2;DP=58;FractionInformativeReads=1;MQ=60;set=variant2-variant23-variant35 GT:AD:DP:GQ:PL:SB 0/1:6,12:18:99:426,0,178:5,1,11,1 chr1 211264140 . A G 599.1 PASS AC=2;AF=0.563;AN=2;DP=321;MQ=60;set=variant2-variant10-variant14-variant17-variant23-variant30-variant31-variant35 GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:1948,164,0:0,0,12,43 chr1 211280737 . A AC 1576.72 PASS AC=2;AF=0.571;AN=2;DP=659;MQ=60;set=variant2-variant10-variant14-variant23-variant30-variant31-variant35 GT:AD:DP:GQ:PL:SB 1/1:1,99:100:99:3683,281,0:1,0,37,62 chr1 211380770 . T C 855.89 PASS AC=1;AF=0.656;AN=2;DP=6197;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant20-variant22-variant24-variant26-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:119,101:220:99:2466,0,2990:69,50,64,37 chr1 211447435 . CT C 191.23 PASS AC=2;AF=0.964;AN=2;DP=351;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:67,9,0:0,0,3,0 chr1 211447625 . G A 1720.99 PASS AC=1;AF=0.735;AN=2;DP=5102;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:70,89:159:99:1875,0,1553:35,35,47,42 chr1 211452529 . TAA TA,T 673.3 PASS AC=2,0;AF=0.989,0.011;AN=2;DP=1044;set=Intersection GT:DP:GQ:SB 1/1:23:43:1,0,16,6 chr1 211452678 . G A 1120.04 PASS AC=1;AF=0.735;AN=2;DP=2628;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,24:70:99:569,0,1139:18,28,9,15 chr1 211452728 . G A 987.98 PASS AC=1;AF=0.735;AN=2;DP=1402;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,11:35:99:297,0,690:7,17,2,9 chr1 211487347 . GT G 3393.26 PASS AC=1;AF=0.735;AN=2;DP=6558;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:89,94:183:99:2971,0,2762:46,43,43,51 chr1 211487676 . CT CTT,C 900.38 PASS AC=1,0;AF=0.375,0.125;AN=2;DP=970;MQ=60;set=variant2-variant6-variant7-variant12-variant16-variant29-variant35-variant39 GT:DP:GQ:SB 0/1:102:99:23,32,15,32 chr1 211488076 . A G 15717.5 PASS AC=2;AF=0.977;AN=2;DP=16649;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,413:413:99:13326,1238,0:0,0,203,210 chr1 211488538 . C A 22314.8 PASS AC=2;AF=0.977;AN=2;DP=28584;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,647:647:99:19585,1938,0:0,0,331,316 chr1 211489187 . T G 7192.61 PASS AC=2;AF=0.977;AN=2;DP=9413;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,228:228:99:7457,683,0:0,0,119,109 chr1 211489591 . A G 387.34 PASS AC=1;AF=0.5;AN=2;DP=98;FractionInformativeReads=1;MQ=60;set=variant30-variant35 GT:AD:DP:GQ:PL:SB 0/1:32,26:58:99:631,0,721:13,19,12,14 chr1 211499911 . G T 729.08 PASS AC=1;AF=0.5;AN=2;DP=502;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant12-variant16-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:40,46:86:99:1045,0,1039:26,14,26,20 chr1 211519576 . C G 108.16 PASS AC=1;AF=0.5;AN=2;DP=80;MQ=60;set=variant2-variant6-variant7-variant12-variant29-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:7,10:17:99:306,0,185:4,3,8,2 chr1 211527609 . C A 895.41 PASS AC=2;AF=1;AN=2;DP=701;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:648,54,0:0,0,14,4 chr1 211527958 . A G 443.67 PASS AC=1;AF=0.5;AN=2;DP=132;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant12-variant16-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:12,11:23:99:336,0,314:3,9,2,9 chr1 211533352 . A G 1518.82 PASS AC=1;AF=0.5;AN=2;DP=870;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant7-variant12-variant16-variant29-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:54,55:109:99:1295,0,1395:19,35,26,29 chr1 211538597 . C A 252.67 PASS AC=1;AF=0.5;AN=2;DP=222;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant12-variant16-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:20,21:41:99:578,0,622:17,3,16,5 chr1 211545442 . CTT C,CT 706.29 PASS AC=0,1;AF=0.013,0.65;AN=2;DP=1426;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:29:99:5,5,12,7 chr1 211649875 . C A 244.34 PASS AC=1;AF=0.5;AN=2;DP=117;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant16-variant31-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:19,6:25:99:141,0,496:12,7,5,1 chr1 211651544 . C A,T 413.28 PASS AC=0,1;AF=0.111,0.389;AN=2;DP=458;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant16-variant28-variant31-variant34-variant35-variant39 GT:DP:GQ:SB 0/2:50:99:17,18,9,6 chr1 211652185 . C G 1671.16 PASS AC=1;AF=0.538;AN=2;DP=1208;set=variant3-variant14-variant18-variant29-variant30-variant31-variant32-variant35-variant37-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:71,49:120:99:1129,0,1792:37,34,23,26 chr1 211654216 . A G 161.56 PASS AC=1;AF=0.538;AN=2;DP=175;FractionInformativeReads=1;MQ=60;set=variant3-variant14-variant18-variant29-variant30-variant31-variant32-variant35-variant37-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,7:14:99:183,0,185:3,4,5,2 chr1 211665298 . A AG 215.16 PASS AC=2;AF=0.797;AN=2;DP=581;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:642,48,0:0,0,6,10 chr1 211665391 . GT G 236.06 PASS AC=1;AF=0.5;AN=2;DP=50;MQ=60;set=variant16-variant28-variant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:1,7:8:18:271,0,18:0,1,6,1 chr1 211665393 . GTGTGTGTGT G 233.05 PASS AC=1;AF=0.5;AN=2;DP=54;MQ=60;set=variant16-variant28-variant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:1,7:8:18:271,0,18:0,1,6,1 chr1 211666218 . A G 566.71 PASS AC=1;AF=0.677;AN=2;DP=1609;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant20-variant22-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:40,24:64:99:679,0,963:17,23,10,14 chr1 211745154 . C G 6071.05 PASS AC=1;AF=0.625;AN=2;DP=4106;MQ=60;set=variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant21-variant26-variant29-variant30-variant31-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:135,89:224:99:1900,0,3374:66,69,40,49 chr1 211745290 . T A 1624.19 PASS AC=1;AF=0.5;AN=2;DP=1163;MQ=60;set=variant7-variant8-variant9-variant10-variant26-variant30-variant35-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:66,44:110:99:1020,0,1913:29,37,20,24 chr1 211747902 . A T 1895.53 PASS AC=1;AF=0.5;AN=2;DP=1282;FractionInformativeReads=1;MQ=60;set=variant7-variant8-variant9-variant10-variant26-variant30-variant35-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:74,48:122:99:1312,0,1922:33,41,20,28 chr1 211748118 . C T 6112.11 PASS AC=1;AF=0.536;AN=2;DP=8279;MQ=60;set=variant6-variant7-variant8-variant9-variant10-variant26-variant29-variant30-variant31-variant35-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:344,261:605:99:5987,0,8350:179,165,145,116 chr1 211752148 . T C 104.18 PASS AC=1;AF=0.571;AN=2;DP=219;FractionInformativeReads=1;MQ=60;set=variant6-variant7-variant8-variant9-variant10-variant26-variant29-variant30-variant31-variant35-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:15,6:21:99:158,0,498:3,12,2,4 chr1 211840278 . T C 1418.11 PASS AC=1;AF=0.548;AN=2;DP=1961;MQ=60;set=variant3-variant5-variant9-variant11-variant13-variant16-variant17-variant19-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:60,45:105:99:891,0,1336:35,25,26,19 chr1 211842808 . A C 194.98 PASS AC=1;AF=0.765;AN=2;DP=249;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,2:7:66:66,0,166:1,4,0,2 chr1 211846876 . A G 3002.71 PASS AC=1;AF=0.609;AN=2;DP=6374;set=variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:108,100:208:99:2593,0,2717:71,37,66,34 chr1 211916895 . A AT 3311.45 PASS AC=2;AF=0.942;AN=2;DP=3605;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,94:94:99:2868,285,0:0,0,50,44 chr1 211918424 . A G 253.01 PASS AC=1;AF=0.5;AN=2;DP=16;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.705;QD=15.81;ReadPosRankSum=1.681;SOR=0.368;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:6,10:16:99:281,0,109:1,5,3,7 chr1 211921767 . C T 1604.49 PASS AC=1;AF=0.617;AN=2;DP=1727;MQ=60;set=variant-variant2-variant5-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,29:70:99:832,0,1199:12,29,8,21 chr1 211922355 . C T 4414.43 PASS AC=1;AF=0.617;AN=2;DP=4454;MQ=60;set=variant-variant2-variant5-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:74,94:168:99:2374,0,1805:31,43,45,49 chr1 211923441 . C A 281.48 PASS AC=1;AF=0.5;AN=2;DP=75;FractionInformativeReads=1;MQ=60;set=variant18-variant35 GT:AD:DP:GQ:PL:SB 0/1:16,25:41:99:619,0,427:5,11,10,15 chr1 211960831 . CAAAAAA CAAAAA,CAAAA,CAAA,C,CAA 39.62 PASS AC=1,0,0,0,0;AF=0.235,0.176,0.029,0.029,0.029;AN=2;DP=191;set=variant-variant2-variant3-variant6-variant12-variant14-variant16-variant19-variant21-variant27-variant28-variant31-variant35-variant39-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:16:38:4,1,8,3 chr1 212004100 . C G 157.42 PASS AC=2;AF=0.667;AN=2;DP=283;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant10-variant11-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:177,12,0:0,0,2,2 chr1 212113995 . G A 3747.04 PASS AC=2;AF=0.762;AN=2;DP=6063;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,141:141:99:3821,422,0:0,0,64,77 chr1 212114662 . A G 3991.23 PASS AC=2;AF=0.641;AN=2;DP=2845;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,75:76:99:3260,193,0:1,0,35,40 chr1 212114663 . G A 3991.23 PASS AC=2;AF=0.641;AN=2;DP=2811;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,72:73:99:3260,193,0:1,0,33,39 chr1 212114666 . C G 3841.77 PASS AC=2;AF=0.641;AN=2;DP=2764;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:3178,184,0:0,0,32,38 chr1 212142054 . GA G 531.24 PASS AC=2;AF=0.686;AN=2;DP=1549;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-filterInvariant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:71:551,71,0:0,0,5,19 chr1 212154688 . C T 295.7 PASS AC=1;AF=0.5;AN=2;DP=12;FS=10.414;FractionInformativeReads=1;MQ=60;MQRankSum=-0.289;QD=24.64;ReadPosRankSum=-1.599;SOR=4.407;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:4,8:12:63:324,0,63:2,2,0,8 chr1 212209367 . T TC 489.23 PASS AC=2;AF=0.641;AN=2;DP=968;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:918,78,0:0,0,1,25 chr1 212217971 . C CTT 1576.82 PASS AC=2;AF=0.72;AN=2;DP=1661;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:2177,150,0:0,0,29,16 chr1 212220847 . G A 697.58 PASS AC=2;AF=0.703;AN=2;DP=775;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,17:18:12:584,12,0:0,1,2,15 chr1 212236157 . G T 1485.24 PASS AC=2;AF=0.955;AN=2;DP=1978;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1164,105,0:0,0,26,9 chr1 212241714 . TAA TA,TAAAA,TAAA,T 1233.05 PASS AC=2,0,0,0;AF=0.538,0.038,0.013,0.013;AN=2;DP=3023;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-filterInvariant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-filterInvariant28-variant29-filterInvariant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-filterInvariant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:51:76:1,2,13,35 chr1 212250820 . T C 61.77 PASS AC=2;AF=0.762;AN=2;DP=88;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant11-variant16-variant20-variant21-variant24-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:100,9,0:0,0,2,1 chr1 212251103 . A G 279.11 PASS AC=2;AF=0.955;AN=2;DP=782;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:545,48,0:0,0,5,11 chr1 212251367 . GT G 782.69 PASS AC=2;AF=0.955;AN=2;DP=863;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:659,69,0:0,0,17,6 chr1 212273639 . C T 3724.38 PASS AC=2;AF=0.955;AN=2;DP=6094;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,146:146:99:4395,435,0:0,0,79,67 chr1 212274413 . A C 2004.5 PASS AC=2;AF=1;AN=2;DP=2773;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:2360,228,0:0,0,33,43 chr1 212277107 . T G 14314.5 PASS AC=2;AF=0.641;AN=2;DP=12823;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,373:375:99:11785,1075,0:1,1,162,211 chr1 212277304 . C G 8681.24 PASS AC=2;AF=0.641;AN=2;DP=8427;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,294:294:99:9077,880,0:0,0,163,131 chr1 212277588 . A ACTGTGTAGACTTTATGTCAGTT,AGTGTGTAGACTTTATGTCAGTT 10823.6 PASS AC=2,0;AF=0.932,0.023;AN=2;DP=9788;set=Intersection GT:DP:GQ:SB 1/1:187:99:0,0,80,107 chr1 212459015 . G T 750.17 PASS AC=1;AF=0.556;AN=2;DP=1675;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:42,28:70:99:617,0,983:23,19,17,11 chr1 212515613 . C T 1433.4 PASS AC=1;AF=0.56;AN=2;DP=2331;set=variant-variant2-variant4-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:53,35:88:99:799,0,1319:22,31,13,22 chr1 212521639 . T G 1497.47 PASS AC=1;AF=0.869;AN=2;DP=1924;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,20:39:99:536,0,511:14,5,12,8 chr1 212526288 . C T 5527.96 PASS AC=1;AF=0.866;AN=2;DP=6801;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:80,100:180:99:2665,0,1970:39,41,42,58 chr1 212530192 . T C 2447.33 PASS AC=2;AF=0.977;AN=2;DP=2944;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:2165,177,0:0,0,20,39 chr1 212534377 . T A 6392.01 PASS AC=1;AF=0.556;AN=2;DP=11964;set=variant-variant2-variant4-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:224,248:472:99:6056,0,5559:102,122,106,142 chr1 212537553 . G A 4703.67 PASS AC=1;AF=0.556;AN=2;DP=7433;MQ=60;set=variant-variant2-variant4-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:123,146:269:99:3704,0,3217:52,71,67,79 chr1 212537702 . G A 2422.65 PASS AC=1;AF=0.556;AN=2;DP=3812;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:96,57:153:99:2031,0,5618:49,47,32,25 chr1 212537707 . C T 2485.63 PASS AC=1;AF=0.574;AN=2;DP=3888;MQ=60;set=variant-variant2-variant4-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:94,55:149:99:1994,0,5566:48,46,32,23 chr1 212538771 . CTTT CTTTTT,CTT,CTTTT,CT,C 135.95 PASS AC=0,1,0,0,0;AF=0.017,0.317,0.05,0.1,0.017;AN=2;DP=1143;set=variant2-variant3-variant4-filterInvariant5-variant6-variant8-filterInvariant9-variant10-filterInvariant11-variant12-filterInvariant15-variant17-filterInvariant18-variant21-variant23-filterInvariant24-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-filterInvariant42-variant43-variant44 GT:DP:GQ:SB 0/2:26:88:2,8,3,13 chr1 212553111 . G C 438.08 PASS AC=1;AF=0.537;AN=2;DP=1053;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:19,26:45:99:836,0,473:13,6,20,6 chr1 212560327 . A G 2052.8 PASS AC=2;AF=0.977;AN=2;DP=7215;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,162:162:99:4807,484,0:0,0,70,92 chr1 212588206 . C G 1908.97 PASS AC=1;AF=0.537;AN=2;DP=4571;MQ=60;set=variant-variant2-variant4-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:78,115:193:99:3046,0,2251:20,58,45,70 chr1 212617860 . CGTGTGTGTGT CGTGT,CGTGTGT,CGTGTGTGTGTGT,CGTGTGTGT,C,CGT 810.5 PASS AC=0,1,0,1,0,0;AF=0.118,0.329,0.039,0.079,0.079,0.039;AN=2;DP=2400;set=variant-variant2-variant4-variant5-filterInvariant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-filterInvariant17-variant18-filterInvariant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-filterInvariant33-variant34-variant35-variant36-variant37-variant38-filterInvariant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 2/4:21:99:0,2,1,18 chr1 212738909 . T C 143.54 PASS AC=1;AF=0.727;AN=2;DP=297;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,8:10:57:289,0,57:0,2,1,7 chr1 212793613 . T C 521.88 PASS AC=1;AF=0.756;AN=2;DP=2026;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,18:50:99:404,0,887:15,17,7,11 chr1 212793849 . A G 156.03 PASS AC=1;AF=0.5;AN=2;DP=125;FractionInformativeReads=1;MQ=60;set=variant-variant24-variant25-variant35 GT:AD:DP:GQ:PL:SB 0/1:20,17:37:99:370,0,581:12,8,7,10 chr1 212799870 . A G 359 PASS AC=1;AF=0.86;AN=2;DP=3522;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,29:75:99:604,0,1172:21,25,16,13 chr1 212799949 . C T 415.48 PASS AC=1;AF=0.692;AN=2;DP=4099;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,39:86:99:818,0,1220:23,24,20,19 chr1 212870017 . G A 444.04 PASS AC=2;AF=0.667;AN=2;DP=96;FS=0;FractionInformativeReads=1;MQ=60;set=variant9-variant10-variant16-variant17-variant19-variant22-variant28-variant31-variant35-variant37-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:437,39,0:0,0,10,3 chr1 212870103 . C G 732.88 PASS AC=2;AF=1;AN=2;DP=881;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:787,66,0:0,0,15,7 chr1 212900311 . G C 677.96 PASS AC=1;AF=0.72;AN=2;DP=1465;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,21:44:99:523,0,547:11,12,9,12 chr1 212900434 . C CG 932.34 PASS AC=1;AF=0.72;AN=2;DP=1163;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,12:28:99:399,0,558:10,6,8,4 chr1 212900487 . A G 1492.59 PASS AC=2;AF=0.966;AN=2;DP=1957;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1877,168,0:0,0,35,21 chr1 212910930 . G A 3916.66 PASS AC=1;AF=0.72;AN=2;DP=4429;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,57:112:99:1470,0,1605:19,36,23,34 chr1 212911366 . CTT CT,C 1868.79 PASS AC=1,0;AF=0.725,0.025;AN=2;DP=4091;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:101:99:19,21,28,33 chr1 212911836 . T C 5707.53 PASS AC=1;AF=0.72;AN=2;DP=7029;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:82,88:170:99:2386,0,2026:37,45,44,44 chr1 212912108 . ATT A,AT,ATTT 483.4 PASS AC=1,0,0;AF=0.405,0.286,0.083;AN=2;DP=1130;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-filterInvariant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:7:39:0,3,1,3 chr1 212955454 . G A 1264.85 PASS AC=1;AF=0.66;AN=2;DP=2226;MQ=60;set=variant-variant3-variant6-variant8-variant9-variant10-variant12-variant15-variant17-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant35-variant37-variant38-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,47:84:99:1065,0,960:24,13,26,21 chr1 212960866 . C T 2411.66 PASS AC=1;AF=0.55;AN=2;DP=1614;MQ=60;set=variant2-variant3-variant4-variant5-variant8-variant11-variant13-variant14-variant15-variant21-variant24-variant26-variant27-variant34-variant35-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,37:85:99:830,0,1185:29,19,24,13 chr1 212969842 . CT CTT,C 100.04 PASS AC=1,0;AF=0.529,0.015;AN=2;DP=983;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant40-filterInvariant41-variant42-variant44 GT:DP:GQ:SB 0/1:18:99:8,2,6,2 chr1 212970375 . A G 1251.44 PASS AC=2;AF=1;AN=2;DP=1725;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,34:35:59:1029,59,0:1,0,23,11 chr1 212985466 . C T 177.55 PASS AC=1;AF=0.638;AN=2;DP=848;FractionInformativeReads=1;set=variant-variant3-variant5-variant6-variant8-variant9-variant10-variant12-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:26,13:39:99:304,0,610:14,12,9,4 chr1 212989107 . C T 293.55 PASS AC=1;AF=0.654;AN=2;DP=310;FractionInformativeReads=1;set=variant-variant3-variant5-variant6-variant8-variant9-variant10-variant12-variant15-variant17-variant18-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,10:20:99:288,0,264:6,4,7,3 chr1 212989840 . C T 292.79 PASS AC=1;AF=0.638;AN=2;DP=851;MQ=60;set=variant-variant3-variant5-variant6-variant8-variant9-variant10-variant12-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:14,12:26:99:303,0,390:7,7,2,10 chr1 212989891 . C T 199.59 PASS AC=1;AF=0.638;AN=2;DP=620;MQ=60;set=variant-variant3-variant5-variant6-variant8-variant9-variant10-variant12-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant38-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,8:20:99:257,0,266:5,7,3,5 chr1 213003372 . A T 224.81 PASS AC=2;AF=0.852;AN=2;DP=145;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant6-variant7-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant24-variant25-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:201,15,0:0,0,5,0 chr1 213003428 . T G 514.78 PASS AC=1;AF=0.583;AN=2;DP=269;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant8-variant11-variant14-variant15-variant21-variant26-variant27-variant34-variant35-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,8:18:99:184,0,346:9,1,5,3 chr1 213009178 . CAA CA,C 57.2 PASS AC=1,0;AF=0.474,0.026;AN=2;DP=1121;set=filterInvariant-variant2-variant3-variant4-filterInvariant5-variant6-filterInvariant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-filterInvariant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42 GT:DP:GQ:SB 0/1:29:99:15,4,8,2 chr1 213009469 . A G 10909.2 PASS AC=1;AF=0.8;AN=2;DP=12347;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:145,180:325:99:4381,0,3288:72,73,90,90 chr1 213020876 . C T 2892.5 PASS AC=1;AF=0.78;AN=2;DP=4927;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,45:112:99:986,0,1686:41,26,29,16 chr1 213021136 . CTTTTTTTTTT C,CTTTTTTTTTTTT,CT,CTTTTTTTTTTTTT,CTTTTTTTT,CTTTTTTTTTTT,CTTTTTTTTTTTTTTT,CTTTTT,CTTTTTT 292.11 PASS AC=0,0,0,0,0,0,0,1,0;AF=0.095,0.119,0.024,0.071,0.095,0.095,0.024,0.024,0.024;AN=2;DP=558;set=variant-variant3-variant7-variant8-variant12-filterInvariant15-filterInvariant17-variant19-variant23-variant24-variant25-filterInvariant29-variant31-variant32-variant33-variant34-variant35-variant36-variant39-filterInvariant41-variant42 GT:DP:GQ:SB 0/8:13:99:2,6,0,5 chr1 213031158 . C T 4074.76 PASS AC=1;AF=0.703;AN=2;DP=5330;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:91,79:170:99:1813,0,2151:52,39,40,39 chr1 213031350 . C T 4768.32 PASS AC=1;AF=0.703;AN=2;DP=5123;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:98,66:164:99:1501,0,2469:48,50,35,31 chr1 213031448 . G C 1644.67 PASS AC=1;AF=0.672;AN=2;DP=3169;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant17-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,63:118:99:2352,0,2215:20,35,28,35 chr1 213031473 . A C 3754.99 PASS AC=1;AF=0.703;AN=2;DP=3038;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,56:97:99:2217,0,1763:16,25,25,31 chr1 213031638 . GT G 1434.31 PASS AC=1;AF=0.5;AN=2;DP=462;MQ=60;set=variant3-variant4-variant13-variant14-variant15-variant27-variant35 GT:AD:DP:GQ:PL:SB 0/1:39,35:74:99:1187,0,1346:18,21,23,12 chr1 213031709 . C T 1490.41 PASS AC=1;AF=0.703;AN=2;DP=1975;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,23:59:99:505,0,956:23,13,12,11 chr1 213031948 . G C 4308.86 PASS AC=1;AF=0.703;AN=2;DP=4993;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:72,68:140:99:1693,0,1798:39,33,31,37 chr1 213032568 . T A,G 2912.49 PASS AC=1,0;AF=0.7,0.014;AN=2;DP=4763;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:138:99:34,38,29,37 chr1 213046236 . G A 448.23 PASS AC=1;AF=0.615;AN=2;DP=146;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant8-variant14-variant15-variant26-variant27-variant28-variant35-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:5,9:14:99:270,0,187:0,5,2,7 chr1 213056819 . A G 3742.79 PASS AC=2;AF=1;AN=2;DP=4829;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,109:109:99:3367,327,0:0,0,52,57 chr1 213056892 . A G 2137.81 PASS AC=1;AF=0.714;AN=2;DP=2387;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,41:68:99:988,0,619:10,17,16,25 chr1 213058852 . T A 564.11 PASS AC=1;AF=0.722;AN=2;DP=408;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,5:9:99:198,0,207:2,2,0,5 chr1 213061362 . T A 2638.45 PASS AC=1;AF=0.556;AN=2;DP=1968;set=variant2-variant3-variant4-variant5-variant8-variant11-variant13-variant14-variant15-variant26-variant27-variant28-variant35-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,53:107:99:1205,0,1287:24,30,23,30 chr1 213061460 . T C 940.71 PASS AC=1;AF=0.556;AN=2;DP=582;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant8-variant11-variant13-variant14-variant15-variant26-variant27-variant28-variant35-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,12:30:99:356,0,548:4,14,1,11 chr1 213062017 . T TTTG 1574.34 PASS AC=2;AF=0.837;AN=2;DP=2260;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1774,125,0:0,0,7,34 chr1 213068192 . T C 1594.38 PASS AC=2;AF=0.943;AN=2;DP=1357;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:1107,90,0:0,0,25,5 chr1 213068233 . C T 1173 PASS AC=2;AF=0.8;AN=2;DP=2564;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:1964,195,0:0,0,39,26 chr1 213068404 . T C 1563.51 PASS AC=1;AF=0.556;AN=2;DP=1165;MQ=60;set=variant2-variant3-variant4-variant5-variant8-variant11-variant13-variant14-variant15-variant26-variant27-variant28-variant35-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,27:63:99:690,0,867:15,21,11,16 chr1 213068436 . A G 1311.35 PASS AC=1;AF=0.556;AN=2;DP=819;MQ=60;set=variant2-variant3-variant4-variant5-variant8-variant11-variant13-variant14-variant15-variant26-variant27-variant28-variant35-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,19:48:99:585,0,776:11,18,8,11 chr1 213068542 . C CTGAT 1841.42 PASS AC=1;AF=0.556;AN=2;DP=894;MQ=60;set=variant2-variant3-variant4-variant5-variant8-variant11-variant13-variant14-variant15-variant26-variant27-variant28-variant35-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,26:40:99:1056,0,507:9,5,16,10 chr1 213068595 . C T 834.89 PASS AC=1;AF=0.667;AN=2;DP=2549;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,26:77:99:519,0,1163:27,24,13,13 chr1 213068971 . T G 2243.98 PASS AC=2;AF=0.8;AN=2;DP=5594;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,145:145:99:5015,435,0:0,0,102,43 chr1 213069258 . T A 4204.11 PASS AC=1;AF=0.677;AN=2;DP=9491;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant17-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:194,162:356:99:3994,0,4996:75,119,68,94 chr1 213069305 . G A 7228.14 PASS AC=1;AF=0.556;AN=2;DP=4216;MQ=60;set=variant2-variant3-variant4-variant5-variant8-variant11-variant13-variant14-variant15-variant26-variant27-variant28-variant35-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:119,137:256:99:3471,0,3010:44,75,59,78 chr1 213069420 . C T 2018.08 PASS AC=1;AF=0.677;AN=2;DP=2874;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant17-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,43:87:99:1227,0,1268:15,29,18,25 chr1 213069476 . T C 2156.75 PASS AC=1;AF=0.556;AN=2;DP=1256;set=variant2-variant3-variant4-variant5-variant8-variant11-variant13-variant14-variant15-variant26-variant27-variant28-variant35-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,34:81:99:877,0,1491:33,14,24,10 chr1 213069563 . C T 4994.13 PASS AC=1;AF=0.556;AN=2;DP=3190;MQ=60;set=variant2-variant3-variant4-variant5-variant8-variant11-variant13-variant14-variant15-variant26-variant27-variant28-variant35-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:101,86:187:99:2191,0,2536:49,52,45,41 chr1 213069738 . C T 2225.79 PASS AC=1;AF=0.556;AN=2;DP=1830;MQ=60;set=variant2-variant3-variant4-variant5-variant8-variant11-variant13-variant14-variant15-variant26-variant27-variant28-variant35-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,39:81:99:1215,0,1208:20,22,13,26 chr1 213069783 . A G 1704.56 PASS AC=2;AF=0.8;AN=2;DP=4232;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:2931,228,0:0,0,50,26 chr1 213071051 . G A 315.79 PASS AC=1;AF=0.667;AN=2;DP=891;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,12:19:99:338,0,158:2,5,7,5 chr1 213071210 . G A 1519.19 PASS AC=1;AF=0.603;AN=2;DP=2586;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant11-variant13-variant14-variant15-variant16-variant18-variant20-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,49:97:99:1280,0,1413:34,14,35,14 chr1 213071341 . T C 4343.28 PASS AC=1;AF=0.603;AN=2;DP=8537;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant11-variant13-variant14-variant15-variant16-variant18-variant20-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:141,134:275:99:3345,0,3574:78,63,76,58 chr1 213071445 . G A 3662.26 PASS AC=1;AF=0.617;AN=2;DP=7542;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant11-variant13-variant14-variant15-variant16-variant18-variant20-variant23-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:136,125:261:99:3168,0,3570:71,65,63,62 chr1 213071600 . G A 10720.4 PASS AC=1;AF=0.556;AN=2;DP=6637;MQ=60;set=variant2-variant3-variant4-variant5-variant8-variant11-variant13-variant14-variant15-variant26-variant27-variant28-variant35-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:197,221:418:99:5414,0,4628:97,100,116,105 chr1 213071761 . A ATAAT 2913.14 PASS AC=1;AF=0.603;AN=2;DP=4009;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant11-variant13-variant14-variant15-variant16-variant18-variant20-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,64:119:99:2609,0,2770:17,38,22,42 chr1 213124871 . G A 578.1 PASS AC=1;AF=0.667;AN=2;DP=1003;MQ=60;set=variant3-variant4-variant7-variant9-variant10-variant11-variant12-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,22:47:99:605,0,940:16,9,11,11 chr1 213139748 . T G 896.5 PASS AC=1;AF=0.719;AN=2;DP=2607;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,44:87:99:1185,0,1090:17,26,13,31 chr1 213140362 . G C,A 167.24 PASS AC=0,1;AF=0.037,0.63;AN=2;DP=856;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant9-variant10-variant11-variant12-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant38-variant40-variant41-variant43-variant44 GT:DP:GQ:SB 0/2:37:99:12,5,13,7 chr1 213140398 . A C 439.44 PASS AC=1;AF=0.683;AN=2;DP=1621;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,25:53:99:561,0,633:18,10,13,12 chr1 213146944 . A G 513.23 PASS AC=1;AF=0.721;AN=2;DP=1095;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,17:27:99:558,0,326:0,10,3,14 chr1 213162146 . G A 3782.57 PASS AC=1;AF=0.528;AN=2;DP=4350;MQ=60;set=variant-variant3-variant5-variant6-variant10-variant11-variant12-variant14-variant15-variant17-variant25-variant27-variant30-variant34-variant35-variant36-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:132,120:252:99:3066,0,3581:80,52,68,52 chr1 213164083 . A G 10095.4 PASS AC=1;AF=0.705;AN=2;DP=12673;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:142,135:277:99:3460,0,3631:69,73,64,71 chr1 213164502 . A AAAGT 7518.57 PASS AC=2;AF=1;AN=2;DP=5376;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,135:135:99:6164,412,0:0,0,61,74 chr1 213164677 . TAC T 4035.64 PASS AC=1;AF=0.5;AN=2;DP=469;MQ=60;set=variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:130,107:237:99:4073,0,5385:65,65,58,49 chr1 213164918 . G A 1974.6 PASS AC=1;AF=0.55;AN=2;DP=3203;MQ=60;set=variant-variant3-variant5-variant6-variant10-variant11-variant12-variant14-variant15-variant17-variant19-variant25-variant27-variant29-variant30-variant34-variant35-variant36-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:75,85:160:99:2097,0,1901:33,42,36,49 chr1 213167422 . G A 61.77 PASS AC=2;AF=1;AN=2;DP=2;FS=0;FractionInformativeReads=1;MQ=60;QD=30.88;SOR=2.303;set=variant35 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:90,6,0:0,0,0,2 chr1 213168190 . C G 1448.95 PASS AC=1;AF=0.589;AN=2;DP=1500;MQ=60;set=variant-variant3-variant5-variant6-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant22-variant24-variant25-variant27-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,30:58:99:845,0,780:14,14,12,18 chr1 213173457 . C T 254.16 PASS AC=1;AF=0.692;AN=2;DP=1110;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,11:26:99:248,0,382:9,6,8,3 chr1 213178340 . G A 1158.55 PASS AC=1;AF=0.692;AN=2;DP=3911;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,57:116:99:1437,0,1437:34,25,36,21 chr1 213180441 . GA G,GAA 438.87 PASS AC=1,0;AF=0.214,0.321;AN=2;DP=2006;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-filterInvariant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:51:99:18,10,15,8 chr1 213224719 . T C 1426.16 PASS AC=1;AF=0.779;AN=2;DP=4813;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,66:131:99:1620,0,1434:38,27,39,27 chr1 213234933 . G GT,GTT 635.52 PASS AC=1,0;AF=0.539,0.013;AN=2;DP=3956;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:76:99:12,28,13,23 chr1 213405414 . GGCAACTGAGGAT G 340.83 PASS AC=1;AF=0.779;AN=2;DP=1554;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,17:34:99:663,0,1800:14,3,13,4 chr1 214161473 . TC T 569.44 PASS AC=2;AF=1;AN=2;DP=917;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1170,99,0:0,0,19,14 chr1 214161754 . AG A 1963.16 PASS AC=1;AF=0.676;AN=2;DP=3813;set=variant-variant2-variant4-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,53:103:99:1685,0,1481:20,30,22,31 chr1 214161820 . G A 1558.58 PASS AC=1;AF=0.652;AN=2;DP=1831;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,19:39:99:510,0,508:8,12,6,13 chr1 214454471 . G A 105.9 PASS AC=1;AF=0.625;AN=2;DP=333;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant23-variant24-variant25-variant26-variant31-variant32-variant35-variant36-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,12:18:94:283,0,94:3,3,7,5 chr1 214478459 . G A 865.73 PASS AC=2;AF=0.55;AN=2;DP=2351;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant22-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,92:92:99:2835,276,0:0,0,58,34 chr1 214492091 . GT G 33.14 PASS AC=1;AF=0.5;AN=2;DP=50;MQ=60;set=variant11-variant19-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:1,6:7:6:125,0,6:1,0,5,1 chr1 214492286 . G A 4147.94 PASS AC=2;AF=0.875;AN=2;DP=5197;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,127:127:99:3624,380,0:0,0,66,61 chr1 214500852 . A T 210.27 PASS AC=1;AF=0.5;AN=2;DP=151;MQ=60;set=variant6-variant11-variant19-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:11,7:18:99:167,0,373:10,1,7,0 chr1 214503489 . T G 982.29 PASS AC=2;AF=0.588;AN=2;DP=3884;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant22-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,120:120:99:3549,359,0:0,0,66,54 chr1 214504604 . T C 3100.34 PASS AC=2;AF=0.884;AN=2;DP=3810;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,74:74:99:2535,222,0:0,0,21,53 chr1 214505596 . C T 780.6 PASS AC=1;AF=0.5;AN=2;DP=1254;MQ=60;set=variant7-variant13-variant18-variant22-variant26-variant27-variant28-variant30-variant32-variant35-variant36-variant37-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:47,61:108:99:1450,0,1145:19,28,30,31 chr1 214505716 . T C 833.12 PASS AC=2;AF=0.898;AN=2;DP=935;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:998,84,0:0,0,5,23 chr1 214510375 . GGACA G 5621.32 PASS AC=1;AF=0.5;AN=2;DP=4230;MQ=60;set=variant7-variant13-variant18-variant22-variant26-variant27-variant28-variant30-variant32-variant35-variant36-variant37-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:172,157:329:99:6010,0,8075:77,95,64,93 chr1 214531078 . GA G 1121.68 PASS AC=2;AF=0.667;AN=2;DP=2597;MQ=60;set=variant-variant5-variant6-variant8-variant11-variant12-variant13-variant17-variant19-variant20-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,95:95:99:2919,285,0:0,0,45,50 chr1 214537627 . C T 138.19 PASS AC=1;AF=0.528;AN=2;DP=286;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant8-variant12-variant13-variant17-variant20-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,10:14:99:312,0,99:3,1,8,2 chr1 214542668 . T C 403.28 PASS AC=2;AF=0.789;AN=2;DP=343;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:375,30,0:0,0,9,1 chr1 214542819 . T C 3229.19 PASS AC=2;AF=0.738;AN=2;DP=4674;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,149:149:99:4574,447,0:0,0,91,58 chr1 214551276 . G A 271.58 PASS AC=2;AF=0.738;AN=2;DP=968;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-filterInvariant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:65:649,65,0:0,0,17,5 chr1 214558228 . A G 463.64 PASS AC=2;AF=0.738;AN=2;DP=803;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:645,60,0:0,0,6,14 chr1 214560293 . G T 689.45 PASS AC=1;AF=0.5;AN=2;DP=343;FractionInformativeReads=1;MQ=60;set=variant6-variant11-variant19-variant33-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:35,31:66:99:773,0,899:11,24,9,22 chr1 214564340 . T C 5435.65 PASS AC=2;AF=0.738;AN=2;DP=7823;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,208:208:99:6225,622,0:0,0,91,117 chr1 214564442 . C G 923.54 PASS AC=1;AF=0.556;AN=2;DP=941;MQ=60;set=variant6-variant7-variant11-variant13-variant18-variant19-variant22-variant23-variant26-variant28-variant30-variant32-variant33-variant35-variant36-variant37-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:29,36:65:99:1087,0,774:8,21,9,27 chr1 214566845 . A G 634.25 PASS AC=2;AF=0.909;AN=2;DP=839;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:759,57,0:0,0,17,2 chr1 214566952 . A G 3409.81 PASS AC=2;AF=0.75;AN=2;DP=3907;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2234,209,0:0,0,42,28 chr1 214567013 . CG C 4479.69 PASS AC=2;AF=0.75;AN=2;DP=5861;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,108:108:99:3363,325,0:0,0,56,52 chr1 214638172 . C T 3605.3 PASS AC=2;AF=0.826;AN=2;DP=8073;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,212:212:99:6802,634,0:0,0,95,117 chr1 214638319 . T C 1047.46 PASS AC=2;AF=0.826;AN=2;DP=1700;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:2068,159,0:0,0,8,45 chr1 214638347 . A G 763.3 PASS AC=2;AF=0.826;AN=2;DP=915;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:965,75,0:0,0,3,22 chr1 214638383 . CCCCCCCCCCCA C 448.16 PASS AC=2;AF=0.905;AN=2;DP=435;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:586,39,0:0,0,1,12 chr1 214638396 . C G 237.22 PASS AC=2;AF=0.727;AN=2;DP=209;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant18-variant19-variant25-variant29-variant31-variant33-variant35-variant36-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:45:635,45,0:0,0,1,12 chr1 214638419 . G T 286.77 PASS AC=2;AF=0.929;AN=2;DP=258;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:30:410,30,0:0,0,1,8 chr1 214724413 . G C 440.18 PASS AC=1;AF=0.762;AN=2;DP=1480;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,27:48:99:1049,0,1094:12,9,16,11 chr1 214724422 . G T 508.04 PASS AC=1;AF=0.762;AN=2;DP=1622;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,27:50:99:1008,0,1175:14,9,17,10 chr1 214786982 . A G 980.6 PASS AC=1;AF=0.5;AN=2;DP=167;FractionInformativeReads=1;MQ=60;set=variant27-variant35 GT:AD:DP:GQ:PL:SB 0/1:33,50:83:99:1457,0,893:21,12,34,16 chr1 214791895 . T C 1689.66 PASS AC=1;AF=0.5;AN=2;DP=323;FractionInformativeReads=1;MQ=60;set=variant27-variant35 GT:AD:DP:GQ:PL:SB 0/1:77,83:160:99:1993,0,1750:41,36,43,40 chr1 214826196 . G A 1375.88 PASS AC=2;AF=0.629;AN=2;DP=3626;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,121:121:99:3687,363,0:0,0,57,64 chr1 214826364 . G A 861.04 PASS AC=2;AF=0.613;AN=2;DP=1680;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:1771,165,0:0,0,19,36 chr1 214826810 . CTTT CTT,C,CT 1793.57 PASS AC=2,0,0;AF=0.943,0.011,0.011;AN=2;DP=4577;MQ=60;set=Intersection GT:DP:GQ:SB 1/1:83:99:2,0,31,50 chr1 214828812 . A G 663.26 PASS AC=2;AF=0.671;AN=2;DP=2677;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,81:82:99:2570,204,0:1,0,27,54 chr1 214830617 . A G 1058.07 PASS AC=2;AF=0.657;AN=2;DP=3852;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,126:126:99:3858,377,0:0,0,58,68 chr1 214837110 . C G 624.26 PASS AC=2;AF=0.671;AN=2;DP=2453;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:2691,225,0:0,0,46,29 chr1 215256537 . TC T,TCCCCCCCCCCCCCC,TCCCCCCCCCCCC 219.43 PASS AC=0,1,0;AF=0.471,0.059,0.059;AN=2;DP=503;set=variant2-variant4-variant7-variant8-variant9-filterInvariant10-variant11-variant14-variant16-variant17-variant19-variant21-variant23-variant35-variant36-variant39-variant44 GT:DP:GQ:SB 0/2:26:99:0,16,10,0 chr1 215260152 . A T 31.67 PASS AC=1;AF=0.629;AN=2;DP=622;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,8:19:99:274,0,397:1,10,1,7 chr1 215345263 . GTCTCTC G 764.85 PASS AC=1;AF=0.798;AN=2;DP=916;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,6:16:99:223,0,523:5,5,4,2 chr1 215368514 . A G 118.39 PASS AC=1;AF=0.606;AN=2;DP=540;set=variant-variant2-variant4-variant5-variant7-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,10:14:99:393,0,99:1,3,0,10 chr1 215409388 . AATCTATCT AATCTATCTATCATCTATCTATCTATCTATCTATCT,A,AATCTATCTATCATCTATCT,AATCTATCTATCATCTATCTATCTATCTATCT,AATCTATCTATCT,AATCT,AATCTATCTATCATCTATCTATCTATCT,AATCTATCTATCATCTATCTATCT,AATCTATCTATCATCTATCTATCTATCTATCTATCTATCT,AATCTATCTATCTATCT 2590.75 PASS AC=0,0,1,0,0,0,0,0,0,0;AF=0.023,0.058,0.221,0.047,0.128,0.151,0.07,0.07,0.012,0.012;AN=2;DP=7170;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/3:97:99:33,28,19,17 chr1 215409399 . CT C 2443.54 PASS AC=1;AF=0.5;AN=2;DP=195;FS=0;FractionInformativeReads=0.697;MQ=59.86;MQRankSum=-2.741;QD=12.53;ReadPosRankSum=2.435;SOR=0.745;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:60,76:136:99:2481,0,2150:34,26,44,32 chr1 215410106 . G C 2734.7 PASS AC=2;AF=0.774;AN=2;DP=4383;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,109:109:99:3262,326,0:0,0,47,62 chr1 215793834 . G A 2756.05 PASS AC=2;AF=0.732;AN=2;DP=4488;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,107:107:99:3241,321,0:0,0,55,52 chr1 215798014 . G A 14498.8 PASS AC=2;AF=1;AN=2;DP=20723;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,464:465:99:14040,1343,0:0,1,215,249 chr1 215814186 . CAAA CAA,CA,C 82.27 PASS AC=2,0,0;AF=0.583,0.1,0.017;AN=2;DP=495;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant23-variant24-variant29-variant31-variant32-variant33-variant35-variant36-variant39-variant40-variant41-variant44 GT:DP:GQ:SB 1/1:9:27:0,0,2,7 chr1 215848587 . T C 1868.42 PASS AC=2;AF=0.63;AN=2;DP=3274;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant15-variant16-variant22-variant23-variant24-variant26-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,147:147:99:4453,440,0:0,0,67,80 chr1 215848641 . T C 4746.7 PASS AC=2;AF=0.807;AN=2;DP=5820;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,159:159:99:4806,475,0:0,0,78,81 chr1 215853748 . GTT GT,G 966.41 PASS AC=2,0;AF=0.92,0.011;AN=2;DP=2679;MQ=60;set=Intersection GT:DP:GQ:SB 1/1:71:99:1,1,22,47 chr1 215901492 . C T 1892.9 PASS AC=1;AF=0.5;AN=2;DP=1325;MQ=60;set=variant-variant7-variant9-variant18-variant22-variant25-variant30-variant35-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:76,90:166:99:2455,0,1984:36,40,43,47 chr1 215916713 . C CAT,CATAT,CATATAT 34.37 PASS AC=0,0,1;AF=0.667,0.083,0.125;AN=2;DP=129;FS=0;MQ=60;set=variant-variant4-variant6-variant7-variant10-variant14-variant19-variant25-variant33-variant35-variant36-variant38 GT:DP:GQ:SB 0/3:3:10:0,1,0,2 chr1 215931928 . T A 535.63 PASS AC=1;AF=0.5;AN=2;DP=450;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant6-variant9-variant16-variant22-variant25-variant30-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,30:48:99:867,0,474:14,4,21,9 chr1 215956304 . A G 492.05 PASS AC=1;AF=0.653;AN=2;DP=1156;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,19:33:99:537,0,365:4,10,5,14 chr1 215960167 . T G 1381.73 PASS AC=1;AF=0.653;AN=2;DP=3219;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,42:95:99:1083,0,1408:22,31,14,28 chr1 215963374 . G A 353.59 PASS AC=1;AF=0.5;AN=2;DP=180;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant6-variant9-variant16-variant22-variant25-variant30-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,11:15:99:385,0,130:4,0,10,1 chr1 216074312 . G A 556.11 PASS AC=1;AF=0.5;AN=2;DP=144;FractionInformativeReads=1;MQ=60;set=variant23-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:39,26:65:99:570,0,913:18,21,12,14 chr1 216107929 . T C 1374.97 PASS AC=1;AF=0.5;AN=2;DP=250;FractionInformativeReads=1;MQ=60;set=variant15-variant23-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:29,34:63:99:911,0,791:23,6,22,12 chr1 216172380 . A G 681.18 PASS AC=1;AF=0.652;AN=2;DP=1898;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,36:59:99:916,0,500:8,15,15,21 chr1 216246675 . AG A 1141.06 PASS AC=2;AF=0.854;AN=2;DP=1996;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1988,169,0:0,0,15,41 chr1 216258213 . A G 376.91 PASS AC=2;AF=0.588;AN=2;DP=513;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant14-variant16-variant17-variant24-variant25-variant28-variant30-variant35-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,29:30:48:1014,48,0:1,0,6,23 chr1 216270618 . G A 688.73 PASS AC=2;AF=0.588;AN=2;DP=1109;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant14-variant16-variant17-variant24-variant25-variant28-variant30-variant35-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1907,167,0:0,0,14,42 chr1 216347452 . C A 1390.03 PASS AC=1;AF=0.579;AN=2;DP=2565;MQ=60;set=variant-variant4-variant9-variant12-variant13-variant15-variant17-variant19-variant20-variant21-variant22-variant25-variant27-variant31-variant32-variant33-variant34-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:59,58:117:99:1561,0,1479:22,37,23,35 chr1 216347556 . A G 249.51 PASS AC=1;AF=0.579;AN=2;DP=1012;MQ=60;set=variant-variant4-variant9-variant12-variant13-variant15-variant17-variant19-variant20-variant21-variant22-variant25-variant27-variant31-variant32-variant33-variant34-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:31,27:58:99:754,0,794:11,20,9,18 chr1 216348449 . A C 5626.74 PASS AC=1;AF=0.6;AN=2;DP=4473;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant16-variant28-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:208,247:455:99:6547,0,5133:99,109,115,132 chr1 216370108 . C T 1652.79 PASS AC=1;AF=0.605;AN=2;DP=745;MQ=60;set=variant-variant4-variant9-variant12-variant13-variant15-variant17-variant19-variant20-variant21-variant22-variant25-variant27-variant31-variant32-variant33-variant34-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:18,18:36:99:614,0,1012:4,14,6,12 chr1 216370130 . T G 916.77 PASS AC=1;AF=0.817;AN=2;DP=1067;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,12:25:99:465,0,849:4,9,4,8 chr1 216371934 . A C 1078.28 PASS AC=1;AF=0.605;AN=2;DP=500;set=variant-variant4-variant9-variant12-variant13-variant15-variant17-variant19-variant20-variant21-variant22-variant25-variant27-variant31-variant32-variant33-variant34-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:8,16:24:99:520,0,229:1,7,3,13 chr1 216495191 . T G 955.78 PASS AC=1;AF=0.619;AN=2;DP=1265;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant6-variant9-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:24,26:50:99:755,0,705:19,5,21,5 chr1 216495400 . A G 1068.79 PASS AC=1;AF=0.619;AN=2;DP=2228;MQ=60;set=variant-variant4-variant6-variant9-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:56,59:115:99:1586,0,1457:17,39,21,38 chr1 216496947 . G A 2968.78 PASS AC=1;AF=0.619;AN=2;DP=5112;MQ=60;set=variant-variant4-variant6-variant9-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:110,118:228:99:2872,0,2911:57,53,61,57 chr1 216500830 . G C 496.25 PASS AC=1;AF=0.679;AN=2;DP=672;MQ=60;set=variant-variant4-variant6-variant9-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,6:12:99:186,0,140:4,2,4,2 chr1 216592003 . T C 1154.33 PASS AC=1;AF=0.686;AN=2;DP=3249;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,68:119:99:1689,0,1094:24,27,34,34 chr1 216595306 . C T 727.26 PASS AC=1;AF=0.689;AN=2;DP=3808;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,52:110:99:1165,0,1531:32,26,26,26 chr1 216677350 . C T 5071.99 PASS AC=2;AF=0.943;AN=2;DP=13628;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,324:324:99:10188,971,0:0,0,144,180 chr1 216679643 . A G 394.14 PASS AC=2;AF=0.943;AN=2;DP=1917;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1338,117,0:0,0,11,28 chr1 216679858 . A AT 100.7 PASS AC=1;AF=0.611;AN=2;DP=734;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant16-variant17-variant18-variant19-variant23-variant25-variant26-variant27-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:14,13:27:99:269,0,321:9,5,8,5 chr1 216692669 . C T 4278.34 PASS AC=1;AF=0.661;AN=2;DP=4428;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant16-variant17-variant18-variant19-variant23-variant25-variant26-variant27-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:95,75:170:99:1730,0,2441:52,43,45,30 chr1 216741314 . C T 1341.08 PASS AC=1;AF=0.594;AN=2;DP=2280;MQ=60;set=variant-variant4-variant6-variant8-variant9-variant12-variant13-variant15-variant16-variant17-variant18-variant27-variant35-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:62,72:134:99:1795,0,1531:33,29,38,34 chr1 216824505 . C G 468.92 PASS AC=1;AF=0.625;AN=2;DP=611;MQ=60;set=variant3-variant4-variant7-variant10-variant11-variant12-variant14-variant16-variant21-variant22-variant23-variant27-variant28-variant29-variant34-variant35-variant36-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,16:29:99:424,0,437:1,12,6,10 chr1 216880662 . G A 1785.78 PASS AC=1;AF=0.615;AN=2;DP=1659;FractionInformativeReads=1;MQ=60;set=variant3-variant10-variant20-variant24-variant25-variant26-variant30-variant31-variant35-variant36-variant37-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:73,47:120:99:1292,0,2275:56,17,37,10 chr1 217038529 . CAAAAAAAAAAAA C,CAAA,CAAAAA,CAA,CAAAAAAAA,CA 262.22 PASS AC=0,0,0,1,0,0;AF=0.182,0.091,0.045,0.182,0.091,0.045;AN=2;DP=337;set=variant4-variant17-variant20-variant22-variant29-filterInvariant32-variant35-variant39-filterInvariant40-variant43-variant44 GT:DP:GQ:SB 0/4:7:99:0,4,1,2 chr1 217113059 . GAA GA,G 1986.66 PASS AC=1,0;AF=0.75,0.045;AN=2;DP=5420;set=Intersection GT:DP:GQ:SB 0/1:96:99:16,36,13,31 chr1 217311068 . C T 1768.13 PASS AC=1;AF=0.6;AN=2;DP=585;MQ=60;set=variant2-variant7-variant10-variant15-variant22-variant29-variant35-variant36-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:32,44:76:99:1117,0,698:15,17,16,28 chr1 217600228 . G A 419.26 PASS AC=1;AF=0.629;AN=2;DP=730;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,7:18:99:231,0,431:11,0,7,0 chr1 217600728 . C G 732.58 PASS AC=1;AF=0.589;AN=2;DP=2588;set=variant-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant23-variant25-variant26-variant27-variant28-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:53,48:101:99:1401,0,1506:21,32,15,33 chr1 217600781 . C A 289.93 PASS AC=1;AF=0.629;AN=2;DP=1980;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:26,24:50:99:720,0,772:10,16,8,16 chr1 217600860 . A G 330.22 PASS AC=1;AF=0.589;AN=2;DP=1269;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant23-variant25-variant26-variant27-variant28-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:18,19:37:99:517,0,487:7,11,11,8 chr1 217600946 . T TA 282.56 PASS AC=1;AF=0.589;AN=2;DP=1260;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant23-variant25-variant26-variant27-variant28-variant34-variant35-variant36-variant37-variant38-filterInvariant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:7,28:35:96:698,0,96:4,3,13,15 chr1 217602867 . C T 280.55 PASS AC=1;AF=0.589;AN=2;DP=619;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant23-variant25-variant26-variant27-variant28-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:17,17:34:99:439,0,424:7,10,7,10 chr1 217603167 . CAAAAAAAAAAAA CAAAAAAAAA,CAAAAAAAA,CAAAAAAAAAAA,CAAAAAAAAAA,C,CAAAAAAAAAAAAA 228.73 PASS AC=0,0,0,0,1,0;AF=0.091,0.061,0.167,0.152,0.045,0.015;AN=2;DP=1385;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-filterInvariant12-variant15-filterInvariant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant29-variant31-filterInvariant32-variant33-variant34-variant35-variant37-variant39-filterInvariant40-variant41-variant42-variant43 GT:DP:GQ:SB 0/5:68:99:21,9,24,14 chr1 217603318 . CATA C 2884.96 PASS AC=1;AF=0.629;AN=2;DP=5389;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:83,72:155:99:2731,0,3406:45,38,38,34 chr1 217603507 . A C,G 3836.45 PASS AC=0,1;AF=0.536,0.054;AN=2;DP=5653;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant23-variant25-variant26-variant27-variant28-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:DP:GQ:SB 0/2:204:99:52,63,36,53 chr1 217603508 . CT C 2058.43 PASS AC=1;AF=0.5;AN=2;DP=559;MQ=60;set=variant6-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:115,84:199:99:3342,0,5369:52,63,35,49 chr1 217603510 . T C 2070.48 PASS AC=1;AF=0.5;AN=2;DP=554;MQ=60;set=variant6-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:115,84:199:99:3181,0,5354:52,63,35,49 chr1 217603539 . T C 1945.22 PASS AC=1;AF=0.629;AN=2;DP=6067;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:89,64:153:99:1758,0,2264:38,51,26,38 chr1 217603706 . C A 661.6 PASS AC=1;AF=0.5;AN=2;DP=199;FractionInformativeReads=1;MQ=60;set=variant6-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:40,28:68:99:828,0,1273:25,15,13,15 chr1 217603847 . C T 4843.31 PASS AC=1;AF=0.589;AN=2;DP=10211;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant23-variant25-variant26-variant27-variant28-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:190,178:368:99:4359,0,4743:108,82,109,69 chr1 217604124 . T C 892.95 PASS AC=1;AF=0.643;AN=2;DP=2537;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:44,32:76:99:1030,0,1354:20,24,15,17 chr1 217604777 . G A 484.14 PASS AC=1;AF=0.589;AN=2;DP=1258;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant23-variant25-variant26-variant27-variant28-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:18,22:40:99:642,0,504:4,14,5,17 chr1 217671524 . A G 202.63 PASS AC=1;AF=0.5;AN=2;DP=17;FS=0;FractionInformativeReads=1;MQ=60;set=variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:7,6:13:99:231,0,568:7,0,6,0 chr1 217671532 . C T 202.63 PASS AC=1;AF=0.5;AN=2;DP=18;FS=0;FractionInformativeReads=1;MQ=60;set=variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:7,6:13:99:231,0,568:7,0,6,0 chr1 217781558 . GA G 928.27 PASS AC=1;AF=0.556;AN=2;DP=2766;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant33-variant35-variant36-variant37-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:53,44:97:99:963,0,1187:40,13,30,14 chr1 217782273 . T C 4691.56 PASS AC=2;AF=0.703;AN=2;DP=12452;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,288:288:99:8675,862,0:0,0,117,171 chr1 217782714 . A C 2168.22 PASS AC=1;AF=0.5;AN=2;DP=1190;MQ=60;set=variant28-variant31-variant35-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:125,125:250:99:3227,0,2943:61,64,55,70 chr1 217782894 . A AG 4400.87 PASS AC=1;AF=0.583;AN=2;DP=5246;MQ=60;set=variant2-variant4-variant5-variant16-variant17-variant24-variant25-variant28-variant31-variant32-variant34-variant35-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:123,145:268:99:5051,0,4157:68,55,78,67 chr1 217783810 . C T 593.83 PASS AC=1;AF=0.556;AN=2;DP=1752;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant33-variant35-variant36-variant37-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:39,20:59:99:452,0,1009:18,21,7,13 chr1 217787730 . T G 49.73 PASS AC=1;AF=0.6;AN=2;DP=29;FS=0;FractionInformativeReads=1;MQ=60;set=variant28-variant31-variant35-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,5:9:99:198,0,148:0,4,1,4 chr1 217793938 . T TTAA 60.83 PASS AC=1;AF=0.656;AN=2;DP=204;MQ=60;set=variant2-variant4-variant5-variant16-variant17-variant24-variant25-variant28-variant31-variant32-variant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,3:7:99:114,0,147:1,3,0,3 chr1 217804325 . G A 2118.76 PASS AC=2;AF=0.703;AN=2;DP=7529;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,264:264:99:7670,789,0:0,0,128,136 chr1 217804635 . T C 1249.29 PASS AC=1;AF=0.556;AN=2;DP=3300;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant33-variant35-variant36-variant37-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:69,45:114:99:1020,0,1749:42,27,25,20 chr1 217804955 . T C 426.83 PASS AC=1;AF=0.556;AN=2;DP=642;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant33-variant35-variant36-variant37-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:8,4:12:99:144,0,246:2,6,0,4 chr1 217842129 . A G 1065.98 PASS AC=1;AF=0.611;AN=2;DP=1320;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant17-variant20-variant24-variant25-variant28-variant31-variant32-variant34-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,39:75:99:1002,0,891:21,15,24,15 chr1 217842575 . C A 496.98 PASS AC=1;AF=0.5;AN=2;DP=211;FractionInformativeReads=1;MQ=60;set=variant28-variant31-variant35-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:17,24:41:99:653,0,521:4,13,7,17 chr1 217856787 . A AT 710.85 PASS AC=1;AF=0.632;AN=2;DP=1090;MQ=60;set=variant-variant3-variant4-variant7-variant12-variant13-variant15-variant18-variant19-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant33-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:25,31:56:99:762,0,596:8,17,14,17 chr1 217856803 . T C 569.52 PASS AC=1;AF=0.611;AN=2;DP=669;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant17-variant20-variant24-variant25-variant28-variant31-variant32-variant34-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,20:44:99:478,0,536:10,14,7,13 chr1 217915593 . G A 285.9 PASS AC=1;AF=0.652;AN=2;DP=723;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,4:10:99:122,0,202:1,5,0,4 chr1 217947738 . G A 2329.71 PASS AC=2;AF=0.825;AN=2;DP=3059;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,86:86:99:2490,257,0:0,0,53,33 chr1 217955355 . ATAT A 112.63 PASS AC=1;AF=0.641;AN=2;DP=650;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,7:15:99:270,0,355:7,1,6,1 chr1 217974998 . A T 512.11 PASS AC=1;AF=0.5;AN=2;DP=79;FractionInformativeReads=1;MQ=60;set=variant29-variant32-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:12,11:23:99:225,0,354:9,3,7,4 chr1 218458551 . T C 121.67 PASS AC=1;AF=0.611;AN=2;DP=396;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant9-variant10-variant11-variant18-variant19-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,6:19:99:247,0,916:9,4,5,1 chr1 218458557 . AG A 403.77 PASS AC=1;AF=0.591;AN=2;DP=362;MQ=60;set=variant2-variant5-variant8-variant9-variant11-variant18-variant19-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:15,8:23:99:272,0,988:10,5,7,1 chr1 218506210 . GAA GA,GAAA,G 189.14 PASS AC=1,0,0;AF=0.111,0.375,0.014;AN=2;DP=4710;set=filterInvariant-variant2-variant3-filterInvariant5-filterInvariant6-variant7-filterInvariant8-filterInvariant9-filterInvariant11-filterInvariant13-variant15-filterInvariant16-filterInvariant17-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-variant24-filterInvariant25-filterInvariant26-filterInvariant27-variant28-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant39-filterInvariant40-variant41-filterInvariant42-filterInvariant44 GT:DP:GQ:SB 0/1:108:99:48,36,14,10 chr1 218509591 . AAC AACAC,A 2057.36 PASS AC=0,1;AF=0.192,0.308;AN=2;DP=3018;MQ=60;set=variant-filterInvariant5-variant6-filterInvariant9-variant19-filterInvariant20-filterInvariant22-filterInvariant26-filterInvariant29-filterInvariant35-variant36-variant41-filterInvariant44 GT:DP:GQ:SB 0/2:225:99:114,88,11,12 chr1 218511041 . A C 4146.42 PASS AC=1;AF=0.591;AN=2;DP=2329;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant8-variant9-variant11-variant18-variant19-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:52,62:114:99:1775,0,1450:33,19,33,29 chr1 218519928 . A AAAAC 6874.33 PASS AC=1;AF=0.6;AN=2;DP=6171;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant19-variant22-variant25-variant28-variant32-variant35-variant36-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:116,133:249:99:5225,0,5395:61,55,68,65 chr1 218578685 . T TTTG,TTTGTTGTTG,TTTGTTG 497.15 PASS AC=0,0,1;AF=0.188,0.063,0.25;AN=2;DP=588;set=variant4-variant5-variant12-variant20-variant23-variant31-variant35-variant36 GT:DP:GQ:SB 0/3:45:99:4,16,5,20 chr1 218610662 . CTT CT,C 950.17 PASS AC=1,0;AF=0.511,0.023;AN=2;DP=2780;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-filterInvariant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-filterInvariant28-variant29-variant30-variant31-variant32-filterInvariant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:55:99:13,12,18,12 chr1 218614905 . A T 10304.8 PASS AC=1;AF=0.609;AN=2;DP=7259;MQ=60;set=variant-variant2-variant4-variant9-variant10-variant12-variant13-variant17-variant20-variant24-variant25-variant26-variant27-variant29-variant31-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:142,175:317:99:4500,0,3697:55,87,67,108 chr1 218615451 . A C 7681.89 PASS AC=1;AF=0.609;AN=2;DP=4755;MQ=60;set=variant-variant2-variant4-variant9-variant10-variant12-variant13-variant17-variant20-variant24-variant25-variant26-variant27-variant29-variant31-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:138,91:229:99:2230,0,3449:64,74,46,45 chr1 218616014 . C T 8217.71 PASS AC=1;AF=0.543;AN=2;DP=10356;set=variant-variant2-variant4-variant9-variant10-variant12-variant13-variant17-variant20-variant24-variant25-variant26-variant27-variant29-variant31-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:221,216:437:99:8182,0,11416:106,115,101,115 chr1 218616019 . T G 8089.18 PASS AC=1;AF=0.5;AN=2;DP=432;FS=0.522;FractionInformativeReads=1;MQ=60;MQRankSum=3.214;QD=18.72;ReadPosRankSum=0.528;SOR=0.642;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:218,214:432:99:8117,0,11456:101,117,102,112 chr1 218616328 . T A 4256.25 PASS AC=1;AF=0.5;AN=2;DP=2551;MQ=60;set=variant-variant10-variant12-variant20-variant31-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:168,155:323:99:3884,0,4096:96,72,92,63 chr1 218617051 . GTTT GTT,GT,GTTTT,G 3025.88 PASS AC=1,0,0,0;AF=0.081,0.339,0.177,0.016;AN=2;DP=3717;set=variant-variant2-variant4-variant6-filterInvariant7-variant9-variant10-variant12-variant13-variant17-variant18-variant20-variant22-filterInvariant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:DP:GQ:SB 0/1:89:99:31,22,23,13 chr1 218617135 . C G 7169.57 PASS AC=1;AF=0.609;AN=2;DP=5737;set=variant-variant2-variant4-variant9-variant10-variant12-variant13-variant17-variant20-variant24-variant25-variant26-variant27-variant29-variant31-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:102,81:183:99:2079,0,2764:55,47,49,32 chr1 218617543 . G A 813.98 PASS AC=1;AF=0.609;AN=2;DP=1003;MQ=60;set=variant-variant2-variant4-variant9-variant10-variant12-variant13-variant17-variant20-variant24-variant25-variant26-variant27-variant29-variant31-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:20,27:47:99:716,0,585:5,15,11,16 chr1 218617900 . C T 564.51 PASS AC=1;AF=0.609;AN=2;DP=604;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant9-variant10-variant12-variant13-variant17-variant20-variant24-variant25-variant26-variant27-variant29-variant31-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:14,12:26:99:317,0,402:7,7,4,8 chr1 218683417 . CT CTTT,CTT,C 1108.05 PASS AC=0,1,0;AF=0.036,0.464,0.071;AN=2;DP=828;MQ=60;set=variant-filterInvariant9-variant10-variant12-filterInvariant13-filterInvariant19-variant20-variant24-variant31-variant34-variant35-variant36-variant37-variant41 GT:DP:GQ:SB 0/2:49:99:7,11,17,14 chr1 218683528 . A G 958.53 PASS AC=1;AF=0.556;AN=2;DP=236;FractionInformativeReads=1;MQ=60;set=variant-variant12-variant20-variant24-variant31-variant34-variant35-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:10,17:27:99:673,0,527:3,7,6,11 chr1 218683536 . A G 916.77 PASS AC=1;AF=0.556;AN=2;DP=222;FractionInformativeReads=1;MQ=60;set=variant-variant12-variant20-variant24-variant31-variant34-variant35-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:9,17:26:99:676,0,493:3,6,6,11 chr1 218698728 . G A 3204.75 PASS AC=1;AF=0.55;AN=2;DP=832;FractionInformativeReads=1;MQ=60;set=variant-variant12-variant20-variant24-variant31-variant34-variant35-variant36-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:51,43:94:99:1053,0,1301:32,19,29,14 chr1 218699059 . TA T,TAA 237 PASS AC=1,0;AF=0.347,0.153;AN=2;DP=2967;set=variant-variant3-filterInvariant4-filterInvariant5-filterInvariant7-filterInvariant8-filterInvariant10-variant11-filterInvariant13-variant14-variant15-variant16-filterInvariant17-variant19-variant20-filterInvariant21-filterInvariant22-filterInvariant23-variant24-variant25-filterInvariant27-variant28-filterInvariant29-variant30-filterInvariant31-variant32-variant33-variant34-filterInvariant35-variant37-filterInvariant39-variant40-variant41-filterInvariant42-variant43-variant44 GT:DP:GQ:SB 0/1:63:87:36,15,8,4 chr1 219366400 . T TG,TGGG,TGG 250.22 PASS AC=2,0,0;AF=0.807,0.011,0.034;AN=2;DP=2307;set=Intersection GT:DP:GQ:SB 1/1:64:99:0,1,44,19 chr1 219383848 . A ACTTTTT 1212.07 PASS AC=2;AF=1;AN=2;DP=1368;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,26:26:93:1366,93,0:0,0,16,10 chr1 219383867 . T C 1350.32 PASS AC=2;AF=1;AN=2;DP=2134;FS=0;MQ=60;MQRankSum=-1.659;ReadPosRankSum=0.258;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1514,153,0:0,0,30,21 chr1 219383905 . A G 1854.71 PASS AC=2;AF=1;AN=2;DP=2926;FS=0;MQ=60;MQRankSum=1.684;ReadPosRankSum=1.444;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,74:74:99:2050,221,0:0,0,41,33 chr1 219706327 . A G 1208.24 PASS AC=1;AF=0.611;AN=2;DP=1887;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant11-variant12-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant30-variant32-variant33-variant35-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,38:63:99:1017,0,648:17,8,23,15 chr1 219706428 . T C 1987.86 PASS AC=1;AF=0.691;AN=2;DP=6911;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:108,98:206:99:2215,0,2761:61,47,57,41 chr1 219783279 . T A 2241.14 PASS AC=1;AF=0.636;AN=2;DP=8400;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:99,122:221:99:2766,0,2054:46,53,42,80 chr1 220101008 . A C 546.57 PASS AC=2;AF=0.684;AN=2;DP=303;set=variant3-variant4-variant10-variant11-variant13-variant15-variant17-variant19-variant20-variant22-filterInvariant27-variant31-variant35-variant36-variant37-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,8:9:14:372,14,0:1,0,7,1 chr1 220101029 . A AC,AAAC,AAAAC,AAC 1445.73 PASS AC=2,0,0,0;AF=0.333,0.125,0.125,0.083;AN=2;DP=696;set=variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant15-variant17-variant19-variant20-variant22-variant26-variant28-variant29-variant31-variant32-variant35-variant38-variant40-variant41-variant44 GT:DP:GQ:SB 1/1:20:63:0,0,18,2 chr1 220141851 . T G 164.91 PASS AC=1;AF=0.66;AN=2;DP=391;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant7-variant8-variant10-variant11-variant13-variant14-variant16-variant18-variant19-variant21-variant22-variant24-variant26-variant27-variant29-variant32-variant34-variant35-variant36-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,10:22:99:300,0,390:10,2,9,1 chr1 220142023 . C T 794.25 PASS AC=1;AF=0.654;AN=2;DP=2873;MQ=60;set=variant2-variant4-variant7-variant8-variant10-variant11-variant13-variant14-variant16-variant18-variant19-variant21-variant22-variant24-variant26-variant27-variant29-variant32-variant34-variant35-variant36-variant37-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,48:97:99:1269,0,1231:24,25,23,25 chr1 220142070 . C T 1119.11 PASS AC=1;AF=0.654;AN=2;DP=3449;MQ=60;set=variant2-variant4-variant7-variant8-variant10-variant11-variant13-variant14-variant16-variant18-variant19-variant21-variant22-variant24-variant26-variant27-variant29-variant32-variant34-variant35-variant36-variant37-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:62,61:123:99:1484,0,1598:31,31,29,32 chr1 220145371 . T G 445.5 PASS AC=2;AF=0.86;AN=2;DP=907;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:810,81,0:0,0,18,9 chr1 220145584 . C T 352.49 PASS AC=1;AF=0.66;AN=2;DP=842;MQ=60;set=variant2-variant4-variant7-variant8-variant10-variant11-variant13-variant14-variant16-variant18-variant19-variant22-variant24-variant26-variant27-variant29-variant32-variant34-variant35-variant36-variant37-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,21:45:99:421,0,610:9,15,8,13 chr1 220145655 . C T 81.18 PASS AC=1;AF=0.674;AN=2;DP=325;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant8-variant10-variant11-variant13-variant16-variant18-variant19-variant21-variant24-variant26-variant27-variant29-variant32-variant34-variant35-variant36-variant37-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,12:22:99:377,0,251:3,7,2,10 chr1 220151808 . C CAA 127.68 PASS AC=1;AF=0.667;AN=2;DP=228;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant7-variant10-variant11-variant13-variant14-variant16-variant18-variant19-variant21-variant22-variant24-variant26-variant27-variant29-variant32-variant34-variant35-variant36-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,4:5:22:165,0,22:1,0,4,0 chr1 220153332 . T TAA 882.2 PASS AC=2;AF=0.841;AN=2;DP=1699;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,25:25:78:1160,78,0:0,0,20,5 chr1 220153403 . G A 863.24 PASS AC=1;AF=0.5;AN=2;DP=137;FractionInformativeReads=1;MQ=60;set=variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:31,32:63:99:820,0,721:17,14,18,14 chr1 220154246 . AT A 92.28 PASS AC=2;AF=0.807;AN=2;DP=1368;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-filterInvariant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,39:41:69:1014,69,0:1,1,12,27 chr1 220154306 . A C 66.47 PASS AC=1;AF=0.7;AN=2;DP=191;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant8-variant10-variant11-variant13-variant14-variant16-variant18-variant19-variant24-variant26-variant29-variant32-variant34-variant35-variant37-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,2:8:63:63,0,246:0,6,0,2 chr1 220154659 . TAAA T 315.43 PASS AC=2;AF=0.841;AN=2;DP=984;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:469,33,0:0,0,8,3 chr1 220154768 . C T 816.15 PASS AC=1;AF=0.645;AN=2;DP=3023;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant12-variant13-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,51:100:99:1130,0,1021:26,23,26,25 chr1 220156090 . T C 1265.3 PASS AC=2;AF=0.841;AN=2;DP=5276;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,128:128:99:3732,384,0:0,0,72,56 chr1 220156427 . T C 31.3 PASS AC=1;AF=0.68;AN=2;DP=216;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant7-variant8-variant10-variant11-variant13-variant14-variant18-variant19-variant21-variant22-variant24-variant26-variant27-variant29-variant32-variant34-variant35-variant36-variant37-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,3:4:34:123,0,34:1,0,3,0 chr1 220156704 . T C 1127.97 PASS AC=1;AF=0.5;AN=2;DP=565;FractionInformativeReads=1;MQ=60;set=variant-variant16-variant17-variant23-variant28-variant31-variant33-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:38,23:61:99:844,0,1830:14,24,9,14 chr1 220156729 . C T 1005.23 PASS AC=1;AF=0.55;AN=2;DP=502;FractionInformativeReads=1;MQ=60;set=variant-variant16-variant17-variant23-variant28-variant31-variant33-variant35-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:31,19:50:99:704,0,1638:12,19,6,13 chr1 220160360 . A G 672.02 PASS AC=2;AF=0.726;AN=2;DP=976;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:763,63,0:0,0,18,3 chr1 220160433 . A G 1226.52 PASS AC=2;AF=0.841;AN=2;DP=3256;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:2499,237,0:0,0,50,29 chr1 220162004 . C T 1134.84 PASS AC=1;AF=0.5;AN=2;DP=254;FractionInformativeReads=1;MQ=60;set=variant33-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:48,37:85:99:822,0,1226:27,21,17,20 chr1 220162195 . T C 380.31 PASS AC=2;AF=0.732;AN=2;DP=732;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:571,51,0:0,0,4,13 chr1 220170238 . C T 679.91 PASS AC=1;AF=0.5;AN=2;DP=147;FractionInformativeReads=1;MQ=60;set=variant33-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:29,20:49:99:602,0,835:20,9,17,3 chr1 220178717 . T TA 726.93 PASS AC=2;AF=0.841;AN=2;DP=2450;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:1611,144,0:0,0,23,25 chr1 220179322 . A T 162.92 PASS AC=2;AF=0.851;AN=2;DP=317;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant24-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:169,15,0:0,0,4,1 chr1 220184150 . CA C,CAAA 325.06 PASS AC=1,0;AF=0.733,0.012;AN=2;DP=752;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:16:99:7,0,9,0 chr1 220184164 . A G,AG 672.36 PASS AC=1,1;AF=0.69,0.103;AN=2;DP=644;set=variant18-variant20-variant21-variant22-variant23-variant2-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant3-variant33-variant34-variant4-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant5-variant43-variant44 GT:DP:GQ:SB 1/2:15:99:0,0,15,0 chr1 220191932 . GA GAA,GAAA,G 103.03 PASS AC=2,0,0;AF=0.679,0.06,0.012;AN=2;DP=1124;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:19:58:0,0,6,13 chr1 220192171 . T TAAA,TAA 87.37 PASS AC=0,2;AF=0.662,0.162;AN=2;DP=232;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 2/2:4:15:0,0,4,0 chr1 220192192 . TAA TA,T 76.23 PASS AC=1,0;AF=0.676,0.054;AN=2;DP=597;set=variant-variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:DP:GQ:SB 0/1:6:7:1,0,4,1 chr1 220192495 . C G 1047.96 PASS AC=2;AF=0.841;AN=2;DP=1904;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:1629,144,0:0,0,11,37 chr1 220197545 . C T 637.19 PASS AC=2;AF=0.807;AN=2;DP=1047;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:944,69,0:0,0,19,4 chr1 220197625 . G T 1495.18 PASS AC=2;AF=0.841;AN=2;DP=4207;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,121:121:99:3485,362,0:0,0,69,52 chr1 220205714 . G GA 615.5 PASS AC=1;AF=0.5;AN=2;DP=150;MQ=60;set=variant33-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:21,16:37:99:369,0,526:13,8,11,5 chr1 220205943 . G A 253.59 PASS AC=2;AF=0.807;AN=2;DP=772;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:663,51,0:0,0,2,15 chr1 220205980 . A C 118.65 PASS AC=2;AF=0.814;AN=2;DP=397;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:364,27,0:0,0,1,8 chr1 220207017 . C T 702.66 PASS AC=2;AF=0.841;AN=2;DP=2295;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1171,114,0:0,0,15,23 chr1 220208154 . C A 402.22 PASS AC=2;AF=0.807;AN=2;DP=1974;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:857,75,0:0,0,19,6 chr1 220231180 . CT C 579.8 PASS AC=1;AF=0.595;AN=2;DP=1116;MQ=60;set=variant-variant3-variant4-variant7-variant8-variant10-variant11-variant16-variant18-variant19-variant20-variant22-variant24-variant26-variant27-variant29-variant34-variant35-variant37-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,20:42:99:683,0,760:9,13,9,11 chr1 220231447 . G A 1419.25 PASS AC=2;AF=0.909;AN=2;DP=1906;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1535,129,0:0,0,34,9 chr1 220231876 . G T 310.86 PASS AC=1;AF=0.5;AN=2;DP=124;FS=1.917;FractionInformativeReads=0.847;MQ=60;MQRankSum=-0.545;QD=2.51;ReadPosRankSum=0.275;SOR=1.019;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:80,25:105:99:339,0,1702:35,45,9,16 chr1 220239448 . T C 2566.75 PASS AC=1;AF=0.881;AN=2;DP=3560;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,49:92:99:1236,0,1051:15,28,17,32 chr1 220284112 . GT GTT,G 351.72 PASS AC=0,1;AF=0.1,0.4;AN=2;DP=257;MQ=60;set=variant2-variant33-variant35-variant39-variant41 GT:DP:GQ:SB 0/2:55:99:12,5,27,11 chr1 220298664 . A G 2311.23 PASS AC=1;AF=0.5;AN=2;DP=633;FractionInformativeReads=1;MQ=60;set=variant33-variant35-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:82,86:168:99:2173,0,2006:29,53,37,49 chr1 220322898 . A ATGT 4990.44 PASS AC=1;AF=0.5;AN=2;DP=2149;MQ=60;set=variant3-variant4-variant11-variant18-variant19-variant20-variant22-variant24-variant27-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:102,96:198:99:3655,0,4751:47,55,47,49 chr1 220323089 . C A 2958.28 PASS AC=1;AF=0.5;AN=2;DP=851;MQ=60;set=variant33-variant35-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:137,55:192:99:1367,0,3760:76,61,30,25 chr1 220323448 . CTT CT,C,CTTT 1489.64 PASS AC=1,0,0;AF=0.5,0.058,0.012;AN=2;DP=6726;set=variant-variant2-filterInvariant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-filterInvariant11-variant12-variant13-variant14-variant15-filterInvariant16-variant17-variant18-filterInvariant19-variant20-variant21-variant22-variant23-variant24-variant25-filterInvariant26-filterInvariant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-filterInvariant37-variant38-variant39-variant40-variant41-filterInvariant42-variant43-variant44 GT:DP:GQ:SB 0/1:119:99:16,34,18,51 chr1 220327444 . AG A 369.52 PASS AC=1;AF=0.5;AN=2;DP=167;MQ=60;set=variant33-variant35-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:16,21:37:99:561,0,399:6,10,7,14 chr1 220332552 . C T 305.58 PASS AC=1;AF=0.586;AN=2;DP=602;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant14-variant15-variant17-variant18-variant20-variant22-variant24-variant25-variant28-variant29-variant31-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,11:14:25:339,0,25:2,1,10,1 chr1 220332835 . T TA 151.45 PASS AC=1;AF=0.667;AN=2;DP=41;MQ=60;set=variant33-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:3,9:12:60:250,0,60:0,3,0,9 chr1 220332876 . G A 61.77 PASS AC=1;AF=0.667;AN=2;DP=89;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant12-variant13-variant14-variant15-variant17-variant22-variant24-variant25-variant33-variant35-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,5:8:99:181,0,113:0,3,0,5 chr1 220345860 . C T 277.55 PASS AC=1;AF=0.5;AN=2;DP=108;FractionInformativeReads=1;MQ=60;set=variant33-variant35-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:11,16:27:99:506,0,319:9,2,13,3 chr1 220375788 . C T 317.6 PASS AC=1;AF=0.5;AN=2;DP=66;FractionInformativeReads=1;MQ=60;set=variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:20,24:44:99:698,0,523:7,13,7,17 chr1 220406291 . A G 884.49 PASS AC=1;AF=0.643;AN=2;DP=865;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant17-variant20-variant22-variant24-variant25-variant28-variant29-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,16:23:99:467,0,243:0,7,6,10 chr1 220603310 . TGTGA T 948.83 PASS AC=1;AF=0.795;AN=2;DP=2013;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:4,29:33:42:868,0,42:2,2,22,7 chr1 220603324 . A G 1058.62 PASS AC=2;AF=0.692;AN=2;DP=684;set=variant6-variant11-variant14-variant15-variant16-variant17-variant20-variant31-variant34-variant35-variant36-variant37-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1151,100,0:0,0,24,9 chr1 220607685 . G A 1654.53 PASS AC=2;AF=0.943;AN=2;DP=3396;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:2115,195,0:0,0,24,41 chr1 220607891 . A G 1047.69 PASS AC=2;AF=0.977;AN=2;DP=1979;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1346,111,0:0,0,26,11 chr1 220608142 . C T 1244.28 PASS AC=2;AF=0.692;AN=2;DP=506;MQ=60;set=variant6-variant11-variant14-variant15-variant16-variant17-variant20-variant31-variant34-variant35-variant36-variant37-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1162,102,0:0,0,8,26 chr1 220789236 . C T 1848.96 PASS AC=2;AF=1;AN=2;DP=2840;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:2113,228,0:0,0,33,43 chr1 220789355 . AT A 145.99 PASS AC=2;AF=0.684;AN=2;DP=506;MQ=60;set=variant2-variant4-variant6-variant8-variant11-variant14-variant15-variant20-variant21-variant22-variant24-variant26-variant34-variant35-variant36-variant37-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:990,78,0:0,0,7,19 chr1 220789362 . T A 226.77 PASS AC=2;AF=0.949;AN=2;DP=860;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,18:20:4:449,4,0:0,2,5,13 chr1 220808666 . CTTT CTT,CT,C 258.57 PASS AC=0,1,0;AF=0.317,0.183,0.017;AN=2;DP=786;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant15-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:DP:GQ:SB 0/2:24:99:5,4,9,6 chr1 220863423 . A G 1091.09 PASS AC=2;AF=0.714;AN=2;DP=647;MQ=60;set=variant8-variant20-variant26-variant35-variant36-variant38-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,86:87:99:2786,234,0:1,0,43,43 chr1 220871123 . A G 802.26 PASS AC=2;AF=0.647;AN=2;DP=1077;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant9-variant11-variant14-variant20-variant26-variant32-variant35-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:2278,225,0:0,0,39,36 chr1 220871320 . T C 736.81 PASS AC=2;AF=0.647;AN=2;DP=1456;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant9-variant11-variant14-variant20-variant26-variant32-variant35-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,91:91:99:2754,273,0:0,0,46,45 chr1 220921945 . G C 1058.67 PASS AC=2;AF=0.714;AN=2;DP=403;FractionInformativeReads=1;set=variant8-variant20-variant26-variant35-variant38-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:2105,168,0:0,0,42,14 chr1 220927771 . C T 780.96 PASS AC=2;AF=0.714;AN=2;DP=375;MQ=60;set=variant8-variant20-variant26-variant35-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,63:64:99:1957,145,0:0,1,19,44 chr1 220934802 . A C 130.7 PASS AC=2;AF=0.75;AN=2;DP=44;FS=0;FractionInformativeReads=1;MQ=60;set=variant8-variant20-variant26-variant35-variant38-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:270,18,0:0,0,5,1 chr1 220935081 . G A 1249.06 PASS AC=2;AF=0.714;AN=2;DP=704;FractionInformativeReads=1;MQ=60;set=variant8-variant20-variant26-variant35-variant38-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,123:124:99:3645,361,0:0,1,60,63 chr1 220970028 . A G 1535.21 PASS AC=2;AF=0.763;AN=2;DP=3418;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,92:93:99:2864,243,0:1,0,45,47 chr1 220986516 . C T,G 543.46 PASS AC=2,0;AF=0.3,0.429;AN=2;DP=1213;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:34:99:0,0,29,5 chr1 220986546 . G A 967.65 PASS AC=2;AF=0.625;AN=2;DP=1024;MQ=60;set=variant-variant3-variant4-variant7-variant8-variant17-variant23-variant25-variant26-variant27-variant29-variant31-variant35-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,66:66:99:2311,198,0:0,0,48,18 chr1 220987155 . A G 1650.04 PASS AC=2;AF=0.85;AN=2;DP=2386;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,67:67:99:2267,201,0:0,0,30,37 chr1 221051713 . C G 775.97 PASS AC=1;AF=0.536;AN=2;DP=700;MQ=60;set=variant9-variant11-variant12-variant13-variant18-variant23-variant25-variant30-variant33-variant34-variant35-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,8:31:99:177,0,629:13,10,6,2 chr1 221052101 . T G 1811.83 PASS AC=2;AF=0.966;AN=2;DP=2636;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,78:78:99:2418,234,0:0,0,40,38 chr1 221052640 . T C 1032.56 PASS AC=2;AF=0.795;AN=2;DP=1353;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1603,132,0:0,0,32,12 chr1 221052765 . A G 922.64 PASS AC=1;AF=0.625;AN=2;DP=2124;set=variant-variant2-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant16-variant18-variant19-variant20-variant23-variant24-variant25-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,60:107:99:1519,0,1579:21,26,33,27 chr1 221052769 . GT G,GTT 1056.22 PASS AC=1,0;AF=0.603,0.017;AN=2;DP=2209;set=variant-variant2-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant16-variant18-variant19-variant20-variant23-variant24-variant25-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:107:99:14,24,37,32 chr1 221052789 . CT C 1043.18 PASS AC=1;AF=0.625;AN=2;DP=2270;set=variant-variant2-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant16-variant18-variant19-variant20-variant23-variant24-variant25-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,62:110:99:1345,0,1158:20,28,27,35 chr1 221052793 . TC T 813.5 PASS AC=1;AF=0.614;AN=2;DP=1836;set=variant-variant3-variant4-variant7-variant8-variant10-variant11-variant14-variant16-variant17-variant25-variant26-variant27-variant31-variant34-variant35-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,41:106:99:744,0,1627:29,36,14,27 chr1 221052937 . A C 1128.19 PASS AC=2;AF=0.795;AN=2;DP=1645;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:1813,162,0:0,0,23,31 chr1 221053545 . T C 1862.13 PASS AC=1;AF=0.533;AN=2;DP=2867;MQ=60;set=variant-variant3-variant4-variant7-variant17-variant25-variant26-variant27-variant31-variant35-variant37-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:127,100:227:99:2254,0,2991:63,64,54,46 chr1 221054761 . C G 1593.36 PASS AC=1;AF=0.533;AN=2;DP=1499;MQ=60;set=variant-variant3-variant4-variant7-variant17-variant25-variant26-variant27-variant31-variant35-variant37-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,41:94:99:1081,0,1570:19,34,21,20 chr1 221055105 . AACACACACACACACAC AACAC,AACACACACACAC,AACACAC,AACACACACACACAC,AACACACAC,AACACACACAC,AAC,AACACACACACACACACACACAC,A,AACACACACACACACACACAC 143.06 PASS AC=2,0,0,0,0,0,0,0,0,0;AF=0.139,0.083,0.069,0.042,0.069,0.125,0.097,0.028,0.083,0.014;AN=2;DP=369;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:7:21:0,0,5,2 chr1 221055463 . G A 854.13 PASS AC=1;AF=0.625;AN=2;DP=3685;MQ=60;set=variant-variant2-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant16-variant18-variant19-variant20-variant23-variant24-variant25-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,90:141:99:2449,0,1201:30,21,41,49 chr1 221057646 . C T 2997.63 PASS AC=1;AF=0.625;AN=2;DP=6206;set=variant-variant2-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant16-variant18-variant19-variant20-variant23-variant24-variant25-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:131,127:258:99:3047,0,3190:63,68,60,67 chr1 221057739 . C G 2322.01 PASS AC=1;AF=0.538;AN=2;DP=1925;set=variant9-variant11-variant12-variant13-variant18-variant23-variant25-variant30-variant33-variant34-variant35-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:100,100:200:99:2550,0,2553:49,51,45,55 chr1 221058059 . C T 2379.84 PASS AC=1;AF=0.536;AN=2;DP=2917;MQ=60;set=variant9-variant11-variant12-variant13-variant18-variant23-variant25-variant30-variant33-variant34-variant35-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:117,139:256:99:3431,0,2996:56,61,71,68 chr1 221058846 . T C 855.86 PASS AC=1;AF=0.536;AN=2;DP=822;MQ=60;set=variant9-variant11-variant12-variant13-variant18-variant23-variant25-variant30-variant33-variant34-variant35-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,19:53:99:450,0,949:20,14,10,9 chr1 221507141 . C T 1544.46 PASS AC=2;AF=1;AN=2;DP=2137;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,67:67:99:2000,200,0:0,0,44,23 chr1 221509335 . A C 2417.51 PASS AC=1;AF=0.5;AN=2;DP=1450;MQ=60;set=variant3-variant7-variant12-variant23-variant24-variant34-variant35-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:63,76:139:99:1763,0,1577:32,31,40,36 chr1 221912361 . T C 749.44 PASS AC=1;AF=0.814;AN=2;DP=2550;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:41,37:78:99:923,0,1032:22,19,22,15 chr1 221912808 . T C 1506.71 PASS AC=1;AF=0.625;AN=2;DP=4083;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant32-variant33-variant35-variant36-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:70,78:148:99:2051,0,1833:33,37,31,47 chr1 222645539 . T C 106.77 PASS AC=2;AF=1;AN=2;DP=193;FS=0;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-filterInvariant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-filterInvariant20-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-filterInvariant43 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:113,12,0:0,0,3,1 chr1 222645619 . G A 37.74 PASS AC=1;AF=0.5;AN=2;DP=106;set=variant2-variant8-variant13-variant14-variant18-variant28-variant33-variant35-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:2,8:10:60:168,0,60:2,0,4,4 chr1 222646927 . G A 437.49 PASS AC=1;AF=0.5;AN=2;DP=190;FractionInformativeReads=1;set=variant2-variant8-variant13-variant14-variant18-variant20-variant28-variant29-variant35-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:6,8:14:99:189,0,152:1,5,3,5 chr1 222646986 . A G 98.32 PASS AC=2;AF=0.977;AN=2;DP=617;FS=0;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-filterInvariant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:234,21,0:0,0,3,4 chr1 222649341 . A C 147.54 PASS AC=2;AF=1;AN=2;DP=558;FS=0;FractionInformativeReads=1;MQRankSum=0.496;ReadPosRankSum=-0.744;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-filterInvariant17-variant18-variant19-variant20-filterInvariant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:144,15,0:0,0,4,1 chr1 222649491 . C G 472.94 PASS AC=1;AF=0.603;AN=2;DP=865;set=variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,21:36:99:496,0,322:8,7,14,7 chr1 222650113 . G A 1244.17 PASS AC=1;AF=0.5;AN=2;DP=1406;FractionInformativeReads=1;set=variant2-variant8-variant13-variant14-variant18-variant20-variant28-variant33-variant35-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:79,69:148:99:1665,0,1907:33,46,30,39 chr1 222650329 . C T 263.05 PASS AC=1;AF=0.63;AN=2;DP=737;FractionInformativeReads=1;set=filterInvariant2-variant4-variant6-filterInvariant8-filterInvariant10-variant11-variant13-filterInvariant14-variant15-filterInvariant18-filterInvariant20-filterInvariant21-variant26-filterInvariant28-variant29-filterInvariant30-filterInvariant32-filterInvariant34-filterInvariant35-filterInvariant40-filterInvariant41-filterInvariant42-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:27,21:48:99:485,0,578:10,17,10,11 chr1 222650534 . T C 268.59 PASS AC=2;AF=0.676;AN=2;DP=1068;FractionInformativeReads=1;set=variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1003,108,0:0,0,13,23 chr1 222697088 . G A 805.29 PASS AC=1;AF=0.568;AN=2;DP=2347;MQ=60;set=variant-variant3-variant4-variant6-variant8-variant12-variant16-variant19-variant22-variant24-variant26-variant27-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:62,61:123:99:1513,0,1471:27,35,28,33 chr1 222700416 . C T 1040.63 PASS AC=1;AF=0.565;AN=2;DP=2968;MQ=60;set=variant-variant3-variant4-variant6-variant8-variant12-variant16-variant19-variant22-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:76,44:120:99:934,0,1789:38,38,21,23 chr1 222705270 . T C 1135.07 PASS AC=1;AF=0.578;AN=2;DP=2216;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,36:65:99:898,0,669:17,12,22,14 chr1 222705546 . G A 173.88 PASS AC=1;AF=0.586;AN=2;DP=360;set=variant-variant3-variant4-variant6-variant7-variant8-variant11-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant26-variant27-variant28-variant30-variant31-variant32-variant35-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,7:11:99:173,0,146:0,4,3,4 chr1 222712354 . C T 253.61 PASS AC=1;AF=0.56;AN=2;DP=752;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant8-variant12-variant16-variant17-variant19-variant22-variant24-variant26-variant27-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,15:26:99:336,0,286:5,6,7,8 chr1 222713208 . G A 155.35 PASS AC=1;AF=0.56;AN=2;DP=437;MQ=60;set=variant-variant3-variant4-variant6-variant8-variant12-variant16-variant17-variant19-variant22-variant24-variant26-variant27-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,11:23:99:358,0,379:10,2,11,0 chr1 222713503 . C G 1794.83 PASS AC=1;AF=0.56;AN=2;DP=4617;MQ=60;set=variant-variant3-variant4-variant6-variant8-variant12-variant16-variant17-variant19-variant22-variant24-variant26-variant27-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:104,113:217:99:2745,0,2593:45,59,48,65 chr1 222713631 . G C 721.95 PASS AC=1;AF=0.56;AN=2;DP=3171;MQ=60;set=variant-variant3-variant4-variant6-variant8-variant12-variant16-variant17-variant19-variant22-variant24-variant26-variant27-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:70,44:114:99:1102,0,1840:37,33,19,25 chr1 222713750 . G A 596.63 PASS AC=1;AF=0.578;AN=2;DP=2397;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,23:76:99:448,0,1396:23,30,11,12 chr1 222721162 . G A 2178.39 PASS AC=1;AF=0.5;AN=2;DP=163;FS=4.627;FractionInformativeReads=1;MQ=60;MQRankSum=0.085;QD=13.36;ReadPosRankSum=3.263;SOR=0.636;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:72,91:163:99:2207,0,1884:32,40,48,43 chr1 222721288 . C T 2543.54 PASS AC=1;AF=0.688;AN=2;DP=3940;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,56:114:99:1471,0,1491:34,24,24,32 chr1 222734628 . C T 455.86 PASS AC=1;AF=0.55;AN=2;DP=143;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant8-variant17-variant26-variant29-variant30-variant35-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,12:18:99:302,0,169:5,1,8,4 chr1 222736498 . C T 449.73 PASS AC=1;AF=0.536;AN=2;DP=738;MQ=60;set=variant2-variant3-variant4-variant8-variant13-variant18-variant20-variant34-variant35-variant36-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,31:47:99:801,0,452:13,3,18,13 chr1 222737265 . G T 625.25 PASS AC=2;AF=1;AN=2;DP=1112;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:842,81,0:0,0,17,10 chr1 222737481 . C G 485.65 PASS AC=1;AF=0.55;AN=2;DP=405;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant8-variant17-variant26-variant29-variant30-variant35-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:26,30:56:99:642,0,616:10,16,14,16 chr1 222737568 . C T 221.49 PASS AC=2;AF=1;AN=2;DP=561;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:610,51,0:0,0,3,14 chr1 222750744 . C T 83.94 PASS AC=1;AF=0.5;AN=2;DP=141;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant8-variant18-variant20-variant34-variant35-variant36-variant41 GT:AD:DP:GQ:PL:SB 0/1:7,8:15:99:264,0,208:7,0,8,0 chr1 222751034 . T C 1656.56 PASS AC=1;AF=0.788;AN=2;DP=2135;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,25:50:99:731,0,721:7,18,6,19 chr1 222761649 . C A 1349.32 PASS AC=1;AF=0.738;AN=2;DP=800;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,9:19:99:315,0,344:9,1,9,0 chr1 222763026 . C T 369.47 PASS AC=1;AF=0.738;AN=2;DP=572;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,9:15:99:350,0,136:4,2,9,0 chr1 222763215 . C G 593.04 PASS AC=1;AF=0.531;AN=2;DP=789;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant8-variant13-variant18-variant20-variant29-variant34-variant35-variant36-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,10:36:99:167,0,591:12,14,4,6 chr1 222763235 . T G 1478.84 PASS AC=1;AF=0.802;AN=2;DP=1633;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,9:31:99:150,0,538:9,13,4,5 chr1 222763249 . C T 650.58 PASS AC=2;AF=0.989;AN=2;DP=1402;FS=0;MQ=60;MQRankSum=0.442;ReadPosRankSum=0.442;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:738,75,0:0,0,10,15 chr1 222798106 . G A 4120.33 PASS AC=2;AF=1;AN=2;DP=5171;FS=0;MQ=60;MQRankSum=-0.751;ReadPosRankSum=1.334;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,81:81:99:2408,243,0:0,0,38,43 chr1 222802006 . A G 1971.42 PASS AC=2;AF=1;AN=2;DP=3686;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,74:74:99:2240,221,0:0,0,40,34 chr1 222802803 . T G 2411.21 PASS AC=1;AF=0.75;AN=2;DP=3120;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,39:74:99:993,0,984:19,16,18,21 chr1 222802926 . C T 2818.59 PASS AC=1;AF=0.898;AN=2;DP=3977;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:50,27:77:99:607,0,1254:25,25,14,13 chr1 222821211 . C T 283.69 PASS AC=1;AF=0.622;AN=2;DP=1514;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,21:35:99:480,0,325:7,7,9,12 chr1 222823529 . A C 1264.65 PASS AC=1;AF=0.744;AN=2;DP=1675;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,16:48:99:371,0,815:21,11,11,5 chr1 222823743 . T G 1072.42 PASS AC=1;AF=0.744;AN=2;DP=1508;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,22:43:99:520,0,566:6,15,10,12 chr1 222825403 . G A 1159.26 PASS AC=1;AF=0.989;AN=2;DP=1688;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:15,21:36:99:577,0,471:6,9,8,13 chr1 222825415 . G A 395.36 PASS AC=1;AF=0.5;AN=2;DP=27;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.529;QD=14.64;ReadPosRankSum=0.558;SOR=0.593;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:14,13:27:99:424,0,367:5,9,5,8 chr1 222825717 . T C 1632.65 PASS AC=1;AF=0.744;AN=2;DP=3762;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,51:104:99:1168,0,1240:24,29,24,27 chr1 222825761 . G A 1023.06 PASS AC=1;AF=0.989;AN=2;DP=2548;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:38,34:72:99:834,0,953:14,24,12,22 chr1 222826481 . G A 3182.62 PASS AC=1;AF=0.744;AN=2;DP=3526;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,40:86:99:1093,0,1307:26,20,20,20 chr1 222832010 . A G 276.29 PASS AC=1;AF=0.567;AN=2;DP=600;MQ=60;set=variant2-variant12-variant13-variant16-variant19-variant22-variant23-variant24-variant31-variant33-variant34-variant35-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,21:45:99:601,0,732:19,5,16,5 chr1 222832295 . T C 567.11 PASS AC=1;AF=0.75;AN=2;DP=689;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,12:17:99:391,0,163:2,3,3,9 chr1 222833601 . T C 3355.75 PASS AC=2;AF=1;AN=2;DP=4532;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,104:104:99:3184,312,0:0,0,57,47 chr1 222837594 . G A 1195.04 PASS AC=1;AF=0.784;AN=2;DP=1831;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:28,24:52:99:755,0,841:7,21,4,20 chr1 222838216 . C T 2969.91 PASS AC=1;AF=0.989;AN=2;DP=3855;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:67,57:124:99:1383,0,1582:29,38,20,37 chr1 222839838 . A G 8720.25 PASS AC=1;AF=0.898;AN=2;DP=12288;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:152,149:301:99:3770,0,3906:60,92,57,92 chr1 222840043 . T TGGG,TGGGG 936.21 PASS AC=1,0;AF=0.898,0.091;AN=2;DP=1456;MQ=60;set=Intersection GT:DP:GQ:SB 0/1:42:99:9,12,17,4 chr1 222846882 . G A 135.97 PASS AC=1;AF=0.797;AN=2;DP=322;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,5:9:99:154,0,114:1,3,2,3 chr1 222860734 . C T 147.98 PASS AC=2;AF=1;AN=2;DP=320;FS=0;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:433,39,0:0,0,10,3 chr1 222886119 . A G 10601.2 PASS AC=2;AF=0.795;AN=2;DP=16270;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,355:355:99:11169,1064,0:0,0,176,179 chr1 222906294 . A G 12588.5 PASS AC=1;AF=0.713;AN=2;DP=15944;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:221,190:411:99:4358,0,5213:97,124,77,113 chr1 222906418 . CTTTTTTTTTTTTTTTTTTTTT CTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTTT,C,CTTTTTTTTTTTTTTTTTT 30.38 PASS AC=0,0,1,0;AF=0.045,0.364,0.045,0.045;AN=2;DP=593;set=filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant13-filterInvariant17-filterInvariant19-filterInvariant21-filterInvariant28-variant35-filterInvariant39-filterInvariant43 GT:DP:GQ:SB 0/3:54:99:3,14,7,30 chr1 222919748 . G A 247.51 PASS AC=1;AF=0.838;AN=2;DP=350;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:3,2:5:72:72,0,86:3,0,2,0 chr1 222919895 . T G 1975.15 PASS AC=1;AF=0.725;AN=2;DP=2103;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,24:46:99:600,0,548:13,9,14,10 chr1 222923001 . A G 2148.17 PASS AC=1;AF=0.725;AN=2;DP=2407;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,55:93:99:1330,0,844:17,21,27,28 chr1 222923183 . A C 666.35 PASS AC=1;AF=0.5;AN=2;DP=71;FS=8.38;FractionInformativeReads=1;MQ=60;MQRankSum=-1.475;QD=9.39;ReadPosRankSum=-2.635;SOR=1.493;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:44,27:71:99:695,0,1126:21,23,18,9 chr1 222923351 . A G 1800.59 PASS AC=1;AF=0.807;AN=2;DP=3244;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:34,28:62:99:636,0,830:16,18,14,14 chr1 222923839 . A G 2473.48 PASS AC=2;AF=0.841;AN=2;DP=3334;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:1732,174,0:0,0,34,24 chr1 223101939 . A C 241.62 PASS AC=1;AF=0.574;AN=2;DP=434;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:6,10:16:99:304,0,184:1,5,2,8 chr1 223152868 . G A 1082.3 PASS AC=2;AF=0.989;AN=2;DP=1189;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:570,42,0:0,0,12,2 chr1 223156280 . C CT,CTT 72.77 PASS AC=0,1;AF=0.033,0.633;AN=2;DP=133;FS=0;MQ=60;set=variant2-variant11-variant15-variant16-variant17-variant18-variant26-variant27-variant29-variant31-variant32-variant33-variant35-variant39-variant41 GT:DP:GQ:SB 0/2:6:58:2,0,3,1 chr1 223156382 . C T 2214.62 PASS AC=2;AF=1;AN=2;DP=2570;FS=0;MQ=60;MQRankSum=1.253;ReadPosRankSum=0.879;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1509,153,0:0,0,31,20 chr1 223168213 . T C 1153.41 PASS AC=1;AF=0.6;AN=2;DP=951;MQ=60;set=variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,21:42:99:509,0,564:13,8,13,8 chr1 223176275 . G A 1669.56 PASS AC=1;AF=0.5;AN=2;DP=1809;FractionInformativeReads=1;MQ=60;set=variant4-variant8-variant14-variant18-variant23-variant24-variant25-variant30-variant35-variant36-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:86,86:172:99:2164,0,2164:44,42,42,44 chr1 223177574 . A G 1470.88 PASS AC=1;AF=0.571;AN=2;DP=2947;MQ=60;set=variant-variant2-variant9-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,53:108:99:1481,0,1364:29,26,30,23 chr1 223178478 . G A 3446.89 PASS AC=1;AF=0.5;AN=2;DP=3078;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant8-variant14-variant18-variant24-variant25-variant30-variant35-variant36-variant37-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:149,117:266:99:2934,0,3872:83,66,64,53 chr1 223178561 . A C 2222.98 PASS AC=1;AF=0.618;AN=2;DP=9905;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:172,118:290:99:2789,0,4486:87,85,59,59 chr1 223283910 . A G 3751.74 PASS AC=2;AF=1;AN=2;DP=4090;FS=0;MQ=60;MQRankSum=1.591;ReadPosRankSum=1.704;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,114:114:99:3491,342,0:0,0,64,50 chr1 223284599 . T C 642.09 PASS AC=1;AF=0.5;AN=2;DP=1366;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant11-variant14-variant23-variant24-variant25-variant28-variant31-variant32-variant35-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:44,46:90:99:1188,0,1056:21,23,23,23 chr1 223537285 . CA C,CAA 101.87 PASS AC=1,0;AF=0.485,0.015;AN=2;DP=2174;set=variant-variant2-variant3-filterInvariant4-variant5-variant6-variant9-variant11-variant13-variant15-variant17-variant18-variant19-filterInvariant20-variant21-filterInvariant22-filterInvariant23-variant24-variant25-variant27-variant29-variant30-variant31-variant33-variant34-variant35-filterInvariant36-variant37-variant38-variant39-variant40-variant41-variant42-filterInvariant44 GT:DP:GQ:SB 0/1:57:99:24,17,11,5 chr1 223537385 . A G 3787.22 PASS AC=2;AF=0.872;AN=2;DP=6148;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,154:154:99:4291,460,0:0,0,80,74 chr1 223712870 . G T 655.25 PASS AC=1;AF=0.5;AN=2;DP=733;FractionInformativeReads=1;MQ=60;set=variant2-variant8-variant16-variant17-variant21-variant23-variant30-variant31-variant32-variant35-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:41,23:64:99:647,0,1170:24,17,15,8 chr1 223714950 . G A 356.06 PASS AC=2;AF=0.878;AN=2;DP=877;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-filterInvariant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:459,42,0:0,0,8,6 chr1 223715248 . GT G 949.48 PASS AC=2;AF=0.697;AN=2;DP=3493;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,96:96:99:3588,289,0:0,0,46,50 chr1 223716349 . G A 1338.7 PASS AC=2;AF=0.854;AN=2;DP=4364;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,128:128:99:4047,384,0:0,0,81,47 chr1 223717379 . A C 895.26 PASS AC=2;AF=1;AN=2;DP=2319;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:1959,194,0:0,0,40,25 chr1 223717484 . G A 515.84 PASS AC=2;AF=0.829;AN=2;DP=3343;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,105:105:99:3164,314,0:0,0,52,53 chr1 223718462 . G A 103.44 PASS AC=2;AF=0.829;AN=2;DP=1536;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1363,111,0:0,0,30,7 chr1 223718518 . C A 377.71 PASS AC=2;AF=0.829;AN=2;DP=2959;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,95:95:99:3039,284,0:0,0,59,36 chr1 223718651 . G A 1045.79 PASS AC=2;AF=0.684;AN=2;DP=3903;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,118:118:99:3847,353,0:0,0,56,62 chr1 223718670 . G A 1155.94 PASS AC=2;AF=0.684;AN=2;DP=3749;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,108:108:99:3518,324,0:0,0,49,59 chr1 223722646 . T TA 120.04 PASS AC=2;AF=0.842;AN=2;DP=533;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-filterInvariant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:27:221,27,0:0,0,7,1 chr1 223722780 . G A 554.78 PASS AC=2;AF=0.684;AN=2;DP=2714;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,82:82:99:2536,246,0:0,0,48,34 chr1 223799857 . C T 1206.46 PASS AC=1;AF=0.711;AN=2;DP=6593;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:106,107:213:99:2535,0,2496:55,51,59,48 chr1 223799871 . C T 1373.02 PASS AC=1;AF=0.684;AN=2;DP=6723;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:111,105:216:99:2404,0,2640:56,55,58,47 chr1 223804932 . A T 537.67 PASS AC=1;AF=0.684;AN=2;DP=989;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,13:19:99:402,0,206:6,0,10,3 chr1 223804973 . C CT,CTT 113.71 PASS AC=1,0;AF=0.438,0.094;AN=2;DP=572;MQ=60;set=variant4-variant5-variant12-variant14-variant16-variant21-variant23-variant25-variant27-variant29-variant32-variant33-variant34-variant35-variant37-variant41 GT:DP:GQ:SB 0/1:31:99:13,5,11,2 chr1 223805032 . T TTTTG 1199.53 PASS AC=1;AF=0.684;AN=2;DP=2821;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,37:73:99:1445,0,1412:23,13,23,14 chr1 223805231 . T G 1875.73 PASS AC=1;AF=0.711;AN=2;DP=4498;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:78,67:145:99:1815,0,2108:39,39,30,37 chr1 223805504 . T C 808.97 PASS AC=1;AF=0.711;AN=2;DP=2558;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,29:62:99:769,0,943:12,21,11,18 chr1 223810318 . G A 1518.83 PASS AC=1;AF=0.654;AN=2;DP=2905;MQ=60;set=variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant13-variant14-variant19-variant22-variant23-variant25-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:78,49:127:99:975,0,2010:44,34,28,21 chr1 223813586 . G T 1154.33 PASS AC=1;AF=0.733;AN=2;DP=2894;MQ=60;set=variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant13-variant14-variant16-variant19-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:48,49:97:99:1230,0,1138:21,27,18,31 chr1 223814671 . A T 1246.44 PASS AC=1;AF=0.733;AN=2;DP=1602;MQ=60;set=variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant13-variant14-variant16-variant19-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:22,22:44:99:644,0,662:18,4,17,5 chr1 223815575 . G A 108.47 PASS AC=1;AF=0.75;AN=2;DP=1421;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,29:47:99:932,0,500:11,7,21,8 chr1 223816322 . A G 921.14 PASS AC=1;AF=0.75;AN=2;DP=4219;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:82,51:133:99:1255,0,2112:39,43,19,32 chr1 223816347 . A G 793.88 PASS AC=1;AF=0.75;AN=2;DP=4264;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:82,47:129:99:1164,0,2026:38,44,21,26 chr1 223841836 . C T 213.36 PASS AC=1;AF=0.5;AN=2;DP=275;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant7-variant9-variant12-variant19-variant23-variant27-variant28-variant29-variant33-variant35-variant36-variant37-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:11,9:20:99:261,0,379:10,1,7,2 chr1 223841877 . C G 358.28 PASS AC=1;AF=0.5;AN=2;DP=582;FractionInformativeReads=1;set=variant2-variant4-variant5-variant7-variant9-variant12-variant13-variant18-variant19-variant23-variant27-variant28-variant29-variant33-variant35-variant36-variant37-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:23,13:36:99:303,0,810:21,2,9,4 chr1 223853440 . A G 996.69 PASS AC=2;AF=1;AN=2;DP=1683;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,31:31:93:1078,93,0:0,0,7,24 chr1 223900408 . C G 9068.64 PASS AC=2;AF=1;AN=2;DP=15689;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,436:436:99:12953,1305,0:0,0,225,211 chr1 223905532 . G A 2095.33 PASS AC=2;AF=0.821;AN=2;DP=4198;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,101:101:99:3118,302,0:0,0,51,50 chr1 223931648 . T C 1625.51 PASS AC=2;AF=1;AN=2;DP=2020;FS=0;MQ=60;MQRankSum=1.33;ReadPosRankSum=1.652;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,69:69:99:2226,207,0:0,0,45,24 chr1 223934720 . G A 5105.78 PASS AC=2;AF=0.898;AN=2;DP=9016;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,199:199:99:6153,597,0:0,0,98,101 chr1 223938565 . A C 1784.77 PASS AC=2;AF=0.625;AN=2;DP=4508;MQ=60;set=variant2-variant3-variant4-variant7-variant8-variant9-variant12-variant13-variant14-variant18-variant20-variant21-variant23-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,185:185:99:5495,554,0:0,0,106,79 chr1 223954080 . A C 3678.44 PASS AC=1;AF=0.588;AN=2;DP=1733;MQ=60;set=variant-variant8-variant11-variant15-variant16-variant19-variant20-variant21-variant25-variant26-variant28-variant35-variant36-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,41:100:99:917,0,1589:32,27,23,18 chr1 223962929 . G A 2218.61 PASS AC=1;AF=0.638;AN=2;DP=2001;MQ=60;set=variant-variant8-variant11-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,48:82:99:1183,0,889:11,23,15,33 chr1 224001963 . G A 1441.56 PASS AC=1;AF=0.5;AN=2;DP=382;FractionInformativeReads=1;MQ=60;set=variant-variant20-variant35 GT:AD:DP:GQ:PL:SB 0/1:64,70:134:99:1752,0,1580:30,34,32,38 chr1 224133240 . G A 919.97 PASS AC=1;AF=0.533;AN=2;DP=425;FractionInformativeReads=1;set=variant-variant7-variant8-variant11-variant12-variant14-variant17-variant20-variant24-variant28-variant29-variant31-variant34-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,6:14:99:152,0,223:3,5,2,4 chr1 224139650 . T C 693.43 PASS AC=1;AF=0.6;AN=2;DP=1041;set=variant-variant7-variant8-variant11-variant12-variant14-variant17-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,16:54:99:277,0,977:22,16,6,10 chr1 224139708 . T C 410.98 PASS AC=1;AF=0.604;AN=2;DP=914;set=variant-variant7-variant8-variant11-variant12-variant14-variant17-variant19-variant20-variant23-variant25-variant26-variant27-variant28-variant29-filterInvariant30-variant31-variant34-variant35-variant36-variant37-variant38-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:34,14:48:99:317,0,800:15,19,4,10 chr1 224191284 . A G 114.83 PASS AC=2;AF=0.988;AN=2;DP=295;FS=0;FractionInformativeReads=1;MQRankSum=-0.731;ReadPosRankSum=0.731;set=variant-filterInvariant2-variant3-filterInvariant4-variant5-filterInvariant6-filterInvariant7-variant8-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant13-variant14-filterInvariant15-filterInvariant16-filterInvariant17-variant18-variant19-filterInvariant20-filterInvariant21-variant22-variant23-variant24-variant25-filterInvariant26-variant27-filterInvariant28-variant29-variant30-variant31-variant32-filterInvariant33-filterInvariant34-variant35-filterInvariant36-variant37-variant38-variant39-filterInvariant40-filterInvariant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:127,12,0:0,0,1,3 chr1 224218429 . G A 133.2 DRAGENHardSNP AC=1;AF=0.6;AN=2;DP=270;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:2,7:9:22:153,0,22:1,1,4,3 chr1 224302154 . T TGAG 997.54 PASS AC=2;AF=1;AN=2;DP=2537;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:3188,214,0:0,0,22,50 chr1 224318151 . T TTTG 2042.05 PASS AC=2;AF=1;AN=2;DP=1619;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1702,117,0:0,0,28,8 chr1 224321984 . C T 1504.42 PASS AC=2;AF=1;AN=2;DP=2147;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.555;ReadPosRankSum=1.2;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:2200,204,0:0,0,21,47 chr1 224345012 . G A 667.58 PASS AC=2;AF=1;AN=2;DP=1141;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1275,102,0:0,0,28,6 chr1 224346489 . G A 834.09 PASS AC=1;AF=0.5;AN=2;DP=210;MQ=60;set=variant4-variant8-variant35 GT:AD:DP:GQ:PL:SB 0/1:42,36:78:99:1075,0,1253:27,15,27,9 chr1 224347291 . G A 5087.87 PASS AC=2;AF=0.988;AN=2;DP=5158;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,114:114:99:3645,341,0:0,0,56,58 chr1 224347391 . C T 6427.51 PASS AC=2;AF=0.988;AN=2;DP=6510;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,125:125:99:4327,374,0:0,0,73,52 chr1 224347433 . C T 8514.41 PASS AC=2;AF=1;AN=2;DP=9806;FS=0;MQ=60;MQRankSum=-0.293;ReadPosRankSum=0.18;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,187:187:99:6106,560,0:0,0,115,72 chr1 224347918 . G C 15904.7 PASS AC=2;AF=0.988;AN=2;DP=15575;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,341:341:99:10572,1021,0:0,0,156,185 chr1 224348506 . A G 14660.4 PASS AC=2;AF=1;AN=2;DP=15919;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,406:406:99:12621,1217,0:0,0,188,218 chr1 224348700 . T C 12643.2 PASS AC=2;AF=0.988;AN=2;DP=13228;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,315:315:99:9616,943,0:0,0,165,150 chr1 224348827 . A G 12976.5 PASS AC=2;AF=0.988;AN=2;DP=13193;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,319:319:99:9407,952,0:0,0,139,180 chr1 224348915 . A G 6720.86 PASS AC=2;AF=0.988;AN=2;DP=7971;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,204:205:99:6648,578,0:1,0,90,114 chr1 224380234 . A G 2465.09 PASS AC=1;AF=0.5;AN=2;DP=1775;MQ=60;set=variant3-variant4-variant6-variant8-variant9-variant16-variant17-variant23-variant29-variant31-variant32-variant34-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:64,47:111:99:1272,0,1641:32,32,19,28 chr1 224380921 . A T 1308.38 PASS AC=1;AF=0.571;AN=2;DP=2323;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant10-variant11-variant14-variant17-variant18-variant19-variant20-variant25-variant29-variant35-variant36-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,58:116:99:1357,0,1379:35,23,38,20 chr1 224381107 . C T 3134.21 PASS AC=1;AF=0.5;AN=2;DP=2797;MQ=60;set=variant3-variant4-variant6-variant8-variant9-variant16-variant17-variant23-variant29-variant31-variant32-variant34-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:82,61:143:99:1499,0,1951:40,42,27,34 chr1 224415509 . A G 1904.08 PASS AC=1;AF=0.5;AN=2;DP=772;MQ=60;set=variant4-variant8-variant9-variant29-variant32-variant35 GT:AD:DP:GQ:PL:SB 0/1:77,68:145:99:1623,0,1862:30,47,31,37 chr1 224415616 . C T 246.56 PASS AC=1;AF=0.583;AN=2;DP=710;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant10-variant13-variant14-variant17-variant19-variant20-variant25-variant26-variant28-variant29-variant31-variant34-variant35-variant36-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,7:33:99:204,0,773:6,20,0,7 chr1 224444628 . C T 3305.16 PASS AC=2;AF=0.977;AN=2;DP=4453;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,115:115:99:3397,345,0:0,0,69,46 chr1 224444901 . G C 129.73 PASS AC=2;AF=1;AN=2;DP=246;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:90,6,0:0,0,0,2 chr1 224468986 . CGT CGTGTGTGT,CGTGT,CGTGTGT,C 310.05 PASS AC=0,2,0,0;AF=0.047,0.469,0.188,0.016;AN=2;DP=876;set=variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant13-variant14-variant15-variant16-variant17-filterInvariant19-variant21-variant22-variant8-variant23-variant6-variant25-variant27-variant29-variant30-variant20-variant32-variant34-variant35-variant36-variant24-variant38-filterInvariant-variant40-variant41 GT:DP:GQ:SB 2/2:12:36:0,0,2,10 chr1 224482216 . T C 1018.5 PASS AC=2;AF=0.932;AN=2;DP=1035;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,18:18:53:595,53,0:0,0,5,13 chr1 224491264 . T A 573.32 PASS AC=2;AF=1;AN=2;DP=860;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:747,51,0:0,0,17,0 chr1 224492381 . C T 1524.39 PASS AC=2;AF=1;AN=2;DP=2155;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1330,126,0:0,0,29,13 chr1 224492746 . C T 4419.33 PASS AC=2;AF=0.943;AN=2;DP=6274;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,166:166:99:4836,498,0:0,0,86,80 chr1 224495852 . C T 4023.93 PASS AC=2;AF=0.943;AN=2;DP=5355;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,115:115:99:3380,344,0:0,0,54,61 chr1 224500860 . CAA CA,C 58 PASS AC=2,0;AF=0.5,0.167;AN=2;DP=25;FS=0;MQ=60;set=variant18-variant35-variant36 GT:DP:GQ:SB 1/1:4:12:0,0,1,3 chr1 224500881 . A G 137.29 PASS AC=2;AF=0.923;AN=2;DP=77;FS=0;MQ=60;set=variant3-variant5-variant6-variant9-variant11-variant14-variant18-variant21-variant28-variant29-variant33-variant34-variant35 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:200,18,0:0,0,2,4 chr1 224505570 . T TAA 1818.86 PASS AC=2;AF=1;AN=2;DP=2023;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:2115,144,0:0,0,22,26 chr1 224505719 . T G 283.54 PASS AC=2;AF=1;AN=2;DP=241;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:311,24,0:0,0,1,7 chr1 224514275 . G A 322.54 PASS AC=2;AF=1;AN=2;DP=499;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:405,27,0:0,0,0,9 chr1 224517842 . C T 2060.99 PASS AC=2;AF=0.943;AN=2;DP=5295;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,117:117:99:3518,349,0:0,0,59,58 chr1 224517907 . A T 1443.27 PASS AC=2;AF=0.943;AN=2;DP=3901;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,89:89:99:2854,266,0:0,0,37,52 chr1 224518074 . T C 572.45 PASS AC=2;AF=0.943;AN=2;DP=1414;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:1020,96,0:0,0,11,21 chr1 224518143 . T C 180.3 PASS AC=2;AF=0.977;AN=2;DP=418;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:519,42,0:0,0,3,11 chr1 224544529 . A G 3274.98 PASS AC=2;AF=0.825;AN=2;DP=4886;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,121:121:99:4118,363,0:0,0,81,40 chr1 224567004 . G A 989.51 PASS AC=2;AF=0.825;AN=2;DP=1381;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:850,78,0:0,0,11,15 chr1 224575373 . G A 6836.53 PASS AC=2;AF=0.955;AN=2;DP=6902;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,170:170:99:5314,508,0:0,0,92,78 chr1 224575831 . C CT 2667.01 PASS AC=2;AF=0.825;AN=2;DP=2677;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:2774,237,0:0,0,45,34 chr1 224600904 . C CA 689.49 PASS AC=1;AF=0.5;AN=2;DP=651;set=variant16-variant17-variant21-variant22-variant35-variant36-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,24:65:99:308,0,871:16,25,11,13 chr1 224600910 . C A 2558.04 PASS AC=1;AF=0.909;AN=2;DP=3701;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:31,37:68:99:815,0,650:13,18,16,21 chr1 224600920 . C A 2613.74 PASS AC=2;AF=0.989;AN=2;DP=3778;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,69:69:99:2678,218,0:0,0,28,41 chr1 224621368 . G C 2445.47 PASS AC=2;AF=1;AN=2;DP=3707;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,119:119:99:3949,356,0:0,0,79,40 chr1 224621906 . C CGGA 1657.15 PASS AC=1;AF=0.619;AN=2;DP=2535;set=variant2-variant3-variant7-variant10-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant28-variant29-variant33-variant35-variant36-variant37-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,68:128:99:2677,0,2366:30,30,37,31 chr1 224805112 . C T 1285.36 PASS AC=2;AF=0.577;AN=2;DP=1048;MQ=60;set=variant3-variant7-variant16-variant17-variant21-variant24-variant25-variant32-variant35-variant36-variant37-variant39-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,96:96:99:3109,286,0:0,0,24,72 chr1 225211684 . G A 5131.07 PASS AC=2;AF=0.942;AN=2;DP=6336;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,155:155:99:4506,464,0:0,0,82,73 chr1 225211934 . G A 2424.3 PASS AC=2;AF=1;AN=2;DP=2755;FS=0;MQ=60;MQRankSum=0.052;ReadPosRankSum=2.346;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,69:69:99:2255,207,0:0,0,38,31 chr1 225212040 . T A 3629.75 PASS AC=2;AF=0.942;AN=2;DP=4482;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,104:104:99:3461,312,0:0,0,62,42 chr1 225230608 . C T 5070.83 PASS AC=2;AF=0.93;AN=2;DP=6115;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,130:130:99:3917,390,0:0,0,61,69 chr1 225237850 . A C 718.23 PASS AC=2;AF=0.93;AN=2;DP=504;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:402,30,0:0,0,10,0 chr1 225266966 . C G 1747.24 PASS AC=2;AF=0.93;AN=2;DP=2595;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:1891,180,0:0,0,33,27 chr1 225268343 . A G 4311.43 PASS AC=2;AF=0.93;AN=2;DP=5654;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,136:136:99:5922,409,0:0,0,61,75 chr1 225268346 . G A 4311.43 PASS AC=2;AF=0.93;AN=2;DP=5591;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,129:129:99:5898,406,0:0,0,55,74 chr1 225270409 . A T 2428.63 PASS AC=2;AF=0.869;AN=2;DP=3065;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,67:67:99:2241,201,0:0,0,24,43 chr1 225273248 . G T 1818.08 PASS AC=2;AF=0.93;AN=2;DP=1908;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1498,129,0:0,0,32,11 chr1 225273633 . T A 189.55 PASS AC=2;AF=0.962;AN=2;DP=235;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:405,27,0:0,0,0,9 chr1 225477491 . C T 709.42 PASS AC=1;AF=0.614;AN=2;DP=295;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant8-variant9-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant26-variant28-variant30-variant32-variant35-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,4:10:99:147,0,202:5,1,4,0 chr1 225477546 . A C 1834.07 PASS AC=1;AF=0.609;AN=2;DP=1044;MQ=60;set=variant-variant2-variant6-variant8-variant9-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant26-variant28-variant30-variant32-variant34-variant35-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,26:42:99:635,0,368:10,6,16,10 chr1 225477793 . T G 856.63 PASS AC=1;AF=0.609;AN=2;DP=704;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant8-variant9-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant26-variant28-variant30-variant32-variant34-variant35-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,13:31:99:378,0,571:4,14,2,11 chr1 225490809 . C T 36.63 PASS AC=1;AF=0.5;AN=2;DP=80;FractionInformativeReads=1;MQ=60;set=variant-variant16-variant21-variant22-variant35-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:80:80,0,134:4,0,3,1 chr1 225492545 . A G 527.54 PASS AC=1;AF=0.609;AN=2;DP=375;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant26-variant28-variant30-variant32-variant35-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,13:21:99:416,0,285:7,1,11,2 chr1 225492845 . C T 750.25 PASS AC=1;AF=0.604;AN=2;DP=654;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant26-variant28-variant30-variant32-variant34-variant35-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,9:22:99:217,0,405:3,10,3,6 chr1 225511905 . T C 1994.81 PASS AC=1;AF=0.567;AN=2;DP=850;FractionInformativeReads=1;MQ=60;set=variant-variant10-variant12-variant13-variant16-variant19-variant20-variant21-variant22-variant24-variant27-variant35-variant37-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:18,25:43:99:605,0,510:13,5,15,10 chr1 225512083 . A G 1018.43 PASS AC=1;AF=0.5;AN=2;DP=674;FractionInformativeReads=1;MQ=60;set=variant-variant10-variant12-variant13-variant16-variant21-variant22-variant24-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:39,41:80:99:1029,0,965:15,24,14,27 chr1 225519445 . G T 385.72 PASS AC=1;AF=0.5;AN=2;DP=210;FractionInformativeReads=1;MQ=60;set=variant-variant10-variant12-variant16-variant21-variant22-variant24-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:15,14:29:99:340,0,553:3,12,5,9 chr1 225525299 . G GA 337.35 PASS AC=1;AF=0.567;AN=2;DP=301;MQ=60;set=variant-variant10-variant12-variant13-variant16-variant19-variant20-variant21-variant22-variant24-variant27-variant35-variant37-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:16,9:25:99:206,0,425:4,12,1,8 chr1 225528175 . G T 1521.77 PASS AC=1;AF=0.5;AN=2;DP=253;FractionInformativeReads=1;MQ=60;set=variant16-variant21-variant35 GT:AD:DP:GQ:PL:SB 0/1:54,27:81:99:1025,0,2891:34,20,18,9 chr1 225528183 . C A 3139.64 PASS AC=1;AF=0.643;AN=2;DP=2807;set=variant-variant2-variant9-variant10-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant32-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,29:84:99:1028,0,2869:32,23,19,10 chr1 225533684 . A G 1852.57 PASS AC=1;AF=0.643;AN=2;DP=1911;MQ=60;set=variant-variant2-variant9-variant10-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant32-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,28:52:99:726,0,595:15,9,19,9 chr1 225533931 . A G 721.53 PASS AC=1;AF=0.5;AN=2;DP=917;MQ=60;set=variant-variant10-variant12-variant13-variant16-variant21-variant22-variant24-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:45,52:97:99:1382,0,1111:23,22,23,29 chr1 225534219 . T C 4200.39 PASS AC=1;AF=0.643;AN=2;DP=3226;MQ=60;set=variant-variant2-variant9-variant10-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant32-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:62,60:122:99:1481,0,1566:30,32,29,31 chr1 225534348 . G A 1494.63 PASS AC=1;AF=0.643;AN=2;DP=1012;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant9-variant10-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant32-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,20:42:99:539,0,624:5,17,6,14 chr1 225539665 . T A 729.81 PASS AC=1;AF=0.708;AN=2;DP=549;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,8:14:99:256,0,190:1,5,1,7 chr1 225555512 . C T 4988.56 PASS AC=2;AF=0.705;AN=2;DP=5650;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,146:147:99:4341,402,0:0,1,76,70 chr1 225555602 . T G 4399.21 PASS AC=2;AF=0.718;AN=2;DP=4330;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,104:104:99:3358,312,0:0,0,39,65 chr1 225562385 . C T 2884.76 PASS AC=2;AF=0.917;AN=2;DP=3275;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:1830,174,0:0,0,34,24 chr1 225565015 . T C 1361.56 PASS AC=2;AF=0.829;AN=2;DP=2173;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:2088,213,0:0,0,41,30 chr1 225565073 . C T 1433.78 PASS AC=2;AF=0.784;AN=2;DP=2185;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,66:66:99:1931,197,0:0,0,30,36 chr1 225569241 . T G 2505.12 PASS AC=2;AF=0.824;AN=2;DP=2219;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,52:52:99:1721,156,0:0,0,21,31 chr1 225576058 . T C 1984.49 PASS AC=2;AF=0.824;AN=2;DP=2168;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:1760,174,0:0,0,33,25 chr1 225576311 . A G 718.07 PASS AC=2;AF=0.784;AN=2;DP=1007;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1460,135,0:0,0,15,30 chr1 225577648 . C T 958.57 PASS AC=2;AF=0.784;AN=2;DP=1253;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1578,128,0:0,0,7,36 chr1 225601647 . C T 1401.32 PASS AC=2;AF=0.838;AN=2;DP=2538;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:2194,224,0:0,0,39,36 chr1 225603103 . C T 530.25 PASS AC=2;AF=0.94;AN=2;DP=602;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:231,24,0:0,0,3,5 chr1 225607144 . C T 931.19 PASS AC=2;AF=0.929;AN=2;DP=1509;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,31:32:50:912,50,0:0,1,11,20 chr1 225609884 . A G 2925.75 PASS AC=2;AF=0.905;AN=2;DP=4147;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,137:137:99:4039,411,0:0,0,64,73 chr1 225611661 . C T 3024.8 PASS AC=2;AF=0.875;AN=2;DP=3398;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,80:80:99:2442,239,0:0,0,51,29 chr1 225611845 . C T 1309.29 PASS AC=2;AF=0.776;AN=2;DP=1294;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1280,114,0:0,0,10,28 chr1 225615566 . G C 1397.97 PASS AC=2;AF=0.897;AN=2;DP=1821;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:2075,171,0:0,0,45,12 chr1 225680555 . C CATTT 3049.93 PASS AC=2;AF=1;AN=2;DP=2404;FS=0;MQ=60;MQRankSum=0.668;ReadPosRankSum=0.911;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1998,138,0:0,0,36,6 chr1 225680980 . A C 8292.94 PASS AC=2;AF=0.955;AN=2;DP=10360;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,263:263:99:8317,789,0:0,0,142,121 chr1 225681766 . CAAA CAAAAAAA,CAAAAAAAA,CAAAAAA,CAAAAAAAAA,CAAAAA,CAAAA,CAAAAAAAAAAA,CAA,CAAAAAAAAAA,CAAAAAAAAAAAA,C,CA 1161.28 PASS AC=0,0,0,0,0,0,0,0,1,0,0,0;AF=0.085,0.159,0.134,0.024,0.073,0.085,0.012,0.012,0.024,0.012,0.012,0.012;AN=2;DP=2403;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-filterInvariant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 0/9:28:99:11,4,11,2 chr1 225682175 . C T 10938.2 PASS AC=2;AF=0.917;AN=2;DP=16361;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,394:394:99:12045,1179,0:0,0,197,197 chr1 225682560 . G A 2525.13 PASS AC=2;AF=0.833;AN=2;DP=3117;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,66:66:99:2189,198,0:0,0,31,35 chr1 225683158 . GTT GTTTT,GTTTTT,G,GTTTTTT,GTTT,GT 2314.66 PASS AC=1,0,0,0,0,0;AF=0.452,0.06,0.06,0.012,0.024,0.012;AN=2;DP=11650;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-filterInvariant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:163:99:38,21,16,88 chr1 225685621 . TAAG T 1248 PASS AC=2;AF=0.833;AN=2;DP=1549;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1621,109,0:0,0,11,25 chr1 225707271 . GAAA GAA,GAAAA,GA,G 62.11 PASS AC=1,0,0,0;AF=0.325,0.125,0.025,0.025;AN=2;DP=669;MQ=60;set=filterInvariant2-filterInvariant3-variant5-variant6-variant8-variant11-variant12-variant13-variant14-variant16-variant19-filterInvariant20-filterInvariant21-variant24-variant28-filterInvariant30-variant33-variant35-variant37-variant41 GT:DP:GQ:SB 0/1:25:99:6,10,3,6 chr1 225840539 . C G 483.33 PASS AC=1;AF=0.5;AN=2;DP=215;FractionInformativeReads=1;MQ=60;set=variant31-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:36,37:73:99:997,0,1035:16,20,15,22 chr1 225840761 . C T 271.5 PASS AC=1;AF=0.5;AN=2;DP=29;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.68;QD=9.36;ReadPosRankSum=-0.807;SOR=0.593;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:15,14:29:99:300,0,380:6,9,6,8 chr1 225965832 . G T 4454.15 PASS AC=1;AF=0.625;AN=2;DP=1194;MQ=60;set=variant3-variant11-variant16-variant18-variant19-variant21-variant27-variant30-variant31-variant33-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:52,66:118:99:1592,0,1237:17,35,23,43 chr1 225974486 . T TG 1080.13 PASS AC=1;AF=0.732;AN=2;DP=2194;MQ=60;set=variant2-variant3-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant21-variant23-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:46,47:93:99:1475,0,1443:24,22,27,20 chr1 225974531 . A G 1158.91 PASS AC=1;AF=0.676;AN=2;DP=2849;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,42:89:99:966,0,1015:22,25,19,23 chr1 225997689 . T C 177.6 PASS AC=1;AF=0.667;AN=2;DP=712;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,10:22:99:223,0,286:9,3,6,4 chr1 225997741 . C A 285.78 PASS AC=1;AF=0.652;AN=2;DP=1332;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant37-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,17:41:99:344,0,548:12,12,10,7 chr1 225997973 . G A 173.94 PASS AC=1;AF=0.703;AN=2;DP=285;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant32-variant34-variant35-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,7:14:99:174,0,195:2,5,4,3 chr1 226013355 . C T 85.48 PASS AC=1;AF=0.615;AN=2;DP=84;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant6-variant15-variant16-variant22-variant23-variant24-variant25-variant29-variant30-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:8,8:16:99:233,0,188:3,5,2,6 chr1 226016381 . G A 3741.01 PASS AC=1;AF=0.722;AN=2;DP=972;FractionInformativeReads=1;MQ=60;set=variant3-variant11-variant14-variant16-variant18-variant19-variant21-variant23-variant25-variant27-variant28-variant30-variant31-variant33-variant35-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:27,25:52:99:1010,0,1441:17,10,17,8 chr1 226016397 . G A 4631.19 PASS AC=1;AF=0.711;AN=2;DP=1347;MQ=60;set=variant3-variant11-variant13-variant14-variant16-variant18-variant19-variant21-variant23-variant25-variant27-variant28-variant30-variant31-variant33-variant35-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:34,35:69:99:1206,0,1594:21,13,22,13 chr1 226027067 . GGTGTGTGT GGTGTGTGTGT,GGTGTGTGTGTGT,GGTGT,GGTGTGT,GGT,GGTGTGTGTGTGTGTGTGT,GGTGTGTGTGTGTGT,GGTGTGTGTGTGTGTGT,G 77.7 PASS AC=1,0,0,0,0,0,0,0,0;AF=0.181,0.125,0.056,0.069,0.028,0.014,0.056,0.056,0.014;AN=2;DP=1111;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant24-filterInvariant25-variant27-variant28-variant29-variant30-variant32-filterInvariant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-filterInvariant44 GT:DP:GQ:SB 0/1:9:92:0,4,1,4 chr1 226033476 . A G 875.11 PASS AC=2;AF=0.611;AN=2;DP=2487;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant11-variant15-variant16-variant20-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:2,103:105:99:3024,265,0:1,1,55,48 chr1 226036309 . A G 1346.1 PASS AC=2;AF=0.725;AN=2;DP=3745;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,113:113:99:3292,338,0:0,0,54,59 chr1 226044028 . GTTT G,GTT,GTTTT 54.02 PASS AC=0,1,0;AF=0.083,0.333,0.167;AN=2;DP=68;set=variant5-variant10-variant12-variant29-variant35-variant43 GT:DP:GQ:SB 0/2:5:5:0,1,2,2 chr1 226044489 . G GC 1089.1 PASS AC=2;AF=1;AN=2;DP=1719;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1302,120,0:0,0,19,20 chr1 226046648 . ATGTGTGTGTGTGTGTG ATGTGTGTG,ATGTGTGTGTG,ATGTG,ATGTGTGTGTGTG,ATGTGTGTGTGTGTG,ATGTGTG,A 322.97 PASS AC=0,2,0,0,0,0,0;AF=0.425,0.188,0.1,0.088,0.038,0.075,0.013;AN=2;DP=506;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 2/2:4:12:0,0,2,2 chr1 226050609 . C A 812.04 PASS AC=2;AF=0.591;AN=2;DP=2346;MQ=60;set=variant-variant3-variant5-variant8-variant9-variant10-variant11-variant12-variant17-variant19-variant20-variant24-variant25-variant26-variant27-variant31-variant33-variant35-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,125:125:99:3509,373,0:0,0,63,62 chr1 226050815 . A G 283.54 PASS AC=2;AF=0.94;AN=2;DP=278;FS=0;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:225,15,0:0,0,0,5 chr1 226050832 . T C 241.77 PASS AC=2;AF=0.94;AN=2;DP=232;FS=0;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:225,15,0:0,0,0,5 chr1 226054681 . T A 1123.35 PASS AC=2;AF=0.932;AN=2;DP=1061;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:1063,84,0:0,0,25,3 chr1 226058534 . C G 439.59 PASS AC=2;AF=0.932;AN=2;DP=840;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:747,63,0:0,0,16,5 chr1 226064846 . A G 152.09 PASS AC=2;AF=0.778;AN=2;DP=527;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:621,51,0:0,0,14,3 chr1 226065409 . G A 760.95 PASS AC=2;AF=0.786;AN=2;DP=1572;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,63:63:99:1960,189,0:0,0,23,40 chr1 226066861 . A C 111.22 PASS AC=2;AF=0.806;AN=2;DP=359;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:177,12,0:0,0,2,2 chr1 226075442 . T G 1637.26 PASS AC=1;AF=0.5;AN=2;DP=476;MQ=60;set=variant11-variant31-variant33-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:45,42:87:99:1436,0,1381:15,30,9,33 chr1 226075608 . G A 1477.11 PASS AC=2;AF=0.625;AN=2;DP=2149;set=variant-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant17-variant19-variant20-variant24-variant25-variant27-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,105:105:99:3092,313,0:0,0,51,54 chr1 226107787 . T C 987.93 PASS AC=1;AF=0.5;AN=2;DP=1521;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant7-variant8-variant9-variant11-variant17-variant20-variant24-variant25-variant27-variant33-variant35-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:43,63:106:99:1769,0,1224:29,14,40,23 chr1 226108200 . C T 1384.98 PASS AC=1;AF=0.5;AN=2;DP=666;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant18-variant21-variant23-variant31-variant33-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:28,30:58:99:910,0,723:16,12,22,8 chr1 226112074 . GC G 3272.2 PASS AC=2;AF=1;AN=2;DP=3793;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,91:91:99:3232,274,0:0,0,27,64 chr1 226125543 . G GA 1459.1 PASS AC=2;AF=1;AN=2;DP=2643;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:2664,217,0:0,0,23,49 chr1 226127443 . G C 2739.95 PASS AC=1;AF=0.565;AN=2;DP=3836;set=variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant13-variant14-variant17-variant18-variant20-variant21-variant23-variant26-variant31-variant32-variant33-variant35-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:127,84:211:99:2270,0,3638:50,77,34,50 chr1 226179909 . A G 436.9 PASS AC=1;AF=0.857;AN=2;DP=340;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,7:10:99:244,0,103:3,0,5,2 chr1 226187129 . C T 2254.72 PASS AC=1;AF=0.5;AN=2;DP=2216;MQ=60;set=variant5-variant6-variant15-variant18-variant22-variant24-variant31-variant33-variant35-variant36-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:104,96:200:99:2335,0,2584:39,65,29,67 chr1 226252232 . C T 903.58 PASS AC=2;AF=1;AN=2;DP=1783;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1618,150,0:0,0,16,34 chr1 226253127 . T G 466.77 PASS AC=2;AF=0.988;AN=2;DP=399;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.742;ReadPosRankSum=0.742;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:316,24,0:0,0,7,1 chr1 226253316 . G T 1621.03 PASS AC=2;AF=1;AN=2;DP=1936;FS=0;MQ=60;MQRankSum=1.238;ReadPosRankSum=1.155;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1564,146,0:0,0,24,25 chr1 226253926 . T C 1005.93 PASS AC=1;AF=0.625;AN=2;DP=3084;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant13-variant15-variant17-variant18-variant21-variant22-variant24-variant25-variant27-variant29-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:49,53:102:99:1474,0,1362:16,33,22,31 chr1 226254036 . T C 1869.8 PASS AC=2;AF=1;AN=2;DP=2887;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,61:61:99:2008,183,0:0,0,34,27 chr1 226332548 . G A 3036.46 PASS AC=1;AF=0.5;AN=2;DP=312;FS=0.859;FractionInformativeReads=1;MQ=60;MQRankSum=5.279;QD=9.73;ReadPosRankSum=-1.936;SOR=0.63;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:166,146:312:99:3065,0,3732:78,88,71,75 chr1 226332692 . T TA 814.75 PASS AC=1;AF=0.548;AN=2;DP=1957;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant9-variant13-variant15-variant21-variant22-variant25-variant27-variant29-variant32-variant33-variant35-variant37-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:36,20:56:99:392,0,843:15,21,9,11 chr1 226333535 . CCAAAA C 3759.5 PASS AC=1;AF=0.563;AN=2;DP=6759;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant13-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:91,82:173:99:3130,0,5386:48,43,53,29 chr1 226334578 . G A 1341.95 PASS AC=2;AF=1;AN=2;DP=1711;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1119,102,0:0,0,8,26 chr1 226334605 . T C 547.57 PASS AC=1;AF=0.531;AN=2;DP=384;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant10-variant14-variant15-variant18-variant24-variant27-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,8:20:99:207,0,306:4,8,2,6 chr1 226414375 . CAAAAAAAA CAA,CA,C 142.87 PASS AC=0,2,0;AF=0.083,0.25,0.458;AN=2;DP=77;FS=0;set=variant2-variant3-variant5-variant15-variant24-variant25-variant27-variant33-variant35-variant39-variant40-variant42 GT:DP:GQ:SB 2/2:8:24:0,0,6,2 chr1 226420536 . C G 1721.05 PASS AC=2;AF=0.705;AN=2;DP=4555;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,130:130:99:3922,390,0:0,0,79,51 chr1 226455934 . C T 265.05 PASS AC=1;AF=0.5;AN=2;DP=115;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant21-variant27-variant29-variant35-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,5:11:99:154,0,200:1,5,0,5 chr1 226497419 . G A 4587.64 PASS AC=1;AF=0.538;AN=2;DP=3534;MQ=60;set=variant3-variant10-variant14-variant15-variant18-variant24-variant27-variant31-variant33-variant34-variant35-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:148,143:291:99:3604,0,3591:65,83,63,80 chr1 226550553 . ATT A,AT 767.33 PASS AC=2,0;AF=0.698,0.14;AN=2;DP=1688;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:36:99:0,0,26,10 chr1 226550924 . G C 1402.35 PASS AC=2;AF=0.789;AN=2;DP=1738;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1218,114,0:0,0,12,26 chr1 226553485 . A C 1186.77 PASS AC=2;AF=0.875;AN=2;DP=658;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:84:1253,84,0:0,0,18,9 chr1 226553486 . C A 1186.77 PASS AC=2;AF=0.878;AN=2;DP=685;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:1253,84,0:0,0,19,9 chr1 226553490 . C A 1186.77 PASS AC=2;AF=0.866;AN=2;DP=747;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:90:1308,90,0:0,0,19,9 chr1 226553494 . C A,CA 1070.14 PASS AC=0,2;AF=0.022,0.913;AN=2;DP=416;set=variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 2/2:31:96:0,0,21,10 chr1 226556094 . T C 722.95 PASS AC=2;AF=0.977;AN=2;DP=1898;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1718,150,0:0,0,19,31 chr1 226557878 . T C 276.11 PASS AC=2;AF=0.638;AN=2;DP=563;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant9-variant11-variant12-variant13-variant15-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:788,63,0:0,0,11,10 chr1 226564691 . T C 1841.85 PASS AC=2;AF=0.789;AN=2;DP=1450;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1316,111,0:0,0,26,11 chr1 226566726 . A C 1231.79 PASS AC=2;AF=0.86;AN=2;DP=1895;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1121,99,0:0,0,21,12 chr1 226570840 . T C 2558.82 PASS AC=2;AF=0.86;AN=2;DP=3494;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,89:89:99:2876,267,0:0,0,49,40 chr1 227058344 . A G 76.53 PASS AC=1;AF=0.64;AN=2;DP=325;MQ=60;set=variant2-variant3-variant4-variant7-variant9-variant12-variant15-variant16-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,5:17:99:133,0,246:6,6,3,2 chr1 227059037 . C T 237.3 PASS AC=1;AF=0.531;AN=2;DP=585;MQ=60;set=variant-variant2-variant3-variant4-variant9-filterInvariant14-variant21-variant22-variant23-variant24-variant27-variant28-variant32-variant33-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:28,8:36:99:168,0,581:13,15,5,3 chr1 227069677 . T C 1993.2 PASS AC=1;AF=0.791;AN=2;DP=10130;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:138,118:256:99:2873,0,3146:63,75,58,60 chr1 227069737 . C T 1328.46 PASS AC=1;AF=0.671;AN=2;DP=5260;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:71,90:161:99:2057,0,1746:25,46,36,54 chr1 227071364 . G A 191.88 PASS AC=1;AF=0.681;AN=2;DP=589;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,9:14:99:343,0,145:4,1,9,0 chr1 227071377 . T C 152.9 PASS AC=1;AF=0.798;AN=2;DP=909;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,12:18:99:392,0,113:4,2,10,2 chr1 227071525 . C T 892.79 PASS AC=1;AF=0.671;AN=2;DP=4050;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,51:102:99:1098,0,1205:30,21,23,28 chr1 227073410 . G C 322.37 PASS AC=1;AF=0.791;AN=2;DP=2952;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,41:70:99:1004,0,884:6,23,15,26 chr1 227078955 . T C 412.55 PASS AC=1;AF=0.791;AN=2;DP=2289;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,20:44:99:548,0,561:14,10,14,6 chr1 227079222 . C G 567.51 PASS AC=1;AF=0.658;AN=2;DP=2025;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,21:52:99:571,0,863:16,15,12,9 chr1 227081622 . A G 1462.18 PASS AC=1;AF=0.791;AN=2;DP=4026;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:76,56:132:99:1425,0,1941:45,31,40,16 chr1 227081850 . G A 1527.59 PASS AC=1;AF=0.671;AN=2;DP=3183;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,44:99:99:1109,0,1502:17,38,14,30 chr1 227083550 . C T 1008.94 PASS AC=1;AF=0.658;AN=2;DP=3404;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,43:77:99:1064,0,921:15,19,18,25 chr1 227085155 . G A 151.23 PASS AC=1;AF=0.613;AN=2;DP=604;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,18:23:99:473,0,114:4,1,13,5 chr1 227086937 . T C 1891.99 PASS AC=1;AF=0.658;AN=2;DP=3047;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,40:84:99:1316,0,1530:7,37,9,31 chr1 227149203 . G A 1564.61 PASS AC=1;AF=0.55;AN=2;DP=4290;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant29-variant31-variant33-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:131,121:252:99:2745,0,3189:64,67,55,66 chr1 227165097 . G A 446.48 PASS AC=1;AF=0.522;AN=2;DP=1302;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant15-variant19-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant32-variant33-variant35-variant36-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,50:82:99:1069,0,712:19,13,27,23 chr1 227165484 . T C 148.52 PASS AC=2;AF=0.929;AN=2;DP=425;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:276,24,0:0,0,3,5 chr1 227170298 . A G 297.45 PASS AC=1;AF=0.667;AN=2;DP=761;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:16,17:33:99:512,0,346:10,6,14,3 chr1 227171584 . GT G 230.19 PASS AC=1;AF=0.629;AN=2;DP=738;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,13:26:99:386,0,381:5,8,6,7 chr1 227171736 . G GT 1038.99 PASS AC=1;AF=0.548;AN=2;DP=1321;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant29-variant31-variant33-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:38,23:61:99:828,0,1629:28,10,20,3 chr1 227171738 . G T 1048.02 PASS AC=1;AF=0.548;AN=2;DP=1372;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant29-variant31-variant33-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:41,23:64:99:828,0,1629:29,12,20,3 chr1 227171739 . G T,C 755.46 PASS AC=0,1;AF=0.267,0.283;AN=2;DP=1982;MQ=60;set=variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant13-variant15-variant17-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant30-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:69:99:23,7,29,10 chr1 227171958 . G C 3037.2 PASS AC=1;AF=0.577;AN=2;DP=3106;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant23-variant25-variant27-variant29-variant31-variant33-variant35-variant36-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:78,67:145:99:1709,0,2082:34,44,29,38 chr1 227172290 . C T 1821.35 PASS AC=1;AF=0.613;AN=2;DP=7789;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:152,122:274:99:2879,0,3470:74,78,66,56 chr1 227172518 . C T 665.63 PASS AC=1;AF=0.545;AN=2;DP=1846;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant25-variant29-variant31-variant33-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:26,44:70:99:1352,0,792:19,7,32,12 chr1 227172903 . G A 230.82 PASS AC=1;AF=0.613;AN=2;DP=1070;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,22:33:99:559,0,267:7,4,12,10 chr1 227172935 . C G 243.59 PASS AC=1;AF=0.617;AN=2;DP=1482;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:20,25:45:99:544,0,592:12,8,14,11 chr1 227174122 . C G 208.66 PASS AC=1;AF=0.545;AN=2;DP=1087;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant25-variant29-variant31-variant33-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:38,33:71:99:911,0,987:26,12,26,7 chr1 227174145 . T C 334.27 PASS AC=1;AF=0.641;AN=2;DP=2503;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:59,46:105:99:1275,0,1336:37,22,35,11 chr1 227174210 . T C 537.19 PASS AC=1;AF=0.625;AN=2;DP=5041;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:102,97:199:99:2335,0,2194:55,47,55,42 chr1 227174549 . G T 1082.12 PASS AC=1;AF=0.5;AN=2;DP=67;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.258;QD=16.15;ReadPosRankSum=0.12;SOR=0.622;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:30,37:67:99:1110,0,874:14,16,18,19 chr1 227174823 . A AT 1126.74 PASS AC=1;AF=0.625;AN=2;DP=2563;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:49,44:93:99:1183,0,1318:24,25,26,18 chr1 227174902 . G A 860.94 PASS AC=1;AF=0.556;AN=2;DP=2719;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant10-variant14-variant15-variant19-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,44:105:99:1090,0,1711:32,29,19,25 chr1 227175245 . C CT 40.66 PASS AC=1;AF=0.633;AN=2;DP=349;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,10:15:99:291,0,127:1,4,2,8 chr1 227175253 . C T 49.73 PASS AC=2;AF=0.713;AN=2;DP=400;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:45:655,45,0:0,0,2,12 chr1 227177444 . A G 853.65 PASS AC=1;AF=0.625;AN=2;DP=1766;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:21,23:44:99:748,0,568:16,5,22,1 chr1 227177731 . A T 1005.02 PASS AC=1;AF=0.613;AN=2;DP=2574;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:50,36:86:99:995,0,1371:19,31,17,19 chr1 227177883 . T TACA 1084.25 PASS AC=1;AF=0.613;AN=2;DP=3008;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:58,29:87:99:1065,0,2834:27,31,11,18 chr1 227178127 . A G 588.53 PASS AC=1;AF=0.613;AN=2;DP=1463;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:22,40:62:99:1141,0,495:12,10,21,19 chr1 227178700 . A G 1637.44 PASS AC=1;AF=0.613;AN=2;DP=4964;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:116,78:194:99:1815,0,2687:60,56,44,34 chr1 227178713 . C T 1822 PASS AC=1;AF=0.613;AN=2;DP=5284;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:112,80:192:99:1928,0,2831:55,57,47,33 chr1 227178948 . G A 13596.2 PASS AC=2;AF=0.821;AN=2;DP=13914;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,322:323:99:11644,962,0:0,1,139,183 chr1 227178962 . T C 3864.57 PASS AC=1;AF=0.613;AN=2;DP=9352;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:156,136:292:99:3386,0,3742:67,89,52,84 chr1 227179037 . G T 2452.03 PASS AC=1;AF=0.613;AN=2;DP=4122;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:66,60:126:99:2118,0,2406:24,42,24,36 chr1 227179054 . G A 2110.77 PASS AC=1;AF=0.613;AN=2;DP=3277;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:52,48:100:99:1805,0,2046:21,31,19,29 chr1 227179358 . T C 1016.19 PASS AC=2;AF=0.92;AN=2;DP=2310;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:2159,213,0:0,0,32,39 chr1 227179501 . AATAAGCACCT A 201.19 PASS AC=1;AF=0.597;AN=2;DP=1036;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:16,18:34:99:653,0,1526:8,8,7,11 chr1 227179707 . GGGAGGGTGGGGAGAGTGA G 97.73 PASS AC=2;AF=0.98;AN=2;DP=129;FS=0;MQ=60;MQRankSum=0.851;ReadPosRankSum=0.47;set=variant2-variant4-variant5-variant7-variant9-variant10-variant11-variant12-variant15-variant18-variant19-variant20-variant22-variant24-variant26-variant29-variant30-variant31-variant33-variant35-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:19:260,19,0:0,0,6,0 chr1 227180858 . T C 824.4 PASS AC=1;AF=0.545;AN=2;DP=1423;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant25-variant29-variant31-variant33-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:46,27:73:99:740,0,1333:30,16,20,7 chr1 227180947 . A C 2189.22 PASS AC=1;AF=0.625;AN=2;DP=5731;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:103,84:187:99:1887,0,2648:56,47,50,34 chr1 227180981 . T C 2440.09 PASS AC=1;AF=0.625;AN=2;DP=6663;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:117,97:214:99:2204,0,2747:57,60,50,47 chr1 227181554 . C G 1773.99 PASS AC=1;AF=0.613;AN=2;DP=2087;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:36,34:70:99:1319,0,2135:20,16,19,15 chr1 227181555 . A G 1773.99 PASS AC=1;AF=0.613;AN=2;DP=2097;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:35,34:69:99:1319,0,2135:20,15,19,15 chr1 227181838 . T G 1309.04 PASS AC=1;AF=0.613;AN=2;DP=3120;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:73,50:123:99:1488,0,1921:23,50,16,34 chr1 227181923 . C T 679.4 PASS AC=1;AF=0.613;AN=2;DP=1648;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:30,26:56:99:679,0,1017:14,16,13,13 chr1 227182033 . G A 1924.07 PASS AC=2;AF=0.943;AN=2;DP=4342;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,131:132:99:3583,380,0:1,0,70,61 chr1 227182179 . C T 420.31 PASS AC=1;AF=0.55;AN=2;DP=1030;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant29-variant31-variant33-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:35,28:63:99:654,0,837:16,19,8,20 chr1 227182575 . A G 1839.74 PASS AC=2;AF=0.884;AN=2;DP=3819;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,86:86:99:2725,258,0:0,0,55,31 chr1 227191656 . A C 49.73 PASS AC=2;AF=0.692;AN=2;DP=75;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant7-variant11-variant13-variant15-variant16-variant18-variant19-variant31-variant33-variant35-variant36 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:90,6,0:0,0,2,0 chr1 227191755 . ATT AT,ATTT,ATTTT,A 342.89 PASS AC=1,0,0,0;AF=0.488,0.15,0.025,0.025;AN=2;DP=1089;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:37:99:10,6,12,9 chr1 227192028 . T C 411.05 PASS AC=1;AF=0.548;AN=2;DP=833;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant29-variant31-variant33-variant35-variant36-variant41 GT:AD:DP:GQ:PL:SB 0/1:27,23:50:99:548,0,639:12,15,10,13 chr1 227192280 . T C 959 PASS AC=1;AF=0.55;AN=2;DP=1584;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant29-variant31-variant33-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:54,39:93:99:887,0,1258:26,28,21,18 chr1 227192477 . C T 529.02 PASS AC=1;AF=0.522;AN=2;DP=693;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant15-variant19-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant32-variant33-variant35-variant36-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,19:32:99:593,0,316:5,8,10,9 chr1 227192579 . A C 331.33 PASS AC=1;AF=0.613;AN=2;DP=1413;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:23,26:49:99:688,0,670:16,7,15,11 chr1 227198775 . C G 255.69 PASS AC=1;AF=0.55;AN=2;DP=676;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant29-variant31-variant33-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:25,17:42:99:426,0,668:8,17,7,10 chr1 227210820 . G A 447.22 PASS AC=1;AF=0.629;AN=2;DP=1214;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:22,17:39:99:367,0,539:13,9,11,6 chr1 227210888 . A T 858.65 PASS AC=1;AF=0.629;AN=2;DP=2249;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:30,32:62:99:753,0,699:16,14,18,14 chr1 227213968 . G T 591.93 PASS AC=2;AF=0.645;AN=2;DP=1259;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:906,87,0:0,0,9,20 chr1 227218069 . C CAT 1349.92 PASS AC=1;AF=0.837;AN=2;DP=1098;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,12:26:99:462,0,603:10,4,8,4 chr1 227221251 . T C 719.36 PASS AC=1;AF=0.525;AN=2;DP=719;MQ=60;set=variant-variant3-variant4-variant7-variant8-variant17-variant19-variant23-variant25-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant37-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,28:48:99:745,0,529:6,14,9,19 chr1 227222515 . G GACAA 2846.16 PASS AC=2;AF=1;AN=2;DP=2939;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:2241,150,0:0,0,21,29 chr1 227227740 . A C 144.08 PASS AC=1;AF=0.525;AN=2;DP=595;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant7-variant8-variant17-variant19-variant23-variant25-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant37-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,16:39:99:455,0,632:16,7,13,3 chr1 227239746 . G T 1186.77 PASS AC=1;AF=0.732;AN=2;DP=1440;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,12:29:99:369,0,582:2,15,2,10 chr1 227246890 . C CA 181.88 PASS AC=1;AF=0.525;AN=2;DP=712;MQ=60;set=variant-variant3-variant4-variant7-variant8-variant17-variant19-variant23-variant25-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant37-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,18:33:99:397,0,320:12,3,10,8 chr1 227247160 . A T 541.32 PASS AC=1;AF=0.5;AN=2;DP=343;FractionInformativeReads=1;MQ=60;set=variant7-variant8-variant19-variant30-variant32-variant33-variant35-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,27:43:99:721,0,422:4,12,10,17 chr1 227288655 . G A 542.78 PASS AC=1;AF=0.826;AN=2;DP=681;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,11:23:99:325,0,340:9,3,7,4 chr1 227330759 . A G 1117.27 PASS AC=2;AF=0.775;AN=2;DP=3910;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,99:99:99:3030,297,0:0,0,39,60 chr1 227330783 . G C 897.89 PASS AC=1;AF=0.533;AN=2;DP=1164;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant7-variant9-variant11-variant12-variant15-variant16-variant19-variant25-variant29-variant33-variant35-variant36-variant40 GT:AD:DP:GQ:PL:SB 0/1:30,40:70:99:943,0,760:11,19,17,23 chr1 227381326 . C T 128.58 PASS AC=2;AF=0.784;AN=2;DP=389;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:356,27,0:0,0,8,1 chr1 227381373 . G T 370.45 PASS AC=2;AF=0.789;AN=2;DP=1053;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:1162,90,0:0,0,26,4 chr1 227381674 . TA T 541.13 PASS AC=1;AF=0.525;AN=2;DP=648;MQ=60;set=variant-variant3-variant4-variant7-variant8-variant17-variant19-variant23-variant25-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant37-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,17:25:99:557,0,216:2,6,2,15 chr1 227387143 . A G 172.47 PASS AC=2;AF=0.848;AN=2;DP=252;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:267,18,0:0,0,6,0 chr1 227387361 . A G 1920.97 PASS AC=2;AF=0.852;AN=2;DP=2200;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:898,87,0:0,0,10,19 chr1 227505212 . TAAAA TAAA,T,TAAAAA 91.3 PASS AC=0,0,1;AF=0.128,0.205,0.244;AN=2;DP=3772;set=filterInvariant-variant2-filterInvariant4-filterInvariant5-variant6-variant8-filterInvariant9-variant10-variant11-variant12-filterInvariant13-variant14-variant15-filterInvariant16-filterInvariant17-variant18-variant20-variant21-variant22-variant23-variant24-filterInvariant25-variant26-variant27-variant28-variant29-variant30-variant31-filterInvariant32-filterInvariant33-variant34-filterInvariant35-variant37-variant38-variant39-filterInvariant40-variant41-variant43-variant44 GT:DP:GQ:SB 0/3:76:97:37,21,8,10 chr1 227505820 . G GC 1975.31 PASS AC=2;AF=1;AN=2;DP=1773;FS=0;MQ=60;MQRankSum=0;ReadPosRankSum=-0.551;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1488,111,0:0,0,24,13 chr1 227505994 . C CG 5465.2 PASS AC=2;AF=1;AN=2;DP=5957;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,176:176:99:7058,530,0:0,0,74,102 chr1 227841981 . A G 160.44 PASS AC=1;AF=0.625;AN=2;DP=23;FS=0;FractionInformativeReads=1;MQ=60;set=variant21-variant24-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:2,3:5:67:120,0,67:2,0,3,0 chr1 227919500 . T C 872.48 PASS AC=1;AF=0.5;AN=2;DP=677;MQ=60;set=variant3-variant7-variant11-variant15-variant16-variant19-variant33-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:51,41:92:99:1055,0,1360:18,33,13,28 chr1 227923081 . G A 8137.41 PASS AC=2;AF=0.989;AN=2;DP=14002;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,362:363:99:10452,1072,0:0,1,169,193 chr1 228004966 . C A 2001.16 PASS AC=1;AF=0.5;AN=2;DP=744;MQ=60;set=variant3-variant7-variant11-variant15-variant35 GT:AD:DP:GQ:PL:SB 0/1:87,61:148:99:1454,0,2404:51,36,37,24 chr1 228033197 . A G 1547.22 PASS AC=2;AF=0.893;AN=2;DP=3285;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:2621,231,0:0,0,54,23 chr1 228107139 . A G 593.85 PASS AC=1;AF=0.646;AN=2;DP=2186;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:22,35:57:99:954,0,640:13,9,14,21 chr1 228107281 . G A 396.48 PASS AC=1;AF=0.646;AN=2;DP=1869;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:43,20:63:99:424,0,1099:18,25,11,9 chr1 228107365 . A G 154.6 PASS AC=1;AF=0.75;AN=2;DP=740;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,11:30:99:361,0,614:5,14,4,7 chr1 228107387 . TACACACACAC T,TACACACAC,TACACAC 79.67 PASS AC=1,0,0;AF=0.515,0.136,0.015;AN=2;DP=464;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant29-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant41-variant43-variant44 GT:DP:GQ:SB 0/1:15:99:0,7,3,5 chr1 228107403 . C T 88.71 PASS AC=1;AF=0.607;AN=2;DP=350;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant29-variant30-variant31-variant34-variant35-variant37-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,8:17:99:309,0,354:1,8,2,6 chr1 228107430 . T C 91.72 PASS AC=1;AF=0.603;AN=2;DP=303;FractionInformativeReads=1;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant34-variant35-variant37-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,6:11:99:234,0,234:1,4,2,4 chr1 228107554 . A AACAC,AAC,AACACAC 316.52 PASS AC=1,0,0;AF=0.547,0.016,0.016;AN=2;DP=1287;MQ=60;set=variant-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43 GT:DP:GQ:SB 0/1:41:99:16,8,13,4 chr1 228107643 . T C 587.62 PASS AC=1;AF=0.756;AN=2;DP=3148;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,45:96:99:1073,0,1299:28,23,25,20 chr1 228108290 . G A 776.46 PASS AC=1;AF=0.5;AN=2;DP=157;FS=0;MQ=60;set=variant3-variant25-variant35 GT:AD:DP:GQ:PL:SB 0/1:21,24:45:99:444,0,448:10,11,12,12 chr1 228108703 . C T 2298.07 PASS AC=1;AF=0.55;AN=2;DP=7319;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant34-variant35-variant36-variant37-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:164,123:287:99:2872,0,4293:95,69,75,48 chr1 228108932 . A G 1885.69 PASS AC=1;AF=0.646;AN=2;DP=7559;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:113,117:230:99:3059,0,2967:54,59,60,57 chr1 228112121 . A G 816.05 PASS AC=2;AF=0.65;AN=2;DP=3736;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,101:101:99:3300,303,0:0,0,40,61 chr1 228112280 . T C 134.32 PASS AC=2;AF=0.653;AN=2;DP=572;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:466,36,0:0,0,2,10 chr1 228112776 . A G 103.54 PASS AC=2;AF=1;AN=2;DP=280;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:184,15,0:0,0,2,3 chr1 228113163 . A G 927.74 PASS AC=2;AF=0.744;AN=2;DP=3869;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,100:101:99:3026,276,0:1,0,42,58 chr1 228129197 . T C 718.53 PASS AC=2;AF=0.663;AN=2;DP=3034;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,78:78:99:2395,233,0:0,0,42,36 chr1 228155008 . T C 101.02 PASS AC=2;AF=0.722;AN=2;DP=46;FractionInformativeReads=1;set=variant3-variant11-variant15-filterInvariant21-variant24-variant28-variant33-variant35-filterInvariant37 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:129,9,0:0,0,3,0 chr1 228156143 . G C 247.99 PASS AC=2;AF=0.593;AN=2;DP=514;set=variant-filterInvariant3-variant5-variant6-variant8-filterInvariant11-variant13-variant14-filterInvariant15-filterInvariant16-filterInvariant19-filterInvariant20-filterInvariant21-variant22-variant23-variant24-variant25-filterInvariant26-variant28-variant29-filterInvariant30-variant33-variant35-variant36-variant37-variant38-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:771,69,0:0,0,8,15 chr1 228159125 . A C 58.24 PASS AC=1;AF=0.5;AN=2;DP=86;FractionInformativeReads=1;set=variant5-variant30-variant35-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:15,8:23:99:149,0,371:8,7,4,4 chr1 228159154 . A G 52.6 PASS AC=1;AF=0.643;AN=2;DP=90;FractionInformativeReads=1;set=variant3-filterInvariant5-variant26-variant30-filterInvariant35-filterInvariant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:17,4:21:69:69,0,405:7,10,1,3 chr1 228159186 . T G 35.02 PASS AC=1;AF=0.5;AN=2;DP=16;FS=2.769;FractionInformativeReads=1;MQ=44.01;MQRankSum=-1.614;QD=2.19;ReadPosRankSum=0.135;SOR=1.609;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:13,3:16:63:63,0,377:4,9,0,3 chr1 228160428 . T C 116.06 PASS AC=2;AF=0.719;AN=2;DP=106;FractionInformativeReads=1;set=variant3-variant5-variant6-variant11-variant13-variant16-variant19-variant20-variant22-variant24-variant26-variant28-variant29-variant33-variant35-variant36 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:190,15,0:0,0,1,4 chr1 228247351 . T C 1129.74 PASS AC=2;AF=0.795;AN=2;DP=5046;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,157:157:99:4923,470,0:0,0,85,72 chr1 228270268 . A G 286.34 PASS AC=2;AF=0.808;AN=2;DP=572;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:915,69,0:0,0,19,4 chr1 228271153 . T A 349.11 PASS AC=2;AF=0.6;AN=2;DP=1172;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1331,110,0:0,0,8,29 chr1 228285579 . C T 3048.37 PASS AC=1;AF=0.5;AN=2;DP=269;FS=2.028;FractionInformativeReads=0.996;MQ=60;MQRankSum=3.256;QD=11.33;ReadPosRankSum=0.449;SOR=0.579;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:131,137:268:99:3077,0,3209:70,61,69,68 chr1 228290033 . T C 2084.09 PASS AC=1;AF=0.5;AN=2;DP=654;FractionInformativeReads=1;MQ=60;set=variant3-variant22-variant25-variant35 GT:AD:DP:GQ:PL:SB 0/1:97,68:165:99:1478,0,2300:51,46,33,35 chr1 228294300 . T C 1597.9 PASS AC=2;AF=0.716;AN=2;DP=2450;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,83:83:99:2814,249,0:0,0,60,23 chr1 228296745 . C T 4733.88 PASS AC=2;AF=0.821;AN=2;DP=5440;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,135:135:99:4507,404,0:0,0,58,77 chr1 228328743 . T C 334.22 PASS AC=2;AF=0.989;AN=2;DP=609;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.58;ReadPosRankSum=0.296;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:548,48,0:0,0,12,4 chr1 228347352 . A G 3410.08 PASS AC=2;AF=0.909;AN=2;DP=5711;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,150:150:99:4456,450,0:0,0,73,77 chr1 228352160 . T C 2384.36 PASS AC=2;AF=0.989;AN=2;DP=4693;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,120:121:99:3459,317,0:1,0,56,64 chr1 228353651 . G C 2279.35 PASS AC=2;AF=0.603;AN=2;DP=4068;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,168:168:99:5515,503,0:0,0,97,71 chr1 228366526 . A G 1361.23 PASS AC=2;AF=0.989;AN=2;DP=2632;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:2591,237,0:0,0,40,39 chr1 228366813 . C T 647.38 PASS AC=2;AF=0.989;AN=2;DP=1831;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:1519,143,0:0,0,23,25 chr1 228368230 . G A 3034.4 PASS AC=2;AF=0.989;AN=2;DP=4082;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,92:92:99:2769,276,0:0,0,51,41 chr1 228369893 . CTTCA C 1594.14 PASS AC=2;AF=0.603;AN=2;DP=3285;set=variant-variant3-variant4-variant6-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,109:109:99:4839,328,0:0,0,50,59 chr1 228391382 . T TA 3438.33 PASS AC=1;AF=0.5;AN=2;DP=11456;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:76,172:248:99:3010,0,891:36,40,83,89 chr1 228391591 . G C 2767.82 PASS AC=2;AF=0.607;AN=2;DP=6580;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant31-variant32-variant34-variant35-variant36-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,217:217:99:6469,647,0:0,0,104,113 chr1 228399482 . C G 3690.38 PASS AC=2;AF=0.743;AN=2;DP=4660;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,133:133:99:4098,399,0:0,0,80,53 chr1 228399766 . T C 5142.97 PASS AC=2;AF=0.743;AN=2;DP=6911;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,240:240:99:6974,718,0:0,0,121,119 chr1 228400646 . T C 2695.8 PASS AC=2;AF=0.743;AN=2;DP=2756;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,93:93:99:3972,280,0:0,0,27,66 chr1 228400653 . A T 2592.79 PASS AC=2;AF=0.743;AN=2;DP=2390;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,78:78:99:3443,237,0:0,0,20,58 chr1 228402047 . A G 13248.9 PASS AC=2;AF=0.743;AN=2;DP=18450;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,482:484:99:14756,1400,0:1,1,232,250 chr1 228402121 . A G 9366.56 PASS AC=2;AF=0.743;AN=2;DP=11755;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:3,323:326:99:10355,861,0:2,1,127,196 chr1 228404997 . C T 1234.11 PASS AC=1;AF=0.5;AN=2;DP=459;MQ=60;set=variant-variant35-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:63,56:119:99:1466,0,1546:24,39,21,35 chr1 228405118 . G GA 328.21 PASS AC=2;AF=1;AN=2;DP=1121;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:590,63,0:0,0,3,18 chr1 228407059 . G T 3189.52 PASS AC=1;AF=0.5;AN=2;DP=1517;MQ=60;set=variant-variant35-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:263,241:504:99:5702,0,6664:152,111,126,115 chr1 228444565 . T A 11741.1 PASS AC=2;AF=1;AN=2;DP=26581;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,663:663:99:19064,1976,0:0,0,301,362 chr1 228456147 . T C 1568.97 PASS AC=1;AF=0.725;AN=2;DP=7980;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:111,100:211:99:2695,0,2958:65,46,56,44 chr1 228461129 . A G 3233.38 PASS AC=1;AF=0.72;AN=2;DP=22602;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:311,274:585:99:6549,0,7789:157,154,146,128 chr1 228461381 . T C 1117.76 PASS AC=1;AF=0.5;AN=2;DP=497;FractionInformativeReads=1;MQ=60;set=variant3-variant22-variant25-variant34-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:43,38:81:99:1152,0,1207:19,24,12,26 chr1 228461408 . A AG 1405.81 PASS AC=2;AF=1;AN=2;DP=2780;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,58:59:99:1943,171,0:0,1,24,34 chr1 228464248 . T G 3602.24 PASS AC=1;AF=0.72;AN=2;DP=10025;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:129,117:246:99:2652,0,3087:71,58,67,50 chr1 228464276 . T C 3972.54 PASS AC=1;AF=0.72;AN=2;DP=11227;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:132,132:264:99:3205,0,3040:66,66,75,57 chr1 228464842 . C G 2767.85 PASS AC=1;AF=0.72;AN=2;DP=8607;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:89,103:192:99:2830,0,2200:49,40,56,47 chr1 228465370 . T G 1557.9 PASS AC=1;AF=0.72;AN=2;DP=7064;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:92,114:206:99:2969,0,2367:43,49,50,64 chr1 228465403 . G T 1316.09 PASS AC=1;AF=0.5;AN=2;DP=1503;MQ=60;set=variant22-variant25-variant26-variant31-variant34-variant35-variant37-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:95,98:193:99:2476,0,2414:44,51,39,59 chr1 228467711 . G A 2604.35 PASS AC=1;AF=0.5;AN=2;DP=1106;MQ=60;set=variant22-variant25-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:118,124:242:99:3222,0,3071:67,51,72,52 chr1 228468244 . G A 3120.85 PASS AC=1;AF=0.5;AN=2;DP=1436;MQ=60;set=variant22-variant25-variant34-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:120,146:266:99:3728,0,2959:55,65,74,72 chr1 228469870 . C T 1799.33 PASS AC=1;AF=0.5;AN=2;DP=672;MQ=60;set=variant22-variant25-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:83,68:151:99:1647,0,2174:29,54,26,42 chr1 228472259 . G T 559.61 PASS AC=1;AF=0.5;AN=2;DP=305;FractionInformativeReads=1;MQ=60;set=variant22-variant25-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:30,27:57:99:691,0,756:13,17,14,13 chr1 228475715 . A G 2863.47 PASS AC=1;AF=0.5;AN=2;DP=753;MQ=60;set=variant22-variant25-variant35 GT:AD:DP:GQ:PL:SB 0/1:146,111:257:99:2682,0,3604:82,64,58,53 chr1 228476366 . G T 3566.82 PASS AC=1;AF=0.5;AN=2;DP=1136;MQ=60;set=variant22-variant25-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:132,112:244:99:4297,0,6468:73,59,54,58 chr1 228476367 . A T 3566.91 PASS AC=1;AF=0.5;AN=2;DP=1134;MQ=60;set=variant22-variant25-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:129,115:244:99:4297,0,6468:70,59,55,60 chr1 228476414 . G A 2731.12 PASS AC=1;AF=0.5;AN=2;DP=1265;MQ=60;set=variant22-variant25-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:151,130:281:99:3204,0,3897:80,71,68,62 chr1 228480282 . A G 1956.99 PASS AC=1;AF=0.707;AN=2;DP=8741;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:115,98:213:99:2542,0,2992:62,53,56,42 chr1 228480964 . A G 5231.05 PASS AC=1;AF=0.633;AN=2;DP=4339;MQ=60;set=variant3-variant6-variant8-variant9-variant10-variant13-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:86,84:170:99:2125,0,2149:54,32,53,31 chr1 228482285 . T C 1611.76 PASS AC=1;AF=0.707;AN=2;DP=3156;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,35:77:99:1078,0,1305:14,28,10,25 chr1 228486524 . G A 1053.32 PASS AC=1;AF=0.5;AN=2;DP=331;FractionInformativeReads=1;MQ=60;set=variant22-variant25-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:41,36:77:99:1057,0,1201:12,29,10,26 chr1 228492220 . C T 4392.46 PASS AC=1;AF=0.5;AN=2;DP=1176;MQ=60;set=variant22-variant25-variant35 GT:AD:DP:GQ:PL:SB 0/1:215,218:433:99:5113,0,5265:106,109,107,111 chr1 228492412 . C T 1159.84 PASS AC=1;AF=0.5;AN=2;DP=88;FS=0.943;FractionInformativeReads=1;MQ=60;MQRankSum=-0.029;QD=13.18;ReadPosRankSum=-0.614;SOR=0.826;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:46,42:88:99:1188,0,1359:11,35,9,33 chr1 228494382 . T G,C 913.18 PASS AC=0,1;AF=0.39,0.317;AN=2;DP=4578;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:116:99:20,40,22,34 chr1 228494696 . G A 2238.09 PASS AC=1;AF=0.565;AN=2;DP=3417;MQ=60;set=variant3-variant6-variant8-variant9-variant10-variant13-variant15-variant16-variant18-variant19-variant22-variant25-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:77,78:155:99:1992,0,1949:45,32,40,38 chr1 228495696 . T C 88.74 PASS AC=1;AF=0.707;AN=2;DP=1047;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,18:33:99:492,0,464:13,2,12,6 chr1 228497053 . A G 813.29 PASS AC=1;AF=0.707;AN=2;DP=3864;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,57:107:99:1543,0,1302:25,25,33,24 chr1 228497286 . C A 1062.76 PASS AC=1;AF=0.5;AN=2;DP=466;FractionInformativeReads=1;MQ=60;set=variant22-variant25-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:54,49:103:99:1176,0,1388:20,34,18,31 chr1 228503677 . A G 2547.96 PASS AC=1;AF=0.707;AN=2;DP=11128;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:130,166:296:99:4175,0,3136:75,55,97,69 chr1 228504472 . T C 1382.52 PASS AC=1;AF=0.707;AN=2;DP=5676;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:96,83:179:99:2064,0,2325:52,44,44,39 chr1 228504701 . G GCTCC 439.95 PASS AC=1;AF=0.713;AN=2;DP=1100;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,19:38:99:720,0,1114:6,13,5,14 chr1 228505204 . G A 3220.02 PASS AC=1;AF=0.565;AN=2;DP=4295;MQ=60;set=variant3-variant6-variant8-variant9-variant10-variant13-variant15-variant16-variant18-variant19-variant22-variant25-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:109,111:220:99:2439,0,2720:60,49,56,55 chr1 228505668 . C G 2999.4 PASS AC=1;AF=0.707;AN=2;DP=10705;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:164,159:323:99:3796,0,4091:90,74,90,69 chr1 228505699 . T C 3038.83 PASS AC=1;AF=0.707;AN=2;DP=12207;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:192,166:358:99:3928,0,4456:104,88,87,79 chr1 228505727 . C T 3116.51 PASS AC=1;AF=0.5;AN=2;DP=1664;MQ=60;set=variant22-variant25-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:205,167:372:99:3965,0,4950:101,104,78,89 chr1 228505925 . G A 574.25 PASS AC=1;AF=0.5;AN=2;DP=149;FractionInformativeReads=1;MQ=60;set=variant22-variant25-variant35 GT:AD:DP:GQ:PL:SB 0/1:26,21:47:99:546,0,825:6,20,6,15 chr1 228509427 . A G 2140.92 PASS AC=1;AF=0.707;AN=2;DP=11236;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:141,157:298:99:4008,0,3391:71,70,76,81 chr1 228522029 . TA T 70.54 PASS AC=1;AF=0.613;AN=2;DP=634;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant12-variant14-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:10,14:24:99:492,0,330:10,0,13,1 chr1 228523412 . G A 734.73 PASS AC=1;AF=0.5;AN=2;DP=413;FractionInformativeReads=1;MQ=60;set=variant9-variant22-variant25-variant27-variant35-variant37-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:21,28:49:99:775,0,553:14,7,19,9 chr1 228523442 . T C 733.14 PASS AC=1;AF=0.597;AN=2;DP=2287;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant12-variant14-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:33,48:81:99:1921,0,1541:19,14,30,18 chr1 228523447 . T C 730.13 PASS AC=1;AF=0.83;AN=2;DP=3406;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:35,50:85:99:1952,0,1570:21,14,31,19 chr1 228523618 . G A 786.57 PASS AC=1;AF=0.597;AN=2;DP=2443;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant12-variant14-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:26,58:84:99:1399,0,622:8,18,24,34 chr1 228525898 . C G 372.19 PASS AC=1;AF=0.597;AN=2;DP=1836;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant12-variant14-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:34,32:66:99:769,0,924:17,17,18,14 chr1 228526665 . T C 640.97 PASS AC=1;AF=0.597;AN=2;DP=2832;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant12-variant14-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:45,44:89:99:1195,0,1065:17,28,17,27 chr1 228526742 . CCACA CCACACA,CCACACACACA,CCACACACA,CCA,C,CCACACACACACA 57.98 PASS AC=0,0,0,0,1,0;AF=0.171,0.186,0.2,0.1,0.043,0.014;AN=2;DP=627;set=variant-variant2-variant3-variant5-variant6-variant8-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/5:8:99:1,3,0,4 chr1 228527970 . C G 57.27 PASS AC=1;AF=0.5;AN=2;DP=145;FractionInformativeReads=1;MQ=60;set=variant9-variant22-variant25-variant27-variant35-variant37-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:23,12:35:99:232,0,676:10,13,6,6 chr1 228528563 . C G 1260.52 PASS AC=1;AF=0.597;AN=2;DP=4911;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant12-variant14-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:127,91:218:99:2085,0,3062:56,71,39,52 chr1 228529129 . C A 907.44 PASS AC=1;AF=0.5;AN=2;DP=875;FractionInformativeReads=1;MQ=60;set=variant9-variant22-variant25-variant27-variant35-variant37-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:67,64:131:99:1942,0,2037:39,28,36,28 chr1 228529429 . A AGACGGCTCAGCCAGCCTGTGGCATGG 497.24 PASS AC=1;AF=0.603;AN=2;DP=967;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant12-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant35-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:21,17:38:99:673,0,1269:3,18,1,16 chr1 228538470 . C G 1234 PASS AC=1;AF=0.5;AN=2;DP=711;set=variant9-variant22-variant25-variant27-variant35-variant37-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:50,47:97:99:1238,0,1254:34,16,31,16 chr1 228538968 . C T 332.37 PASS AC=1;AF=0.55;AN=2;DP=195;FractionInformativeReads=1;MQ=60;set=variant9-variant12-variant20-variant22-variant25-variant27-variant35-variant37-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:5,10:15:99:263,0,138:4,1,6,4 chr1 228539300 . G A 134.62 PASS AC=2;AF=0.72;AN=2;DP=1137;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1114,107,0:0,0,13,23 chr1 228543800 . C T 992.35 PASS AC=1;AF=0.5;AN=2;DP=699;MQ=60;set=variant9-variant22-variant25-variant27-variant35-variant37-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:40,65:105:99:1753,0,908:26,14,43,22 chr1 228547256 . G A 917.72 PASS AC=1;AF=0.5;AN=2;DP=809;MQ=60;set=variant9-variant22-variant25-variant27-variant35-variant37-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:48,61:109:99:1529,0,1198:30,18,28,33 chr1 228547901 . C T 2618.09 PASS AC=1;AF=0.556;AN=2;DP=4886;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant31-variant32-variant35-variant36-variant37-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:139,92:231:99:2192,0,3693:70,69,46,46 chr1 228548197 . G A 2191.16 PASS AC=1;AF=0.5;AN=2;DP=1611;set=variant9-variant22-variant25-variant27-variant35-variant37-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:101,105:206:99:2772,0,2920:58,43,67,38 chr1 228550426 . C T 1506.45 PASS AC=1;AF=0.5;AN=2;DP=731;MQ=60;set=variant9-variant22-variant25-variant27-variant35-variant37-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:61,60:121:99:1503,0,1537:19,42,20,40 chr1 228552571 . T C 1900.63 PASS AC=1;AF=0.556;AN=2;DP=1444;MQ=60;set=variant9-variant22-variant25-variant27-variant35-variant37-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:87,114:201:99:2654,0,2004:51,36,63,51 chr1 228553651 . T C 475.1 PASS AC=1;AF=0.556;AN=2;DP=364;MQ=60;set=variant9-variant22-variant25-variant27-variant35-variant37-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:35,27:62:99:962,0,1013:28,7,26,1 chr1 228553675 . C T 829.11 PASS AC=1;AF=0.556;AN=2;DP=570;FractionInformativeReads=1;MQ=60;set=variant9-variant22-variant25-variant27-variant35-variant37-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:43,44:87:99:1413,0,1431:36,7,37,7 chr1 228555794 . A G 187.37 PASS AC=1;AF=0.556;AN=2;DP=140;MQ=60;set=variant9-variant22-variant25-variant27-variant35-variant37-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:8,8:16:99:265,0,226:4,4,4,4 chr1 228556403 . C T 1244.09 PASS AC=1;AF=0.5;AN=2;DP=837;FractionInformativeReads=1;MQ=60;set=variant9-variant22-variant25-variant27-variant35-variant37-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:60,55:115:99:1275,0,1483:37,23,29,26 chr1 228556788 . C T 421.27 PASS AC=1;AF=0.583;AN=2;DP=1615;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,21:55:99:563,0,933:22,12,11,10 chr1 228559994 . C T 3026.26 PASS AC=2;AF=0.645;AN=2;DP=11916;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,358:358:99:10486,1068,0:0,0,172,186 chr1 228560139 . A G 3565.31 PASS AC=2;AF=0.943;AN=2;DP=5330;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,145:145:99:4668,434,0:0,0,64,81 chr1 228560700 . T C 1357.63 PASS AC=2;AF=0.707;AN=2;DP=5200;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,164:164:99:4825,490,0:0,0,89,75 chr1 228564884 . G A 5054.78 PASS AC=1;AF=0.5;AN=2;DP=2693;MQ=60;set=variant9-variant22-variant25-variant27-variant35-variant37-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:216,217:433:99:5096,0,5411:100,116,99,118 chr1 228565445 . C A 1364.42 PASS AC=1;AF=0.5;AN=2;DP=758;MQ=60;set=variant9-variant22-variant25-variant27-variant35-variant37-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:46,61:107:99:1541,0,1195:13,33,25,36 chr1 228583954 . GGGTCTGA G 608.61 PASS AC=1;AF=0.5;AN=2;DP=464;MQ=60;set=variant9-variant22-variant25-variant27-variant35-variant37-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:31,32:63:99:1251,0,2607:14,17,15,17 chr1 228588654 . G A 757.69 PASS AC=1;AF=0.5;AN=2;DP=409;MQ=60;set=variant9-variant22-variant25-variant27-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:48,33:81:99:735,0,1337:27,21,17,16 chr1 228588680 . A C 983.34 PASS AC=1;AF=0.5;AN=2;DP=911;MQ=60;set=variant3-variant9-variant10-variant18-variant22-variant25-variant27-variant35-variant37-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,29:88:99:709,0,1563:32,27,17,12 chr1 228593222 . T G 1370.08 PASS AC=1;AF=0.5;AN=2;DP=797;MQ=60;set=variant9-variant22-variant25-variant27-variant35-variant37-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:56,45:101:99:1028,0,1174:32,24,26,19 chr1 228594569 . G T 376.72 PASS AC=1;AF=0.571;AN=2;DP=70;set=variant3-variant12-variant13-variant35-variant37-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:7,5:12:99:118,0,164:3,4,2,3 chr1 228597130 . G A 284.11 PASS AC=1;AF=0.5;AN=2;DP=84;FractionInformativeReads=1;MQ=60;set=variant9-variant22-variant25-variant27-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:6,8:14:99:237,0,167:1,5,2,6 chr1 228601638 . T C 1133.15 PASS AC=1;AF=0.563;AN=2;DP=2448;set=variant3-variant6-variant8-variant9-variant10-variant13-variant16-variant18-variant19-variant22-variant25-variant27-variant28-variant29-variant30-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:75,66:141:99:1408,0,1875:30,45,30,36 chr1 228602660 . G C 2071.72 PASS AC=1;AF=0.545;AN=2;DP=1706;MQ=60;set=variant9-variant10-variant18-variant22-variant25-variant27-variant35-variant37-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:105,94:199:99:2293,0,2325:51,54,44,50 chr1 228603029 . C A 713.92 PASS AC=1;AF=0.537;AN=2;DP=2803;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant21-variant23-variant25-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:80,82:162:99:1859,0,1984:37,43,40,42 chr1 228604248 . A G 424.2 PASS AC=1;AF=0.545;AN=2;DP=646;MQ=60;set=variant9-variant10-variant18-variant22-variant25-variant27-variant35-variant37-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:46,37:83:99:843,0,1125:18,28,15,22 chr1 228612444 . A G 896.49 PASS AC=1;AF=0.886;AN=2;DP=1483;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:19,18:37:99:505,0,578:14,5,14,4 chr1 228612838 . G T 2635.69 PASS AC=1;AF=0.849;AN=2;DP=8146;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:149,109:258:99:2788,0,4241:79,70,59,50 chr1 228613052 . T C 2394.73 PASS AC=1;AF=0.886;AN=2;DP=5635;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:77,91:168:99:2150,0,1951:32,45,36,55 chr1 228645063 . A G 4309.36 PASS AC=1;AF=0.841;AN=2;DP=5718;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:88,96:184:99:2183,0,2371:58,30,56,40 chr1 228645252 . G A 671.45 PASS AC=1;AF=0.5;AN=2;DP=1916;set=variant-variant13-filterInvariant14-variant16-variant20-variant28-filterInvariant35 GT:AD:DP:GQ:PL:SB 0/1:311,29:340:99:277,0,16385:156,155,12,17 chr1 228645267 . C A 583.28 PASS AC=1;AF=0.5;AN=2;DP=1922;FractionInformativeReads=1;set=variant-variant13-filterInvariant14-variant16-variant20-filterInvariant28-filterInvariant35 GT:AD:DP:GQ:PL:SB 0/1:314,30:344:99:290,0,17118:153,161,10,20 chr1 228681749 . C T 3828.71 PASS AC=2;AF=0.65;AN=2;DP=4033;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant31-variant33-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,155:155:99:4709,464,0:0,0,77,78 chr1 228682330 . C G 2867.51 PASS AC=2;AF=0.852;AN=2;DP=3833;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,78:78:99:2573,234,0:0,0,48,30 chr1 228699477 . T C 2201.92 PASS AC=2;AF=0.691;AN=2;DP=7645;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,224:224:99:6960,670,0:0,0,125,99 chr1 228871693 . C T 2890.71 PASS AC=1;AF=0.529;AN=2;DP=4320;MQ=60;set=variant4-variant8-variant12-variant17-variant21-variant23-variant24-variant26-variant31-variant32-variant35-variant36-variant37-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:148,154:302:99:3281,0,3567:90,58,91,63 chr1 228873640 . GT G 421.75 PASS AC=1;AF=0.652;AN=2;DP=513;MQ=60;set=variant4-variant8-variant10-variant12-variant13-variant17-variant18-variant21-variant23-variant24-variant26-variant27-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,10:18:99:320,0,245:2,6,1,9 chr1 228880021 . C T 3267.89 PASS AC=1;AF=0.529;AN=2;DP=3733;MQ=60;set=variant4-variant8-variant12-variant17-variant21-variant23-variant24-variant26-variant31-variant32-variant35-variant36-variant37-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:150,88:238:99:1930,0,3665:77,73,37,51 chr1 228880098 . T A 1729.37 PASS AC=1;AF=0.529;AN=2;DP=2061;MQ=60;set=variant4-variant8-variant12-variant17-variant21-variant23-variant24-variant26-variant31-variant32-variant35-variant36-variant37-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:86,39:125:99:814,0,2350:37,49,15,24 chr1 228880135 . C T 923.44 PASS AC=1;AF=0.529;AN=2;DP=1324;MQ=60;set=variant4-variant8-variant12-variant17-variant21-variant23-variant24-variant26-variant31-variant32-variant35-variant36-variant37-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,20:85:99:542,0,1905:27,38,7,13 chr1 228880296 . G A 358.56 PASS AC=1;AF=0.526;AN=2;DP=1069;MQ=60;set=variant4-variant8-variant10-variant12-variant13-variant17-variant21-variant23-variant24-variant26-variant31-variant32-variant35-variant36-variant37-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,24:69:99:578,0,1238:21,24,14,10 chr1 228880466 . G A 814.34 PASS AC=1;AF=0.529;AN=2;DP=962;MQ=60;set=variant4-variant8-variant12-variant17-variant21-variant23-variant24-variant26-variant31-variant32-variant35-variant36-variant37-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,27:61:99:751,0,1062:19,15,18,9 chr1 228881129 . A G 794.09 PASS AC=1;AF=0.652;AN=2;DP=926;FractionInformativeReads=1;MQ=60;set=variant4-variant8-variant10-variant12-variant13-variant17-variant18-variant21-variant23-variant24-variant26-variant27-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,17:41:99:439,0,668:12,12,8,9 chr1 229178058 . C T 104.64 PASS AC=1;AF=0.652;AN=2;DP=365;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,4:6:74:113,0,74:2,0,3,1 chr1 229385256 . G A 277.83 PASS AC=1;AF=0.655;AN=2;DP=547;MQ=60;set=variant-variant2-variant5-variant7-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant33-variant35-variant37-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,8:17:99:257,0,287:7,2,7,1 chr1 229385897 . C CGTGTGT,CGT,CGTGTGTGTGT,CGTGT,CGTGTGTGT 79.67 PASS AC=0,0,1,0,0;AF=0.212,0.154,0.308,0.038,0.038;AN=2;DP=250;MQ=60;set=variant2-variant4-variant5-variant12-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant33-variant34-variant35-variant36-variant39-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/3:10:99:3,4,2,1 chr1 229386237 . T A 814.21 PASS AC=1;AF=0.65;AN=2;DP=1185;MQ=60;set=variant-variant5-variant7-variant11-variant12-variant15-variant18-variant19-variant21-variant22-variant23-variant24-variant27-variant29-variant33-variant35-variant37-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:32,34:66:99:962,0,950:17,15,22,12 chr1 229407233 . G C 318.41 PASS AC=1;AF=0.655;AN=2;DP=550;MQ=60;set=variant2-variant5-variant7-variant10-variant11-variant12-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant35-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,6:15:99:139,0,337:2,7,1,5 chr1 229422193 . T C 2240.65 PASS AC=1;AF=0.773;AN=2;DP=1752;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant10-variant11-variant12-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,36:77:99:880,0,957:24,17,22,14 chr1 229438530 . CT C 39.45 DRAGENHardINDEL AC=1;AF=0.5;AN=2;DP=30;FS=0;FractionInformativeReads=0.933;MQ=60;MQRankSum=-0.252;QD=1.31;ReadPosRankSum=0.308;SOR=0.927;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:22,6:28:77:77,0,433:16,6,5,1 chr1 229438828 . G A 507.1 PASS AC=1;AF=0.79;AN=2;DP=506;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant10-variant11-variant12-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,4:13:99:100,0,276:2,7,1,3 chr1 229439639 . T A 5064.62 PASS AC=1;AF=0.672;AN=2;DP=12199;MQ=60;set=variant2-variant5-variant7-variant10-variant11-variant12-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:217,214:431:99:5369,0,5048:114,103,106,108 chr1 229440190 . C T 2279.87 PASS AC=1;AF=0.672;AN=2;DP=4155;MQ=60;set=variant2-variant5-variant7-variant10-variant11-variant12-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:79,77:156:99:2021,0,2161:29,50,29,48 chr1 229457208 . C A 9313.95 PASS AC=2;AF=1;AN=2;DP=11875;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,289:289:99:8465,863,0:0,0,144,145 chr1 229460176 . TA TAA,T 207.39 PASS AC=1,0;AF=0.517,0.017;AN=2;DP=1320;set=variant2-variant5-variant7-variant10-variant11-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant42-variant44 GT:DP:GQ:SB 0/1:26:99:10,8,6,2 chr1 229460246 . A T 1672.86 PASS AC=1;AF=0.672;AN=2;DP=3312;MQ=60;set=variant2-variant5-variant7-variant10-variant11-variant12-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,41:98:99:1217,0,1499:35,22,31,10 chr1 229461024 . C T 2336.31 PASS AC=1;AF=0.672;AN=2;DP=5474;MQ=60;set=variant2-variant5-variant7-variant10-variant11-variant12-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:115,103:218:99:2683,0,3041:44,71,38,65 chr1 229568231 . T G 685.47 PASS AC=2;AF=1;AN=2;DP=1233;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:1120,84,0:0,0,2,26 chr1 229569803 . A G 1171.48 PASS AC=2;AF=0.694;AN=2;DP=3059;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,100:100:99:4316,301,0:0,0,45,55 chr1 229569804 . G A 1171.48 PASS AC=2;AF=0.694;AN=2;DP=3023;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,100:100:99:4316,301,0:0,0,45,55 chr1 229623292 . G A 607.22 PASS AC=1;AF=0.5;AN=2;DP=58;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.322;QD=10.47;ReadPosRankSum=-0.731;SOR=0.833;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:29,29:58:99:635,0,695:13,16,12,17 chr1 229663064 . GAGGAA G 4062.01 PASS AC=2;AF=1;AN=2;DP=3625;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:3316,229,0:0,0,39,37 chr1 229730452 . G A 4087.09 PASS AC=1;AF=0.625;AN=2;DP=3582;MQ=60;set=variant2-variant3-variant4-variant6-variant8-variant9-variant11-variant14-variant15-variant16-variant17-variant18-variant20-variant23-variant24-variant27-variant29-variant34-variant35-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:93,76:169:99:1723,0,2296:47,46,35,41 chr1 229735022 . G GT 2832.15 PASS AC=2;AF=0.636;AN=2;DP=5618;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:9,144:153:99:3560,243,0:3,6,50,94 chr1 229737227 . G A 7026.46 PASS AC=2;AF=0.625;AN=2;DP=7189;MQ=60;set=variant2-variant3-variant4-variant6-variant8-variant9-variant11-variant14-variant15-variant16-variant17-variant18-variant20-variant23-variant24-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,319:319:99:10169,955,0:0,0,122,197 chr1 229738170 . T G 3605.86 PASS AC=2;AF=0.652;AN=2;DP=4405;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,140:140:99:4285,420,0:0,0,74,66 chr1 229738236 . G A 1369.73 PASS AC=2;AF=0.788;AN=2;DP=5426;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,149:149:99:4551,446,0:0,0,78,71 chr1 229746019 . C T 3088.17 PASS AC=2;AF=0.652;AN=2;DP=3079;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,93:93:99:2761,278,0:0,0,42,51 chr1 229750343 . T G 580.7 PASS AC=2;AF=0.591;AN=2;DP=1848;MQ=60;set=variant2-variant4-variant6-variant8-variant9-variant11-variant14-variant15-variant16-variant20-variant23-variant24-variant27-variant28-variant29-variant33-variant34-variant35-variant37-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,103:104:99:3251,301,0:0,1,33,70 chr1 229762054 . T A 3191.04 PASS AC=2;AF=0.643;AN=2;DP=3613;MQ=60;set=variant2-variant3-variant4-variant6-variant8-variant9-variant11-variant14-variant15-variant16-variant17-variant18-variant20-variant23-variant24-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,153:153:99:4460,454,0:0,0,73,80 chr1 229768297 . C T 398.91 PASS AC=2;AF=0.652;AN=2;DP=904;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:1053,90,0:0,0,5,25 chr1 229772693 . T G 3468.93 PASS AC=2;AF=0.652;AN=2;DP=4790;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,173:173:99:5794,519,0:0,0,100,73 chr1 229781532 . T G 591.69 PASS AC=2;AF=0.661;AN=2;DP=548;MQ=60;set=variant2-variant3-variant4-variant6-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant27-variant28-variant29-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:638,51,0:0,0,14,3 chr1 229781744 . T C 4710.12 PASS AC=2;AF=0.652;AN=2;DP=7106;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,241:241:99:7223,722,0:0,0,110,131 chr1 229783236 . T C 3333.64 PASS AC=2;AF=0.932;AN=2;DP=3436;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,73:73:99:3318,226,0:0,0,42,31 chr1 229783240 . T C 4417.22 PASS AC=2;AF=0.636;AN=2;DP=2574;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:3368,232,0:0,0,45,31 chr1 229790048 . A G 1783.76 PASS AC=2;AF=0.653;AN=2;DP=4892;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,129:129:99:3978,387,0:0,0,64,65 chr1 229795070 . T G 661.86 PASS AC=2;AF=0.653;AN=2;DP=3291;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,88:88:99:2683,264,0:0,0,35,53 chr1 229795330 . T C 939.01 PASS AC=2;AF=0.625;AN=2;DP=2493;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant35-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,98:98:99:3109,294,0:0,0,54,44 chr1 229795683 . AT A 695.61 PASS AC=2;AF=0.609;AN=2;DP=2005;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant35-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:1800,180,0:0,0,41,19 chr1 229795714 . T C 1075.02 PASS AC=2;AF=0.579;AN=2;DP=1817;MQ=60;set=variant2-variant6-variant9-variant11-variant12-variant14-variant15-variant16-variant23-variant24-variant27-variant28-variant29-variant33-variant35-variant37-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,94:94:99:3448,282,0:0,0,70,24 chr1 229795966 . AT A 1223.67 PASS AC=2;AF=0.625;AN=2;DP=3344;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant35-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,105:105:99:3595,316,0:0,0,27,78 chr1 230415025 . A G 2412.05 PASS AC=2;AF=0.65;AN=2;DP=6726;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,238:238:99:6835,711,0:0,0,125,113 chr1 230415293 . C T 779.12 PASS AC=1;AF=0.536;AN=2;DP=1020;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant10-variant11-variant12-variant18-variant23-variant29-variant31-variant32-variant34-variant35-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:56,31:87:99:809,0,1798:37,19,19,12 chr1 230416320 . C T 511.37 PASS AC=1;AF=0.5;AN=2;DP=314;FractionInformativeReads=1;MQ=60;set=variant10-variant11-variant12-variant18-variant23-variant29-variant31-variant32-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:16,17:33:99:570,0,413:6,10,7,10 chr1 230416399 . G T 39.19 PASS AC=1;AF=0.625;AN=2;DP=642;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant18-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:14,15:29:99:379,0,395:7,7,7,8 chr1 230416744 . G A 847.07 PASS AC=1;AF=0.542;AN=2;DP=1220;MQ=60;set=variant2-variant10-variant11-variant12-variant18-variant23-variant29-variant31-variant32-variant35-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:52,72:124:99:1649,0,1339:21,31,38,34 chr1 230416832 . T A 920.65 PASS AC=1;AF=0.542;AN=2;DP=1138;MQ=60;set=variant2-variant10-variant11-variant12-variant18-variant23-variant29-variant31-variant32-variant35-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:49,61:110:99:1418,0,1246:27,22,32,29 chr1 230416950 . C T 1081.22 PASS AC=1;AF=0.5;AN=2;DP=1062;FractionInformativeReads=1;MQ=60;set=variant10-variant11-variant12-variant18-variant23-variant31-variant32-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:74,59:133:99:1429,0,1882:40,34,29,30 chr1 230416953 . A G 1086.16 PASS AC=2;AF=0.625;AN=2;DP=3360;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant18-variant22-variant23-variant25-variant26-variant28-variant31-variant32-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,131:131:99:4866,394,0:0,0,67,64 chr1 230417294 . A G 791.28 PASS AC=1;AF=0.5;AN=2;DP=783;MQ=60;set=variant10-variant11-variant12-variant18-variant23-variant31-variant32-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:43,42:85:99:1020,0,1066:23,20,20,22 chr1 230417371 . C T 953.45 PASS AC=1;AF=0.5;AN=2;DP=1838;MQ=60;set=variant3-variant5-variant6-variant8-variant9-variant12-variant13-variant16-variant19-variant20-variant21-variant22-variant25-variant26-variant30-variant32-variant33-variant34-variant35-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:41,54:95:99:1290,0,956:23,18,26,28 chr1 230417408 . T C 723.97 PASS AC=2;AF=0.586;AN=2;DP=2532;MQ=60;set=variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,88:88:99:2705,262,0:0,0,44,44 chr1 230417557 . T C 1517.35 PASS AC=2;AF=0.845;AN=2;DP=3359;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:3144,214,0:0,0,37,34 chr1 230417560 . A G 1517.35 PASS AC=2;AF=0.845;AN=2;DP=3349;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:3144,214,0:0,0,36,35 chr1 230417664 . C G 2224.78 PASS AC=1;AF=0.556;AN=2;DP=4161;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant18-variant22-variant23-variant25-variant26-variant28-variant31-variant32-variant34-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:74,80:154:99:1918,0,1785:43,31,42,38 chr1 230417990 . T C 632.68 PASS AC=1;AF=0.5;AN=2;DP=792;MQ=60;set=variant3-variant5-variant6-variant8-variant9-variant12-variant13-variant16-variant19-variant20-variant21-variant22-variant25-variant26-variant30-variant32-variant33-variant34-variant35-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:33,13:46:99:281,0,1007:9,24,6,7 chr1 230417999 . C T 334.39 PASS AC=2;AF=0.689;AN=2;DP=1181;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,36:37:99:1428,106,0:1,0,10,26 chr1 230451331 . T C 110.44 PASS AC=1;AF=0.594;AN=2;DP=123;FractionInformativeReads=1;MQ=60;set=variant5-variant6-variant7-variant10-variant11-variant15-variant20-variant25-variant26-variant27-variant28-variant30-variant35-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:5,3:8:99:111,0,249:3,2,1,2 chr1 230451349 . T C 132.17 PASS AC=1;AF=0.594;AN=2;DP=141;FractionInformativeReads=1;MQ=60;set=variant5-variant6-variant7-variant10-variant11-variant15-variant20-variant25-variant26-variant27-variant28-variant30-variant35-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:5,3:8:99:111,0,266:3,2,1,2 chr1 230451517 . G GATGT 89.09 PASS AC=2;AF=0.833;AN=2;DP=40;FS=0;MQ=60;set=variant3-variant16-variant19-variant21-variant22-variant23-variant29-variant31-variant35 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:90,6,0:0,0,1,1 chr1 230451935 . C CAT 673.24 PASS AC=2;AF=0.878;AN=2;DP=2001;set=variant-variant2-variant3-variant4-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:2358,162,0:0,0,30,20 chr1 230451978 . G A 993.77 PASS AC=2;AF=0.888;AN=2;DP=2885;set=variant-variant2-variant3-variant4-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:2108,204,0:0,0,34,34 chr1 230457347 . G A 1802.8 PASS AC=1;AF=0.5;AN=2;DP=1519;FractionInformativeReads=1;set=variant-variant7-variant9-variant11-variant14-variant18-variant20-variant23-variant24-variant27-variant30-variant34-variant35-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:60,64:124:99:1589,0,1512:36,24,37,27 chr1 230459433 . GC G 650.31 PASS AC=2;AF=0.719;AN=2;DP=2153;MQ=60;set=variant2-variant3-variant4-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1177,114,0:0,0,8,30 chr1 230460830 . T C 371.28 PASS AC=1;AF=0.5;AN=2;DP=19;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.479;QD=19.54;ReadPosRankSum=-2.24;SOR=0.593;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:7,12:19:99:400,0,213:5,2,8,4 chr1 230473103 . A C 377.27 PASS AC=2;AF=0.641;AN=2;DP=1310;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1477,129,0:0,0,10,33 chr1 230497940 . G T 1827.68 PASS AC=1;AF=0.763;AN=2;DP=3384;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,77:131:99:1814,0,1322:37,17,51,26 chr1 230498232 . C T 1084.63 PASS AC=1;AF=0.763;AN=2;DP=1426;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,22:47:99:761,0,753:5,20,2,20 chr1 230503684 . C T 1188.6 PASS AC=1;AF=0.756;AN=2;DP=2360;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,37:66:99:939,0,885:24,5,24,13 chr1 230504070 . C G 235.14 PASS AC=1;AF=0.792;AN=2;DP=363;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:99:156,0,131:0,4,0,4 chr1 230513128 . G A 2007.27 PASS AC=1;AF=0.763;AN=2;DP=2594;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,35:76:99:842,0,1084:25,16,21,14 chr1 230561700 . G GC 459.58 PASS AC=2;AF=1;AN=2;DP=681;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:658,63,0:0,0,6,15 chr1 230819155 . TAAAAA TAAAA,TAAA,TA,TAA,T 153.87 PASS AC=2,0,0,0,0;AF=0.286,0.345,0.024,0.071,0.012;AN=2;DP=693;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:DP:GQ:SB 1/1:12:2:1,1,8,2 chr1 230819479 . G T,GT 1089.82 PASS AC=0,2;AF=0.056,0.611;AN=2;DP=426;MQ=60;set=variant29-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:DP:GQ:SB 2/2:32:69:1,0,7,24 chr1 230820763 . C CACATT 3831.97 PASS AC=2;AF=0.685;AN=2;DP=1782;MQ=60;set=variant3-variant5-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant23-variant24-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39 GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:3581,243,0:0,0,55,21 chr1 230822607 . G A 203.7 PASS AC=2;AF=0.837;AN=2;DP=920;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:939,69,0:0,0,20,3 chr1 230822903 . C T 240.14 PASS AC=1;AF=0.5;AN=2;DP=138;FractionInformativeReads=1;MQ=60;set=variant5-variant13-variant16-variant18-variant26-variant33-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:5,14:19:99:504,0,168:0,5,1,13 chr1 230825942 . A G 938.31 PASS AC=2;AF=0.685;AN=2;DP=910;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant23-variant24-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39 GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1072,107,0:0,0,12,24 chr1 230828987 . C A 2067.53 PASS AC=2;AF=0.685;AN=2;DP=1268;MQ=60;set=variant3-variant5-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant23-variant24-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39 GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1164,117,0:0,0,25,14 chr1 230838258 . G A 6969.93 PASS AC=1;AF=0.577;AN=2;DP=4478;MQ=60;set=variant3-variant4-variant5-variant7-variant9-variant12-variant14-variant15-variant18-variant19-variant21-variant22-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:93,87:180:99:2087,0,2299:58,35,53,34 chr1 230838331 . G T 11127.1 PASS AC=1;AF=0.577;AN=2;DP=7098;MQ=60;set=variant3-variant4-variant5-variant7-variant9-variant12-variant14-variant15-variant18-variant19-variant21-variant22-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:152,130:282:99:3071,0,3761:85,67,70,60 chr1 230841687 . T C 1895.07 PASS AC=1;AF=0.92;AN=2;DP=4390;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:38,56:94:99:1419,0,931:22,16,32,24 chr1 230883484 . T C 564.74 PASS AC=2;AF=0.671;AN=2;DP=2838;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2132,210,0:0,0,25,45 chr1 230883499 . T C 446.73 PASS AC=2;AF=0.671;AN=2;DP=2337;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,61:61:99:1808,182,0:0,0,22,39 chr1 230910481 . CTTTCTTT CT,C 130.9 PASS AC=1,0;AF=0.357,0.143;AN=2;DP=272;set=variant2-variant7-filterInvariant29-variant33-variant35-variant37-variant39 GT:DP:GQ:SB 0/1:38:99:4,22,1,11 chr1 230914706 . C A 1552.73 PASS AC=1;AF=0.5;AN=2;DP=827;FractionInformativeReads=1;MQ=60;set=variant2-variant9-variant14-variant21-variant24-variant29-variant34-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:68,51:119:99:1740,0,3500:32,36,24,27 chr1 230914729 . A C 1521.49 PASS AC=1;AF=0.579;AN=2;DP=1628;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant9-variant12-variant14-variant20-variant21-variant22-variant23-variant24-variant25-variant29-variant34-variant35-variant37-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:62,46:108:99:1655,0,3313:27,35,17,29 chr1 230916260 . C T 1008.59 PASS AC=1;AF=0.5;AN=2;DP=509;FractionInformativeReads=1;MQ=60;set=variant2-variant9-variant14-variant21-variant24-variant29-variant34-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:28,29:57:99:738,0,619:13,15,16,13 chr1 230923151 . T C 683.42 PASS AC=1;AF=0.5;AN=2;DP=590;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant9-variant14-variant21-variant24-variant29-variant34-variant35-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:19,15:34:99:388,0,562:14,5,9,6 chr1 230923187 . C G 1388.17 PASS AC=1;AF=0.5;AN=2;DP=897;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant9-variant14-variant21-variant24-variant29-variant34-variant35-variant37-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:31,28:59:99:687,0,856:21,10,17,11 chr1 230923313 . C T 1622.17 PASS AC=1;AF=0.5;AN=2;DP=1471;MQ=60;set=variant2-variant7-variant9-variant14-variant21-variant24-variant29-variant34-variant35-variant37-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:81,49:130:99:1103,0,1996:40,41,22,27 chr1 230927353 . T A 219.11 PASS AC=1;AF=0.641;AN=2;DP=721;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,9:17:99:347,0,269:7,1,9,0 chr1 230927871 . T C 233.38 PASS AC=1;AF=0.641;AN=2;DP=955;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,22:37:99:473,0,338:7,8,10,12 chr1 230928512 . C G 1323.61 PASS AC=1;AF=0.597;AN=2;DP=3539;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant10-variant11-variant12-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant30-variant32-variant33-variant34-variant35-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:73,54:127:99:1386,0,1736:46,27,33,21 chr1 230973407 . G T 115.45 PASS AC=2;AF=0.782;AN=2;DP=903;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:967,99,0:0,0,15,18 chr1 230974261 . A T 493.17 PASS AC=2;AF=0.563;AN=2;DP=769;set=variant3-variant4-variant9-variant10-variant14-variant15-variant16-variant18-variant21-variant24-variant25-variant26-variant28-variant29-variant31-filterInvariant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:79:858,79,0:0,0,17,10 chr1 230974774 . T C 1428.04 PASS AC=2;AF=0.768;AN=2;DP=4779;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,120:120:99:3922,359,0:0,0,71,49 chr1 230975454 . A G 2750.1 PASS AC=2;AF=0.788;AN=2;DP=7002;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,176:176:99:5175,527,0:0,0,99,77 chr1 231003898 . G A 428.26 PASS AC=1;AF=0.5;AN=2;DP=37;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.974;QD=11.57;ReadPosRankSum=0.603;SOR=0.368;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:22,15:37:99:456,0,770:20,2,13,2 chr1 231004431 . T C 50.26 PASS AC=2;AF=1;AN=2;DP=73;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant9-variant12-variant13-variant15-variant21-variant22-variant23-variant25-variant35-variant36-variant39-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:239,21,0:0,0,2,5 chr1 231004471 . C T 128.9 PASS AC=1;AF=0.75;AN=2;DP=35;MQ=60;set=variant16-variant35-variant36-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,4:5:30:117,0,30:0,1,3,1 chr1 231004888 . T C 996 PASS AC=1;AF=0.558;AN=2;DP=1552;MQ=60;set=variant5-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant35-variant36-variant37-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,26:76:99:565,0,1366:24,26,12,14 chr1 231042732 . T A 697.57 PASS AC=1;AF=0.691;AN=2;DP=2702;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,52:100:99:1168,0,1029:21,27,26,26 chr1 231047143 . A G 306.25 PASS AC=1;AF=0.536;AN=2;DP=495;FractionInformativeReads=1;MQ=60;set=variant5-variant7-variant9-variant13-variant18-variant21-variant22-variant24-variant26-variant28-variant35-variant36-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:20,12:32:99:270,0,455:10,10,8,4 chr1 231047310 . TAC T 400.56 PASS AC=2;AF=0.8;AN=2;DP=703;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:537,39,0:0,0,4,9 chr1 231057287 . A C 182.6 PASS AC=1;AF=0.538;AN=2;DP=177;FractionInformativeReads=1;MQ=60;set=variant5-variant7-variant9-variant13-variant18-variant21-variant22-variant24-variant26-variant35-variant36-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,4:9:99:112,0,195:0,5,1,3 chr1 231057310 . C T 43.44 PASS AC=2;AF=0.839;AN=2;DP=245;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:184,15,0:0,0,1,4 chr1 231059784 . C T 268.18 PASS AC=2;AF=0.788;AN=2;DP=801;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:414,33,0:0,0,2,9 chr1 231060736 . T C 1004.97 PASS AC=1;AF=0.703;AN=2;DP=2808;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant16-variant17-variant20-variant21-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,43:90:99:1128,0,1118:18,29,16,27 chr1 231064578 . T TCTC 253.6 PASS AC=2;AF=0.833;AN=2;DP=339;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:42:630,42,0:0,0,13,0 chr1 231064611 . G A 617.2 PASS AC=1;AF=0.719;AN=2;DP=616;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant16-variant17-variant20-variant21-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,12:24:99:441,0,313:9,3,12,0 chr1 231067236 . C T 613.27 PASS AC=1;AF=0.703;AN=2;DP=2296;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant16-variant17-variant20-variant21-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,27:66:99:675,0,1012:16,23,9,18 chr1 231067318 . G T 264.07 PASS AC=1;AF=0.703;AN=2;DP=887;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant16-variant17-variant20-variant21-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,10:30:99:267,0,550:9,11,3,7 chr1 231069348 . C T 121.23 PASS AC=1;AF=0.542;AN=2;DP=120;FractionInformativeReads=1;MQ=60;set=variant5-variant7-variant9-variant13-variant21-variant22-variant24-variant26-variant35-variant36-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,9:17:99:327,0,246:7,1,8,1 chr1 231069652 . A C 566.74 PASS AC=2;AF=0.788;AN=2;DP=1099;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,26:27:35:863,35,0:0,1,5,21 chr1 231071876 . C T 357.01 PASS AC=1;AF=0.563;AN=2;DP=361;FractionInformativeReads=1;MQ=60;set=variant5-variant18-variant21-variant26-variant35-variant36-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:26,22:48:99:554,0,749:20,6,14,8 chr1 231079429 . C T 57.42 PASS AC=1;AF=0.5;AN=2;DP=7;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.937;QD=8.2;ReadPosRankSum=0.55;SOR=0.941;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:3,4:7:86:86,0,107:3,0,4,0 chr1 231081269 . T TA 468.75 PASS AC=1;AF=0.5;AN=2;DP=164;MQ=60;set=variant20-variant21-variant35 GT:AD:DP:GQ:PL:SB 0/1:28,25:53:99:681,0,823:10,18,4,21 chr1 231081304 . T G 274.65 PASS AC=1;AF=0.686;AN=2;DP=771;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,17:34:99:569,0,525:4,13,2,15 chr1 231091972 . C T 250.87 PASS AC=1;AF=0.646;AN=2;DP=493;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant12-variant14-variant15-variant17-variant20-variant21-variant23-variant24-variant27-variant28-variant29-variant33-variant35-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,11:31:99:237,0,580:14,6,7,4 chr1 231093785 . CT C 366.45 PASS AC=1;AF=0.77;AN=2;DP=784;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,13:24:99:303,0,244:9,2,10,3 chr1 231094050 . GAA GA,GAAA,G 355.26 PASS AC=1,0,0;AF=0.443,0.071,0.043;AN=2;DP=1839;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-filterInvariant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-filterInvariant20-variant22-variant23-variant25-variant26-filterInvariant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-filterInvariant39-filterInvariant40-variant41-variant42-variant43 GT:DP:GQ:SB 0/1:32:99:5,12,4,11 chr1 231154921 . C CT,CTT,CTTT 5210.18 PASS AC=1,1,0;AF=0.545,0.398,0.011;AN=2;DP=11192;set=Intersection GT:DP:GQ:SB 1/2:252:99:8,4,109,131 chr1 231161817 . TA TAA,T,TAAA 36.59 PASS AC=1,0,0;AF=0.21,0.242,0.113;AN=2;DP=710;set=variant-variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-filterInvariant15-variant17-variant20-variant22-variant23-variant24-variant26-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:17:52:4,2,6,5 chr1 231176064 . GC G 248.13 PASS AC=1;AF=0.591;AN=2;DP=232;MQ=60;set=variant2-variant4-variant7-variant10-variant15-variant18-variant21-variant24-variant25-variant27-variant28-variant31-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,8:10:32:218,0,32:0,2,3,5 chr1 231297992 . A G 788.23 PASS AC=2;AF=1;AN=2;DP=1109;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:709,78,0:0,0,14,12 chr1 231298031 . C G 1031.49 PASS AC=2;AF=1;AN=2;DP=1172;FS=0;MQ=60;MQRankSum=-1.448;ReadPosRankSum=0.869;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,26:26:81:1212,81,0:0,0,15,11 chr1 231298037 . T G 1031.49 PASS AC=2;AF=1;AN=2;DP=1158;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:1273,87,0:0,0,17,12 chr1 231323140 . T A 151.77 PASS AC=2;AF=1;AN=2;DP=311;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:189,18,0:0,0,4,2 chr1 231352767 . A G 1577.36 PASS AC=1;AF=0.625;AN=2;DP=1689;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant16-variant18-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,30:61:99:753,0,856:17,14,16,14 chr1 231353589 . A G 2918.67 PASS AC=1;AF=0.583;AN=2;DP=3335;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant13-variant14-variant16-variant18-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant33-variant35-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:89,77:166:99:1731,0,2188:40,49,33,44 chr1 231355058 . C T 1067.13 PASS AC=1;AF=0.583;AN=2;DP=1553;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant13-variant14-variant16-variant18-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant33-variant35-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,36:76:99:845,0,1004:19,21,19,17 chr1 231355070 . G A 978.27 PASS AC=1;AF=0.638;AN=2;DP=1864;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant16-variant18-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,34:72:99:739,0,948:18,20,17,17 chr1 231355912 . G T 1204.33 PASS AC=1;AF=0.533;AN=2;DP=1359;MQ=60;set=variant-variant3-variant6-variant8-variant14-variant16-variant20-variant21-variant23-variant27-variant30-variant35-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,51:98:99:1929,0,3686:22,25,19,32 chr1 231355918 . C G 4342.72 PASS AC=1;AF=0.625;AN=2;DP=2425;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant10-variant13-variant14-variant16-variant18-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,48:95:99:1911,0,3670:22,25,18,30 chr1 231355919 . G T 4342.72 PASS AC=1;AF=0.625;AN=2;DP=2394;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant10-variant13-variant14-variant16-variant18-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,48:94:99:1890,0,3673:21,25,18,30 chr1 231356559 . A G 753.41 PASS AC=1;AF=0.625;AN=2;DP=1521;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant10-variant13-variant14-variant16-variant18-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,31:73:99:785,0,1104:21,21,19,12 chr1 231357102 . G C 4557.02 PASS AC=1;AF=0.58;AN=2;DP=2154;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant13-variant14-variant16-variant18-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant33-variant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,38:91:99:1499,0,2897:22,31,17,21 chr1 231357109 . C G 4744.67 PASS AC=1;AF=0.58;AN=2;DP=2047;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant13-variant14-variant16-variant18-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant33-variant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,39:88:99:1467,0,2884:21,28,20,19 chr1 231360962 . T C 1493.3 PASS AC=1;AF=0.583;AN=2;DP=1113;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant6-variant8-variant13-variant14-variant16-variant18-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant33-variant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,22:64:99:613,0,1078:21,21,8,14 chr1 231361110 . C T 1438.05 PASS AC=1;AF=0.5;AN=2;DP=792;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant21-variant24-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:51,37:88:99:989,0,1289:29,22,25,12 chr1 231362923 . G A 1409.18 PASS AC=1;AF=0.583;AN=2;DP=1868;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant8-variant13-variant14-variant16-variant18-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant33-variant35-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,46:82:99:1137,0,887:15,21,18,28 chr1 231377081 . C T 2116.78 PASS AC=1;AF=0.694;AN=2;DP=3330;MQ=60;set=variant-variant2-variant4-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,37:87:99:770,0,1349:30,20,21,16 chr1 231400905 . A G 103.54 PASS AC=1;AF=0.781;AN=2;DP=68;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant7-variant10-variant16-variant17-variant20-variant21-variant25-variant27-variant28-variant29-variant32-variant35-variant37-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:77:114,0,77:2,1,2,1 chr1 231401596 . T C 2097.64 PASS AC=1;AF=0.681;AN=2;DP=2898;MQ=60;set=variant-variant2-variant4-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,44:80:99:1124,0,844:13,23,17,27 chr1 231401902 . G A 4926.56 PASS AC=1;AF=0.708;AN=2;DP=5534;MQ=60;set=variant-variant2-variant4-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:81,91:172:99:2089,0,1899:44,37,50,41 chr1 231406295 . T C 694.22 PASS AC=1;AF=0.681;AN=2;DP=535;MQ=60;set=variant-variant2-variant4-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,5:20:99:125,0,427:11,4,4,1 chr1 231408091 . A G 1671.78 PASS AC=1;AF=0.55;AN=2;DP=2425;MQ=60;set=variant-variant2-variant4-variant8-variant15-variant16-variant19-variant20-variant21-variant23-variant25-variant29-variant32-variant35-variant36-variant37-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:63,82:145:99:2098,0,1615:38,25,45,37 chr1 231410866 . T A 76.69 PASS AC=1;AF=0.5;AN=2;DP=6;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.406;QD=12.78;ReadPosRankSum=0.406;SOR=0.693;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:99:105,0,105:3,0,3,0 chr1 231468606 . A G 5952.04 PASS AC=2;AF=0.684;AN=2;DP=15319;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,418:420:99:12413,1208,0:1,1,233,185 chr1 231468953 . G A 3514.47 PASS AC=2;AF=0.718;AN=2;DP=9835;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,264:264:99:8498,791,0:0,0,125,139 chr1 231470650 . T C 6602.35 PASS AC=2;AF=0.684;AN=2;DP=16783;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,475:475:99:14111,1423,0:0,0,225,250 chr1 231470772 . A G 1936.45 PASS AC=2;AF=0.684;AN=2;DP=3448;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,94:94:99:3521,281,0:0,0,15,79 chr1 231472835 . A C 3652.63 PASS AC=1;AF=0.5;AN=2;DP=257;FS=0;FractionInformativeReads=0.996;MQ=60;MQRankSum=1.585;QD=14.21;ReadPosRankSum=0.502;SOR=0.718;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:115,141:256:99:3681,0,2864:58,57,72,69 chr1 231480507 . A G 387.7 PASS AC=2;AF=0.697;AN=2;DP=1667;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1496,150,0:0,0,25,25 chr1 231486951 . TAAAA TAAA,TA,TAA,T 110.85 PASS AC=0,0,2,0;AF=0.058,0.288,0.327,0.058;AN=2;DP=475;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant15-variant16-variant18-variant19-variant21-variant22-variant24-variant25-variant31-variant33-variant35-variant37-variant38-variant39-variant42-variant44 GT:DP:GQ:SB 3/3:9:26:0,0,8,1 chr1 231486989 . A C 709.82 PASS AC=2;AF=0.718;AN=2;DP=2133;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:1681,161,0:0,0,38,16 chr1 231487017 . T C 1080.6 PASS AC=2;AF=0.692;AN=2;DP=3154;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:2229,212,0:0,0,49,22 chr1 231488524 . C T 1277.86 PASS AC=2;AF=0.684;AN=2;DP=4848;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,135:135:99:4377,404,0:0,0,60,75 chr1 231489353 . G T 5356.22 PASS AC=2;AF=0.711;AN=2;DP=13074;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,325:325:99:9791,974,0:0,0,140,185 chr1 231490105 . C T 2466.59 PASS AC=2;AF=0.718;AN=2;DP=6644;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,146:146:99:4375,437,0:0,0,61,85 chr1 231490819 . A AT 39.79 PASS AC=2;AF=0.726;AN=2;DP=320;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:437,39,0:0,0,0,13 chr1 231500353 . A AT 6108.21 PASS AC=2;AF=0.679;AN=2;DP=16886;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:3,376:379:99:11358,1067,0:3,0,185,191 chr1 231502244 . AT A,AGT 64.13 PASS AC=0,1;AF=0.233,0.267;AN=2;DP=2855;set=filterInvariant3-variant5-variant9-filterInvariant10-variant13-variant14-filterInvariant16-variant21-variant22-variant26-filterInvariant31-variant35-variant37-filterInvariant39-variant44 GT:DP:GQ:SB 0/2:167:99:31,55,25,56 chr1 231502245 . T A 1174.94 PASS AC=2;AF=0.526;AN=2;DP=6751;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:18,145:163:26:4753,26,0:7,11,46,99 chr1 231502310 . T C 1019.67 PASS AC=2;AF=0.676;AN=2;DP=2438;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:2195,179,0:0,0,11,49 chr1 231506557 . G A 734.14 PASS AC=2;AF=0.676;AN=2;DP=1067;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:748,66,0:0,0,5,17 chr1 231664607 . C T 2056.5 PASS AC=1;AF=0.571;AN=2;DP=3838;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant6-variant9-variant10-variant11-variant13-variant14-variant15-variant21-variant22-variant24-variant25-variant26-variant31-variant34-variant35-variant36-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:93,98:191:99:2458,0,2315:46,47,48,50 chr1 231699398 . ATTT AT,ATT,A 74.07 PASS AC=0,2,0;AF=0.226,0.419,0.048;AN=2;DP=613;MQ=60;set=variant-variant3-variant4-variant6-variant9-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 2/2:13:17:0,1,3,9 chr1 231727447 . A G 1428.4 PASS AC=1;AF=0.742;AN=2;DP=4469;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant21-variant22-variant24-variant25-variant26-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:81,91:172:99:2348,0,2054:30,51,35,56 chr1 231747989 . G A 115.49 PASS AC=2;AF=0.789;AN=2;DP=621;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:688,57,0:0,0,3,16 chr1 231762413 . T TGTGTGCGC,TGTGTGTGTGC,TGTGTGTGTGTGC,TGTATGTCTGTGTGTGTGTGTGTGTGTGCGC,TGTATGTCTGTGTGTGTGTGTGTGTGTGTGC,TGTATGTCTGTGTGTGTGTGTGTGTGTGTGTGC 267.92 PASS AC=0,1,0,1,0,0;AF=0.013,0.474,0.115,0.051,0.013,0.013;AN=2;DP=1157;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-filterInvariant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 2/4:25:99:2,1,17,5 chr1 231858993 . GA G 451.89 PASS AC=2;AF=0.966;AN=2;DP=1824;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:1631,162,0:0,0,26,28 chr1 231906589 . C T 1257.34 PASS AC=1;AF=0.5;AN=2;DP=1834;MQ=60;set=variant2-variant7-variant13-variant14-variant16-variant21-variant23-variant25-variant27-variant28-variant29-variant33-variant35-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:49,76:125:99:1923,0,1010:27,22,47,29 chr1 231931048 . T C 1311.67 PASS AC=1;AF=0.538;AN=2;DP=926;MQ=60;set=variant-variant14-variant18-variant19-variant21-variant23-variant24-variant27-variant29-variant35-variant37-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,28:72:99:700,0,1160:15,29,7,21 chr1 231936016 . A G 1849.76 PASS AC=2;AF=1;AN=2;DP=2552;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1769,168,0:0,0,18,38 chr1 231954101 . C T 726.08 PASS AC=1;AF=0.5;AN=2;DP=592;FractionInformativeReads=1;MQ=60;set=variant-variant18-variant19-variant21-variant23-variant24-variant27-variant30-variant35-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,29:59:99:672,0,848:23,7,20,9 chr1 231954427 . C T 799.89 PASS AC=1;AF=0.731;AN=2;DP=2670;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,41:80:99:1343,0,1224:13,26,16,25 chr1 231954609 . G A 1241.41 PASS AC=1;AF=0.5;AN=2;DP=1517;MQ=60;set=variant2-variant3-variant7-variant12-variant16-variant17-variant18-variant24-variant25-variant26-variant27-variant32-variant35-variant36-variant37-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:53,43:96:99:1172,0,1302:26,27,23,20 chr1 231955906 . G A 124.68 PASS AC=1;AF=0.571;AN=2;DP=90;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant8-variant16-variant19-variant21-variant23-variant25-variant26-variant27-variant29-variant35-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,2:6:72:72,0,161:4,0,2,0 chr1 231956086 . A T 1928.79 PASS AC=1;AF=0.684;AN=2;DP=2437;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,24:63:99:520,0,961:18,21,12,12 chr1 232094729 . G A 555.98 PASS AC=1;AF=0.587;AN=2;DP=320;MQ=60;set=variant2-variant3-variant4-variant5-variant10-variant11-variant13-variant15-variant17-variant19-variant21-variant22-variant23-variant25-variant28-variant29-variant30-variant33-variant35-variant36-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:5,6:11:99:237,0,192:0,5,0,6 chr1 232098847 . C T 509.23 PASS AC=1;AF=0.5;AN=2;DP=384;FractionInformativeReads=1;MQ=60;set=variant10-variant23-variant29-variant30-variant33-variant35-variant36-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:30,26:56:99:816,0,908:9,21,3,23 chr1 232098859 . C G 362.91 PASS AC=1;AF=0.556;AN=2;DP=313;FractionInformativeReads=1;MQ=60;set=variant10-variant23-variant29-variant30-variant33-variant35-variant36-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:23,23:46:99:767,0,738:6,17,2,21 chr1 232144598 . A T 3950.95 PASS AC=1;AF=0.571;AN=2;DP=2711;MQ=60;set=variant2-variant3-variant4-variant5-variant10-variant11-variant13-variant15-variant17-variant19-variant22-variant23-variant25-variant28-variant29-variant30-variant33-variant35-variant36-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:58,57:115:99:1428,0,1463:33,25,33,24 chr1 232144887 . A G 1953.07 PASS AC=1;AF=0.571;AN=2;DP=1143;MQ=60;set=variant2-variant3-variant4-variant5-variant10-variant11-variant13-variant15-variant17-variant19-variant22-variant23-variant25-variant28-variant29-variant30-variant33-variant35-variant36-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:26,19:45:99:532,0,804:12,14,8,11 chr1 232145181 . G A 326.96 PASS AC=1;AF=0.583;AN=2;DP=132;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant11-variant13-variant15-variant17-variant19-variant22-variant23-variant25-variant28-variant29-variant33-variant35-variant36-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:2,3:5:76:117,0,76:2,0,2,1 chr1 232145203 . T TTTAC,TTTAA 592.73 PASS AC=1,0;AF=0.478,0.217;AN=2;DP=197;MQ=60;set=variant2-variant3-variant4-variant10-variant11-variant13-variant14-variant15-variant17-variant19-variant22-variant23-variant25-variant27-variant28-variant29-variant33-variant35-variant36-variant37-variant40-variant41-variant42 GT:DP:GQ:SB 0/1:9:99:3,2,2,2 chr1 232145221 . A G 896.19 PASS AC=1;AF=0.579;AN=2;DP=243;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant10-variant11-variant13-variant15-variant17-variant19-variant22-variant23-variant25-variant28-variant29-variant33-variant35-variant36-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:5,5:10:99:195,0,286:3,2,3,2 chr1 232145222 . T C 896.19 PASS AC=1;AF=0.579;AN=2;DP=248;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant10-variant11-variant13-variant15-variant17-variant19-variant22-variant23-variant25-variant28-variant29-variant33-variant35-variant36-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:5,5:10:99:195,0,286:3,2,3,2 chr1 232145424 . C T 740.83 PASS AC=1;AF=0.571;AN=2;DP=412;MQ=60;set=variant2-variant3-variant4-variant5-variant10-variant11-variant13-variant15-variant17-variant19-variant22-variant23-variant25-variant28-variant29-variant30-variant33-variant35-variant36-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:13,6:19:99:189,0,356:6,7,1,5 chr1 232172374 . G A 311.55 PASS AC=1;AF=0.545;AN=2;DP=389;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant8-variant11-variant13-variant17-variant19-variant24-variant35-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:16,24:40:99:508,0,464:13,3,13,11 chr1 232173560 . G T 1926.28 PASS AC=2;AF=0.591;AN=2;DP=2773;set=variant4-variant5-variant8-variant10-variant11-variant13-variant15-variant17-variant19-variant23-variant24-variant25-variant27-variant31-variant33-variant34-variant35-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,131:133:99:4178,378,0:1,1,61,70 chr1 232173665 . AAC A 1419.12 PASS AC=1;AF=0.5;AN=2;DP=362;MQ=60;set=variant-variant29-variant35 GT:AD:DP:GQ:PL:SB 0/1:81,55:136:99:2026,0,2613:40,41,27,28 chr1 232173717 . CAGTA C 2317.09 PASS AC=1;AF=0.538;AN=2;DP=1874;set=variant10-variant15-variant16-variant19-variant23-variant25-variant27-variant31-variant33-variant34-variant35-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:95,70:165:99:2628,0,3165:43,52,43,27 chr1 232176769 . C T 2452.45 PASS AC=1;AF=0.55;AN=2;DP=1945;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant8-variant13-variant17-variant19-variant24-variant35-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:132,107:239:99:2747,0,3652:70,62,54,53 chr1 232533667 . T C 725.37 PASS AC=1;AF=0.575;AN=2;DP=819;MQ=60;set=variant2-variant3-variant7-variant8-variant14-variant18-variant22-variant23-variant24-variant26-variant27-variant29-variant35-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,32:49:99:1157,0,581:16,1,30,2 chr1 232534303 . CT C,CTT 147.56 DRAGENHardINDEL AC=0,1;AF=0.483,0.017;AN=2;DP=17946;set=FilteredInAll GT:DP:GQ:SB 0/2:516:99:216,230,38,32 chr1 232534957 . T C 1202.18 PASS AC=1;AF=0.575;AN=2;DP=2684;MQ=60;set=variant2-variant3-variant7-variant8-variant14-variant18-variant22-variant23-variant24-variant26-variant27-variant29-variant35-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,53:121:99:1215,0,1695:32,36,26,27 chr1 232535030 . C T 3366.55 PASS AC=2;AF=1;AN=2;DP=4642;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,105:105:99:3054,313,0:0,0,43,62 chr1 232564096 . CTTTT CTTT,CTT,CTTTTT,C 95.49 PASS AC=1,1,0,0;AF=0.3,0.2,0.02,0.02;AN=2;DP=601;set=variant-variant4-variant5-variant8-filterInvariant9-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant23-variant24-filterInvariant25-variant27-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant41 GT:DP:GQ:SB 2/1:21:75:3,0,12,6 chr1 232568293 . A G 1511.77 PASS AC=2;AF=0.92;AN=2;DP=2859;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:2177,195,0:0,0,17,48 chr1 232577281 . T G 102.1 PASS AC=1;AF=0.565;AN=2;DP=789;FractionInformativeReads=1;set=variant-variant4-variant6-variant8-variant9-variant10-variant11-variant15-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant30-variant31-variant33-variant35-variant36-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:17,13:30:99:316,0,529:10,7,9,4 chr1 232650750 . A G 8663.53 PASS AC=2;AF=0.977;AN=2;DP=12375;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,309:310:99:9541,883,0:1,0,151,158 chr1 232650867 . C T 2098.45 PASS AC=1;AF=0.78;AN=2;DP=9129;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:124,118:242:99:2806,0,2903:58,66,52,66 chr1 232697081 . C T 46.75 PASS AC=2;AF=0.714;AN=2;DP=61;FS=0;FractionInformativeReads=1;MQ=60;set=variant10-variant11-variant12-variant15-variant17-variant19-variant21-variant22-variant32-variant33-variant34-variant35-variant39-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:90,6,0:0,0,1,1 chr1 232697340 . T C 503.69 PASS AC=1;AF=0.5;AN=2;DP=104;FractionInformativeReads=1;MQ=60;set=variant23-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:19,22:41:99:575,0,443:9,10,7,15 chr1 232941153 . C T 793.97 PASS AC=2;AF=0.782;AN=2;DP=3997;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,118:118:99:3475,353,0:0,0,59,59 chr1 232944569 . C T 4287.79 PASS AC=2;AF=0.78;AN=2;DP=12446;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,314:314:99:9735,938,0:0,0,130,184 chr1 233086239 . T G 669.18 PASS AC=1;AF=0.583;AN=2;DP=165;FractionInformativeReads=1;MQ=60;set=variant8-variant25-variant28-variant35-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:19,15:34:99:552,0,615:16,3,15,0 chr1 233086456 . T C 1616.47 PASS AC=1;AF=0.55;AN=2;DP=4164;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant13-variant18-variant20-variant21-variant25-variant28-variant30-variant32-variant33-variant34-variant35-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:112,123:235:99:2834,0,2600:53,59,56,67 chr1 233091276 . CTTT CTT,C,CT,CTTTT 214.73 PASS AC=1,0,0,0;AF=0.393,0.018,0.071,0.018;AN=2;DP=1164;set=variant-variant2-variant5-variant7-filterInvariant10-variant11-variant12-variant13-variant14-variant15-variant17-filterInvariant19-variant20-variant21-filterInvariant22-variant24-variant26-variant27-variant29-variant31-variant33-filterInvariant35-variant36-variant38-variant39-variant41-variant42-variant43 GT:DP:GQ:SB 0/1:32:99:12,8,8,4 chr1 233112095 . A G 622.92 PASS AC=1;AF=0.583;AN=2;DP=450;MQ=60;set=variant8-variant25-variant28-variant35-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:42,23:65:99:555,0,1160:25,17,14,9 chr1 233134086 . C T 3536.21 PASS AC=1;AF=0.563;AN=2;DP=2189;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant11-variant15-variant16-variant18-variant20-variant25-variant27-variant28-variant33-variant34-variant35-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:90,66:156:99:1480,0,2389:53,37,36,30 chr1 233150270 . T C 455.29 PASS AC=1;AF=0.636;AN=2;DP=268;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant16-variant18-variant21-variant22-variant25-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,5:7:70:160,0,70:2,0,4,1 chr1 233152910 . A AAAAGCAAGATTTTGAGTCCTCACAGCTATTCT 1069.08 PASS AC=1;AF=0.62;AN=2;DP=993;set=variant-variant2-variant3-variant4-variant5-variant8-variant11-variant15-variant16-variant18-variant20-variant21-variant22-variant25-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,24:43:99:954,0,3446:6,13,7,17 chr1 233189946 . A G 261.85 PASS AC=1;AF=0.545;AN=2;DP=255;FractionInformativeReads=1;MQ=60;set=variant7-variant8-variant10-variant19-variant25-variant29-variant35-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:16,11:27:99:362,0,479:12,4,10,1 chr1 233193599 . C CA,CAA 1254.67 PASS AC=1,0;AF=0.744,0.012;AN=2;DP=5143;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:119:50:11,5,63,40 chr1 233225957 . CA C 220.22 PASS AC=1;AF=0.5;AN=2;DP=640;MQ=60;set=variant-variant2-variant5-variant6-variant9-variant12-variant17-variant22-variant27-variant33-variant34-variant35-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:27,16:43:99:322,0,617:10,17,4,12 chr1 233231323 . A T 11116.1 PASS AC=1;AF=0.526;AN=2;DP=5868;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant12-variant13-variant17-variant19-variant21-variant22-variant27-variant29-variant33-variant34-variant35-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:153,169:322:99:4210,0,3706:66,87,81,88 chr1 233296399 . A AG 129.82 PASS AC=2;AF=0.782;AN=2;DP=819;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:1187,90,0:0,0,7,23 chr1 233296891 . T C 1043.81 PASS AC=2;AF=0.731;AN=2;DP=3186;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,86:86:99:2605,258,0:0,0,49,37 chr1 233296908 . T G 1276.03 PASS AC=2;AF=0.731;AN=2;DP=3499;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,91:91:99:2821,273,0:0,0,53,38 chr1 233336129 . CTTT CTTTT,CTT,CTTTTT,C 66.12 PASS AC=0,0,0,1;AF=0.077,0.269,0.077,0.077;AN=2;DP=354;set=variant2-filterInvariant3-variant4-variant6-filterInvariant13-filterInvariant28-filterInvariant29-variant32-filterInvariant35-filterInvariant38-variant39-variant41-variant44 GT:DP:GQ:SB 0/4:12:80:1,8,1,2 chr1 233353951 . A G 482.58 PASS AC=1;AF=0.542;AN=2;DP=211;MQ=60;set=variant2-variant4-variant9-variant11-variant22-variant25-variant26-variant33-variant35-variant37-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:3,10:13:99:371,0,102:1,2,4,6 chr1 233353955 . CAAAAAAAA C,CAA 401.88 PASS AC=1,0;AF=0.538,0.038;AN=2;DP=208;set=variant2-variant4-variant9-variant11-variant22-variant25-variant26-variant33-variant34-variant35-variant37-variant40-variant41 GT:DP:GQ:SB 0/1:16:99:1,5,4,6 chr1 233362930 . G A 2305.81 PASS AC=1;AF=0.545;AN=2;DP=2436;MQ=60;set=variant2-variant4-variant6-variant7-variant9-variant10-variant11-variant15-variant16-variant17-variant25-variant26-variant27-variant28-variant29-variant33-variant34-variant35-variant36-variant37-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:56,77:133:99:1815,0,1309:34,22,40,37 chr1 233395214 . T A 588.62 PASS AC=1;AF=0.705;AN=2;DP=635;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,6:18:99:205,0,333:2,10,0,6 chr1 233397752 . T C 4099.22 PASS AC=1;AF=0.577;AN=2;DP=3865;MQ=60;set=variant2-variant6-variant8-variant10-variant12-variant15-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant29-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:87,71:158:99:1793,0,2136:51,36,39,32 chr1 233398636 . A G 336.22 PASS AC=1;AF=0.55;AN=2;DP=112;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant8-variant12-variant15-variant19-variant20-variant24-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,2:6:72:72,0,163:4,0,2,0 chr1 233398670 . C A 624 PASS AC=1;AF=0.577;AN=2;DP=524;FractionInformativeReads=1;set=variant2-variant6-variant8-variant10-variant12-variant15-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant29-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,7:12:99:224,0,190:5,0,6,1 chr1 233398713 . C T 1123.39 PASS AC=1;AF=0.577;AN=2;DP=1118;FractionInformativeReads=1;set=variant2-variant6-variant8-variant10-variant12-variant15-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant29-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,23:34:99:641,0,337:8,3,16,7 chr1 233398918 . AG A 2132.11 PASS AC=1;AF=0.542;AN=2;DP=583;MQ=60;set=variant2-variant6-variant8-variant12-variant15-variant19-variant20-variant24-variant25-variant29-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:29,27:56:99:984,0,1465:12,17,12,15 chr1 233398927 . C G 2151.69 PASS AC=1;AF=0.577;AN=2;DP=1030;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant8-variant10-variant12-variant15-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant29-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,24:49:99:926,0,1430:9,16,10,14 chr1 233398931 . G GC 2032.26 PASS AC=1;AF=0.577;AN=2;DP=964;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant8-variant10-variant12-variant15-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant29-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,22:48:99:846,0,1403:9,17,8,14 chr1 233398993 . C A 635.56 PASS AC=1;AF=0.604;AN=2;DP=271;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant8-variant10-variant12-variant15-variant17-variant18-variant19-variant20-variant24-variant25-variant29-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,7:18:99:220,0,392:1,10,1,6 chr1 233489499 . A G 785.29 PASS AC=1;AF=0.569;AN=2;DP=2558;MQ=60;set=variant-variant2-variant3-variant4-variant8-variant9-variant13-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,54:97:99:1288,0,879:24,19,30,24 chr1 233489529 . G A 942.89 PASS AC=1;AF=0.569;AN=2;DP=3039;MQ=60;set=variant-variant2-variant3-variant4-variant8-variant9-variant13-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,62:107:99:1528,0,1116:26,19,33,29 chr1 233489707 . G T 624 PASS AC=1;AF=0.569;AN=2;DP=1770;MQ=60;set=variant-variant2-variant3-variant4-variant8-variant9-variant13-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,30:76:99:832,0,1256:18,28,10,20 chr1 233490536 . A AATGTCTTGGGGATAATCTG 832.49 PASS AC=1;AF=0.569;AN=2;DP=1178;MQ=60;set=variant-variant2-variant3-variant4-variant8-variant9-variant13-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,23:52:99:1165,0,1877:20,9,16,7 chr1 233490543 . G A 879.43 PASS AC=1;AF=0.569;AN=2;DP=1529;MQ=60;set=variant-variant2-variant3-variant4-variant8-variant9-variant13-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,37:69:99:1282,0,1907:21,11,22,15 chr1 233490764 . G T 592.52 PASS AC=1;AF=0.548;AN=2;DP=731;MQ=60;set=variant3-variant4-variant8-variant13-variant17-variant18-variant19-variant21-variant25-variant26-variant27-variant29-variant30-variant33-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,18:36:99:459,0,595:3,15,7,11 chr1 233490776 . C T 436.3 PASS AC=1;AF=0.548;AN=2;DP=568;MQ=60;set=variant3-variant4-variant8-variant13-variant17-variant18-variant19-variant21-variant25-variant26-variant27-variant29-variant30-variant33-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,14:29:99:354,0,438:3,12,4,10 chr1 233508298 . C T 3479.83 PASS AC=1;AF=0.5;AN=2;DP=276;FS=0.928;FractionInformativeReads=1;MQ=60;MQRankSum=1.245;QD=12.61;ReadPosRankSum=1.198;SOR=0.765;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:127,149:276:99:3508,0,3087:55,72,62,87 chr1 233508430 . G A 1875.92 PASS AC=1;AF=0.52;AN=2;DP=2411;MQ=60;set=variant-variant2-variant4-variant5-variant9-variant10-variant12-variant13-variant15-variant16-variant19-variant20-variant21-variant24-variant26-variant27-variant31-variant32-variant35-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,33:84:99:957,0,1473:25,26,18,15 chr1 233508564 . G A 3584.58 PASS AC=1;AF=0.618;AN=2;DP=8516;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:142,131:273:99:3033,0,3475:69,73,69,62 chr1 233509581 . G A 628.84 PASS AC=1;AF=0.5;AN=2;DP=464;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant10-variant15-variant20-variant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:28,19:47:99:469,0,778:13,15,12,7 chr1 233515413 . G A 1436.99 PASS AC=1;AF=0.567;AN=2;DP=3511;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant15-variant16-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant35-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,71:126:99:1704,0,1354:24,31,32,39 chr1 233518682 . G A 7637.01 PASS AC=1;AF=0.636;AN=2;DP=15534;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:235,209:444:99:5207,0,6284:113,122,104,105 chr1 233518753 . T C 6832.5 PASS AC=1;AF=0.636;AN=2;DP=16304;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:260,262:522:99:6158,0,6231:122,138,124,138 chr1 233518885 . T C 1981.53 PASS AC=1;AF=0.679;AN=2;DP=4983;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:54,56:110:99:1703,0,1759:11,43,10,46 chr1 233518983 . G GT 3228.75 PASS AC=1;AF=0.636;AN=2;DP=5176;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:72,70:142:99:2750,0,4072:38,34,41,29 chr1 233518998 . C T 3573.12 PASS AC=1;AF=0.636;AN=2;DP=5865;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:75,83:158:99:3082,0,4071:40,35,49,34 chr1 233519277 . A G 1315.41 PASS AC=1;AF=0.636;AN=2;DP=2800;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,38:94:99:1009,0,1526:34,22,24,14 chr1 233519393 . C T 3412.15 PASS AC=1;AF=0.744;AN=2;DP=10604;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:142,124:266:99:3232,0,3718:75,67,75,49 chr1 233519825 . C T 4138.08 PASS AC=1;AF=0.636;AN=2;DP=9804;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:177,122:299:99:2904,0,4563:76,101,54,68 chr1 233520144 . A G 5028.39 PASS AC=1;AF=0.636;AN=2;DP=12444;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:222,176:398:99:4521,0,5699:120,102,94,82 chr1 233520199 . T G 5293.46 PASS AC=1;AF=0.636;AN=2;DP=13290;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:220,196:416:99:4560,0,5580:105,115,101,95 chr1 233520316 . A AG 5874.76 PASS AC=1;AF=0.744;AN=2;DP=12869;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:163,163:326:99:5095,0,5023:73,90,74,89 chr1 233520845 . T C 3012.12 PASS AC=1;AF=0.636;AN=2;DP=6361;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:99,102:201:99:2545,0,2579:35,64,36,66 chr1 233520909 . T C 990.25 PASS AC=1;AF=0.636;AN=2;DP=2378;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,38:84:99:1049,0,1386:10,36,9,29 chr1 233520965 . G A 196.99 PASS AC=1;AF=0.636;AN=2;DP=620;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,7:20:99:237,0,495:0,13,0,7 chr1 233749855 . A G 267.33 PASS AC=2;AF=0.802;AN=2;DP=846;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:646,51,0:0,0,15,2 chr1 233749896 . C CTTGGCTTTGGCT 1210.13 PASS AC=1;AF=0.611;AN=2;DP=1370;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant10-variant11-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant25-variant26-variant31-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:26,21:47:99:949,0,1011:20,6,16,5 chr1 234040742 . A C 2353.78 PASS AC=2;AF=0.656;AN=2;DP=6018;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,238:238:99:6991,714,0:0,0,139,99 chr1 234041422 . G C 3261.85 PASS AC=2;AF=0.641;AN=2;DP=11899;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,428:428:99:12441,1281,0:0,0,221,207 chr1 234442376 . G A 566.48 PASS AC=1;AF=0.743;AN=2;DP=1006;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant26-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,15:37:99:320,0,505:9,13,7,8 chr1 234444761 . TA T,TAAAAA,TAAAA,TAA 369.39 PASS AC=1,0,0,0;AF=0.486,0.243,0.057,0.029;AN=2;DP=287;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant44 GT:DP:GQ:SB 0/1:10:22:2,0,7,1 chr1 234454405 . A C 345.81 PASS AC=2;AF=1;AN=2;DP=593;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:583,42,0:0,0,12,2 chr1 234458668 . G A 106.42 PASS AC=1;AF=0.586;AN=2;DP=653;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant25-variant28-variant30-variant31-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,7:21:99:178,0,420:11,3,5,2 chr1 234509259 . G C 4129.57 PASS AC=1;AF=0.771;AN=2;DP=5359;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:62,87:149:99:2352,0,1796:45,17,54,33 chr1 234509858 . GT G 187.73 PASS AC=1;AF=0.711;AN=2;DP=580;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,8:10:16:161,0,16:1,1,4,4 chr1 234519452 . C CT 1093.32 PASS AC=1;AF=0.771;AN=2;DP=1137;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:19,22:41:99:508,0,413:14,5,18,4 chr1 234528006 . A G 279.76 PASS AC=1;AF=0.773;AN=2;DP=375;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,7:11:99:201,0,130:4,0,5,2 chr1 234528087 . C CA 1012.2 PASS AC=1;AF=0.545;AN=2;DP=481;MQ=60;set=variant3-variant5-variant6-variant9-variant12-variant18-variant20-variant29-variant35-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:18,17:35:99:365,0,412:13,5,12,5 chr1 234546354 . C T 258.58 PASS AC=1;AF=0.5;AN=2;DP=242;MQ=60;set=variant3-variant5-variant6-variant16-variant18-variant20-variant35-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:10,18:28:99:490,0,247:6,4,6,12 chr1 234561590 . T A 240.61 PASS AC=1;AF=0.676;AN=2;DP=203;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant11-variant13-variant16-variant18-variant19-variant20-variant29-variant35-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:3,2:5:75:75,0,118:0,3,0,2 chr1 234573357 . G C 558.8 PASS AC=1;AF=0.597;AN=2;DP=860;FractionInformativeReads=1;set=variant-variant2-variant3-variant5-variant7-variant10-variant11-variant12-variant13-variant16-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,16:31:99:432,0,464:5,10,4,12 chr1 234582457 . C T 313.43 PASS AC=1;AF=0.683;AN=2;DP=401;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant10-variant11-variant12-variant13-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,7:13:99:273,0,420:5,1,6,1 chr1 234582461 . G A 92.44 PASS AC=1;AF=0.528;AN=2;DP=311;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant7-variant10-variant11-variant12-variant13-variant19-variant23-variant25-variant27-variant28-variant33-variant34-variant35-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,9:16:99:340,0,414:6,1,8,1 chr1 234582651 . T C 1396.02 PASS AC=1;AF=0.542;AN=2;DP=3780;MQ=60;set=variant2-variant5-variant7-variant10-variant11-variant12-variant13-variant17-variant18-variant19-variant20-variant23-variant25-variant27-variant28-variant30-variant33-variant34-variant35-variant36-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:73,77:150:99:1831,0,1670:41,32,37,40 chr1 234584231 . C T 1342.7 PASS AC=1;AF=0.542;AN=2;DP=4352;MQ=60;set=variant2-variant5-variant7-variant10-variant11-variant12-variant13-variant17-variant18-variant19-variant20-variant23-variant25-variant27-variant28-variant30-variant33-variant34-variant35-variant36-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:124,117:241:99:2568,0,2929:69,55,61,56 chr1 234584445 . C T 103.16 PASS AC=1;AF=0.563;AN=2;DP=424;MQ=60;set=variant2-variant5-variant7-variant10-variant11-variant12-variant13-variant17-variant18-variant19-variant20-variant23-variant25-variant27-variant28-variant30-variant33-variant34-variant35-variant36-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,6:16:99:222,0,392:1,9,1,5 chr1 234594947 . T C 450.89 PASS AC=1;AF=0.545;AN=2;DP=528;MQ=60;set=variant2-variant10-variant13-variant17-variant18-variant23-variant34-variant35-variant36-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,27:55:99:679,0,795:20,8,18,9 chr1 234601296 . T C 680.57 PASS AC=1;AF=0.5;AN=2;DP=395;FractionInformativeReads=1;MQ=60;set=variant14-variant17-variant31-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:26,46:72:99:1158,0,547:11,15,24,22 chr1 234601456 . TA T 170.8 PASS AC=1;AF=0.5;AN=2;DP=1146;MQ=60;set=variant-filterInvariant2-filterInvariant3-filterInvariant5-variant6-variant7-variant8-variant9-filterInvariant11-variant14-variant15-variant16-variant17-variant21-variant24-variant25-filterInvariant27-filterInvariant28-variant29-variant30-variant31-filterInvariant33-variant35-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:21,13:34:99:152,0,237:14,7,7,6 chr1 234603075 . G T 311.87 PASS AC=2;AF=0.703;AN=2;DP=381;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant10-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:264,21,0:0,0,6,1 chr1 234606644 . A G 233.92 PASS AC=1;AF=0.531;AN=2;DP=366;set=variant-variant2-variant3-variant4-variant10-variant13-variant19-variant22-variant23-variant30-variant32-variant35-variant36-variant37-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:18,6:24:99:109,0,500:12,6,4,2 chr1 234606705 . C G 757.97 PASS AC=1;AF=0.5;AN=2;DP=425;MQ=60;set=variant-variant3-variant13-variant19-variant23-variant35-variant36-variant42 GT:AD:DP:GQ:PL:SB 0/1:31,29:60:99:753,0,819:22,9,20,9 chr1 234606799 . C T 947.4 PASS AC=1;AF=0.5;AN=2;DP=635;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant13-variant19-variant23-variant35-variant36-variant42 GT:AD:DP:GQ:PL:SB 0/1:44,46:90:99:955,0,1077:21,23,22,24 chr1 234607055 . TG T 278.67 PASS AC=1;AF=0.5;AN=2;DP=297;MQ=60;set=variant-variant3-variant13-variant19-variant23-variant35-variant36-variant42 GT:AD:DP:GQ:PL:SB 0/1:13,27:40:99:971,0,404:5,8,12,15 chr1 234607086 . G A 141.4 PASS AC=1;AF=0.5;AN=2;DP=193;MQ=60;set=variant-variant3-variant13-variant19-variant23-variant35-variant36-variant42 GT:AD:DP:GQ:PL:SB 0/1:7,16:23:99:496,0,163:2,5,4,12 chr1 234607104 . C T 154.68 PASS AC=1;AF=0.5;AN=2;DP=122;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant13-variant19-variant23-variant35-variant36-variant42 GT:AD:DP:GQ:PL:SB 0/1:4,7:11:99:238,0,136:0,4,2,5 chr1 234608725 . A AT,ATT 205.29 PASS AC=2,0;AF=0.714,0.167;AN=2;DP=164;FS=0;MQ=60;set=variant2-variant3-variant6-variant10-variant13-variant17-variant21-variant22-variant23-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43 GT:DP:GQ:SB 1/1:3:9:0,0,0,3 chr1 234614390 . G C 507.85 PASS AC=1;AF=0.5;AN=2;DP=398;MQ=60;set=variant2-variant4-variant10-variant13-variant22-variant23-variant32-variant35-variant36-variant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:21,13:34:99:310,0,485:9,12,6,7 chr1 234740141 . G A 9313.05 PASS AC=1;AF=0.816;AN=2;DP=10244;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:136,110:246:99:2684,0,3463:72,64,61,49 chr1 234740917 . C CAGTTATAAT 21857.9 PASS AC=1;AF=0.816;AN=2;DP=14154;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:256,184:440:99:7270,0,27059:151,105,103,81 chr1 234742218 . C A 579.54 PASS AC=1;AF=0.5;AN=2;DP=270;set=variant2-filterInvariant35 GT:AD:DP:GQ:PL:SB 0/1:87,22:109:99:162,0,2076:38,49,9,13 chr1 234744250 . G A 1747.14 PASS AC=1;AF=0.607;AN=2;DP=2494;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant12-variant16-variant18-variant19-variant20-variant21-variant28-variant29-variant35-variant36-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:83,125:208:99:3034,0,1946:46,37,68,57 chr1 234744413 . C A 3172.86 PASS AC=1;AF=0.66;AN=2;DP=2449;MQ=60;set=variant-variant5-variant6-variant7-variant11-variant12-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant35-variant36-variant37-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,55:113:99:1430,0,1583:22,36,20,35 chr1 234745009 . A G 2957.74 PASS AC=1;AF=0.816;AN=2;DP=4130;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,61:118:99:1525,0,1214:26,31,35,26 chr1 234953834 . A C 515.54 PASS AC=2;AF=0.882;AN=2;DP=664;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-filterInvariant9-filterInvariant10-variant12-variant13-variant14-filterInvariant15-variant16-variant17-variant18-variant20-variant23-variant24-filterInvariant25-filterInvariant26-variant27-filterInvariant28-filterInvariant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-filterInvariant39-variant40-variant41-variant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:426,36,0:0,0,1,11 chr1 234953875 . C CA 136.53 PASS AC=2;AF=0.98;AN=2;DP=158;MQRankSum=-2.653;ReadPosRankSum=-0.094;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant16-variant20-variant23-filterInvariant24-variant26-variant28-variant30-variant31-variant33-variant35-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:107,9,0:0,0,1,2 chr1 235273179 . G A 20791.4 PASS AC=1;AF=0.738;AN=2;DP=16126;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:212,198:410:99:4957,0,5379:101,111,103,95 chr1 235285740 . C T 176.57 PASS AC=1;AF=0.524;AN=2;DP=940;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant10-variant12-variant13-variant15-variant16-variant21-variant23-variant25-variant28-variant31-variant32-variant35-variant36-variant37-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:23,10:33:99:229,0,561:13,10,7,3 chr1 235350207 . T C 46.72 PASS AC=1;AF=0.711;AN=2;DP=108;FS=0;FractionInformativeReads=1;set=variant2-variant3-variant4-variant5-variant9-variant10-variant15-variant18-variant20-variant21-variant23-variant24-variant26-variant31-variant32-variant35-variant37-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:1,4:5:31:124,0,31:1,0,3,1 chr1 235350458 . G A 51.2 PASS AC=1;AF=0.5;AN=2;DP=5;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.358;QD=10.24;ReadPosRankSum=0.358;SOR=0.859;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:2,3:5:77:79,0,77:0,2,2,1 chr1 235357303 . A ATG 855.54 PASS AC=1;AF=0.621;AN=2;DP=706;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant12-variant14-variant15-variant16-variant18-variant20-variant21-variant23-variant24-variant26-variant28-variant29-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,8:17:99:349,0,392:8,1,8,0 chr1 235357314 . AT A 417.38 PASS AC=1;AF=0.543;AN=2;DP=740;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant10-variant12-variant15-variant16-variant20-variant21-variant23-variant26-variant28-variant29-variant31-variant32-variant35-variant36-variant37-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,13:24:99:415,0,338:9,2,12,1 chr1 235357543 . A G 226.33 PASS AC=1;AF=0.543;AN=2;DP=721;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant10-variant12-variant15-variant16-variant20-variant21-variant23-variant26-variant28-variant29-variant31-variant32-variant35-variant36-variant37-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,21:34:99:503,0,325:4,9,8,13 chr1 235383188 . A G 3509.65 PASS AC=1;AF=0.621;AN=2;DP=2648;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant12-variant14-variant15-variant16-variant18-variant20-variant21-variant23-variant24-variant26-variant28-variant29-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:48,45:93:99:1086,0,1101:19,29,19,26 chr1 235392546 . T C 1212.75 PASS AC=1;AF=0.621;AN=2;DP=1187;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant12-variant14-variant15-variant16-variant18-variant20-variant21-variant23-variant24-variant26-variant28-variant29-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:23,15:38:99:428,0,623:15,8,11,4 chr1 235394541 . A C 589.24 PASS AC=1;AF=0.625;AN=2;DP=570;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant9-variant10-variant12-variant14-variant15-variant16-variant18-variant20-variant21-variant23-variant24-variant26-variant28-variant29-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:10,9:19:99:175,0,219:3,7,4,5 chr1 235397937 . GCA G 392.31 PASS AC=1;AF=0.63;AN=2;DP=432;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant20-variant21-variant23-variant26-variant28-variant29-variant31-variant32-variant35-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,3:8:93:93,0,169:1,4,0,3 chr1 235490391 . CA C 374.91 PASS AC=1;AF=0.621;AN=2;DP=809;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant12-variant14-variant15-variant16-variant18-variant20-variant21-variant23-variant24-variant26-variant28-variant29-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:16,10:26:99:276,0,520:11,5,5,5 chr1 235492546 . T G 1337.18 PASS AC=1;AF=0.621;AN=2;DP=1677;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant12-variant14-variant15-variant16-variant18-variant20-variant21-variant23-variant24-variant26-variant28-variant29-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:28,30:58:99:765,0,660:13,15,15,15 chr1 235492972 . T G 337.25 PASS AC=1;AF=0.543;AN=2;DP=579;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant10-variant12-variant14-variant15-variant16-variant20-variant21-variant23-variant26-variant28-variant29-variant31-variant32-variant35-variant36-variant37-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,6:19:99:192,0,441:9,4,2,4 chr1 235505313 . A AT 244.12 PASS AC=1;AF=0.542;AN=2;DP=998;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant10-variant12-variant14-variant15-variant16-variant20-variant21-variant23-variant26-variant28-variant29-variant31-variant32-variant35-variant36-variant37-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:27,15:42:99:329,0,698:18,9,9,6 chr1 235506853 . G A 46.68 PASS AC=1;AF=0.563;AN=2;DP=168;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant10-variant12-variant15-variant16-variant23-variant24-variant26-variant28-variant31-variant32-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:4,7:11:66:160,0,66:2,2,3,4 chr1 235506865 . C CA 89.83 PASS AC=1;AF=0.571;AN=2;DP=165;MQ=60;set=variant2-filterInvariant3-variant5-variant10-variant12-variant15-variant16-variant23-variant26-variant28-variant31-variant32-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:4,10:14:78:244,0,78:2,2,6,4 chr1 235506918 . G C 362.91 PASS AC=1;AF=0.635;AN=2;DP=438;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant9-variant10-variant12-variant14-variant15-variant16-variant18-variant20-variant21-variant23-variant24-variant26-variant28-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:4,14:18:45:365,0,45:2,2,8,6 chr1 235543262 . CA CAA,C 140.31 PASS AC=0,1;AF=0.397,0.103;AN=2;DP=937;set=variant2-filterInvariant4-filterInvariant5-variant6-variant7-variant8-filterInvariant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant41-variant42-variant43 GT:DP:GQ:SB 0/2:33:99:15,6,8,4 chr1 235543476 . TTGTGTGTGTGTGTGTGTGTGTG T,TTGTGTGTG,TTGTGTG,TTGTGTGTGTGTGTGTGTGTG,TTGTGTGTGTGTGTGTGTG,TTGTG,TTGTGTGTGTG,TTGTGTGTGTGTG,TTGTGTGTGTGTGTGTG,TTGTGTGTGTGTGTG 1103.38 PASS AC=0,1,0,0,1,0,0,0,0,0;AF=0.102,0.398,0.08,0.045,0.057,0.068,0.045,0.011,0.034,0.034;AN=2;DP=3568;set=Intersection GT:DP:GQ:SB 2/5:38:99:0,1,9,28 chr1 235564924 . G T 627.1 PASS AC=1;AF=0.5;AN=2;DP=816;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant16-variant18-variant19-variant21-variant22-variant25-variant29-variant33-variant34-variant35-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:38,39:77:99:1055,0,946:16,22,15,24 chr1 235594182 . A G 420.32 PASS AC=1;AF=0.756;AN=2;DP=1539;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,24:41:99:543,0,407:5,12,9,15 chr1 235594250 . A G 287.37 PASS AC=1;AF=0.706;AN=2;DP=332;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant25-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,3:8:94:94,0,200:0,5,0,3 chr1 235597252 . T G 1843.58 PASS AC=1;AF=0.716;AN=2;DP=2476;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,53:89:99:1444,0,883:27,9,38,15 chr1 235598973 . C T 1377.32 PASS AC=1;AF=0.722;AN=2;DP=1998;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,25:42:99:752,0,507:13,4,17,8 chr1 235601958 . G T 394.87 PASS AC=1;AF=0.744;AN=2;DP=1250;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,17:32:99:503,0,441:12,3,13,4 chr1 235612023 . G C 1606.61 PASS AC=1;AF=0.5;AN=2;DP=126;FS=3.758;FractionInformativeReads=1;MQ=60;MQRankSum=1.12;QD=12.75;ReadPosRankSum=-0.64;SOR=0.419;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:67,59:126:99:1635,0,2104:52,15,42,17 chr1 235612320 . C T 3211.2 PASS AC=1;AF=0.756;AN=2;DP=10128;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:125,108:233:99:3201,0,3624:34,91,26,82 chr1 235628718 . T G 40.9 PASS AC=1;AF=0.5;AN=2;DP=254;set=filterInvariant6-filterInvariant7-filterInvariant15-variant28-variant30-filterInvariant31-filterInvariant32-filterInvariant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:20,5:25:60:60,0,498:16,4,0,5 chr1 235628908 . G A 732.17 PASS AC=2;AF=0.629;AN=2;DP=1646;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1730,150,0:0,0,32,18 chr1 235647631 . G T 287.58 PASS AC=2;AF=0.613;AN=2;DP=1249;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1179,105,0:0,0,26,9 chr1 235652513 . T C 1237.79 PASS AC=2;AF=0.629;AN=2;DP=2977;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:2379,237,0:0,0,49,30 chr1 235659478 . G A 93.19 PASS AC=1;AF=0.5;AN=2;DP=65;FractionInformativeReads=1;MQ=60;set=variant4-variant7-variant8-variant9-variant11-variant17-variant25-variant34-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:2,6:8:63:202,0,63:2,0,5,1 chr1 235659621 . GA G,GAA 42.76 PASS AC=0,1;AF=0.143,0.357;AN=2;DP=418;MQ=60;set=filterInvariant3-variant4-variant8-variant9-filterInvariant10-variant11-filterInvariant12-variant25-filterInvariant26-filterInvariant27-variant29-variant34-variant35-variant41 GT:DP:GQ:SB 0/2:24:99:7,7,3,7 chr1 235667398 . AC A 628.63 PASS AC=1;AF=0.5;AN=2;DP=300;MQ=60;set=variant7-variant8-variant9-variant11-variant17-variant25-variant34-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:21,17:38:99:405,0,538:18,3,15,2 chr1 235667690 . A G 716.37 PASS AC=2;AF=0.617;AN=2;DP=2230;MQ=60;set=variant-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,78:78:99:2685,234,0:0,0,22,56 chr1 235714042 . G A 134.96 PASS AC=1;AF=0.6;AN=2;DP=28;FS=0;FractionInformativeReads=1;MQ=60;set=variant8-variant17-variant24-variant29-variant35 GT:AD:DP:GQ:PL:SB 0/1:4,2:6:72:72,0,121:3,1,2,0 chr1 235714076 . G A 77.76 PASS AC=1;AF=0.5;AN=2;DP=50;FS=0;FractionInformativeReads=1;MQ=60;set=variant5-variant10-variant14-variant16-variant32-variant35 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:75:75,0,136:3,1,2,2 chr1 235714162 . G A 375.1 PASS AC=2;AF=0.559;AN=2;DP=578;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant14-variant16-variant17-variant24-variant29-variant32-variant35-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:830,72,0:0,0,13,11 chr1 235714440 . A G 1654.98 PASS AC=1;AF=0.5;AN=2;DP=537;FractionInformativeReads=1;MQ=60;set=variant8-variant29-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:83,81:164:99:1994,0,1861:44,39,39,42 chr1 235714569 . T C 2069.57 PASS AC=2;AF=0.658;AN=2;DP=1130;set=variant-variant3-variant5-variant7-variant8-variant10-variant11-variant14-variant16-variant17-variant18-variant20-variant24-variant29-variant32-variant34-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:2594,178,0:0,0,18,41 chr1 235714571 . T C 2069.57 PASS AC=2;AF=0.632;AN=2;DP=1085;set=variant-variant3-variant5-variant7-variant8-variant10-variant11-variant14-variant16-variant17-variant18-variant20-variant24-variant29-variant32-variant34-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:2594,178,0:0,0,16,40 chr1 235714859 . CAAA C 432.09 PASS AC=2;AF=0.6;AN=2;DP=463;MQ=60;set=variant-variant3-variant7-variant8-variant10-variant11-variant14-variant16-variant18-variant24-variant32-variant35-variant37-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1534,108,0:0,0,27,9 chr1 235715029 . G A 1040.69 PASS AC=1;AF=0.5;AN=2;DP=1459;MQ=60;set=variant2-variant3-variant7-variant10-variant11-variant14-variant16-variant18-variant24-variant32-variant35-variant37-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:66,52:118:99:1286,0,1583:33,33,24,28 chr1 235715064 . A T 2292.06 PASS AC=2;AF=0.813;AN=2;DP=3527;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,85:87:99:2152,211,0:1,1,38,47 chr1 235715523 . A G 826.35 PASS AC=1;AF=0.653;AN=2;DP=5307;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:80,63:143:99:1422,0,1994:29,51,28,35 chr1 235715556 . C G 687.25 PASS AC=1;AF=0.657;AN=2;DP=3317;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,40:90:99:1067,0,1342:15,35,13,27 chr1 235715601 . A G 324.22 PASS AC=1;AF=0.657;AN=2;DP=1471;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,18:41:99:535,0,793:4,19,3,15 chr1 235758911 . A G 193.54 PASS AC=2;AF=0.744;AN=2;DP=566;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:556,51,0:0,0,6,11 chr1 235826382 . TA T 990.04 PASS AC=1;AF=0.689;AN=2;DP=1355;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,22:37:99:468,0,281:5,10,5,17 chr1 235827443 . T C 410.1 PASS AC=1;AF=0.682;AN=2;DP=362;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,8:15:99:185,0,263:0,7,3,5 chr1 235827641 . C T 500.3 PASS AC=1;AF=0.694;AN=2;DP=464;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,9:14:99:360,0,183:5,0,9,0 chr1 235856901 . G A 1034.98 PASS AC=1;AF=0.686;AN=2;DP=1582;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,14:37:99:313,0,719:6,17,4,10 chr1 235860340 . C T 2859.75 PASS AC=1;AF=0.708;AN=2;DP=3291;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,38:89:99:937,0,1393:27,24,17,21 chr1 235918688 . CAAAAGAAAAG CAAAAG,CAAAAGAAAAGAAAAG,CAAAAGAAAAGAAAAGAAAAG,C 627.4 PASS AC=0,2,0,0;AF=0.442,0.337,0.023,0.012;AN=2;DP=710;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 2/2:4:21:0,0,3,1 chr1 236016475 . A C 67.94 PASS AC=1;AF=0.5;AN=2;DP=56;FractionInformativeReads=1;MQ=60;set=variant6-variant32-variant35 GT:AD:DP:GQ:PL:SB 0/1:10,15:25:99:313,0,204:4,6,7,8 chr1 236141213 . C T 1270.01 PASS AC=1;AF=0.5;AN=2;DP=102;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.362;QD=12.45;ReadPosRankSum=2.045;SOR=0.69;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:50,52:102:99:1298,0,1219:26,24,27,25 chr1 236142565 . T C 351.5 PASS AC=1;AF=0.845;AN=2;DP=1382;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,16:43:99:404,0,774:7,20,4,12 chr1 236144919 . G T 1759.11 PASS AC=1;AF=0.5;AN=2;DP=110;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.494;QD=15.99;ReadPosRankSum=-1.862;SOR=0.74;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:39,71:110:99:1787,0,928:21,18,39,32 chr1 236205090 . C T 239.06 PASS AC=2;AF=0.577;AN=2;DP=240;MQ=60;set=variant4-variant5-variant7-variant8-variant16-variant23-variant26-variant27-variant29-variant31-variant35-variant38-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:856,63,0:0,0,20,1 chr1 236205121 . T C 1329.7 PASS AC=2;AF=0.603;AN=2;DP=1035;FractionInformativeReads=1;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant16-variant18-variant19-variant20-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1660,123,0:0,0,38,3 chr1 236208688 . A G 871.77 PASS AC=2;AF=0.6;AN=2;DP=493;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant16-variant18-variant19-variant20-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:270,18,0:0,0,6,0 chr1 236208689 . T A 871.77 PASS AC=2;AF=0.6;AN=2;DP=508;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant16-variant18-variant19-variant20-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:270,18,0:0,0,6,0 chr1 236208773 . C T 2041.02 PASS AC=2;AF=0.6;AN=2;DP=2598;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant16-variant18-variant19-variant20-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:1900,165,0:0,0,39,16 chr1 236209024 . C G 1189.07 PASS AC=2;AF=0.6;AN=2;DP=1435;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant16-variant18-variant19-variant20-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:1613,144,0:0,0,13,35 chr1 236209081 . G A 248.05 PASS AC=2;AF=0.603;AN=2;DP=494;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant16-variant18-variant19-variant20-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:523,51,0:0,0,5,12 chr1 236305689 . CGGGGCGCGCGGGCCGGGGCGGGGGCGCGCGGGCCGGGGCG C,CGGGGCGCGCGGGCCGGGGCG 308.56 PASS AC=2,0;AF=0.76,0.04;AN=2;DP=254;set=variant2-variant3-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant35-variant38-variant39-variant40-variant41 GT:DP:GQ:SB 1/1:12:37:0,0,10,2 chr1 236368391 . C CT 1092.61 PASS AC=2;AF=0.639;AN=2;DP=1408;MQ=60;set=variant-variant2-variant5-variant7-variant9-variant15-variant17-variant20-variant23-variant24-variant26-variant28-variant29-variant30-variant35-variant37-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,89:89:99:3355,271,0:0,0,55,34 chr1 236368708 . T C 76.67 PASS AC=2;AF=0.7;AN=2;DP=265;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant7-variant9-variant12-variant14-variant15-variant17-variant20-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant34-variant35-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:585,48,0:0,0,4,12 chr1 236379034 . TG T 7386.88 PASS AC=2;AF=0.639;AN=2;DP=6361;MQ=60;set=variant-variant2-variant5-variant7-variant9-variant15-variant17-variant20-variant23-variant24-variant26-variant28-variant29-variant30-variant35-variant37-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,316:316:99:12764,951,0:0,0,168,148 chr1 236379149 . A C 5169.3 PASS AC=2;AF=0.639;AN=2;DP=6264;MQ=60;set=variant-variant2-variant5-variant7-variant9-variant15-variant17-variant20-variant23-variant24-variant26-variant28-variant29-variant30-variant35-variant37-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:2,361:363:99:10865,1051,0:1,1,171,190 chr1 236379221 . TACAG T 5670.76 PASS AC=2;AF=0.639;AN=2;DP=4831;MQ=60;set=variant-variant2-variant5-variant7-variant9-variant15-variant17-variant20-variant23-variant24-variant26-variant28-variant29-variant30-variant35-variant37-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,247:248:99:10978,702,0:0,1,105,142 chr1 236379623 . G A 4163.01 PASS AC=2;AF=0.632;AN=2;DP=5853;MQ=60;set=variant-variant2-variant5-variant7-variant9-variant15-variant17-variant20-variant23-variant24-variant26-variant28-variant29-variant30-variant35-variant37-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,303:303:99:9753,909,0:0,0,146,157 chr1 236380077 . G A 2262.17 PASS AC=1;AF=0.609;AN=2;DP=5888;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant11-variant13-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:96,66:162:99:1622,0,2502:44,52,29,37 chr1 236380611 . C T 1117.63 PASS AC=2;AF=0.673;AN=2;DP=2567;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant10-variant15-variant16-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant35-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,93:93:99:2937,278,0:0,0,36,57 chr1 236380653 . ACTGTTGGTATGAATCACAGAAAGTCCT A 447.79 PASS AC=2;AF=0.673;AN=2;DP=1550;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant10-variant15-variant16-variant17-filterInvariant18-variant20-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant35-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1623,114,0:0,0,10,26 chr1 236380744 . T G 293.11 PASS AC=2;AF=0.673;AN=2;DP=841;MQ=60;set=variant-filterInvariant2-variant4-variant5-variant7-variant9-variant10-variant15-variant16-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant35-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:1006,87,0:0,0,13,16 chr1 236380913 . T C 199.29 PASS AC=2;AF=0.674;AN=2;DP=408;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant15-variant16-variant18-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant35-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:415,36,0:0,0,6,6 chr1 236381349 . C G 1425.82 PASS AC=2;AF=0.673;AN=2;DP=3063;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant10-variant15-variant16-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant35-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,119:119:99:3891,356,0:0,0,49,70 chr1 236381825 . G C 586.05 PASS AC=2;AF=0.673;AN=2;DP=1153;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant10-variant15-variant16-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant35-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1123,111,0:0,0,18,19 chr1 236381897 . T A 360.54 PASS AC=2;AF=0.673;AN=2;DP=571;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant10-variant15-variant16-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant35-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:706,66,0:0,0,8,14 chr1 236381917 . T A 364.57 PASS AC=2;AF=0.673;AN=2;DP=414;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant10-variant15-variant16-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant35-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:423,39,0:0,0,5,8 chr1 236381987 . A G 49.73 PASS AC=2;AF=0.688;AN=2;DP=80;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant7-variant9-variant15-variant16-variant23-variant24-variant25-variant26-variant28-variant30-variant35-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:127,9,0:0,0,0,3 chr1 236381989 . C A 49.73 PASS AC=2;AF=0.688;AN=2;DP=76;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant7-variant9-variant15-variant16-variant23-variant24-variant25-variant26-variant28-variant30-variant35-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:9:127,9,0:0,0,0,2 chr1 236383425 . C A 1153.62 PASS AC=2;AF=0.673;AN=2;DP=1782;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant10-variant15-variant16-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant35-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,64:64:99:2412,192,0:0,0,55,9 chr1 236383623 . A G 3775.47 PASS AC=2;AF=0.673;AN=2;DP=7955;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant10-variant15-variant16-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant35-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,303:304:99:8917,879,0:1,0,134,169 chr1 236383650 . C G 3546.08 PASS AC=2;AF=0.673;AN=2;DP=6524;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant10-variant15-variant16-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant35-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,233:233:99:7176,699,0:0,0,101,132 chr1 236383889 . T A 3240.57 PASS AC=2;AF=0.673;AN=2;DP=6749;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant10-variant15-variant16-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant35-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:2,237:239:99:6568,664,0:1,1,130,107 chr1 236383910 . G A 3290.2 PASS AC=2;AF=0.673;AN=2;DP=7446;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant10-variant15-variant16-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant35-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:2,258:260:99:7219,727,0:1,1,138,120 chr1 236384022 . A ATTT 4007.26 PASS AC=2;AF=0.673;AN=2;DP=7063;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant10-variant15-variant16-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant35-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,200:200:99:8707,602,0:0,0,104,96 chr1 236384278 . G C 357.23 PASS AC=2;AF=0.673;AN=2;DP=740;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant10-variant15-variant16-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant35-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:816,63,0:0,0,3,18 chr1 236385116 . C T 300.83 PASS AC=2;AF=0.673;AN=2;DP=457;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant10-variant15-variant16-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant35-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:742,51,0:0,0,17,0 chr1 236385165 . G C 530.34 PASS AC=2;AF=0.673;AN=2;DP=1169;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant10-variant15-variant16-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant35-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1535,135,0:0,0,34,11 chr1 236385360 . C T 1042.35 PASS AC=2;AF=0.673;AN=2;DP=1990;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant10-variant15-variant16-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant35-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,74:74:99:2202,220,0:0,0,25,49 chr1 236385379 . A G 637.02 PASS AC=2;AF=0.673;AN=2;DP=1466;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant10-variant15-variant16-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant35-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:1940,177,0:0,0,16,43 chr1 236393654 . A G 877.81 PASS AC=2;AF=0.989;AN=2;DP=1059;FS=0;MQRankSum=0.474;ReadPosRankSum=1.107;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:973,96,0:0,0,11,21 chr1 236413147 . T C 921.94 PASS AC=2;AF=0.658;AN=2;DP=863;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant7-variant9-variant15-variant16-variant17-variant20-variant23-variant24-variant26-variant28-variant29-variant30-variant35-variant37-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1636,153,0:0,0,34,17 chr1 236413282 . G A 1103.81 PASS AC=2;AF=0.658;AN=2;DP=1391;MQ=60;set=variant-variant2-variant5-variant7-variant9-variant15-variant16-variant17-variant20-variant23-variant24-variant26-variant28-variant29-variant30-variant35-variant37-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,61:61:99:1960,183,0:0,0,22,39 chr1 236413362 . C T 313.57 PASS AC=2;AF=0.658;AN=2;DP=406;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant7-variant9-variant15-variant16-variant17-variant20-variant23-variant24-variant26-variant28-variant29-variant30-variant35-variant37-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:680,57,0:0,0,6,13 chr1 236413384 . T C 235.59 PASS AC=2;AF=0.676;AN=2;DP=230;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant7-variant9-variant15-variant17-variant20-variant23-variant24-variant26-variant28-variant29-variant30-variant35-variant37-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:498,45,0:0,0,4,11 chr1 236415347 . T C 614.64 PASS AC=2;AF=0.658;AN=2;DP=1429;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant7-variant9-variant15-variant16-variant17-variant20-variant23-variant24-variant26-variant28-variant29-variant30-variant35-variant37-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:2,82:84:99:2346,202,0:1,1,34,48 chr1 236415444 . G A 239.4 PASS AC=2;AF=0.676;AN=2;DP=324;MQ=60;set=variant-variant2-variant5-variant7-variant9-variant15-variant16-variant17-variant20-variant23-variant24-variant28-variant29-variant30-variant35-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:431,33,0:0,0,1,10 chr1 236416921 . C T 224.43 PASS AC=2;AF=0.658;AN=2;DP=391;MQ=60;set=variant-variant2-variant5-variant7-variant9-variant15-variant16-variant17-variant20-variant23-variant24-variant26-variant28-variant29-variant30-variant35-variant37-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:611,51,0:0,0,3,14 chr1 236433135 . AT A 1620.78 PASS AC=2;AF=0.886;AN=2;DP=1930;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,32:33:90:1262,90,0:1,0,17,15 chr1 236444879 . G GGCCCGGCCCT 81.16 PASS AC=2;AF=0.737;AN=2;DP=1046;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,23:24:70:1111,70,0:1,0,12,11 chr1 236444973 . C T 532.06 PASS AC=2;AF=0.596;AN=2;DP=1466;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant20-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant35-variant37-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,63:63:99:2041,189,0:0,0,37,26 chr1 236445212 . A G 1435.47 PASS AC=2;AF=0.989;AN=2;DP=2772;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,53:54:99:1607,137,0:0,1,28,25 chr1 236557771 . G A 1444.61 PASS AC=1;AF=0.791;AN=2;DP=5645;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:62,81:143:99:1806,0,1355:27,35,44,37 chr1 236557928 . G A 121.25 PASS AC=1;AF=0.798;AN=2;DP=719;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,8:13:99:304,0,186:0,5,0,8 chr1 236572368 . TAA TA,T,TAAA 152.72 PASS AC=1,0,0;AF=0.421,0.079,0.026;AN=2;DP=265;MQ=60;set=variant3-variant4-variant7-variant11-variant13-variant14-variant16-variant19-variant21-variant23-variant24-variant25-variant28-variant30-variant35-variant37-variant41-variant42-variant43 GT:DP:GQ:SB 0/1:18:71:6,0,11,1 chr1 236572389 . G A 869.5 PASS AC=1;AF=0.675;AN=2;DP=1080;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,23:30:99:777,0,189:7,0,21,2 chr1 236572475 . A G 2728.98 PASS AC=1;AF=0.628;AN=2;DP=3579;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,66:111:99:1662,0,931:28,17,36,30 chr1 236577762 . C T,CT 234.78 PASS AC=0,1;AF=0.474,0.41;AN=2;DP=324;FS=0;MQ=60;set=variant7-variant9-variant4-variant3-variant14-variant15-variant-variant5-variant16-variant8-variant6-variant17-variant18-variant2-variant19-variant13-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:4:20:0,1,0,3 chr1 236590497 . C G 612.09 PASS AC=1;AF=0.622;AN=2;DP=727;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,11:29:99:278,0,465:12,6,8,3 chr1 236590563 . C T 1395.41 PASS AC=1;AF=0.618;AN=2;DP=1719;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-filterInvariant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,16:48:99:341,0,827:20,12,7,9 chr1 236590629 . C T 1827.88 PASS AC=1;AF=0.618;AN=2;DP=2418;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,22:71:99:479,0,1336:24,25,11,11 chr1 236590659 . G C 2188.64 PASS AC=1;AF=0.632;AN=2;DP=2425;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,22:66:99:468,0,1153:21,23,9,13 chr1 236590816 . T G 783.1 PASS AC=1;AF=0.618;AN=2;DP=959;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,10:22:99:222,0,342:3,9,4,6 chr1 236645670 . C T 3607.62 PASS AC=1;AF=0.605;AN=2;DP=2904;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant20-variant23-variant24-variant25-variant29-variant30-variant31-variant33-variant35-variant37-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:76,82:158:99:2150,0,1830:41,35,51,31 chr1 236648062 . G A 509.99 PASS AC=1;AF=0.625;AN=2;DP=69;FractionInformativeReads=1;MQ=60;set=variant8-variant25-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:6,9:15:99:264,0,145:2,4,3,6 chr1 236681581 . G A 419.53 PASS AC=1;AF=0.594;AN=2;DP=313;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant7-variant9-variant12-variant13-variant17-variant22-variant25-variant29-variant32-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,15:28:99:350,0,336:6,7,9,6 chr1 236681634 . A G 573.96 PASS AC=1;AF=0.614;AN=2;DP=626;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant6-variant8-variant10-variant12-variant13-variant18-variant19-variant21-variant24-variant26-variant27-variant29-variant31-variant33-variant35-variant36-variant37-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,9:28:99:234,0,530:9,10,5,4 chr1 236681719 . T C 596.86 PASS AC=1;AF=0.522;AN=2;DP=896;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant12-variant16-variant18-variant20-variant22-variant23-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:16,20:36:99:464,0,362:8,8,9,11 chr1 236681750 . G A 173.45 PASS AC=2;AF=0.691;AN=2;DP=1268;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:987,102,0:0,0,13,21 chr1 236686575 . T C 373.54 PASS AC=2;AF=1;AN=2;DP=376;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:266,21,0:0,0,6,1 chr1 236688177 . G T 156.15 PASS AC=2;AF=0.706;AN=2;DP=90;FS=0;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant7-variant9-variant11-variant16-variant18-variant21-variant23-variant26-variant27-variant28-variant31-variant32-variant35-variant37-variant39 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:216,15,0:0,0,0,5 chr1 236700807 . T A 3112.21 PASS AC=1;AF=0.743;AN=2;DP=2827;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,38:75:99:1477,0,1811:22,15,23,15 chr1 236700823 . T C 3257.13 PASS AC=1;AF=0.743;AN=2;DP=3155;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,42:83:99:1581,0,1941:23,18,26,16 chr1 236700857 . C T 3095.66 PASS AC=1;AF=0.743;AN=2;DP=3443;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,35:82:99:900,0,1135:23,24,16,19 chr1 236700982 . T C 1068.3 PASS AC=1;AF=0.743;AN=2;DP=1751;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,20:53:99:512,0,832:12,21,7,13 chr1 236702374 . G A,C 1469.75 PASS AC=1,0;AF=0.686,0.057;AN=2;DP=1658;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:43:99:16,14,8,5 chr1 236702447 . T G 1304.07 PASS AC=1;AF=0.735;AN=2;DP=999;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,9:32:99:299,0,948:8,15,6,3 chr1 236702450 . T C 1304.07 PASS AC=1;AF=0.743;AN=2;DP=997;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,9:32:99:299,0,948:8,15,5,4 chr1 236702475 . A G 740.98 PASS AC=1;AF=0.743;AN=2;DP=741;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,6:25:99:147,0,505:6,13,3,3 chr1 236702517 . T C 480.23 PASS AC=1;AF=0.758;AN=2;DP=331;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,6:16:99:138,0,304:2,8,2,4 chr1 236703767 . C T 474.96 PASS AC=1;AF=0.758;AN=2;DP=316;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,6:9:96:222,0,96:3,0,6,0 chr1 236703832 . CG C,CGG 1273.44 PASS AC=1,0;AF=0.743,0.043;AN=2;DP=1273;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:39:99:11,5,16,7 chr1 236704888 . A AACAGGT 367.73 PASS AC=1;AF=0.797;AN=2;DP=230;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,3:9:99:108,0,285:3,3,2,1 chr1 236704891 . TAAA T 367.73 PASS AC=1;AF=0.781;AN=2;DP=277;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,2:8:99:131,0,279:3,3,1,1 chr1 236704897 . ATT A 367.68 PASS AC=1;AF=0.766;AN=2;DP=299;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,5:11:99:131,0,279:3,3,2,3 chr1 236706352 . A C 2066.85 PASS AC=1;AF=0.743;AN=2;DP=1905;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,37:65:99:851,0,685:9,19,14,23 chr1 236706371 . A G 1572.32 PASS AC=1;AF=0.743;AN=2;DP=1483;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,29:48:99:784,0,551:4,15,9,20 chr1 236706425 . G A 679.61 PASS AC=1;AF=0.743;AN=2;DP=558;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,12:17:99:383,0,170:0,5,1,11 chr1 236706671 . T A 1320.55 PASS AC=1;AF=0.803;AN=2;DP=1017;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,9:28:99:252,0,661:17,2,8,1 chr1 236706780 . C T 4322.3 PASS AC=1;AF=0.803;AN=2;DP=5279;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:90,72:162:99:1716,0,2317:55,35,45,27 chr1 236706862 . G C 6504.16 PASS AC=1;AF=0.803;AN=2;DP=8916;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:131,118:249:99:2705,0,3090:64,67,61,57 chr1 236707007 . C T 2654.63 PASS AC=1;AF=0.706;AN=2;DP=3860;MQ=60;set=variant-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:69,64:133:99:1528,0,1712:29,40,24,40 chr1 236707036 . A T 2760.5 PASS AC=1;AF=0.743;AN=2;DP=2778;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,44:93:99:1656,0,2406:20,29,15,29 chr1 236707045 . C T 2578.54 PASS AC=1;AF=0.743;AN=2;DP=2467;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,41:86:99:1599,0,2411:16,29,13,28 chr1 236708022 . GT G,GTTTT 1211.09 PASS AC=1,0;AF=0.722,0.028;AN=2;DP=1394;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:31:99:11,7,8,5 chr1 236708224 . A C 1969.91 PASS AC=1;AF=0.743;AN=2;DP=3094;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,53:86:99:1259,0,713:13,20,22,31 chr1 236708316 . A G 804.65 PASS AC=1;AF=0.743;AN=2;DP=1199;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,14:24:99:393,0,298:2,8,4,10 chr1 236708357 . C CCCTT 502.38 PASS AC=1;AF=0.743;AN=2;DP=571;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,8:10:95:330,0,95:0,2,2,6 chr1 236711297 . A T 461.97 PASS AC=1;AF=0.743;AN=2;DP=476;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,4:14:84:84,0,308:8,2,3,1 chr1 236711323 . T C 768.91 PASS AC=1;AF=0.743;AN=2;DP=717;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,10:26:99:279,0,421:11,5,8,2 chr1 236711586 . G A 4985.18 PASS AC=1;AF=0.743;AN=2;DP=4847;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,72:129:99:1938,0,1524:29,28,43,29 chr1 236711810 . A G 5253.92 PASS AC=1;AF=0.803;AN=2;DP=5172;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:78,77:155:99:2024,0,1944:31,47,30,47 chr1 236711882 . G T 2855.38 PASS AC=1;AF=0.743;AN=2;DP=2175;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,30:65:99:1125,0,1348:11,24,13,17 chr1 236711886 . C T 2770.47 PASS AC=1;AF=0.743;AN=2;DP=2121;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,28:61:99:1134,0,1327:11,22,12,16 chr1 236711951 . T A 1854.04 PASS AC=1;AF=0.743;AN=2;DP=1940;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,28:58:99:1095,0,1149:15,15,14,14 chr1 236711956 . A C 1878.77 PASS AC=1;AF=0.743;AN=2;DP=1974;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,29:57:99:1095,0,1149:13,15,15,14 chr1 236711981 . C T 1776.2 PASS AC=1;AF=0.743;AN=2;DP=2046;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,26:54:99:732,0,730:14,14,13,13 chr1 236712074 . TTTTC T 1158.26 PASS AC=1;AF=0.743;AN=2;DP=1556;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,21:40:99:825,0,1051:8,11,8,13 chr1 236712857 . C T 5183.53 PASS AC=1;AF=0.706;AN=2;DP=5827;MQ=60;set=variant-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:113,93:206:99:2377,0,2635:62,51,49,44 chr1 236713556 . G A 911.6 PASS AC=1;AF=0.743;AN=2;DP=1588;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,23:57:99:485,0,848:18,16,15,8 chr1 236713828 . G A 14212.8 PASS AC=1;AF=0.743;AN=2;DP=13689;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:204,173:377:99:4278,0,5191:112,92,96,77 chr1 236714064 . A C 8739.1 PASS AC=1;AF=0.743;AN=2;DP=8889;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:110,131:241:99:3226,0,2736:59,51,63,68 chr1 236714292 . TA TAA,TAAA,T 731.68 PASS AC=0,1,0;AF=0.22,0.195,0.171;AN=2;DP=3144;set=variant-variant2-variant3-variant4-variant5-variant6-filterInvariant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-filterInvariant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:43:99:3,23,4,13 chr1 236714335 . C T 1043.36 PASS AC=1;AF=0.706;AN=2;DP=1113;set=variant-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,16:32:99:574,0,492:4,12,4,12 chr1 236714384 . G A 568.27 PASS AC=1;AF=0.743;AN=2;DP=839;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,11:18:99:351,0,199:4,3,5,6 chr1 236714709 . TC T 3309.3 PASS AC=1;AF=0.743;AN=2;DP=2641;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,34:79:99:1146,0,1572:32,13,26,8 chr1 236714747 . T C 4260.13 PASS AC=1;AF=0.706;AN=2;DP=3807;MQ=60;set=variant-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:76,57:133:99:1548,0,1990:49,27,41,16 chr1 236714916 . T C 10663.4 PASS AC=1;AF=0.743;AN=2;DP=11291;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:182,170:352:99:4111,0,4653:92,90,83,87 chr1 236715517 . T C 12896.2 PASS AC=1;AF=0.743;AN=2;DP=11801;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:178,189:367:99:4813,0,4302:97,81,102,87 chr1 236715710 . G A 4669.9 PASS AC=1;AF=0.706;AN=2;DP=4140;MQ=60;set=variant-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:66,75:141:99:2065,0,1932:17,49,21,54 chr1 236715842 . A G 732.47 PASS AC=1;AF=0.743;AN=2;DP=918;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,9:33:99:201,0,635:11,13,5,4 chr1 236715863 . G A 728.59 PASS AC=1;AF=0.743;AN=2;DP=879;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,11:35:99:234,0,595:13,11,6,5 chr1 236716370 . C T 283.53 PASS AC=1;AF=0.697;AN=2;DP=363;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:99:117,0,110:1,2,0,3 chr1 236716686 . G A 368.16 PASS AC=1;AF=0.819;AN=2;DP=678;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,10:24:99:288,0,388:10,4,8,2 chr1 236716741 . G A 1691.09 PASS AC=1;AF=0.743;AN=2;DP=1617;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,31:68:99:861,0,1017:28,9,23,8 chr1 236716959 . C T 5995.27 PASS AC=1;AF=0.743;AN=2;DP=5663;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:87,86:173:99:2131,0,2266:37,50,39,47 chr1 236717104 . A G 1708.64 PASS AC=1;AF=0.743;AN=2;DP=1480;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,23:51:99:612,0,783:7,21,6,17 chr1 236717926 . T C 2662.22 PASS AC=1;AF=0.743;AN=2;DP=2419;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,25:75:99:515,0,1271:28,22,10,15 chr1 236718524 . G C 899.65 PASS AC=1;AF=0.703;AN=2;DP=540;MQ=60;set=variant-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,4:14:99:138,0,312:8,2,4,0 chr1 236718561 . G A 1607.55 PASS AC=1;AF=0.743;AN=2;DP=1105;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,13:29:99:389,0,487:12,4,11,2 chr1 236718620 . T C 2957.33 PASS AC=1;AF=0.743;AN=2;DP=2461;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,37:76:99:876,0,825:21,18,24,13 chr1 236719135 . T C 1537.3 PASS AC=1;AF=0.81;AN=2;DP=2996;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:62,16:78:99:243,0,1701:38,24,9,7 chr1 236719193 . A G 2921.25 PASS AC=1;AF=0.743;AN=2;DP=3965;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:94,35:129:99:710,0,2321:51,43,20,15 chr1 236719259 . G A 3016.81 PASS AC=1;AF=0.697;AN=2;DP=3831;MQ=60;set=variant-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:86,45:131:99:1009,0,2172:36,50,25,20 chr1 236719688 . A G 505.21 PASS AC=1;AF=0.797;AN=2;DP=810;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,8:20:99:250,0,397:2,10,1,7 chr1 236720761 . T C 1687.73 PASS AC=1;AF=0.797;AN=2;DP=2369;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,32:57:99:891,0,684:10,15,11,21 chr1 236720833 . C T 940.72 PASS AC=1;AF=0.743;AN=2;DP=1124;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,15:31:99:402,0,456:4,12,4,11 chr1 236721610 . G A 1431.72 PASS AC=1;AF=0.797;AN=2;DP=1997;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,29:54:99:791,0,721:18,7,20,9 chr1 236721660 . T C 2301.46 PASS AC=1;AF=0.803;AN=2;DP=3106;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,42:95:99:1164,0,1496:31,22,27,15 chr1 236721731 . T C 2608.11 PASS AC=2;AF=1;AN=2;DP=4919;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,149:149:99:4570,446,0:0,0,80,69 chr1 236722182 . A T 1365.98 PASS AC=2;AF=1;AN=2;DP=1968;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1466,129,0:0,0,30,13 chr1 236722489 . C T 356.48 PASS AC=1;AF=0.809;AN=2;DP=390;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,5:14:81:81,0,282:3,6,2,3 chr1 236723177 . G A 1573.66 PASS AC=1;AF=0.706;AN=2;DP=1642;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,28:63:99:1050,0,1791:14,21,11,17 chr1 236723178 . C A 1573.66 PASS AC=1;AF=0.706;AN=2;DP=1631;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,27:60:99:1050,0,1791:14,19,10,17 chr1 236724504 . G A 2212.22 PASS AC=1;AF=0.797;AN=2;DP=2014;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,27:55:99:671,0,785:19,9,16,11 chr1 236724605 . G T 3264.04 PASS AC=1;AF=0.797;AN=2;DP=3449;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,51:112:99:1203,0,1462:28,33,22,29 chr1 236724715 . T G 1651.86 PASS AC=1;AF=0.797;AN=2;DP=1415;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,24:48:99:674,0,773:4,20,6,18 chr1 236724766 . C T 424.21 PASS AC=1;AF=0.833;AN=2;DP=443;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:7,5:12:99:148,0,242:1,6,1,4 chr1 236729867 . C T 1923.74 PASS AC=1;AF=0.706;AN=2;DP=1950;MQ=60;set=variant-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,40:64:99:973,0,494:14,10,24,16 chr1 236729956 . T C 3430.85 PASS AC=1;AF=0.563;AN=2;DP=1504;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant7-variant9-variant12-variant16-variant21-variant23-variant24-variant25-variant26-variant32-variant35-variant36-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,40:86:99:963,0,1089:22,24,21,19 chr1 236735939 . T C 4586.42 PASS AC=1;AF=0.712;AN=2;DP=3792;MQ=60;set=variant-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,55:110:99:1444,0,1522:34,21,30,25 chr1 236739416 . C T 1808.39 PASS AC=1;AF=0.77;AN=2;DP=1926;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,28:52:99:785,0,664:18,6,20,8 chr1 236740039 . G C 1241.2 PASS AC=1;AF=0.77;AN=2;DP=1275;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,27:48:99:759,0,551:13,8,18,9 chr1 236744424 . A AT 134.04 PASS AC=1;AF=0.75;AN=2;DP=340;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,7:10:56:170,0,56:2,1,5,2 chr1 236744712 . C A 1038.2 PASS AC=1;AF=0.743;AN=2;DP=749;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,13:24:99:327,0,332:2,9,5,8 chr1 236746275 . G C 3565.36 PASS AC=1;AF=0.771;AN=2;DP=3429;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,65:123:99:1706,0,1492:28,30,25,40 chr1 236746443 . C T 933.34 PASS AC=1;AF=0.771;AN=2;DP=1980;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,33:63:99:893,0,780:9,21,14,19 chr1 236748505 . T C 2790.74 PASS AC=1;AF=0.771;AN=2;DP=4941;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:73,73:146:99:1795,0,1787:35,38,31,42 chr1 236748570 . T C 1215.4 PASS AC=1;AF=0.5;AN=2;DP=1008;MQ=60;set=variant3-variant6-variant7-variant13-variant16-variant23-variant24-variant25-variant26-variant32-variant35-variant36-variant41 GT:AD:DP:GQ:PL:SB 0/1:43,48:91:99:1171,0,1011:15,28,17,31 chr1 236748630 . C T 678.09 PASS AC=1;AF=0.771;AN=2;DP=701;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,14:31:99:533,0,663:1,16,2,12 chr1 236748636 . G A 581.5 PASS AC=1;AF=0.706;AN=2;DP=596;MQ=60;set=variant-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,13:29:99:498,0,633:1,15,2,11 chr1 236749022 . G A 751.82 PASS AC=1;AF=0.765;AN=2;DP=431;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,5:9:99:226,0,270:4,0,5,0 chr1 236749026 . T A 514.35 PASS AC=1;AF=0.734;AN=2;DP=467;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,6:10:99:152,0,272:4,0,6,0 chr1 236749348 . C T 488.68 PASS AC=1;AF=0.771;AN=2;DP=669;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,4:19:99:123,0,555:0,15,0,4 chr1 236749451 . TA T 178.29 PASS AC=1;AF=0.838;AN=2;DP=250;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,3:8:93:93,0,374:4,1,2,1 chr1 236749649 . T C 3029.73 PASS AC=1;AF=0.712;AN=2;DP=3019;MQ=60;set=variant-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,58:115:99:1434,0,1477:35,22,32,26 chr1 236749817 . C T 888.68 PASS AC=1;AF=0.771;AN=2;DP=1226;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,24:47:99:630,0,799:3,20,7,17 chr1 236751519 . GA G 641.29 PASS AC=1;AF=0.706;AN=2;DP=655;MQ=60;set=variant-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-filterInvariant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,10:15:99:360,0,157:0,5,3,7 chr1 236755170 . G T 1319.14 PASS AC=1;AF=0.77;AN=2;DP=1130;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,12:21:99:312,0,265:7,2,8,4 chr1 236755427 . A G 1953.57 PASS AC=1;AF=0.77;AN=2;DP=1274;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,11:25:99:329,0,358:5,9,4,7 chr1 236755690 . G A 156.22 PASS AC=1;AF=0.788;AN=2;DP=243;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:3,4:7:99:115,0,108:3,0,3,1 chr1 236755814 . G A 1603.89 PASS AC=1;AF=0.77;AN=2;DP=1567;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,14:42:99:423,0,1453:17,11,8,6 chr1 236755837 . C T 1648.89 PASS AC=1;AF=0.77;AN=2;DP=1665;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,13:40:99:424,0,1434:16,11,6,7 chr1 236755937 . TA T 442.52 PASS AC=1;AF=0.757;AN=2;DP=878;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-filterInvariant40-variant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:13,10:23:99:213,0,296:2,11,4,6 chr1 236757200 . A G 847.02 PASS AC=1;AF=0.77;AN=2;DP=951;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,12:22:99:338,0,298:8,2,8,4 chr1 236757229 . G A 1245.84 PASS AC=1;AF=0.77;AN=2;DP=1632;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,20:41:99:554,0,566:16,5,13,7 chr1 236757507 . A G 766.95 PASS AC=1;AF=0.719;AN=2;DP=327;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant8-variant10-variant14-variant15-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,5:9:99:198,0,156:0,4,0,5 chr1 236758887 . T C 3057.73 PASS AC=1;AF=0.77;AN=2;DP=3819;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,73:120:99:1703,0,1006:24,23,36,37 chr1 236759060 . T C 1040.7 PASS AC=1;AF=0.771;AN=2;DP=955;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,8:20:99:282,0,386:8,4,3,5 chr1 236763031 . C T 310.97 PASS AC=1;AF=0.5;AN=2;DP=210;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant7-variant16-variant23-variant24-variant25-variant26-variant32-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:9,7:16:99:245,0,266:2,7,0,7 chr1 236767072 . A G 177.07 PASS AC=1;AF=0.821;AN=2;DP=190;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant8-variant10-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant22-variant24-variant26-variant28-variant29-variant30-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:1,3:4:34:123,0,34:1,0,2,1 chr1 236767176 . C G 1711.58 PASS AC=1;AF=0.706;AN=2;DP=1455;MQ=60;set=variant-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,10:26:99:356,0,908:12,4,8,2 chr1 236767178 . AG A 1702.63 PASS AC=1;AF=0.689;AN=2;DP=1687;MQ=60;set=variant-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,10:27:99:356,0,908:13,4,8,2 chr1 236767330 . A G 3615.1 PASS AC=1;AF=0.743;AN=2;DP=4681;MQ=60;set=variant-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,55:120:99:1174,0,1534:32,33,25,30 chr1 236767826 . T C 708.35 PASS AC=1;AF=0.691;AN=2;DP=1428;MQ=60;set=variant-variant4-variant5-variant6-variant8-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,11:26:99:284,0,453:6,9,3,8 chr1 236881403 . C T 406.52 PASS AC=2;AF=0.73;AN=2;DP=306;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:91,9,0:0,0,1,2 chr1 236882110 . G A 2734.81 PASS AC=2;AF=1;AN=2;DP=3536;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:2136,203,0:0,0,41,27 chr1 236882303 . T C 1280.54 PASS AC=2;AF=1;AN=2;DP=3036;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:2506,231,0:0,0,27,50 chr1 236883161 . A G 923.66 PASS AC=2;AF=1;AN=2;DP=967;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:769,69,0:0,0,17,6 chr1 236883240 . T C 2765.35 PASS AC=2;AF=1;AN=2;DP=3989;FS=0;MQ=60;MQRankSum=1.55;ReadPosRankSum=-0.547;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,83:83:99:2636,249,0:0,0,54,29 chr1 236883421 . C T 3599.44 PASS AC=2;AF=1;AN=2;DP=4963;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,105:105:99:3173,317,0:0,0,42,63 chr1 236883564 . G A 1256.36 PASS AC=2;AF=1;AN=2;DP=1437;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:686,66,0:0,0,8,14 chr1 236890781 . A G 632.31 PASS AC=2;AF=1;AN=2;DP=1102;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:1242,96,0:0,0,27,5 chr1 236897633 . A G 1822.56 PASS AC=2;AF=1;AN=2;DP=2362;FS=0;MQ=60;MQRankSum=0.426;ReadPosRankSum=1.505;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:1991,165,0:0,0,41,14 chr1 236899899 . TC T 2870.98 PASS AC=2;AF=0.797;AN=2;DP=3720;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,94:94:99:3088,283,0:0,0,39,55 chr1 236900018 . G A 702.27 PASS AC=2;AF=0.706;AN=2;DP=764;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1199,117,0:0,0,12,27 chr1 236900598 . C T 139.61 PASS AC=2;AF=0.845;AN=2;DP=345;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant35-variant36-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:274,21,0:0,0,0,7 chr1 236902560 . C T,G 2293.48 PASS AC=2,0;AF=0.694,0.069;AN=2;DP=2690;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:73:99:0,0,48,25 chr1 236902594 . C G 4104.2 PASS AC=2;AF=0.842;AN=2;DP=4427;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,123:123:99:3676,368,0:0,0,74,49 chr1 236902865 . A C 3858.13 PASS AC=2;AF=0.764;AN=2;DP=5590;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,200:200:99:5973,598,0:0,0,99,101 chr1 236902955 . T C 3131.02 PASS AC=2;AF=0.764;AN=2;DP=4291;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,143:143:99:4529,429,0:0,0,61,82 chr1 236912286 . G A 502.07 PASS AC=2;AF=0.942;AN=2;DP=486;FS=0;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:425,33,0:0,0,10,1 chr1 236914610 . G C 186.1 PASS AC=2;AF=0.798;AN=2;DP=954;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:1018,81,0:0,0,22,5 chr1 236924506 . A G 680.85 PASS AC=2;AF=0.872;AN=2;DP=3390;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,89:89:99:2927,266,0:0,0,40,49 chr1 236924732 . CGTGTGTGT C,CGTGTGTGTGTGT,CGT,CGTGTGTGTGT,CGTGTGTGTGTGTGT,CGTGT 272.02 PASS AC=0,0,2,0,0,0;AF=0.013,0.115,0.564,0.064,0.026,0.026;AN=2;DP=398;MQ=60;set=variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 3/3:9:27:0,0,2,7 chr1 236924740 . T C 48.88 PASS AC=2;AF=0.703;AN=2;DP=302;MQ=60;set=variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:345,27,0:0,0,2,7 chr1 236925883 . G A 1952.14 PASS AC=1;AF=0.5;AN=2;DP=174;FS=2.658;FractionInformativeReads=1;MQ=60;MQRankSum=0.716;QD=11.22;ReadPosRankSum=-3.598;SOR=0.512;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:92,82:174:99:1980,0,2347:38,54,38,44 chr1 236926030 . A G 1320.86 PASS AC=2;AF=0.697;AN=2;DP=5499;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:3,129:132:99:3213,304,0:1,2,67,62 chr1 236926366 . C G 3893.62 PASS AC=2;AF=0.697;AN=2;DP=11892;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:3,256:259:99:7670,680,0:2,1,140,116 chr1 236926445 . T C 4008.94 PASS AC=2;AF=0.763;AN=2;DP=13127;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:5,309:314:99:9483,811,0:3,2,151,158 chr1 236926667 . A G 721.39 PASS AC=2;AF=0.697;AN=2;DP=2387;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1927,149,0:0,0,10,40 chr1 236958532 . G T 347.39 PASS AC=2;AF=0.65;AN=2;DP=1238;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant9-variant11-variant13-variant15-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1888,168,0:0,0,38,18 chr1 236978992 . T TTCTG 580.66 PASS AC=2;AF=0.729;AN=2;DP=1002;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:576,39,0:0,0,3,10 chr1 236987790 . G T 185.88 PASS AC=2;AF=0.63;AN=2;DP=594;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant9-variant11-variant13-variant15-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:743,60,0:0,0,4,16 chr1 236988593 . A AT 359.72 PASS AC=2;AF=0.63;AN=2;DP=1093;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant9-variant11-variant13-variant15-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1270,120,0:0,0,26,14 chr1 237001926 . A G 503.99 PASS AC=2;AF=0.63;AN=2;DP=1522;MQ=60;set=variant2-variant3-variant4-variant5-variant9-variant11-variant13-variant15-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,43:44:93:1478,93,0:1,0,14,29 chr1 237002032 . A C 105.22 PASS AC=2;AF=0.652;AN=2;DP=239;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant9-variant11-variant13-variant15-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant35-variant36-variant37-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:444,39,0:0,0,4,9 chr1 237013550 . AT A 40.69 PASS AC=2;AF=0.769;AN=2;DP=52;FS=0;FractionInformativeReads=1;MQ=60;set=variant3-variant9-variant15-variant21-variant23-variant24-variant27-variant29-variant30-variant32-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:225,15,0:0,0,4,1 chr1 237013553 . T A 49.73 PASS AC=2;AF=0.75;AN=2;DP=61;FS=0;FractionInformativeReads=1;MQ=60;set=variant3-variant9-variant13-variant15-variant21-variant23-variant24-variant27-variant29-variant30-variant32-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:225,15,0:0,0,4,1 chr1 237023333 . T C 139.14 PASS AC=2;AF=0.671;AN=2;DP=558;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:562,42,0:0,0,3,11 chr1 237037998 . CTTT CTT,CT,C 143.27 PASS AC=2,0,0;AF=0.609,0.016,0.047;AN=2;DP=879;set=variant2-variant4-variant5-variant7-variant9-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:DP:GQ:SB 1/1:34:4:2,2,20,10 chr1 237038008 . TA AA,TAAA,T 915.19 PASS AC=2,0,0;AF=0.533,0.1,0.033;AN=2;DP=513;set=variant21-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant35-variant4-variant36-variant37-variant41-variant43 GT:DP:GQ:SB 1/1:40:46:2,1,25,12 chr1 237048562 . G A 186.13 PASS AC=2;AF=0.714;AN=2;DP=1198;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,32:32:95:1091,95,0:0,0,7,25 chr1 237049879 . C T 722.7 PASS AC=2;AF=0.63;AN=2;DP=1719;MQ=60;set=variant2-variant3-variant4-variant5-variant9-variant11-variant13-variant15-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,73:73:99:2463,219,0:0,0,20,53 chr1 237054569 . A G 1106.71 PASS AC=2;AF=0.63;AN=2;DP=2849;MQ=60;set=variant2-variant3-variant4-variant5-variant9-variant11-variant13-variant15-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,125:126:99:3614,339,0:1,0,52,73 chr1 237057608 . G A 465.02 PASS AC=2;AF=0.672;AN=2;DP=2469;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,99:99:99:2998,297,0:0,0,59,40 chr1 237058744 . C A 2037.59 PASS AC=2;AF=0.63;AN=2;DP=5570;set=variant2-variant3-variant4-variant5-variant9-variant11-variant13-variant15-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,245:245:99:7379,731,0:0,0,112,133 chr1 237058828 . C T 1268.69 PASS AC=1;AF=0.638;AN=2;DP=3846;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant12-variant15-variant16-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:80,83:163:99:2076,0,2174:32,48,37,46 chr1 237058996 . C CTATT 508.33 PASS AC=2;AF=0.729;AN=2;DP=1586;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:2036,138,0:0,0,14,32 chr1 237060433 . G T 1046.6 PASS AC=2;AF=0.714;AN=2;DP=3448;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,99:99:99:2830,297,0:0,0,39,60 chr1 237061056 . A C 574.95 PASS AC=2;AF=0.672;AN=2;DP=1884;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1705,150,0:0,0,21,29 chr1 237061704 . GT G 38.84 PASS AC=2;AF=0.76;AN=2;DP=304;MQ=60;set=variant3-variant4-variant7-variant9-variant11-variant12-variant13-variant15-variant16-variant18-variant21-variant24-variant25-variant26-variant28-variant29-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,8:9:17:185,17,0:1,0,1,7 chr1 237062198 . A C 314.8 PASS AC=2;AF=0.729;AN=2;DP=1594;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:1788,143,0:0,0,35,13 chr1 237062305 . A G 1903.77 PASS AC=2;AF=0.729;AN=2;DP=5575;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,177:177:99:5461,531,0:0,0,106,71 chr1 237063335 . G C 3318.72 PASS AC=2;AF=0.7;AN=2;DP=8656;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,259:259:99:8099,775,0:0,0,138,121 chr1 237063504 . A G 2950.44 PASS AC=2;AF=0.63;AN=2;DP=7738;MQ=60;set=variant2-variant3-variant4-variant5-variant9-variant11-variant13-variant15-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,278:279:99:8847,794,0:0,1,143,135 chr1 237063709 . T TA,TAA 1238.61 PASS AC=2,0;AF=0.7,0.029;AN=2;DP=4939;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:DP:GQ:SB 1/1:132:99:0,1,57,74 chr1 237064626 . T G 583.29 PASS AC=2;AF=0.672;AN=2;DP=1125;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1205,102,0:0,0,12,22 chr1 237065326 . C T 682.02 PASS AC=2;AF=0.688;AN=2;DP=2637;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,82:82:99:2729,245,0:0,0,37,45 chr1 237065583 . G T 906.82 PASS AC=2;AF=0.729;AN=2;DP=2477;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:2445,234,0:0,0,30,49 chr1 237065810 . T G 446.09 PASS AC=1;AF=0.5;AN=2;DP=326;FractionInformativeReads=1;MQ=60;set=variant11-variant13-variant18-variant28-variant29-variant35 GT:AD:DP:GQ:PL:SB 0/1:38,28:66:99:610,0,1042:17,21,11,17 chr1 237065879 . GCAGGGGCCCTGCCT G 1577.3 PASS AC=1;AF=0.5;AN=2;DP=359;MQ=60;set=variant3-variant21-variant24-variant27-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:22,40:62:99:1586,0,803:9,13,19,21 chr1 237433625 . C T 769.9 PASS AC=1;AF=0.595;AN=2;DP=1454;MQ=60;set=variant2-variant3-variant5-variant10-variant11-variant12-variant13-variant15-variant19-variant22-variant23-variant25-variant26-variant28-variant30-variant31-variant33-variant35-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:34,40:74:99:1059,0,804:18,16,20,20 chr1 237504708 . A G 282.03 PASS AC=2;AF=0.6;AN=2;DP=438;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant9-variant12-variant13-variant15-variant18-variant19-variant20-variant21-variant22-variant28-variant29-variant33-variant34-variant35-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:562,45,0:0,0,12,3 chr1 237504759 . T C 810.75 PASS AC=1;AF=0.545;AN=2;DP=708;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant12-variant18-variant19-variant20-variant21-variant22-variant35-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,22:40:99:569,0,559:12,6,15,7 chr1 237516073 . T C 846.51 PASS AC=2;AF=0.611;AN=2;DP=1353;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant9-variant12-variant13-variant15-variant19-variant20-variant21-variant22-variant28-variant29-variant33-variant35-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:1847,162,0:0,0,35,19 chr1 237516180 . A C 1080.76 PASS AC=1;AF=0.5;AN=2;DP=1248;MQ=60;set=variant9-variant12-variant13-variant15-variant20-variant21-variant28-variant29-variant33-variant35-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:58,46:104:99:938,0,1263:28,30,23,23 chr1 237519137 . T A 40.7 PASS AC=2;AF=0.643;AN=2;DP=110;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant12-variant13-variant15-variant19-variant20-variant21-variant22-variant28-variant33-variant35-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:398,27,0:0,0,9,0 chr1 237519165 . G T 50.22 PASS AC=2;AF=0.611;AN=2;DP=270;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant9-variant12-variant13-variant15-variant19-variant20-variant21-variant22-variant28-variant29-variant33-variant35-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:443,33,0:0,0,10,1 chr1 237540615 . A C 1046.74 PASS AC=1;AF=0.594;AN=2;DP=1690;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant10-variant12-variant17-variant19-variant20-variant22-variant25-variant27-variant28-variant35-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,36:80:99:877,0,1084:28,16,21,15 chr1 237551241 . G GTC 688.29 PASS AC=2;AF=0.757;AN=2;DP=1240;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant35-variant36-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1591,108,0:0,0,24,12 chr1 237551376 . T A 1216.98 PASS AC=2;AF=0.757;AN=2;DP=4418;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant35-variant36-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,118:118:99:3421,352,0:0,0,61,57 chr1 237580606 . G T 376.77 PASS AC=2;AF=0.829;AN=2;DP=453;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:261,18,0:0,0,0,6 chr1 237580612 . G C 376.77 PASS AC=2;AF=0.829;AN=2;DP=417;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:15:225,15,0:0,0,0,3 chr1 237586242 . G T 338.45 PASS AC=1;AF=0.5;AN=2;DP=22;FS=2.103;FractionInformativeReads=1;MQ=60;MQRankSum=-0.668;QD=15.38;ReadPosRankSum=-0.735;SOR=0.317;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:9,13:22:99:367,0,268:8,1,10,3 chr1 237586384 . T C 501.05 PASS AC=1;AF=0.5;AN=2;DP=709;MQ=60;set=variant-variant10-variant17-variant22-variant24-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:51,59:110:99:1421,0,1141:27,24,32,27 chr1 237617757 . C T 1126.56 PASS AC=1;AF=0.697;AN=2;DP=3526;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,54:98:99:1464,0,1079:28,16,37,17 chr1 237619875 . AT ATT,A,ATTT 538.87 PASS AC=1,1,0;AF=0.475,0.213,0.013;AN=2;DP=5142;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 2/1:145:99:2,4,89,50 chr1 237620049 . T C 1904.71 PASS AC=1;AF=0.681;AN=2;DP=4545;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:77,42:119:99:1014,0,2051:27,50,14,28 chr1 237632285 . A AT 415.75 PASS AC=1;AF=0.681;AN=2;DP=819;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,10:18:99:413,0,264:6,2,9,1 chr1 237632558 . CAAAA CA,CAAA,CAA,CAAAAAAA,C 43.31 PASS AC=0,0,1,0,0;AF=0.118,0.147,0.206,0.029,0.029;AN=2;DP=638;set=filterInvariant-filterInvariant3-variant9-variant10-variant11-variant13-variant21-variant22-variant24-filterInvariant25-filterInvariant29-variant30-variant31-variant33-variant35-filterInvariant37-variant40 GT:DP:GQ:SB 0/3:24:99:3,7,4,10 chr1 237632595 . T TGTG 154.45 PASS AC=1;AF=0.691;AN=2;DP=447;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:7,3:10:97:97,0,292:0,7,0,3 chr1 237654831 . G T 1034.67 PASS AC=2;AF=0.768;AN=2;DP=1289;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1362,119,0:0,0,30,10 chr1 237656185 . A AAGGGAGGG,AAGGGAGGGAGGG,AAGGG 607.43 PASS AC=2,0,0;AF=0.705,0.013,0.051;AN=2;DP=870;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43 GT:DP:GQ:SB 1/1:25:84:0,0,25,0 chr1 237670140 . A G 3662.52 PASS AC=2;AF=0.727;AN=2;DP=3285;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant9-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,85:85:99:2648,254,0:0,0,42,43 chr1 237675150 . A G,AG 73.45 PASS AC=0,2;AF=0.167,0.583;AN=2;DP=55;MQ=60;set=variant13-variant16-variant27-variant28-variant35-variant40 GT:DP:GQ:SB 2/2:9:28:0,0,2,7 chr1 237711644 . T C 366.49 PASS AC=2;AF=0.965;AN=2;DP=1040;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:1055,90,0:0,0,23,7 chr1 237711797 . A G 2293.18 PASS AC=2;AF=0.965;AN=2;DP=5194;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,110:110:99:3343,330,0:0,0,59,51 chr1 237714071 . G T 725.16 PASS AC=1;AF=0.5;AN=2;DP=103;FractionInformativeReads=1;MQ=60;set=variant22-variant35 GT:AD:DP:GQ:PL:SB 0/1:37,22:59:99:565,0,1033:14,23,6,16 chr1 237730124 . A G 2581.66 PASS AC=2;AF=0.977;AN=2;DP=3147;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:2629,204,0:0,0,10,58 chr1 237730169 . C T 1098.23 PASS AC=2;AF=0.989;AN=2;DP=1427;MQ=60;MQRankSum=-1.017;ReadPosRankSum=2.444;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1577,114,0:0,0,2,36 chr1 237732395 . G A 978.71 PASS AC=2;AF=0.825;AN=2;DP=1061;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:1125,84,0:0,0,26,2 chr1 237788862 . T C 274.74 PASS AC=2;AF=0.882;AN=2;DP=301;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:406,30,0:0,0,9,1 chr1 237794603 . A G 500.3 PASS AC=2;AF=0.842;AN=2;DP=610;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:768,63,0:0,0,14,7 chr1 237794913 . ATTTTTTTTTTTTTT ATT,A,ATTT,AT,ATTTTTTTTTTTTTTTT 486.27 PASS AC=1,1,0,0,0;AF=0.333,0.083,0.125,0.104,0.042;AN=2;DP=465;set=variant2-variant3-variant5-variant6-variant7-variant11-variant12-variant13-variant15-variant18-variant19-variant20-variant25-variant26-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:DP:GQ:SB 2/1:11:92:0,0,2,9 chr1 237794986 . T TGAA 62.42 PASS AC=2;AF=0.722;AN=2;DP=80;FS=0;set=variant2-variant3-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant25-variant33-variant35-variant36-variant39-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:135,9,0:0,0,0,3 chr1 237794989 . ACG A 172.69 PASS AC=2;AF=0.75;AN=2;DP=75;FS=0;set=variant2-variant3-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant25-variant33-variant35-variant36-variant39-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:135,9,0:0,0,0,3 chr1 237796759 . G C 525.33 PASS AC=1;AF=0.56;AN=2;DP=1212;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant24-variant25-variant27-variant30-variant32-variant33-variant35-variant36-variant37-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:28,18:46:99:466,0,720:17,11,12,6 chr1 237796837 . G A 825.57 PASS AC=1;AF=0.578;AN=2;DP=2210;MQ=60;set=variant2-variant3-variant5-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant24-variant25-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,30:73:99:708,0,1012:23,20,18,12 chr1 237797082 . T G 171.61 PASS AC=2;AF=0.614;AN=2;DP=140;MQ=60;set=variant2-variant3-variant5-variant7-variant9-variant10-variant12-variant13-variant14-variant16-variant19-variant20-variant24-variant27-variant28-variant32-variant35-variant37-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:86,6,0:0,0,0,2 chr1 237798450 . G A 326.82 PASS AC=1;AF=0.565;AN=2;DP=478;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant24-variant25-variant27-variant28-variant30-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,3:7:99:114,0,158:0,4,0,3 chr1 237801770 . T C 5355.09 PASS AC=2;AF=0.966;AN=2;DP=8149;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,223:223:99:6647,668,0:0,0,96,127 chr1 237802559 . T C 1567.79 PASS AC=2;AF=1;AN=2;DP=2648;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:1952,177,0:0,0,21,38 chr1 237813126 . A G 180.37 PASS AC=1;AF=0.606;AN=2;DP=380;MQ=60;set=variant3-variant4-variant5-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,11:14:91:328,0,91:3,0,8,3 chr1 237814783 . C T 973.77 PASS AC=1;AF=0.603;AN=2;DP=2690;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,28:66:99:693,0,944:14,24,9,19 chr1 237814898 . C A 106.89 PASS AC=1;AF=0.613;AN=2;DP=299;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant7-variant9-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:99:102,0,159:0,4,1,3 chr1 237817514 . GA G 261.65 PASS AC=2;AF=0.609;AN=2;DP=693;MQ=60;set=variant3-variant5-variant9-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant22-variant27-variant29-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:419,42,0:0,0,14,0 chr1 237817784 . A G 466.46 PASS AC=1;AF=0.548;AN=2;DP=577;MQ=60;set=variant3-variant9-variant12-variant13-variant14-variant15-variant18-variant20-variant22-variant27-variant29-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,11:30:99:304,0,649:3,16,2,9 chr1 237819014 . C G 469.97 PASS AC=1;AF=0.571;AN=2;DP=370;MQ=60;set=variant3-variant9-variant12-variant13-variant14-variant15-variant18-variant20-variant22-variant27-variant29-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,9:19:99:299,0,331:9,1,8,1 chr1 237821109 . T A 91.5 PASS AC=1;AF=0.6;AN=2;DP=49;FS=0;FractionInformativeReads=1;MQ=60;set=variant3-variant9-variant12-variant15-variant18-variant32-variant33-variant35-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,4:5:31:158,0,31:1,0,4,0 chr1 237823256 . A C 924.33 PASS AC=1;AF=0.5;AN=2;DP=500;MQ=60;set=variant5-variant19-variant22-variant23-variant32-variant35 GT:AD:DP:GQ:PL:SB 0/1:40,24:64:99:559,0,997:21,19,14,10 chr1 237824332 . G A 332.98 PASS AC=2;AF=1;AN=2;DP=405;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:216,18,0:0,0,1,5 chr1 237831103 . C A 510.44 PASS AC=2;AF=1;AN=2;DP=675;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:513,45,0:0,0,11,4 chr1 237841390 . A G 798.85 PASS AC=1;AF=0.5;AN=2;DP=1552;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant20-variant21-variant24-variant26-variant28-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:42,26:68:99:593,0,1112:16,26,11,15 chr1 237850666 . C CT,CTT 594.53 PASS AC=1,0;AF=0.347,0.181;AN=2;DP=1371;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43 GT:DP:GQ:SB 0/1:33:99:10,6,11,6 chr1 237862164 . G C 1577.79 PASS AC=2;AF=0.774;AN=2;DP=1693;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1507,132,0:0,0,31,13 chr1 237862436 . T C 151.77 PASS AC=2;AF=0.919;AN=2;DP=103;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:129,9,0:0,0,0,3 chr1 237863439 . G A 1416.83 PASS AC=2;AF=0.774;AN=2;DP=1430;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1320,117,0:0,0,29,10 chr1 237863718 . T G 2441.52 PASS AC=2;AF=1;AN=2;DP=3448;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,84:84:99:2629,252,0:0,0,37,47 chr1 237865203 . C T 2314.22 PASS AC=2;AF=1;AN=2;DP=2470;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:1641,141,0:0,0,35,12 chr1 237872714 . GT G 576.49 PASS AC=2;AF=0.989;AN=2;DP=1161;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1084,117,0:0,0,26,13 chr1 237881770 . C T 2312.87 PASS AC=2;AF=1;AN=2;DP=4126;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,91:91:99:2621,272,0:0,0,41,50 chr1 237890437 . C T 5356.7 PASS AC=2;AF=1;AN=2;DP=9201;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,175:175:99:5303,525,0:0,0,90,85 chr1 237893674 . C T 1980.16 PASS AC=2;AF=1;AN=2;DP=2523;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:2219,212,0:0,0,30,41 chr1 237905568 . T TC 219.53 PASS AC=1;AF=0.5;AN=2;DP=526;MQ=60;set=variant-filterInvariant2-variant3-variant5-variant6-variant8-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant32-variant33-variant35-filterInvariant36-variant37-filterInvariant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:20,12:32:99:201,0,573:11,9,8,4 chr1 237923053 . C T 2856.52 PASS AC=1;AF=0.744;AN=2;DP=4040;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,44:90:99:989,0,1018:24,22,25,19 chr1 237951451 . A G 698.95 PASS AC=1;AF=0.694;AN=2;DP=1941;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant15-variant16-variant17-variant18-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,26:39:99:839,0,411:1,12,7,19 chr1 237951482 . G A 318.58 PASS AC=1;AF=0.6;AN=2;DP=779;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant8-variant10-variant12-variant14-variant15-variant16-variant18-variant20-variant21-variant24-variant25-variant26-variant28-variant29-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,16:24:99:541,0,290:0,8,2,14 chr1 237955649 . CTGTGTGTGTG CTGTGTGTG,CTGTGTG,C,CTG,CTGTG 523.66 PASS AC=1,1,0,0,0;AF=0.303,0.348,0.106,0.076,0.03;AN=2;DP=1249;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-filterInvariant11-variant12-variant15-variant16-variant17-variant20-variant21-variant22-variant23-filterInvariant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant44 GT:DP:GQ:SB 2/1:19:99:0,0,3,16 chr1 237955678 . T C 345.89 PASS AC=1;AF=0.611;AN=2;DP=445;set=variant-variant3-variant5-variant7-variant8-variant10-variant12-variant17-variant21-variant22-variant23-variant28-variant31-variant33-variant34-variant35-variant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:9,14:23:99:460,0,336:1,8,2,12 chr1 237955680 . T C 345.8 PASS AC=1;AF=0.632;AN=2;DP=440;set=variant-variant3-variant5-variant7-variant8-variant10-variant12-variant17-variant21-variant22-variant23-variant28-variant30-variant31-variant33-variant34-variant35-variant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:9,10:19:99:460,0,336:1,8,1,9 chr1 237955698 . CGT C,TGT 1037.34 PASS AC=1,0;AF=0.647,0.118;AN=2;DP=290;set=variant18-variant5-variant19-variant8-variant21-variant23-variant28-variant29-variant31-variant33-variant34-variant35-variant37-variant38-variant17-variant40-variant41 GT:DP:GQ:SB 0/1:4:19:0,1,0,3 chr1 237957146 . G A 104.69 PASS AC=1;AF=0.75;AN=2;DP=917;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,7:22:99:180,0,397:10,5,6,1 chr1 237957161 . A G 109.49 PASS AC=1;AF=0.744;AN=2;DP=1273;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,11:30:99:317,0,526:13,6,9,2 chr1 237957309 . A C 775.96 PASS AC=1;AF=0.744;AN=2;DP=2717;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:42,38:80:99:931,0,1009:19,23,16,22 chr1 237964934 . A G 340.43 PASS AC=1;AF=0.716;AN=2;DP=520;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,10:13:98:330,0,98:3,0,8,2 chr1 237965035 . C A 505.3 PASS AC=1;AF=0.621;AN=2;DP=1473;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant12-variant16-variant17-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:37,20:57:99:725,0,1610:22,15,15,5 chr1 237965043 . A G 564.42 PASS AC=1;AF=0.621;AN=2;DP=1609;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant12-variant16-variant17-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:40,24:64:99:847,0,1669:25,15,18,6 chr1 237965094 . G T 647.92 PASS AC=1;AF=0.621;AN=2;DP=2185;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant12-variant16-variant17-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:52,32:84:99:766,0,1356:27,25,20,12 chr1 237965131 . G A 789.06 PASS AC=1;AF=0.603;AN=2;DP=2324;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant12-variant16-variant17-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:54,42:96:99:1037,0,1419:25,29,22,20 chr1 237965133 . AT ATT,ATTT,A 1264.76 PASS AC=1,0,0;AF=0.431,0.121,0.017;AN=2;DP=2340;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant12-variant16-variant17-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-filterInvariant36-variant37-variant38-variant39-variant41-variant42-variant43 GT:DP:GQ:SB 0/1:85:99:23,26,19,17 chr1 237969638 . A G 841.1 PASS AC=1;AF=0.563;AN=2;DP=810;MQ=60;set=variant-variant2-variant5-variant9-variant10-variant11-variant12-variant22-variant26-variant30-variant33-variant34-variant35-variant37-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:35,30:65:99:703,0,783:14,21,12,18 chr1 237996581 . GA GAA,G,GAAA 650.32 PASS AC=1,0,0;AF=0.539,0.066,0.013;AN=2;DP=1610;set=variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:38:99:5,11,5,17 chr1 237996661 . C G 215.04 PASS AC=1;AF=0.615;AN=2;DP=401;set=variant2-variant3-variant4-variant5-variant6-variant11-variant13-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant32-variant33-variant35-variant36-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,5:10:70:116,0,70:3,2,1,4 chr1 237997087 . A G 5076.62 PASS AC=1;AF=0.574;AN=2;DP=11091;MQ=60;set=variant2-variant3-variant4-variant6-variant11-variant13-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:221,209:430:99:5141,0,5401:118,103,117,92 chr1 238045590 . C T 84.96 PASS AC=1;AF=0.609;AN=2;DP=207;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant19-variant21-variant25-variant26-variant29-variant35-variant36-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:3,6:9:97:202,0,97:3,0,4,2 chr1 238048325 . A G 1300.54 PASS AC=1;AF=0.895;AN=2;DP=2388;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,26:55:99:703,0,847:12,17,13,13 chr1 238051933 . C T 193.2 PASS AC=1;AF=0.643;AN=2;DP=659;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,8:17:99:287,0,352:0,9,0,8 chr1 238053129 . A C 168.33 PASS AC=1;AF=0.5;AN=2;DP=931;set=variant3-variant4-variant5-filterInvariant6-variant7-variant8-variant10-variant11-filterInvariant14-filterInvariant15-variant16-variant17-filterInvariant18-variant21-filterInvariant22-filterInvariant23-filterInvariant26-filterInvariant27-variant29-variant30-variant31-variant32-filterInvariant35-filterInvariant38-variant39-variant40-filterInvariant41 GT:AD:DP:GQ:PL:SB 0/1:34,22:56:99:462,0,1144:6,28,22,0 chr1 238053132 . A C 387.49 PASS AC=1;AF=0.5;AN=2;DP=644;set=variant4-variant5-filterInvariant6-variant7-filterInvariant8-variant10-variant11-filterInvariant14-filterInvariant18-filterInvariant19-variant21-variant23-filterInvariant26-variant29-variant30-variant31-variant32-filterInvariant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:35,14:49:93:93,0,1514:7,28,14,0 chr1 238053138 . A C 370.54 PASS AC=1;AF=0.5;AN=2;DP=485;set=variant4-variant5-variant6-filterInvariant8-variant10-filterInvariant14-variant16-variant18-variant19-variant21-variant29-variant31-filterInvariant35 GT:AD:DP:GQ:PL:SB 0/1:34,18:52:99:433,0,1227:5,29,18,0 chr1 238053524 . T C 162.61 PASS AC=1;AF=0.596;AN=2;DP=500;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant19-variant20-variant21-variant25-variant26-variant29-variant31-variant34-variant35-variant36-variant37-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,10:23:99:297,0,392:3,10,2,8 chr1 238107361 . C T 54.21 PASS AC=1;AF=0.784;AN=2;DP=522;FS=0;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,4:12:63:63,0,200:4,4,2,2 chr1 238108482 . C T 3102.8 PASS AC=1;AF=0.756;AN=2;DP=9082;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:110,136:246:99:3320,0,2509:61,49,82,54 chr1 240072721 . G GAA,GAAA 4067.09 PASS AC=0,1;AF=0.242,0.455;AN=2;DP=2491;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42 GT:DP:GQ:SB 0/2:77:99:18,24,16,19 chr1 240073226 . C T 7427.32 PASS AC=1;AF=0.667;AN=2;DP=5415;set=variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:105,101:206:99:2277,0,2481:53,52,51,50 chr1 240073884 . GA GAA,G 949.16 PASS AC=1,0;AF=0.528,0.028;AN=2;DP=1559;MQ=60;set=variant3-variant4-variant7-variant8-variant13-variant16-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant30-variant32-variant34-variant35 GT:DP:GQ:SB 0/1:71:99:14,14,22,21 chr1 240074847 . T TA 1012.85 PASS AC=1;AF=0.529;AN=2;DP=1715;MQ=60;set=variant3-variant4-variant7-variant8-variant13-variant16-variant20-variant21-variant25-variant26-variant27-variant28-variant30-variant32-variant34-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:41,35:76:99:639,0,838:22,19,13,22 chr1 240074981 . A G 10164.4 PASS AC=1;AF=0.607;AN=2;DP=7345;MQ=60;set=variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant13-variant16-variant17-variant19-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:150,117:267:99:2532,0,3422:82,68,65,52 chr1 240076608 . A G 2286.94 PASS AC=1;AF=0.529;AN=2;DP=2218;MQ=60;set=variant3-variant4-variant7-variant8-variant13-variant16-variant20-variant21-variant25-variant26-variant27-variant28-variant30-variant32-variant34-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:72,67:139:99:1536,0,1670:37,35,40,27 chr1 240077309 . A G 932.6 PASS AC=1;AF=0.605;AN=2;DP=930;MQ=60;set=variant3-variant4-variant5-variant7-variant8-variant13-variant16-variant19-variant20-variant21-variant25-variant26-variant27-variant28-variant30-variant32-variant34-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:23,31:54:99:887,0,630:8,15,10,21 chr1 240077669 . A G 6500.99 PASS AC=1;AF=0.531;AN=2;DP=6584;MQ=60;set=variant3-variant4-variant7-variant8-variant13-variant16-variant20-variant21-variant25-variant26-variant27-variant28-variant30-variant32-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:188,216:404:99:5407,0,4378:88,100,100,116 chr1 240254828 . T C 335.77 PASS AC=2;AF=0.872;AN=2;DP=302;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:271,21,0:0,0,6,1 chr1 240254874 . T C 644.47 PASS AC=2;AF=0.85;AN=2;DP=706;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:443,39,0:0,0,10,3 chr1 240255203 . G T 700.52 PASS AC=1;AF=0.691;AN=2;DP=973;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,29:46:99:700,0,431:6,11,14,15 chr1 240255568 . GGGC G 1502.47 PASS AC=2;AF=0.821;AN=2;DP=2516;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-filterInvariant17-variant18-variant19-variant20-variant21-variant22-filterInvariant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,51:53:99:2084,104,0:0,2,37,14 chr1 240256822 . C A 2691.05 PASS AC=1;AF=0.691;AN=2;DP=4287;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,90:154:99:2381,0,1806:18,46,32,58 chr1 240286453 . T C 1028.86 PASS AC=1;AF=0.5;AN=2;DP=477;FractionInformativeReads=1;MQ=60;set=variant9-variant18-variant26-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:30,44:74:99:1382,0,816:18,12,31,13 chr1 240286774 . T C 155.13 PASS AC=1;AF=0.5;AN=2;DP=106;FractionInformativeReads=1;MQ=60;set=variant9-variant18-variant26-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:12,10:22:99:335,0,413:2,10,2,8 chr1 240341119 . A G 336.22 PASS AC=1;AF=0.556;AN=2;DP=125;MQ=60;set=variant2-variant3-variant15-variant18-variant26-variant31-variant34-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:4,6:10:99:232,0,149:4,0,6,0 chr1 240341164 . C T 695.36 PASS AC=1;AF=0.55;AN=2;DP=302;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant15-variant18-variant26-variant30-variant31-variant34-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:12,16:28:99:500,0,283:8,4,13,3 chr1 240341268 . A G 3531.54 PASS AC=1;AF=0.545;AN=2;DP=1408;MQ=60;set=variant2-variant3-variant15-variant18-variant26-variant30-variant31-variant34-variant35-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:69,64:133:99:1570,0,1815:45,24,36,28 chr1 240341423 . G T 1860.02 PASS AC=1;AF=0.545;AN=2;DP=731;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant15-variant18-variant26-variant30-variant31-variant34-variant35-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:56,27:83:99:689,0,1686:19,37,6,21 chr1 240343621 . A G 750.77 PASS AC=1;AF=0.545;AN=2;DP=325;MQ=60;set=variant2-variant3-variant15-variant18-variant26-variant30-variant31-variant34-variant35-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:17,18:35:99:449,0,429:4,13,6,12 chr1 240351628 . T C 2795.91 PASS AC=1;AF=0.639;AN=2;DP=7455;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:117,109:226:99:2587,0,2710:52,65,44,65 chr1 240370629 . C G 3521.42 PASS AC=1;AF=0.596;AN=2;DP=7076;MQ=60;set=variant3-variant5-variant8-variant9-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant22-variant24-variant25-variant26-variant28-variant29-variant33-variant34-variant35-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:172,132:304:99:3253,0,4380:87,85,64,68 chr1 240421383 . G A 1612.52 PASS AC=1;AF=0.763;AN=2;DP=1556;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:18,17:35:99:385,0,486:5,13,6,11 chr1 240421437 . C T 235.37 PASS AC=1;AF=0.597;AN=2;DP=375;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:5,5:10:99:180,0,195:0,5,0,5 chr1 240457973 . G T 364.82 PASS AC=2;AF=0.542;AN=2;DP=312;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant6-variant11-variant12-variant13-variant16-variant21-variant26-variant28-variant31-variant35 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:910,78,0:0,0,19,7 chr1 240492543 . G A 2867.43 PASS AC=2;AF=0.676;AN=2;DP=2679;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,84:84:99:2961,252,0:0,0,36,48 chr1 240492952 . G C 281.81 PASS AC=1;AF=0.621;AN=2;DP=465;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant17-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:10,8:18:99:166,0,232:4,6,3,5 chr1 240497265 . A C 2181.69 PASS AC=2;AF=0.7;AN=2;DP=2413;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1576,159,0:0,0,30,23 chr1 240497598 . T C 276.9 PASS AC=1;AF=0.596;AN=2;DP=374;MQ=60;set=variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant17-variant20-variant22-variant23-variant24-variant26-variant27-variant30-variant31-variant35-variant36-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,8:14:99:258,0,176:1,5,1,7 chr1 240519251 . CAAAAAAAAAAAAAAAAAAAAA CA,CAA,C,CAAA 360.19 PASS AC=0,1,0,1;AF=0.19,0.452,0.024,0.024;AN=2;DP=823;MQ=60;set=variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant14-variant17-variant22-variant23-variant24-variant27-variant30-variant31-variant35-variant36-variant38-variant39-variant41-variant42 GT:DP:GQ:SB 2/4:17:99:0,1,5,11 chr1 240601269 . A G 733.76 PASS AC=2;AF=0.953;AN=2;DP=1253;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1134,99,0:0,0,22,11 chr1 240635491 . G C 381.9 PASS AC=2;AF=0.988;AN=2;DP=273;FS=0;MQ=60;MQRankSum=0.358;ReadPosRankSum=0.358;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:304,21,0:0,0,7,0 chr1 240643167 . A C 428.67 PASS AC=1;AF=0.621;AN=2;DP=479;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant11-variant13-variant14-variant15-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,9:16:99:332,0,242:7,0,9,0 chr1 240643184 . C T 496.03 PASS AC=1;AF=0.638;AN=2;DP=654;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant11-variant13-variant14-variant15-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,11:21:99:355,0,330:9,1,10,1 chr1 240643435 . A T,ACCCTTGGGAGGTGTTATCTCAAAATCCTTCTCCAAGGTGAAACCATT 849.88 PASS AC=0,1;AF=0.565,0.065;AN=2;DP=784;set=variant8-variant13-variant14-variant15-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant43-variant44 GT:DP:GQ:SB 0/2:18:99:2,7,2,7 chr1 240652889 . A G 824.76 PASS AC=1;AF=0.533;AN=2;DP=660;FractionInformativeReads=1;MQ=60;set=variant8-variant10-variant20-variant23-variant24-variant25-variant27-variant28-variant30-variant35-variant36-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:22,25:47:99:837,0,741:19,3,22,3 chr1 240652947 . A G 5709.78 PASS AC=2;AF=0.833;AN=2;DP=5514;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,131:131:99:4182,392,0:0,0,86,45 chr1 240654627 . A G 1186.35 PASS AC=1;AF=0.542;AN=2;DP=743;FractionInformativeReads=1;MQ=60;set=variant10-variant20-variant23-variant25-variant27-variant28-variant30-variant34-variant35-variant36-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:31,40:71:99:1138,0,909:10,21,18,22 chr1 240654931 . C A 4566.92 PASS AC=1;AF=0.5;AN=2;DP=3640;MQ=60;set=variant5-variant11-variant24-variant25-variant33-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:287,194:481:99:4116,0,7019:142,145,102,92 chr1 240655015 . C T 18503.6 PASS AC=1;AF=0.712;AN=2;DP=12478;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant17-variant18-variant22-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:234,184:418:99:4210,0,5725:99,135,88,96 chr1 240655330 . G A 901.88 PASS AC=2;AF=0.681;AN=2;DP=1935;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant17-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:2531,230,0:0,0,34,43 chr1 240655791 . T C 617.79 PASS AC=1;AF=0.5;AN=2;DP=355;MQ=60;set=variant10-variant23-variant25-variant28-variant35-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:33,14:47:99:360,0,802:18,15,8,6 chr1 240656797 . G A 1350.36 PASS AC=1;AF=0.5;AN=2;DP=1140;FractionInformativeReads=1;MQ=60;set=variant5-variant8-variant11-variant20-variant24-variant25-variant33-variant35-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:71,49:120:99:1212,0,1798:26,45,15,34 chr1 240656838 . C CT 77.32 PASS AC=1;AF=0.5;AN=2;DP=366;MQ=60;set=filterInvariant22-variant23-variant25-variant28-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:26,21:47:99:304,0,681:8,18,2,19 chr1 240656841 . A T 609.41 PASS AC=2;AF=0.563;AN=2;DP=928;MQ=60;set=variant5-variant8-variant10-variant11-variant20-variant22-variant23-variant24-variant25-variant28-variant33-variant35-variant36-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,66:66:99:2468,197,0:0,0,20,46 chr1 240656852 . T TA 507.48 PASS AC=1;AF=0.5;AN=2;DP=463;MQ=60;set=variant5-variant8-variant11-variant20-variant24-variant25-variant33-variant35-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:28,20:48:99:455,0,891:5,23,5,15 chr1 240775103 . C T 656.95 PASS AC=2;AF=0.837;AN=2;DP=1378;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1213,111,0:0,0,23,14 chr1 240975213 . T C 2405.74 PASS AC=1;AF=0.708;AN=2;DP=2239;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant33-variant34-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,29:56:99:925,0,607:17,10,24,5 chr1 240975435 . C T 675.73 PASS AC=1;AF=0.708;AN=2;DP=917;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant33-variant34-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,17:28:99:641,0,258:1,10,0,17 chr1 240977964 . G T 1021.91 PASS AC=2;AF=0.78;AN=2;DP=1056;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:749,72,0:0,0,15,9 chr1 240979803 . G A 151.77 PASS AC=2;AF=0.833;AN=2;DP=392;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:353,27,0:0,0,1,8 chr1 241100122 . G T 402.73 PASS AC=1;AF=0.7;AN=2;DP=151;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant6-variant9-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant32-variant35-variant36-variant37-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,5:8:77:161,0,77:0,3,2,3 chr1 241519098 . T A 1858.54 PASS AC=2;AF=0.989;AN=2;DP=3363;FS=0;MQ=60;MQRankSum=0.259;ReadPosRankSum=-2.058;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,102:102:99:3043,305,0:0,0,49,53 chr1 241520188 . T C 1896.62 PASS AC=2;AF=0.989;AN=2;DP=2917;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,93:93:99:2575,278,0:0,0,54,39 chr1 241663902 . TGAGA TGAGAGA,TGAGAGAGA,TGAGAGAGAGA,TGA,TGAGAGAGAGAGAGAGAGA,TGAGAGAGAGAGA,TGAGAGAGAGAGAGAGA,TGAGAGAGAGAGAGA,T 991.71 PASS AC=0,1,0,0,0,0,0,0,0;AF=0.148,0.284,0.159,0.023,0.068,0.034,0.034,0.011,0.011;AN=2;DP=4382;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-filterInvariant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-filterInvariant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:39:99:6,6,9,18 chr1 241667233 . C T 690.41 PASS AC=1;AF=0.548;AN=2;DP=672;MQ=60;set=variant-variant6-variant8-variant9-variant11-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant29-variant35-variant36-variant37-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,17:33:99:457,0,480:13,3,13,4 chr1 241667244 . G T 1989.07 PASS AC=2;AF=0.756;AN=2;DP=1664;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1462,126,0:0,0,34,8 chr1 241675119 . G C 154.44 PASS AC=1;AF=0.545;AN=2;DP=214;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant8-variant9-variant11-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant29-variant35-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,3:14:93:93,0,410:10,1,3,0 chr1 241676758 . C T 688.9 PASS AC=1;AF=0.604;AN=2;DP=1242;MQ=60;set=variant-variant6-variant8-variant9-variant11-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant29-variant35-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,27:67:99:678,0,1081:28,12,19,8 chr1 241729614 . T G 412.07 PASS AC=2;AF=0.927;AN=2;DP=440;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:615,42,0:0,0,13,1 chr1 241729687 . AAGCTCCCTGGTCAC A 350.81 PASS AC=1;AF=0.524;AN=2;DP=886;MQ=60;set=variant-variant3-variant7-variant12-variant15-variant16-variant18-variant20-variant21-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant37-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,20:42:99:774,0,853:14,8,14,6 chr1 241730153 . G T 602.96 PASS AC=2;AF=0.898;AN=2;DP=1022;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1117,102,0:0,0,9,25 chr1 241755348 . C T 1643.68 PASS AC=1;AF=0.526;AN=2;DP=2228;MQ=60;set=variant-variant3-variant7-variant15-variant16-variant18-variant20-variant21-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant37-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,45:97:99:1257,0,1402:27,25,25,20 chr1 241756057 . C CATCT,CATCTATCT 140.9 PASS AC=0,2;AF=0.7,0.28;AN=2;DP=548;FS=0;MQ=60;MQRankSum=0.322;ReadPosRankSum=0.322;set=variant2-variant3-variant4-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant21-variant24-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant38-variant40-variant41-variant44 GT:DP:GQ:SB 2/2:4:10:0,0,1,3 chr1 241757549 . G T 1370.48 PASS AC=1;AF=0.575;AN=2;DP=1694;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant17-variant19-variant25-variant27-variant30-variant32-variant34-variant35-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:32,60:92:99:1618,0,942:7,25,25,35 chr1 241761349 . T C 279.21 PASS AC=1;AF=0.526;AN=2;DP=562;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant7-variant15-variant16-variant18-variant20-variant21-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant37-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,18:34:99:494,0,463:4,12,5,13 chr1 241767930 . G A 1494.71 PASS AC=2;AF=0.966;AN=2;DP=4390;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,101:101:99:3064,303,0:0,0,38,63 chr1 241794056 . C A 4423.55 PASS AC=2;AF=0.606;AN=2;DP=8218;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,256:256:99:8536,765,0:0,0,116,140 chr1 241794231 . C T 2863.38 PASS AC=2;AF=0.6;AN=2;DP=8617;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,223:223:99:7284,668,0:0,0,104,119 chr1 241796284 . A G 1717.46 PASS AC=2;AF=0.711;AN=2;DP=5197;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,154:154:99:5245,462,0:0,0,86,68 chr1 241796947 . ATGC A 8420.9 PASS AC=2;AF=0.595;AN=2;DP=8758;MQ=60;set=variant-variant3-variant7-variant9-variant12-variant13-variant17-variant24-variant26-variant28-variant29-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,381:381:99:17056,1147,0:0,0,203,178 chr1 241803636 . T C 464.99 PASS AC=2;AF=0.703;AN=2;DP=1406;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1839,129,0:0,0,22,21 chr1 241803658 . A G 504.26 PASS AC=2;AF=0.716;AN=2;DP=1406;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:2000,141,0:0,0,22,25 chr1 241803731 . AC A 62.96 PASS AC=2;AF=0.714;AN=2;DP=684;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant26-variant28-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:696,66,0:0,0,7,15 chr1 241815647 . T G 1445.4 PASS AC=1;AF=0.5;AN=2;DP=284;FractionInformativeReads=1;MQ=60;set=variant3-variant26-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:33,39:72:99:1527,0,1625:18,15,20,19 chr1 241815651 . A T 1451.39 PASS AC=1;AF=0.5;AN=2;DP=286;FractionInformativeReads=1;MQ=60;set=variant3-variant26-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:35,40:75:99:1505,0,1628:19,16,21,19 chr1 241838057 . C T 3417.3 PASS AC=2;AF=0.759;AN=2;DP=1694;FractionInformativeReads=1;set=variant3-variant5-variant6-variant7-variant9-variant10-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant31-variant33-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:2389,171,0:0,0,22,35 chr1 241838065 . T C 3334.16 PASS AC=2;AF=0.742;AN=2;DP=1700;FractionInformativeReads=1;set=variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:2214,153,0:0,0,16,31 chr1 241847018 . C T,G 121.7 PASS AC=2,0;AF=0.743,0.043;AN=2;DP=448;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:DP:GQ:SB 1/1:6:18:0,0,0,6 chr1 241886754 . T C 1108.8 PASS AC=1;AF=0.5;AN=2;DP=711;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant6-variant7-variant12-variant17-variant25-variant26-variant33-variant35-variant37-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:39,20:59:99:651,0,2367:11,28,7,13 chr1 241886764 . A G 1079.07 PASS AC=1;AF=0.5;AN=2;DP=595;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant6-variant7-variant12-variant17-variant25-variant26-variant33-variant35-variant37-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:37,15:52:99:540,0,2291:10,27,4,11 chr1 241907691 . A G 432.64 PASS AC=1;AF=0.543;AN=2;DP=1143;MQ=60;set=variant2-variant4-variant5-variant6-variant9-variant11-variant14-variant17-variant18-variant21-variant22-variant26-variant27-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,23:37:99:641,0,306:9,5,17,6 chr1 241907706 . C T 390.2 PASS AC=1;AF=0.5;AN=2;DP=196;FractionInformativeReads=1;MQ=60;set=variant6-variant17-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:14,25:39:99:680,0,340:9,5,17,8 chr1 241907817 . T C 714.63 PASS AC=1;AF=0.645;AN=2;DP=2524;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant26-variant27-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,48:86:99:1249,0,914:22,16,21,27 chr1 241913062 . C CT 346.52 PASS AC=2;AF=0.722;AN=2;DP=1713;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1352,129,0:0,0,15,27 chr1 241933876 . A G 652.24 PASS AC=2;AF=0.736;AN=2;DP=1981;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:1986,194,0:0,0,44,21 chr1 241946766 . A C 723.35 PASS AC=1;AF=0.763;AN=2;DP=2259;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,37:60:99:945,0,580:7,16,13,24 chr1 241954005 . TAA TA,T 218.45 PASS AC=1,0;AF=0.5,0.171;AN=2;DP=1432;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:25:38:2,3,5,15 chr1 241958738 . G A 471.62 PASS AC=1;AF=0.5;AN=2;DP=175;FractionInformativeReads=1;MQ=60;set=variant6-variant17-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:25,17:42:99:435,0,794:6,19,5,12 chr1 241964559 . C T,G 5568.47 PASS AC=1,1;AF=0.643,0.114;AN=2;DP=5578;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:DP:GQ:SB 2/1:142:99:0,0,76,66 chr1 242011534 . A G 654.11 PASS AC=1;AF=0.694;AN=2;DP=2738;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,36:88:99:829,0,1346:26,26,20,16 chr1 242012033 . G A 652.91 PASS AC=1;AF=0.7;AN=2;DP=1518;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,16:40:99:526,0,816:20,4,13,3 chr1 242012385 . C T 1002.53 PASS AC=1;AF=0.5;AN=2;DP=417;MQ=60;set=variant3-variant4-variant19-variant20-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,35:69:99:1083,0,1164:7,27,7,28 chr1 242012606 . T A 131.95 PASS AC=1;AF=0.5;AN=2;DP=63;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant19-variant20-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,10:13:73:286,0,73:0,3,4,6 chr1 242013581 . CA CAA,C 181.48 PASS AC=1,0;AF=0.4,0.1;AN=2;DP=196;set=variant3-variant19-variant33-variant35-variant44 GT:DP:GQ:SB 0/1:38:99:17,4,15,2 chr1 242015820 . A G 115.66 PASS AC=1;AF=0.697;AN=2;DP=336;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,6:11:99:196,0,135:1,4,1,5 chr1 242020495 . C T 689.09 PASS AC=1;AF=0.681;AN=2;DP=1192;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,20:35:99:577,0,447:11,4,15,5 chr1 242020804 . A G 751.24 PASS AC=1;AF=0.5;AN=2;DP=255;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant19-variant20-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,22:48:99:617,0,747:8,18,6,16 chr1 242024923 . A G 750.22 PASS AC=1;AF=0.5;AN=2;DP=398;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant19-variant20-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,32:63:99:978,0,884:7,24,7,25 chr1 242030151 . A G 1117.66 PASS AC=1;AF=0.686;AN=2;DP=3334;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,40:90:99:991,0,1128:28,22,25,15 chr1 242035382 . C T 1339.37 PASS AC=1;AF=0.5;AN=2;DP=679;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant19-variant20-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,64:128:99:1439,0,1613:38,26,37,27 chr1 242042301 . G A 2153.86 PASS AC=1;AF=0.672;AN=2;DP=4462;set=variant-variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant15-variant16-variant17-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:83,70:153:99:1777,0,2075:46,37,30,40 chr1 242042364 . A AG 2415.03 PASS AC=1;AF=0.5;AN=2;DP=135;FS=5.444;FractionInformativeReads=0.97;MQ=60;MQRankSum=0.9;QD=17.89;ReadPosRankSum=-2.247;SOR=0.365;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:54,77:131:99:2452,0,1622:21,33,38,39 chr1 242042545 . A G 1472.27 PASS AC=1;AF=0.671;AN=2;DP=4694;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:57,69:126:99:1459,0,1430:27,30,37,32 chr1 242042690 . A G 1751.8 PASS AC=1;AF=0.805;AN=2;DP=2002;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,17:31:99:472,0,341:4,10,4,13 chr1 242045275 . C T 4356.29 PASS AC=2;AF=0.989;AN=2;DP=5320;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,114:114:99:3382,342,0:0,0,60,54 chr1 242048674 . C T 2471.82 PASS AC=1;AF=0.55;AN=2;DP=1508;MQ=60;set=variant3-variant11-variant15-variant20-variant22-variant24-variant26-variant31-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:69,64:133:99:1346,0,1491:38,31,37,27 chr1 242052685 . C G 305.67 PASS AC=1;AF=0.55;AN=2;DP=286;MQ=60;set=variant3-variant11-variant15-variant20-variant22-variant24-variant26-variant31-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,8:21:99:238,0,437:11,2,7,1 chr1 242053030 . AT A 2026.74 PASS AC=1;AF=0.55;AN=2;DP=1673;MQ=60;set=variant3-variant11-variant15-variant20-variant22-variant24-variant26-variant31-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:75,76:151:99:2152,0,2063:33,42,32,44 chr1 242053042 . A G 6341.63 PASS AC=1;AF=0.872;AN=2;DP=6856;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:84,69:153:99:1694,0,2184:35,49,32,37 chr1 242053182 . C CTACT 1923.97 PASS AC=1;AF=0.5;AN=2;DP=107;FS=4.861;FractionInformativeReads=0.963;MQ=60;MQRankSum=-0.709;QD=17.98;ReadPosRankSum=-1.29;SOR=0.826;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:53,50:103:99:1961,0,2686:24,29,28,22 chr1 242120870 . C G 34.68 PASS AC=2;AF=0.652;AN=2;DP=191;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant9-variant11-variant13-variant14-variant15-variant16-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant32-variant33-variant34-variant35-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:259,18,0:0,0,6,0 chr1 242120953 . T C 394.52 PASS AC=2;AF=0.611;AN=2;DP=992;MQ=60;set=variant-variant4-variant5-variant9-variant11-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant32-variant33-variant34-variant35-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:1073,81,0:0,0,23,4 chr1 242121011 . ATAAG A 1749.1 PASS AC=2;AF=0.66;AN=2;DP=2367;MQ=60;set=variant-variant4-variant5-variant9-variant11-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant32-variant33-variant34-variant35-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:3240,217,0:0,0,45,27 chr1 242121052 . C G 2864.97 PASS AC=2;AF=0.66;AN=2;DP=3162;MQ=60;set=variant-variant4-variant5-variant9-variant11-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant32-variant33-variant34-variant35-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,103:103:99:4592,313,0:0,0,63,40 chr1 242121061 . C T 2993.91 PASS AC=2;AF=0.66;AN=2;DP=3439;MQ=60;set=variant-variant4-variant5-variant9-variant11-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant32-variant33-variant34-variant35-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,111:111:99:4798,337,0:0,0,64,47 chr1 242121540 . G A 1839.03 PASS AC=2;AF=0.66;AN=2;DP=5145;MQ=60;set=variant-variant4-variant5-variant9-variant11-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant32-variant33-variant34-variant35-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,192:194:99:6187,524,0:0,2,88,104 chr1 242121796 . G T 1335.63 PASS AC=2;AF=0.66;AN=2;DP=3754;MQ=60;set=variant-variant4-variant5-variant9-variant11-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant32-variant33-variant34-variant35-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,174:174:99:5587,520,0:0,0,90,84 chr1 242161553 . G A 148.72 PASS AC=2;AF=0.976;AN=2;DP=312;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:271,21,0:0,0,6,1 chr1 242161619 . C A 509.23 PASS AC=2;AF=0.966;AN=2;DP=931;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:980,90,0:0,0,21,9 chr1 242161679 . G A 1585.37 PASS AC=2;AF=0.966;AN=2;DP=2139;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:1818,180,0:0,0,34,26 chr1 242253024 . T C 3093.28 PASS AC=1;AF=0.6;AN=2;DP=5763;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant21-variant25-variant28-variant29-variant34-variant35-variant36-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:122,135:257:99:3150,0,3149:61,61,67,68 chr1 242264102 . A G 616.61 PASS AC=1;AF=0.531;AN=2;DP=1101;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant11-variant14-variant15-variant17-variant18-variant25-variant29-variant34-variant35-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:35,28:63:99:598,0,883:12,23,12,16 chr1 242511556 . AACAAAG A 2961.67 PASS AC=1;AF=0.837;AN=2;DP=3857;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,40:82:99:1533,0,2932:18,24,18,22 chr1 242687390 . G A 1006.94 PASS AC=1;AF=0.636;AN=2;DP=4792;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:112,91:203:99:1903,0,2580:62,50,51,40 chr1 242687720 . G C 315.85 PASS AC=1;AF=0.5;AN=2;DP=246;MQ=60;set=variant2-variant8-variant12-variant19-variant23-variant25-variant27-variant32-variant34-variant35-variant36-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:12,15:27:99:340,0,304:4,8,6,9 chr1 243219965 . G C 61.85 PASS AC=1;AF=0.5;AN=2;DP=2407;set=filterInvariant3-filterInvariant4-filterInvariant5-variant8-variant9-variant10-filterInvariant13-filterInvariant14-filterInvariant15-filterInvariant16-filterInvariant17-variant18-variant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant26-filterInvariant27-filterInvariant29-filterInvariant30-filterInvariant31-variant32-filterInvariant33-filterInvariant35-variant38-filterInvariant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:92,16:108:72:72,0,2554:43,49,8,8 chr1 243327520 . A T 69 PASS AC=1;AF=0.643;AN=2;DP=130;FractionInformativeReads=1;set=variant2-variant3-variant6-variant8-variant9-variant13-variant14-variant16-variant17-variant21-variant25-variant28-variant29-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:4,6:10:99:117,0,114:3,1,5,1 chr1 243328887 . G T 178.96 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=1423;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:167,22:189:99:134,0,3996:99,68,17,5 chr1 243329049 . G A 1578.1 PASS AC=1;AF=0.5;AN=2;DP=9905;set=variant-variant2-filterInvariant3-variant4-variant5-variant6-filterInvariant8-variant9-filterInvariant10-variant11-variant13-filterInvariant14-filterInvariant15-filterInvariant16-variant18-filterInvariant20-variant21-variant23-filterInvariant24-variant26-filterInvariant27-variant28-variant31-variant32-variant33-variant34-variant35-filterInvariant37-variant38-variant39-filterInvariant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:215,109:324:99:2039,0,5827:112,103,48,61 chr1 243329075 . T C 932.91 PASS AC=1;AF=0.5;AN=2;DP=8415;set=variant-filterInvariant2-filterInvariant3-filterInvariant4-variant5-filterInvariant6-filterInvariant8-variant9-filterInvariant10-variant11-variant13-filterInvariant16-variant18-filterInvariant21-filterInvariant23-filterInvariant24-variant26-filterInvariant28-variant31-variant32-filterInvariant33-filterInvariant34-variant35-filterInvariant37-variant38-variant39-filterInvariant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:240,83:323:99:1483,0,6377:120,120,31,52 chr1 243332884 . AAG A 511.93 PASS AC=1;AF=0.552;AN=2;DP=430;set=variant-variant2-variant3-variant4-variant6-variant8-variant12-variant14-variant16-variant17-variant18-variant20-variant21-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,10:20:99:378,0,383:8,2,7,3 chr1 243335940 . GA G 392.16 PASS AC=1;AF=0.542;AN=2;DP=467;set=variant2-variant4-variant5-variant11-variant12-variant13-variant19-variant21-variant22-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,16:28:99:375,0,221:6,6,9,7 chr1 243336180 . C T 104.77 PASS AC=1;AF=0.5;AN=2;DP=8;FS=0;FractionInformativeReads=1;MQ=50.98;MQRankSum=-2.017;QD=13.1;ReadPosRankSum=-0.421;SOR=1.981;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:99:133,0,150:1,3,0,4 chr1 243362331 . C T 1630.25 PASS AC=2;AF=0.872;AN=2;DP=1838;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:1941,173,0:0,0,47,11 chr1 243363991 . C T 435.9 PASS AC=1;AF=0.5;AN=2;DP=29;FS=6.964;FractionInformativeReads=1;MQ=35.36;MQRankSum=-0.354;QD=15.03;ReadPosRankSum=-2.522;SOR=0.098;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:9,20:29:99:464,0,257:8,1,12,8 chr1 243388370 . A T 1810.46 PASS AC=1;AF=0.643;AN=2;DP=1557;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant20-variant21-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,16:41:99:504,0,863:22,3,15,1 chr1 243419429 . T A 2740.38 PASS AC=1;AF=0.558;AN=2;DP=4300;MQ=60;set=variant2-variant4-variant5-variant7-variant11-variant12-variant13-variant19-variant21-variant22-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:91,88:179:99:2068,0,2382:48,43,41,47 chr1 243433654 . A G 863.63 PASS AC=1;AF=0.629;AN=2;DP=671;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant16-variant17-variant18-variant20-variant21-variant23-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,6:20:99:129,0,388:4,10,3,3 chr1 243449881 . G A 253.61 PASS AC=1;AF=0.574;AN=2;DP=980;FractionInformativeReads=1;set=variant2-variant3-variant4-variant5-variant7-variant8-variant11-variant12-variant13-variant19-variant21-variant22-variant26-variant27-variant28-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,10:22:99:227,0,395:2,10,1,9 chr1 243481431 . A G 3071.34 PASS AC=1;AF=0.648;AN=2;DP=2854;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant11-variant12-variant13-variant19-variant21-variant22-variant24-variant26-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,49:114:99:1211,0,1572:29,36,18,31 chr1 243493907 . A T 1404.33 PASS AC=1;AF=0.633;AN=2;DP=2176;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant12-variant13-variant14-variant16-variant17-variant18-variant20-variant21-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,27:63:99:624,0,889:19,17,12,15 chr1 243507680 . C CA 816.44 PASS AC=1;AF=0.648;AN=2;DP=934;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant13-variant14-variant16-variant17-variant18-variant20-variant21-variant23-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,14:41:99:364,0,847:6,21,2,12 chr1 243579112 . G A 1588.74 PASS AC=1;AF=0.617;AN=2;DP=1346;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant17-variant18-variant19-variant22-variant24-variant25-variant26-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,15:47:99:337,0,854:13,19,5,10 chr1 243589977 . T C 311.6 PASS AC=1;AF=0.5;AN=2;DP=129;FractionInformativeReads=1;MQ=60;set=variant13-variant17-variant21-variant29-variant30-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:13,8:21:99:248,0,398:3,10,1,7 chr1 243651806 . C T 233.53 PASS AC=1;AF=0.583;AN=2;DP=209;MQ=60;set=variant3-variant6-variant8-variant15-variant16-variant22-variant24-variant27-variant29-variant35-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,12:27:99:282,0,389:5,10,4,8 chr1 243666694 . GCT G 1102.25 PASS AC=1;AF=0.575;AN=2;DP=1047;MQ=60;set=variant3-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant21-variant22-variant24-variant27-variant29-variant35-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,26:58:99:985,0,1273:12,20,9,17 chr1 243667216 . C T 6436.11 PASS AC=1;AF=0.583;AN=2;DP=4882;set=variant3-variant8-variant11-variant15-variant16-variant22-variant24-variant27-variant29-variant35-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:200,178:378:99:4094,0,5543:78,122,85,93 chr1 243667900 . T G 264.48 PASS AC=1;AF=0.571;AN=2;DP=615;set=variant3-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant21-variant22-variant24-variant27-variant29-variant35-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,12:24:99:363,0,381:3,9,2,10 chr1 243736210 . CT CTT,C 61.16 PASS AC=0,1;AF=0.063,0.438;AN=2;DP=781;MQ=60;set=variant2-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant21-variant22-variant24-variant25-variant29-filterInvariant31-variant33-variant35-filterInvariant36-variant37-variant42-variant43-filterInvariant44 GT:DP:GQ:SB 0/2:24:99:8,4,9,3 chr1 243777066 . G A 395.52 PASS AC=1;AF=0.5;AN=2;DP=419;FractionInformativeReads=1;MQ=60;set=variant6-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant21-variant22-variant29-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:8,9:17:99:209,0,255:2,6,3,6 chr1 243828266 . T C 86.95 PASS AC=1;AF=0.5;AN=2;DP=7;FS=3.68;FractionInformativeReads=1;MQ=60;MQRankSum=-0.937;QD=12.42;ReadPosRankSum=0.55;SOR=0.061;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:3,4:7:98:115,0,98:0,3,2,2 chr1 244219563 . A G 1714.15 PASS AC=2;AF=1;AN=2;DP=3051;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:2663,225,0:0,0,23,52 chr1 244219893 . CTCTT C 680.29 PASS AC=1;AF=0.5;AN=2;DP=443;MQ=60;set=variant-variant7-variant8-variant15-variant17-variant18-variant21-variant24-variant28-variant30-variant32-variant34-variant35-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,8:19:99:272,0,438:5,6,3,5 chr1 244516090 . T C 811.91 PASS AC=2;AF=0.837;AN=2;DP=903;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:860,78,0:0,0,9,17 chr1 244527857 . T C 752.86 PASS AC=2;AF=0.636;AN=2;DP=1079;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:956,75,0:0,0,20,5 chr1 244528127 . T C 1514.76 PASS AC=2;AF=0.818;AN=2;DP=1513;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:1792,162,0:0,0,15,39 chr1 244572632 . G GA 888.63 PASS AC=2;AF=0.786;AN=2;DP=3518;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,84:84:99:2279,251,0:0,0,46,38 chr1 244595746 . G A 208.34 PASS AC=1;AF=0.5;AN=2;DP=16;FS=2.307;FractionInformativeReads=1;MQ=60;MQRankSum=0.705;QD=13.02;ReadPosRankSum=-2.332;SOR=0.197;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:6,10:16:99:237,0,185:5,1,6,4 chr1 244601152 . C T 2227.05 PASS AC=2;AF=0.857;AN=2;DP=2664;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1624,150,0:0,0,22,28 chr1 244624635 . G C 2276.28 PASS AC=1;AF=0.708;AN=2;DP=2669;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant22-variant23-variant24-variant26-variant27-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,56:98:99:1623,0,1095:27,15,40,16 chr1 244624887 . T C 2844.68 PASS AC=1;AF=0.679;AN=2;DP=4029;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:63,57:120:99:1422,0,1661:24,39,23,34 chr1 244626948 . CA C 122.86 PASS AC=1;AF=0.588;AN=2;DP=212;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant15-variant23-variant27-variant32-variant35-variant36-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:5,8:13:56:115,0,56:3,2,7,1 chr1 244723920 . C G 268.33 PASS AC=1;AF=0.5;AN=2;DP=90;FractionInformativeReads=1;MQ=60;set=variant26-variant28-variant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:12,12:24:99:294,0,296:8,4,8,4 chr1 244724092 . G A 1707.3 PASS AC=1;AF=0.5;AN=2;DP=508;MQ=60;set=variant26-variant28-variant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:57,55:112:99:1486,0,1381:30,27,33,22 chr1 244735858 . A G 1645.51 PASS AC=1;AF=0.5;AN=2;DP=489;FractionInformativeReads=1;MQ=60;set=variant26-variant28-variant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:55,46:101:99:1148,0,1499:27,28,20,26 chr1 244747051 . G C 101.22 PASS AC=1;AF=0.5;AN=2;DP=53;FS=0;FractionInformativeReads=1;MQ=60;set=variant26-variant28-variant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:6,4:10:99:150,0,167:5,1,4,0 chr1 244747150 . G A 790.43 PASS AC=1;AF=0.5;AN=2;DP=326;FractionInformativeReads=1;MQ=60;set=variant26-variant28-variant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:41,33:74:99:732,0,1110:28,13,20,13 chr1 244747293 . C T 517.64 PASS AC=1;AF=0.5;AN=2;DP=232;FractionInformativeReads=1;MQ=60;set=variant26-variant28-variant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:42,20:62:99:713,0,2066:14,28,6,14 chr1 244747294 . G A 517.64 PASS AC=1;AF=0.5;AN=2;DP=228;FractionInformativeReads=1;MQ=60;set=variant26-variant28-variant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:42,20:62:99:713,0,2066:14,28,6,14 chr1 244747339 . G A 138.85 PASS AC=1;AF=0.5;AN=2;DP=107;MQ=60;set=variant26-variant28-variant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:24,12:36:99:385,0,673:7,17,1,11 chr1 244754961 . C A 609.42 PASS AC=1;AF=0.5;AN=2;DP=260;FractionInformativeReads=1;MQ=60;set=variant26-variant28-variant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:39,36:75:99:925,0,1003:27,12,24,12 chr1 244773784 . T C 1170.1 PASS AC=2;AF=0.795;AN=2;DP=1081;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:792,69,0:0,0,9,14 chr1 244773803 . T C 876.22 PASS AC=1;AF=0.739;AN=2;DP=786;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:10,8:18:99:216,0,272:2,8,2,6 chr1 244803205 . CTTT CT,CTT,C 2919.06 PASS AC=1,1,0;AF=0.727,0.25,0.023;AN=2;DP=4095;MQ=60;set=Intersection GT:DP:GQ:SB 1/2:127:99:2,0,67,58 chr1 244803490 . C CGTA 12172.2 PASS AC=1;AF=0.756;AN=2;DP=10479;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:102,111:213:99:4395,0,4585:44,58,51,60 chr1 244803821 . AT A 461.36 PASS AC=2;AF=0.955;AN=2;DP=1081;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:841,81,0:0,0,9,18 chr1 244849568 . A G 97.15 PASS AC=1;AF=0.575;AN=2;DP=165;set=variant-variant4-variant7-variant9-variant10-variant14-variant15-variant16-variant20-variant21-variant26-variant30-variant31-variant32-variant35-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,5:8:99:180,0,210:3,0,3,2 chr1 244852819 . C CT 215.35 PASS AC=1;AF=0.667;AN=2;DP=99;FS=0;MQ=60;set=variant4-variant10-variant14-variant15-variant16-variant20-variant26-variant29-variant30-variant31-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,9:11:23:220,0,23:1,1,1,8 chr1 244869479 . A G 1613.72 PASS AC=1;AF=0.587;AN=2;DP=2736;MQ=60;set=variant-variant4-variant5-variant7-variant9-variant10-variant12-variant14-variant15-variant16-variant20-variant21-variant22-variant26-variant29-variant30-variant32-variant35-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:82,60:142:99:1538,0,2138:34,48,24,36 chr1 244871041 . T A 1935.21 PASS AC=1;AF=0.583;AN=2;DP=3187;MQ=60;set=variant-variant4-variant5-variant7-variant9-variant10-variant12-variant14-variant15-variant16-variant20-variant21-variant22-variant26-variant29-variant30-variant31-variant32-variant35-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,68:128:99:1803,0,1476:38,22,47,21 chr1 244999153 . T C 1580.66 PASS AC=1;AF=0.5;AN=2;DP=142;FS=2.992;FractionInformativeReads=1;MQ=60;MQRankSum=0.243;QD=11.13;ReadPosRankSum=0.614;SOR=0.679;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:72,70:142:99:1609,0,1734:33,39,37,33 chr1 245025697 . T TA,TAA,TAAA,TAAAAAAAAA 485.6 PASS AC=1,0,0,0;AF=0.405,0.119,0.131,0.012;AN=2;DP=1359;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-filterInvariant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:35:71:7,4,19,5 chr1 245027728 . A T 3074.2 PASS AC=1;AF=0.5;AN=2;DP=243;FS=2.86;FractionInformativeReads=0.996;MQ=60;MQRankSum=-2.067;QD=12.65;ReadPosRankSum=3.85;SOR=0.722;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:107,135:242:99:3102,0,2826:56,51,64,71 chr1 245133489 . T G 988.8 PASS AC=1;AF=0.682;AN=2;DP=3256;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,32:92:99:742,0,1424:26,34,14,18 chr1 245133539 . A G 3079.18 PASS AC=2;AF=1;AN=2;DP=3384;FS=0;MQ=60;MQRankSum=0.385;ReadPosRankSum=1.655;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:2919,228,0:0,0,32,44 chr1 245133549 . GGC G 769.67 PASS AC=1;AF=0.682;AN=2;DP=2474;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,29:73:99:972,0,1572:21,23,11,18 chr1 245133623 . T TCCTCC 1497.25 PASS AC=1;AF=0.697;AN=2;DP=2570;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,39:95:99:1469,0,2114:28,28,17,22 chr1 245133662 . G C 1181.39 PASS AC=1;AF=0.655;AN=2;DP=2914;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant15-variant16-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:64,42:106:99:1079,0,1676:28,36,18,24 chr1 245179011 . CAA CA,C 284.77 PASS AC=1,0;AF=0.571,0.129;AN=2;DP=1332;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-filterInvariant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:DP:GQ:SB 0/1:35:41:3,3,19,10 chr1 245179171 . C T 453.45 PASS AC=1;AF=0.727;AN=2;DP=1571;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,24:41:99:798,0,924:6,11,8,16 chr1 245179188 . G T 420.59 PASS AC=1;AF=0.757;AN=2;DP=1274;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,15:31:99:568,0,986:4,12,3,12 chr1 245222634 . C G 1228.52 PASS AC=2;AF=0.966;AN=2;DP=1377;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1326,105,0:0,0,29,6 chr1 245222839 . G T 1889.44 PASS AC=2;AF=1;AN=2;DP=3134;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,89:89:99:2634,265,0:0,0,33,56 chr1 245245378 . T C 1481.42 PASS AC=1;AF=0.682;AN=2;DP=2697;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,35:87:99:1210,0,2753:25,27,21,14 chr1 245245402 . C T 1344.47 PASS AC=1;AF=0.682;AN=2;DP=2511;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,35:83:99:1246,0,2591:21,27,18,17 chr1 245247180 . G A 2910.74 PASS AC=1;AF=0.667;AN=2;DP=5405;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant15-variant16-variant19-variant21-variant23-variant24-variant25-variant27-variant31-variant35-variant36-variant38-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:116,90:206:99:2423,0,3084:40,76,24,66 chr1 245251020 . G T 78.67 PASS AC=1;AF=0.688;AN=2;DP=671;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,6:19:99:164,0,277:5,8,2,4 chr1 245251140 . T G 61.77 PASS AC=2;AF=0.986;AN=2;DP=191;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:91,9,0:0,0,1,2 chr1 245284995 . G A 622.92 PASS AC=1;AF=0.5;AN=2;DP=73;MQ=60;set=variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:16,13:29:99:406,0,444:12,4,11,2 chr1 245286313 . G A 1110.54 PASS AC=2;AF=0.65;AN=2;DP=1281;MQ=60;set=variant3-variant7-variant8-variant11-variant13-variant15-variant16-variant19-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant33-variant35-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:2984,237,0:0,0,53,26 chr1 245318385 . G C 1462.88 PASS AC=2;AF=0.943;AN=2;DP=2696;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:2445,227,0:0,0,44,32 chr1 245703819 . T C 931.9 PASS AC=1;AF=0.6;AN=2;DP=690;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant12-variant14-variant16-variant18-variant22-variant23-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,8:27:99:267,0,554:14,5,8,0 chr1 245703990 . G T 3246.65 PASS AC=1;AF=0.622;AN=2;DP=4691;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,51:116:99:1280,0,1758:35,30,26,25 chr1 245765800 . T A 778.3 PASS AC=2;AF=0.646;AN=2;DP=1257;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant12-variant13-variant14-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant31-variant32-variant35-variant37-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1783,153,0:0,0,38,13 chr1 245775356 . TTGTGTGTGTGTGTGTGTGTG TTGTGTGTGTG,TTGTGTGTGTGTG,TTGTGTGTGTGTGTGTGTG,TTGTGTGTGTGTGTGTG,TTGTGTGTGTGTGTGTGTGTGTG,TTGTGTGTGTGTGTG,T,TTGTGTG 173.6 PASS AC=0,0,0,0,0,1,0,0;AF=0.023,0.114,0.136,0.114,0.045,0.159,0.023,0.023;AN=2;DP=944;set=variant2-variant4-filterInvariant5-variant7-variant10-variant12-variant13-variant17-variant19-variant20-variant21-variant23-variant25-variant26-filterInvariant29-variant32-variant34-variant35-variant36-variant40-variant41-variant43 GT:DP:GQ:SB 0/6:11:11:1,2,2,6 chr1 245849969 . C T 6371.66 PASS AC=1;AF=0.5;AN=2;DP=1634;MQ=60;set=variant10-variant32-variant35 GT:AD:DP:GQ:PL:SB 0/1:303,282:585:99:6905,0,7424:162,141,157,125 chr1 245851304 . A G 4698.41 PASS AC=2;AF=0.977;AN=2;DP=8916;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,208:208:99:6742,623,0:0,0,96,112 chr1 245861571 . C T 616.14 PASS AC=1;AF=0.75;AN=2;DP=1855;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,19:64:99:335,0,1209:18,27,7,12 chr1 245866511 . T C 2240.89 PASS AC=1;AF=0.548;AN=2;DP=3606;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant13-variant15-variant16-variant17-variant18-variant26-variant27-variant28-variant30-variant32-variant35-variant37-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:81,84:165:99:2301,0,2047:35,46,32,52 chr1 245866584 . G C 1206.17 PASS AC=1;AF=0.548;AN=2;DP=1722;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant13-variant15-variant16-variant17-variant18-variant26-variant27-variant28-variant30-variant32-variant35-variant37-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:43,49:92:99:1493,0,971:17,26,14,35 chr1 245867357 . G GTGAT 708.93 PASS AC=1;AF=0.563;AN=2;DP=1241;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant10-variant13-variant15-variant16-variant17-variant18-variant24-variant26-variant27-variant28-variant30-variant32-variant34-variant35-variant37-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:26,20:46:99:761,0,1419:12,14,10,10 chr1 245867743 . G A 142.33 PASS AC=1;AF=0.548;AN=2;DP=928;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant7-variant10-variant13-variant15-variant16-variant17-variant18-variant26-variant27-variant28-variant32-variant34-variant35-variant37-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:25,23:48:99:635,0,643:10,15,7,16 chr1 245867921 . G A 470.59 PASS AC=1;AF=0.565;AN=2;DP=2071;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant13-variant15-variant16-variant17-variant18-variant24-variant26-variant27-variant28-variant30-variant32-variant34-variant35-variant37-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:29,36:65:99:925,0,782:18,11,20,16 chr1 245868167 . G GTCTT 2142.97 PASS AC=1;AF=0.543;AN=2;DP=2877;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant10-variant13-variant15-variant16-variant17-variant18-variant24-variant26-variant27-variant28-variant30-variant32-variant35-variant37-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:74,75:149:99:2933,0,4149:34,40,36,39 chr1 245868363 . G T 639.88 PASS AC=1;AF=0.5;AN=2;DP=924;MQ=60;set=variant2-variant3-variant13-variant15-variant16-variant17-variant18-variant24-variant26-variant27-variant28-variant30-variant32-variant35-variant37-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:26,31:57:99:850,0,669:12,14,17,14 chr1 245869299 . T C 988 PASS AC=1;AF=0.525;AN=2;DP=1213;FractionInformativeReads=1;MQ=60;set=variant-variant7-variant10-variant13-variant15-variant16-variant17-variant18-variant21-variant25-variant27-variant28-variant32-variant34-variant35-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,31:58:99:880,0,772:10,17,11,20 chr1 245872219 . T C 3645.71 PASS AC=1;AF=0.617;AN=2;DP=8856;MQ=60;set=variant2-variant4-variant6-variant9-variant10-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:148,169:317:99:4190,0,3836:76,72,79,90 chr1 245912840 . C T 2519.62 PASS AC=1;AF=0.5;AN=2;DP=2315;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant6-variant8-variant10-variant16-variant19-variant22-variant26-variant27-variant29-variant30-variant35-variant36-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:70,47:117:99:1216,0,1783:31,39,26,21 chr1 245927242 . G A 704.04 PASS AC=1;AF=0.5;AN=2;DP=209;FractionInformativeReads=1;MQ=60;set=variant12-variant22-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,34:66:99:910,0,822:22,10,23,11 chr1 246021941 . T C 3874.14 PASS AC=2;AF=0.81;AN=2;DP=5249;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,142:142:99:4398,426,0:0,0,66,76 chr1 246022071 . C T 1402.53 PASS AC=2;AF=0.81;AN=2;DP=1770;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1379,128,0:0,0,13,30 chr1 246022159 . G A 482.92 PASS AC=2;AF=0.951;AN=2;DP=540;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:361,33,0:0,0,4,7 chr1 246027024 . A G 2626.77 PASS AC=2;AF=0.81;AN=2;DP=2833;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,63:63:99:2835,190,0:0,0,45,18 chr1 246027029 . A T 3115.31 PASS AC=2;AF=0.81;AN=2;DP=3061;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,67:67:99:3109,211,0:0,0,49,18 chr1 246027034 . G C 3297.52 PASS AC=2;AF=1;AN=2;DP=3443;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:3234,228,0:0,0,53,23 chr1 246091457 . T C 1163.96 PASS AC=2;AF=0.92;AN=2;DP=2727;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:2228,216,0:0,0,25,47 chr1 246091515 . C T 626.49 PASS AC=2;AF=0.907;AN=2;DP=964;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:954,69,0:0,0,3,20 chr1 246091531 . T C 466.77 PASS AC=2;AF=0.977;AN=2;DP=755;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:694,48,0:0,0,2,14 chr1 246093465 . GA G 750.08 PASS AC=1;AF=0.791;AN=2;DP=3068;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,33:39:41:697,0,41:4,2,15,18 chr1 246110573 . A G 2456.42 PASS AC=2;AF=0.802;AN=2;DP=3206;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,73:73:99:2346,219,0:0,0,48,25 chr1 246489196 . C T 9274.84 PASS AC=1;AF=0.83;AN=2;DP=12755;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:170,118:288:99:2531,0,4171:82,88,56,62 chr1 246489706 . GA G 1771.89 PASS AC=1;AF=0.702;AN=2;DP=3324;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,35:66:99:794,0,676:14,17,15,20 chr1 246490438 . T C 1591.77 PASS AC=1;AF=0.83;AN=2;DP=2820;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:41,35:76:99:1417,0,3395:26,15,26,9 chr1 246490442 . A G 1793.26 PASS AC=1;AF=0.83;AN=2;DP=3015;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:44,36:80:99:1395,0,3552:27,17,28,8 chr1 246490452 . G A 1892.15 PASS AC=1;AF=0.697;AN=2;DP=2962;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,44:93:99:1552,0,3664:31,18,32,12 chr1 246498866 . A C 1514.27 PASS AC=1;AF=0.692;AN=2;DP=1326;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,15:27:99:496,0,342:3,9,2,13 chr1 246580688 . AG A 166.53 PASS AC=1;AF=0.577;AN=2;DP=557;MQ=60;set=variant-variant5-variant6-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:22,10:32:99:248,0,633:10,12,5,5 chr1 246580718 . G A 119.97 PASS AC=1;AF=0.58;AN=2;DP=591;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant6-variant9-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:20,11:31:99:227,0,554:7,13,7,4 chr1 246670281 . G C 1152.15 PASS AC=2;AF=1;AN=2;DP=1829;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:2512,169,0:0,0,45,10 chr1 246670297 . CCCT C 112.57 PASS AC=1;AF=0.5;AN=2;DP=845;MQ=60;set=filterInvariant3-variant4-filterInvariant14-filterInvariant17-filterInvariant19-variant23-filterInvariant24-filterInvariant26-filterInvariant27-filterInvariant34-filterInvariant35-variant39-filterInvariant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,11:64:92:92,0,1351:43,10,7,4 chr1 246670298 . CCT C 300.19 PASS AC=1;AF=0.5;AN=2;DP=1881;MQ=60;set=variant-filterInvariant2-variant3-variant4-variant5-variant6-variant10-variant11-variant12-variant13-variant14-filterInvariant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-filterInvariant24-variant25-variant26-variant27-variant28-variant29-variant32-filterInvariant33-variant34-variant35-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,39:56:99:536,0,229:12,5,30,9 chr1 246670333 . A G 3552.91 PASS AC=2;AF=1;AN=2;DP=3773;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,109:109:99:3979,327,0:0,0,66,43 chr1 246670481 . C G 5019.18 PASS AC=2;AF=0.849;AN=2;DP=18619;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,497:497:99:14894,1488,0:0,0,249,248 chr1 246670626 . A AGGGGC 1885.75 PASS AC=2;AF=0.849;AN=2;DP=5994;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,136:136:99:6015,410,0:0,0,41,95 chr1 246704563 . C T 1084.89 PASS AC=1;AF=0.62;AN=2;DP=909;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant10-variant11-variant12-variant14-variant15-variant16-variant20-variant21-variant25-variant26-variant27-variant28-variant31-variant34-variant35-variant36-variant37-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:18,24:42:99:695,0,517:6,12,5,19 chr1 246707816 . T C 1012.37 PASS AC=1;AF=0.64;AN=2;DP=579;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant10-variant11-variant12-variant14-variant15-variant16-variant20-variant21-variant25-variant26-variant27-variant28-variant31-variant34-variant35-variant36-variant37-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:11,10:21:99:289,0,351:9,2,8,2 chr1 246707858 . A G 1920.12 PASS AC=1;AF=0.64;AN=2;DP=1098;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant10-variant11-variant12-variant14-variant15-variant16-variant20-variant21-variant25-variant26-variant27-variant28-variant31-variant34-variant35-variant36-variant37-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:22,21:43:99:594,0,520:13,9,17,4 chr1 246711789 . T A 714.06 PASS AC=1;AF=0.686;AN=2;DP=888;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,11:23:99:405,0,260:7,5,11,0 chr1 246711816 . GA G 2257.18 PASS AC=1;AF=0.645;AN=2;DP=1323;MQ=60;set=variant4-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,24:40:99:663,0,400:11,5,16,8 chr1 246712033 . A G 873.97 PASS AC=2;AF=1;AN=2;DP=788;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.552;ReadPosRankSum=1.552;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:733,66,0:0,0,6,16 chr1 246714426 . A G 198.1 PASS AC=1;AF=0.591;AN=2;DP=92;FractionInformativeReads=1;MQ=60;set=variant4-variant7-variant13-variant27-variant29-variant32-variant35-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,6:9:99:167,0,107:3,0,5,1 chr1 246714587 . G A 1836.49 PASS AC=1;AF=0.656;AN=2;DP=1709;MQ=60;set=variant4-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,23:58:99:439,0,765:17,18,10,13 chr1 246714631 . T A 1816.77 PASS AC=1;AF=0.656;AN=2;DP=1256;MQ=60;set=variant4-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,10:31:99:357,0,1379:8,13,4,6 chr1 246714632 . G A 1816.77 PASS AC=1;AF=0.656;AN=2;DP=1236;MQ=60;set=variant4-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,10:31:99:357,0,1379:8,13,4,6 chr1 246714636 . T A 1852.79 PASS AC=1;AF=0.656;AN=2;DP=1173;MQ=60;set=variant4-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,9:29:99:357,0,1379:8,12,3,6 chr1 246714728 . G A 293.05 PASS AC=2;AF=0.854;AN=2;DP=334;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:157,12,0:0,0,0,4 chr1 246720174 . A G 328.54 PASS AC=2;AF=0.989;AN=2;DP=306;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.044;ReadPosRankSum=1.393;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:287,21,0:0,0,0,7 chr1 246720798 . G A 1453.14 PASS AC=2;AF=1;AN=2;DP=2334;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,52:52:99:1430,155,0:0,0,25,27 chr1 246727558 . G T 1281.74 PASS AC=2;AF=1;AN=2;DP=1604;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1125,105,0:0,0,23,12 chr1 246729990 . A G 1634.69 PASS AC=1;AF=0.553;AN=2;DP=2625;MQ=60;set=variant2-variant5-variant6-variant7-variant9-variant11-variant17-variant19-variant23-variant24-variant26-variant29-variant31-variant32-variant35-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:76,75:151:99:2785,0,3421:32,44,33,42 chr1 246729993 . G A 2737.77 PASS AC=1;AF=0.5;AN=2;DP=147;FS=0.619;FractionInformativeReads=0.993;MQ=60;MQRankSum=-0.09;QD=18.62;ReadPosRankSum=2.337;SOR=0.604;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:75,71:146:99:2766,0,3400:31,44,31,40 chr1 246730090 . G C 1157.06 PASS AC=2;AF=0.966;AN=2;DP=1889;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:1796,165,0:0,0,18,37 chr1 246754778 . G GA 2719.98 PASS AC=1;AF=0.538;AN=2;DP=2909;MQ=60;set=variant5-variant6-variant7-variant11-variant23-variant24-variant29-variant31-variant32-variant35-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:133,119:252:99:3134,0,3585:81,52,77,42 chr1 246755124 . T C 2094.74 PASS AC=2;AF=0.909;AN=2;DP=3628;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,114:114:99:3483,342,0:0,0,54,60 chr1 246797710 . G T 58.6 PASS AC=1;AF=0.536;AN=2;DP=339;MQ=60;set=variant5-variant6-variant7-variant11-variant24-variant25-variant27-variant29-variant31-variant32-variant35-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,9:26:99:327,0,1031:13,4,4,5 chr1 246797714 . G GT 74.04 PASS AC=1;AF=0.538;AN=2;DP=340;FractionInformativeReads=1;MQ=60;set=variant5-variant6-variant7-variant11-variant24-variant27-variant29-variant31-variant32-variant35-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,10:28:99:351,0,1055:14,4,5,5 chr1 246797974 . T A 161.91 PASS AC=1;AF=0.536;AN=2;DP=411;MQ=60;set=variant5-variant6-variant7-variant11-variant24-variant25-variant27-variant29-variant31-variant32-variant35-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,17:32:99:419,0,521:1,14,6,11 chr1 246804824 . T C 382.29 PASS AC=1;AF=0.538;AN=2;DP=226;FractionInformativeReads=1;MQ=60;set=variant5-variant6-variant7-variant11-variant24-variant27-variant29-variant31-variant32-variant35-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,8:21:99:240,0,391:10,3,6,2 chr1 246805434 . GGTT GT,GTTGTT,G 92.57 PASS AC=1,0,0;AF=0.25,0.167,0.083;AN=2;DP=76;MQ=60;set=variant11-variant14-variant21-variant31-variant32-variant35 GT:DP:GQ:SB 0/1:17:99:2,5,1,9 chr1 246829616 . T C 272.82 PASS AC=1;AF=0.649;AN=2;DP=1027;MQ=60;set=variant2-variant3-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,20:36:99:482,0,424:6,10,12,8 chr1 246829742 . T C 56.94 PASS AC=1;AF=0.645;AN=2;DP=877;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant6-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,22:32:99:522,0,204:5,5,8,14 chr1 246829873 . G A 154.69 PASS AC=1;AF=0.649;AN=2;DP=890;set=variant2-variant3-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,7:18:99:185,0,313:8,3,3,4 chr1 246830293 . A G 4289.46 PASS AC=1;AF=0.641;AN=2;DP=14095;set=variant2-variant3-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:162,186:348:99:4613,0,3986:70,92,87,99 chr1 246830488 . T C 3043.45 PASS AC=1;AF=0.641;AN=2;DP=9533;MQ=60;set=variant2-variant3-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:135,125:260:99:3439,0,3634:80,55,75,50 chr1 246903654 . G C 179.69 PASS AC=1;AF=0.635;AN=2;DP=820;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant21-variant23-variant25-variant29-variant31-variant32-variant35-variant36-variant37-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:14,16:30:99:448,0,449:4,10,4,12 chr1 246929483 . A G 554.65 PASS AC=1;AF=0.635;AN=2;DP=1290;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:21,22:43:99:683,0,583:5,16,5,17 chr1 246931057 . A G 1754.3 PASS AC=1;AF=0.545;AN=2;DP=3194;MQ=60;set=variant2-variant3-variant8-variant9-variant11-variant13-variant15-variant16-variant17-variant20-variant23-variant25-variant26-variant27-variant29-variant30-variant35-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:82,77:159:99:2160,0,2344:54,28,51,26 chr1 246931242 . C T 2898.91 PASS AC=1;AF=0.635;AN=2;DP=6972;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:141,128:269:99:3048,0,3424:63,78,54,74 chr1 246939610 . A ATATT 1812.21 PASS AC=1;AF=0.645;AN=2;DP=3714;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:56,50:106:99:1931,0,2808:27,29,25,25 chr1 246939856 . G A 815.43 PASS AC=1;AF=0.655;AN=2;DP=3212;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant24-variant25-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:74,71:145:99:1585,0,1883:42,32,39,32 chr1 246939943 . T C 1364.11 PASS AC=1;AF=0.652;AN=2;DP=2971;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant21-variant31-variant32-variant35-variant36-variant37-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:89,64:153:99:1495,0,2245:45,44,31,33 chr1 246940179 . G A 2415.7 PASS AC=1;AF=0.652;AN=2;DP=3608;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant21-variant31-variant32-variant35-variant36-variant37-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:78,88:166:99:3487,0,4018:45,33,50,38 chr1 246940182 . C A 2456.15 PASS AC=1;AF=0.635;AN=2;DP=4044;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:83,91:174:99:3484,0,4061:46,37,50,41 chr1 246940442 . T C 1466.45 PASS AC=1;AF=0.65;AN=2;DP=923;MQ=60;set=variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:17,22:39:99:645,0,516:9,8,11,11 chr1 246943547 . A C 201.65 PASS AC=1;AF=0.565;AN=2;DP=694;MQ=60;set=variant2-variant3-variant6-variant8-variant9-variant11-variant13-variant15-variant16-variant17-variant20-variant23-variant25-variant26-variant27-variant29-variant30-variant35-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,19:35:99:459,0,386:11,5,11,8 chr1 247004031 . T C 254.83 PASS AC=1;AF=0.5;AN=2;DP=244;FractionInformativeReads=1;set=variant4-variant6-variant8-variant10-variant12-variant15-variant18-variant20-variant31-variant32-variant34-variant35-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,10:21:99:291,0,281:8,3,9,1 chr1 247006160 . G T 1128.62 PASS AC=1;AF=0.692;AN=2;DP=1684;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,20:45:99:481,0,546:11,14,7,13 chr1 247016787 . G A 1361.78 PASS AC=1;AF=0.684;AN=2;DP=2016;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,29:56:99:747,0,680:9,18,10,19 chr1 247019277 . T C 728.59 PASS AC=1;AF=0.529;AN=2;DP=650;MQ=60;set=variant4-variant6-variant8-variant9-variant10-variant12-variant15-variant18-variant20-variant32-variant34-variant35-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:19,15:34:99:367,0,585:4,15,6,9 chr1 247021266 . C CTTCT,CTTCTT 157.5 PASS AC=2,0;AF=0.97,0.03;AN=2;DP=198;FS=0;set=variant-variant3-variant4-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant37-variant38-variant40-variant41-variant42 GT:DP:GQ:SB 1/1:7:21:0,0,2,5 chr1 247024691 . T C 248.3 PASS AC=1;AF=0.571;AN=2;DP=111;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant9-variant10-variant12-variant15-variant18-variant20-variant32-variant35-variant37-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,6:11:97:197,0,97:3,2,1,5 chr1 247025531 . C T 135.2 PASS AC=1;AF=0.559;AN=2;DP=480;set=variant-variant2-variant3-variant5-variant11-variant14-variant15-variant17-variant18-variant21-variant23-variant27-variant30-variant33-variant35-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:24,12:36:99:237,0,688:7,17,4,8 chr1 247031204 . CACACA CCACA,C,CCA 268.01 PASS AC=2,0,0;AF=0.475,0.075,0.05;AN=2;DP=328;set=variant-variant3-variant5-variant10-variant11-variant21-variant22-variant23-variant24-variant27-variant29-variant30-variant32-variant33-variant35-variant38-variant39-variant40-variant41-variant42 GT:DP:GQ:SB 1/1:4:12:0,0,0,4 chr1 247031206 . CACA C 267.97 PASS AC=2;AF=0.563;AN=2;DP=133;set=variant-variant3-variant21-variant23-variant27-variant33-variant35-variant39 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:168,12,0:0,0,0,4 chr1 247031237 . C G 587.07 PASS AC=2;AF=0.717;AN=2;DP=256;FS=0;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant21-variant22-variant23-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:219,15,0:0,0,0,5 chr1 247048834 . T C 172 PASS AC=2;AF=0.691;AN=2;DP=464;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:365,33,0:0,0,8,3 chr1 247054530 . T C 34.26 PASS AC=2;AF=0.7;AN=2;DP=271;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:302,21,0:0,0,0,7 chr1 247067139 . CAA CA,CAAA,C 285.51 PASS AC=1,0,1;AF=0.553,0.026,0.013;AN=2;DP=1090;set=variant-variant2-variant3-variant4-variant5-variant6-filterInvariant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 3/1:27:99:1,0,21,5 chr1 247067492 . AG A 172.1 PASS AC=2;AF=0.667;AN=2;DP=143;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant10-variant11-variant23-variant27-variant29-variant32-variant33-variant35-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:388,30,0:0,0,2,8 chr1 247091604 . CAAA CAA,CA,C 78.77 PASS AC=1,0,0;AF=0.4,0.143,0.029;AN=2;DP=1006;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:DP:GQ:SB 0/1:27:99:8,7,8,4 chr1 247109014 . G C 1134.77 PASS AC=1;AF=0.639;AN=2;DP=1194;MQ=60;set=variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,25:42:99:716,0,550:15,2,19,6 chr1 247109267 . A C 5224.22 PASS AC=1;AF=0.635;AN=2;DP=4646;MQ=60;set=variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:74,59:133:99:2030,0,4019:32,42,24,35 chr1 247109291 . CG C 4167.91 PASS AC=1;AF=0.569;AN=2;DP=2620;set=variant2-variant3-variant5-variant8-variant10-variant11-variant12-variant13-variant15-variant18-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:58,46:104:99:1797,0,3663:22,36,16,30 chr1 247109296 . A G 3951.13 PASS AC=1;AF=0.569;AN=2;DP=2452;FractionInformativeReads=1;set=variant2-variant3-variant5-variant8-variant10-variant11-variant12-variant13-variant15-variant18-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:57,44:101:99:1718,0,3609:21,36,14,30 chr1 247129945 . A G 106.77 PASS AC=1;AF=0.691;AN=2;DP=305;MQ=60;set=variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,9:16:99:299,0,221:6,1,8,1 chr1 247143029 . GTTAGT G 43.7 PASS AC=2;AF=0.816;AN=2;DP=65;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant7-variant12-variant13-variant15-variant16-variant17-variant24-variant25-variant27-variant29-variant32-variant34-variant35-variant36-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:135,9,0:0,0,3,0 chr1 247143092 . T A 115.49 PASS AC=1;AF=0.75;AN=2;DP=247;MQ=60;set=variant-variant4-variant6-variant7-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,11:17:99:309,0,178:5,1,7,4 chr1 247143130 . G A 152.96 PASS AC=1;AF=0.676;AN=2;DP=486;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant6-variant7-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,19:28:99:474,0,178:6,3,10,9 chr1 247143268 . T C 85.75 PASS AC=1;AF=0.724;AN=2;DP=287;set=variant-variant6-variant7-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant22-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,7:11:99:238,0,144:1,3,2,5 chr1 247143308 . TAA TA,T 41.33 PASS AC=1,0;AF=0.875,0.083;AN=2;DP=68;FS=0;MQRankSum=-0.731;ReadPosRankSum=-0.731;set=variant7-variant9-variant12-variant15-variant17-variant24-variant29-variant31-variant32-variant35-variant38-variant39 GT:DP:GQ:SB 0/1:5:11:0,1,0,4 chr1 247148627 . T G 5755.95 PASS AC=1;AF=0.7;AN=2;DP=6329;set=variant-variant4-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:107,86:193:99:1993,0,2893:69,38,55,31 chr1 247148911 . A ATTT 7112.32 PASS AC=1;AF=0.7;AN=2;DP=4632;MQ=60;set=variant-variant4-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:62,49:111:99:1871,0,3107:28,34,16,33 chr1 247149918 . G A 6857.75 PASS AC=1;AF=0.716;AN=2;DP=7190;MQ=60;set=variant-variant4-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:115,96:211:99:2286,0,2964:49,66,44,52 chr1 247149996 . A G 5347.45 PASS AC=1;AF=0.7;AN=2;DP=5677;MQ=60;set=variant-variant4-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:107,79:186:99:1897,0,2781:48,59,33,46 chr1 247150740 . T C 2577.98 PASS AC=1;AF=0.7;AN=2;DP=3220;MQ=60;set=variant-variant4-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,39:100:99:1016,0,1900:35,26,17,22 chr1 247151557 . A G 1561.95 PASS AC=1;AF=0.689;AN=2;DP=1593;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,15:39:99:436,0,657:7,17,3,12 chr1 247162658 . C T 12344.9 PASS AC=2;AF=0.864;AN=2;DP=16951;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,414:414:99:12682,1241,0:0,0,180,234 chr1 247200173 . TAC TACACACACACACAC,TACACACACAC,TACACACACACACACAC,TACACACACACAC,TACACAC,TACACACAC,TACACACACACACACACAC,TACAC,TACACACACACACACACACAC,T,TAGAC 773.12 PASS AC=0,0,1,0,0,0,0,0,0,0,0;AF=0.25,0.079,0.079,0.145,0.013,0.053,0.053,0.053,0.013,0.013,0.013;AN=2;DP=1435;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:DP:GQ:SB 0/3:26:99:8,6,10,2 chr1 247202032 . G T 147.99 PASS AC=1;AF=0.643;AN=2;DP=173;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant21-variant23-variant24-variant25-variant26-variant31-variant33-variant35-variant37-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:2,6:8:25:205,0,25:1,1,5,1 chr1 247241795 . C A 3405.33 PASS AC=1;AF=0.587;AN=2;DP=2318;MQ=60;set=variant2-variant3-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant18-variant21-variant23-variant24-variant25-variant26-variant27-variant31-variant33-variant34-variant35-variant37-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:68,49:117:99:1294,0,1702:42,26,38,11 chr1 247285224 . A G 1685.96 PASS AC=1;AF=0.643;AN=2;DP=1892;set=variant2-variant4-variant5-variant6-variant7-variant9-variant12-variant16-variant17-variant18-variant21-variant23-variant24-variant31-variant32-variant34-variant35-variant37-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:59,53:112:99:1647,0,1625:48,11,44,9 chr1 247285395 . T A 4729.04 PASS AC=1;AF=0.605;AN=2;DP=9979;MQ=60;set=variant2-variant4-variant6-variant7-variant9-variant12-variant16-variant17-variant18-variant21-variant23-variant24-variant31-variant32-variant35-variant37-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:263,260:523:99:6035,0,6258:123,140,121,139 chr1 247285681 . T C 619.89 PASS AC=1;AF=0.658;AN=2;DP=1170;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant6-variant7-variant9-variant12-variant16-variant17-variant18-variant21-variant23-variant24-variant31-variant32-variant35-variant37-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:24,35:59:99:864,0,729:10,14,13,22 chr1 247287256 . T A 254.2 PASS AC=1;AF=0.5;AN=2;DP=1743;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant16-variant17-variant18-variant21-variant23-variant24-variant31-variant32-variant33-variant35-variant37-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:73,25:98:99:499,0,2297:33,40,10,15 chr1 247287260 . A G 447.46 PASS AC=1;AF=0.5;AN=2;DP=1985;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant16-variant17-variant18-variant21-filterInvariant23-variant24-variant26-variant28-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:64,32:96:99:649,0,2705:27,37,14,18 chr1 247287269 . T C 1185.32 PASS AC=1;AF=0.615;AN=2;DP=1837;FractionInformativeReads=1;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant16-variant17-variant18-variant21-variant23-variant24-variant26-variant28-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:36,53:89:99:1875,0,777:15,21,22,31 chr1 247287276 . A T 469.92 PASS AC=1;AF=0.5;AN=2;DP=413;set=variant2-variant18-filterInvariant21-variant34-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:52,33:85:99:698,0,2106:20,32,14,19 chr1 247319190 . AT A 145.58 PASS AC=1;AF=0.563;AN=2;DP=155;set=variant2-variant17-variant21-variant32-variant34-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:17,13:30:99:268,0,363:11,6,11,2 chr1 247319774 . GA G 1235.2 PASS AC=1;AF=0.563;AN=2;DP=832;MQ=60;set=variant2-variant17-variant21-variant32-variant34-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:50,55:105:99:1533,0,1364:13,37,17,38 chr1 247319830 . G A 1179.64 PASS AC=1;AF=0.563;AN=2;DP=659;FractionInformativeReads=1;set=variant2-variant17-variant21-variant32-variant34-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:40,45:85:99:1291,0,1224:18,22,18,27 chr1 247320258 . A G 1202.98 PASS AC=1;AF=0.563;AN=2;DP=887;FractionInformativeReads=1;MQ=60;set=variant2-variant17-variant21-variant32-variant34-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:45,67:112:99:1813,0,1159:20,25,31,36 chr1 247320868 . G A 2826 PASS AC=1;AF=0.563;AN=2;DP=1707;FractionInformativeReads=1;MQ=60;set=variant2-variant17-variant21-variant32-variant34-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:123,123:246:99:3206,0,3062:67,56,66,57 chr1 247322130 . C T 123.17 PASS AC=1;AF=0.583;AN=2;DP=43;FS=0;MQ=60;set=variant17-variant21-variant34-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:6,6:12:99:187,0,169:5,1,4,2 chr1 247322298 . G T 972.68 PASS AC=1;AF=0.673;AN=2;DP=1193;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant16-variant17-variant18-variant21-variant23-variant24-variant26-variant28-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:14,24:38:99:667,0,349:6,8,14,10 chr1 247323195 . T C 994.51 PASS AC=1;AF=0.563;AN=2;DP=824;MQ=60;set=variant2-variant17-variant21-variant32-variant34-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:60,57:117:99:1448,0,1641:18,42,22,35 chr1 247337159 . A G 2145.02 PASS AC=1;AF=0.5;AN=2;DP=2264;FractionInformativeReads=1;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant16-variant17-variant21-variant23-variant24-variant31-variant32-variant33-variant34-variant35-variant37-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:86,29:115:99:555,0,2151:48,38,13,16 chr1 247365430 . A G 841.02 PASS AC=2;AF=0.688;AN=2;DP=1813;MQ=60;set=variant-variant2-variant4-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant22-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:1984,173,0:0,0,19,39 chr1 247419509 . T C 3167.1 PASS AC=2;AF=0.907;AN=2;DP=4561;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,100:100:99:3076,299,0:0,0,64,36 chr1 247419664 . C T 4348 PASS AC=2;AF=0.907;AN=2;DP=4913;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,114:114:99:3634,342,0:0,0,53,61 chr1 247420421 . C T 288.59 PASS AC=1;AF=0.625;AN=2;DP=465;FractionInformativeReads=1;MQ=60;set=variant2-variant8-variant10-variant11-filterInvariant17-variant18-variant20-variant21-variant25-variant26-variant27-variant28-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,8:23:99:271,0,442:3,12,0,8 chr1 247460660 . T C 231.01 PASS AC=2;AF=0.782;AN=2;DP=494;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:521,39,0:0,0,11,2 chr1 247460727 . A G 669.59 PASS AC=1;AF=0.565;AN=2;DP=731;MQ=60;set=variant3-variant8-variant10-variant11-variant12-variant17-variant18-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,20:37:99:523,0,393:11,6,14,6 chr1 247461158 . CAAG C 691.44 PASS AC=1;AF=0.571;AN=2;DP=975;MQ=60;set=variant3-variant8-variant10-variant11-variant12-variant17-variant18-variant20-variant21-variant24-variant26-variant27-variant28-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,21:52:99:754,0,1582:14,17,10,11 chr1 247462048 . A G 1335.34 PASS AC=2;AF=0.762;AN=2;DP=2875;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:2122,204,0:0,0,36,32 chr1 247462273 . A G 677 PASS AC=2;AF=0.762;AN=2;DP=2004;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1622,153,0:0,0,19,32 chr1 247473889 . C T 316.24 PASS AC=1;AF=0.643;AN=2;DP=404;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant13-variant14-variant15-variant17-variant19-variant22-variant23-variant24-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,4:14:99:135,0,373:1,9,0,4 chr1 247485932 . A G 1718.71 PASS AC=2;AF=0.977;AN=2;DP=1650;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1430,146,0:0,0,30,19 chr1 247486213 . G A 1178.29 PASS AC=1;AF=0.641;AN=2;DP=1158;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant12-variant13-variant14-variant15-variant17-variant19-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,30:43:99:678,0,294:5,8,14,16 chr1 247486421 . G C 1511.19 PASS AC=2;AF=0.78;AN=2;DP=1388;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1055,99,0:0,0,22,11 chr1 247486736 . C T 525.96 PASS AC=1;AF=0.571;AN=2;DP=483;MQ=60;set=variant3-variant8-variant10-variant11-variant12-variant17-variant18-variant20-variant21-variant24-variant26-variant27-variant28-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,22:30:99:661,0,212:2,6,6,16 chr1 247581692 . T C 61.77 PASS AC=2;AF=1;AN=2;DP=90;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant11-variant12-variant14-variant17-variant19-variant20-variant22-variant23-variant25-variant27-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:94,9,0:0,0,2,1 chr1 247582466 . A T 174.95 PASS AC=2;AF=0.76;AN=2;DP=208;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant16-variant18-variant20-variant21-variant23-variant27-variant28-variant30-variant32-variant34-variant35-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:129,12,0:0,0,1,3 chr1 247586336 . T C 320.4 PASS AC=1;AF=0.54;AN=2;DP=381;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant9-variant13-variant14-variant15-variant18-variant19-variant20-variant22-variant24-variant26-variant27-variant28-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:16,9:25:99:228,0,390:12,4,7,2 chr1 247587531 . A G 3041.45 PASS AC=1;AF=0.943;AN=2;DP=7491;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:93,112:205:99:2777,0,2221:42,51,51,61 chr1 247597329 . C T 55.3 PASS AC=1;AF=0.932;AN=2;DP=259;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,9:15:99:360,0,380:5,1,9,0 chr1 247597365 . G A,GTGTTCTGAGGCCTTCTCTATTCCAGAGCTCTCTGGTCAGA 983.6 PASS AC=1,0;AF=0.393,0.548;AN=2;DP=700;set=variant3-variant4-variant7-variant8-variant9-variant2-variant-variant10-variant6-variant5-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:34:99:12,3,17,2 chr1 247597656 . TG T 299.71 PASS AC=1;AF=0.705;AN=2;DP=2070;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,30:63:99:843,0,909:8,25,5,25 chr1 247607642 . C T 373.26 PASS AC=1;AF=0.625;AN=2;DP=1379;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,33:52:99:1007,0,499:7,12,12,21 chr1 247611570 . CTTT CT,CTT,C,CTTTT,CTTTTTT 275.48 PASS AC=1,0,0,0,0;AF=0.328,0.172,0.047,0.016,0.016;AN=2;DP=1631;set=variant-variant3-variant4-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:40:99:11,8,12,9 chr1 247612036 . G C 3069.37 PASS AC=1;AF=0.639;AN=2;DP=7439;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:104,108:212:99:2664,0,2507:57,47,51,57 chr1 247612151 . C CT 5709.29 PASS AC=1;AF=0.688;AN=2;DP=8115;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:109,102:211:99:2504,0,2773:47,62,41,61 chr1 247612295 . C T 1632.69 PASS AC=1;AF=0.671;AN=2;DP=2416;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,19:52:99:452,0,878:14,19,7,12 chr1 247612435 . A T 180.18 PASS AC=1;AF=0.587;AN=2;DP=211;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant12-variant13-variant16-variant17-variant21-variant26-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:3,5:8:71:160,0,71:1,2,1,4 chr1 247614194 . A G 147.15 PASS AC=1;AF=0.5;AN=2;DP=469;MQ=60;set=variant2-variant4-variant6-variant8-variant10-variant11-variant19-variant20-variant22-variant23-variant26-variant30-variant33-variant34-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,11:29:99:266,0,442:11,7,7,4 chr1 247614386 . T C 793.91 PASS AC=1;AF=0.5;AN=2;DP=1268;MQ=60;set=variant2-variant4-variant6-variant8-variant10-variant11-variant19-variant20-variant22-variant23-variant26-variant30-variant33-variant34-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,36:78:99:1038,0,1092:22,20,24,12 chr1 247614407 . G A 888.37 PASS AC=1;AF=0.5;AN=2;DP=1439;MQ=60;set=variant2-variant4-variant6-variant8-variant10-variant11-variant19-variant20-variant22-variant23-variant26-variant30-variant33-variant34-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,36:83:99:843,0,1230:24,23,19,17 chr1 247614553 . C T 1269.66 PASS AC=1;AF=0.5;AN=2;DP=2002;MQ=60;set=variant2-variant4-variant6-variant8-variant10-variant11-variant19-variant20-variant22-variant23-variant26-variant30-variant33-variant34-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,62:107:99:1685,0,1109:21,24,34,28 chr1 247614617 . C T 1089.78 PASS AC=1;AF=0.571;AN=2;DP=3300;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:81,47:128:99:976,0,2289:48,33,25,22 chr1 247614693 . C T 1785.79 PASS AC=2;AF=0.977;AN=2;DP=5367;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,134:134:99:4369,401,0:0,0,72,62 chr1 247614896 . A C 642.08 PASS AC=1;AF=0.594;AN=2;DP=3334;MQ=60;set=variant-variant2-variant5-variant7-variant9-variant10-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:70,62:132:99:1668,0,1791:38,32,29,33 chr1 247615261 . GA G 1789.9 PASS AC=2;AF=0.625;AN=2;DP=3585;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,107:107:99:4004,322,0:0,0,45,62 chr1 247615470 . T C 232.49 PASS AC=2;AF=0.864;AN=2;DP=590;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:316,24,0:0,0,1,7 chr1 247681687 . C T 38.47 PASS AC=1;AF=0.722;AN=2;DP=717;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,15:22:99:462,0,120:5,2,10,5 chr1 247693819 . T TCCCC,TC,TCCC,TCC 226.68 PASS AC=0,1,0,0;AF=0.083,0.167,0.347,0.069;AN=2;DP=1540;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:34:99:4,10,5,15 chr1 247693828 . C CA 416.65 PASS AC=1;AF=0.529;AN=2;DP=652;MQ=60;set=variant-variant2-variant3-variant5-variant9-variant14-variant15-variant16-variant18-variant24-variant27-variant28-variant29-variant34-variant35-variant36-variant40 GT:AD:DP:GQ:PL:SB 0/1:20,13:33:99:268,0,563:5,15,4,9 chr1 247693966 . T C 788.67 PASS AC=2;AF=0.989;AN=2;DP=2050;MQ=60;MQRankSum=1.439;ReadPosRankSum=-0.558;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:898,87,0:0,0,19,10 chr1 247694106 . C CTCCGTGGCCTAAACGGGCAGCCGAGCCCG,CTCCGTGGCCTAAATGGGCAGCCGAGCCCG 1817.27 PASS AC=2,0;AF=0.667,0.202;AN=2;DP=3257;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:79:99:0,0,39,40 chr1 247694370 . G C 1155.26 PASS AC=1;AF=0.591;AN=2;DP=1145;MQ=60;set=variant2-variant4-variant9-variant10-variant13-variant22-variant30-variant31-variant32-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:60,57:117:99:1338,0,1476:31,29,27,30 chr1 247694550 . C G 2753.15 PASS AC=1;AF=0.768;AN=2;DP=8156;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:134,108:242:99:2628,0,3331:78,56,61,47 chr1 247694949 . G C 3258.79 PASS AC=1;AF=0.538;AN=2;DP=2565;MQ=60;set=variant-variant2-variant3-variant5-variant14-variant16-variant18-variant24-variant28-variant34-variant35-variant36-variant40 GT:AD:DP:GQ:PL:SB 0/1:120,105:225:99:3991,0,6613:62,58,54,51 chr1 247694958 . G A 3279.69 PASS AC=1;AF=0.531;AN=2;DP=3219;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant14-variant15-variant16-variant18-variant24-variant27-variant28-variant29-variant34-variant35-variant36-variant40 GT:AD:DP:GQ:PL:SB 0/1:121,107:228:99:4033,0,6663:62,59,55,52 chr1 247695612 . G A 2852.79 PASS AC=2;AF=1;AN=2;DP=5751;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,146:146:99:4526,435,0:0,0,68,78 chr1 247695756 . T C 2822.29 PASS AC=2;AF=0.989;AN=2;DP=5096;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,123:123:99:3813,368,0:0,0,54,69 chr1 247695958 . T C 142.43 PASS AC=2;AF=1;AN=2;DP=415;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:634,63,0:0,0,8,13 chr1 247696857 . G C 2746.62 PASS AC=2;AF=0.942;AN=2;DP=3527;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,81:81:99:2767,241,0:0,0,60,21 chr1 247726822 . CTTTT C 2148.79 PASS AC=2;AF=0.643;AN=2;DP=4111;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,117:117:99:5207,352,0:0,0,64,53 chr1 247729206 . CT C,CTT 76.42 PASS AC=1,0;AF=0.468,0.032;AN=2;DP=1834;MQ=60;set=filterInvariant6-filterInvariant8-variant10-variant11-variant13-filterInvariant15-variant16-variant17-variant18-variant19-variant20-filterInvariant21-filterInvariant22-variant25-variant26-filterInvariant27-variant28-filterInvariant29-variant30-variant31-filterInvariant32-variant33-variant34-filterInvariant35-filterInvariant36-filterInvariant37-variant38-filterInvariant39-variant40-variant42-variant43 GT:DP:GQ:SB 0/1:61:99:20,24,9,8 chr1 247729391 . G T 46.72 PASS AC=2;AF=0.571;AN=2;DP=34;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant11-variant21-variant35-variant37-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:79,6,0:0,0,0,2 chr1 247751731 . C G 1211.53 PASS AC=2;AF=0.571;AN=2;DP=1779;MQ=60;set=variant-variant2-variant9-variant11-variant18-variant22-variant23-variant24-variant26-variant35-variant37-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,127:127:99:4170,381,0:0,0,65,62 chr1 247752019 . G C 1988.44 PASS AC=2;AF=0.75;AN=2;DP=6711;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,198:198:99:6362,593,0:0,0,91,107 chr1 247752367 . A G 3915.18 PASS AC=2;AF=0.744;AN=2;DP=5697;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,141:141:99:4666,422,0:0,0,69,72 chr1 247769062 . A G 2429.26 PASS AC=2;AF=0.545;AN=2;DP=1701;MQ=60;set=variant-variant2-variant11-variant17-variant18-variant22-variant24-variant26-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,152:152:99:4933,455,0:0,0,82,70 chr1 247769752 . A G 3085.3 PASS AC=2;AF=0.75;AN=2;DP=7949;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant28-variant30-variant31-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,251:253:99:7738,708,0:1,1,136,115 chr1 247835352 . C T 766.45 PASS AC=2;AF=0.86;AN=2;DP=1368;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-filterInvariant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:1085,87,0:0,0,21,8 chr1 247835674 . G A 1239.59 PASS AC=1;AF=0.595;AN=2;DP=3380;MQ=60;set=variant-variant5-variant7-variant9-variant11-variant13-variant14-variant16-variant18-variant23-variant24-variant25-variant27-variant29-variant30-variant32-variant35-variant37-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:80,91:171:99:2254,0,2053:35,45,42,49 chr1 247835779 . C G 1718.12 PASS AC=1;AF=0.5;AN=2;DP=888;MQ=60;set=variant11-variant22-variant26-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,68:135:99:1988,0,1749:37,30,39,29 chr1 247835908 . T A 910.31 PASS AC=1;AF=0.595;AN=2;DP=2943;MQ=60;set=variant-variant5-variant7-variant9-variant11-variant13-variant14-variant16-variant18-variant23-variant24-variant25-variant27-variant29-variant30-variant32-variant35-variant37-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:81,71:152:99:1833,0,2193:40,41,31,40 chr1 247836008 . G A 964.76 PASS AC=1;AF=0.595;AN=2;DP=2458;MQ=60;set=variant-variant5-variant7-variant9-variant11-variant13-variant14-variant16-variant18-variant23-variant24-variant25-variant27-variant29-variant30-variant32-variant35-variant37-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:60,57:117:99:1536,0,1874:26,34,26,31 chr1 247836207 . T A 1493 PASS AC=1;AF=0.595;AN=2;DP=2558;MQ=60;set=variant-variant5-variant7-variant9-variant11-variant13-variant14-variant16-variant18-variant23-variant24-variant25-variant27-variant29-variant30-variant32-variant35-variant37-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:63,58:121:99:1517,0,1625:35,28,32,26 chr1 247875314 . C A 1665.95 PASS AC=1;AF=0.5;AN=2;DP=1470;FractionInformativeReads=1;MQ=60;set=variant7-variant11-variant21-variant22-variant26-variant30-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:99,74:173:99:1988,0,2777:47,52,44,30 chr1 247875415 . A G 988.97 PASS AC=1;AF=0.56;AN=2;DP=4639;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant7-variant9-variant11-variant14-variant16-variant18-variant21-variant22-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:99,99:198:99:2444,0,2232:47,52,49,50 chr1 247875608 . C G 584.3 PASS AC=1;AF=0.563;AN=2;DP=2168;MQ=60;set=variant-variant3-variant5-variant7-variant9-variant11-variant14-variant16-variant18-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant33-variant35-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,42:80:99:1192,0,951:20,18,17,25 chr1 247875689 . A G 1105.28 PASS AC=1;AF=0.542;AN=2;DP=903;MQ=60;set=variant5-variant7-variant11-variant16-variant21-variant22-variant26-variant28-variant30-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,37:67:99:1047,0,886:17,13,20,17 chr1 247886648 . G A 1119.26 PASS AC=1;AF=0.5;AN=2;DP=496;FractionInformativeReads=1;MQ=60;set=variant11-variant22-variant26-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:56,28:84:99:774,0,1650:24,32,15,13 chr1 247921100 . T G 2540.34 PASS AC=1;AF=0.849;AN=2;DP=4607;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:71,59:130:99:1557,0,1705:36,35,28,31 chr1 247921352 . C T 1582.83 PASS AC=2;AF=0.93;AN=2;DP=3783;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,97:97:99:3313,291,0:0,0,39,58 chr1 247921717 . C A 784.76 PASS AC=2;AF=0.93;AN=2;DP=2017;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:1805,165,0:0,0,17,38 chr1 247921789 . AGT AGTGT,AGTGTGT,A,AGTGTGTGT 198.31 PASS AC=1,0,1,0;AF=0.434,0.145,0.066,0.013;AN=2;DP=817;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 3/1:15:99:0,0,8,7 chr1 247921888 . C T 620.93 PASS AC=2;AF=0.989;AN=2;DP=742;FractionInformativeReads=1;MQ=60;MQRankSum=0.376;ReadPosRankSum=0.612;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:751,75,0:0,0,11,14 chr1 247978087 . G A 873.44 PASS AC=2;AF=0.905;AN=2;DP=1739;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:999,90,0:0,0,19,11 chr1 247978135 . C A 660.73 PASS AC=2;AF=0.583;AN=2;DP=740;MQ=60;set=variant-variant4-variant6-variant8-variant9-variant12-variant26-variant29-variant35-variant36-variant38-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:1528,141,0:0,0,28,19 chr1 247978319 . A G 3434.94 PASS AC=2;AF=1;AN=2;DP=5641;FS=0;MQ=60;MQRankSum=0.144;ReadPosRankSum=0.52;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,130:130:99:3899,389,0:0,0,66,64 chr1 247978541 . AAGG A 3431.99 PASS AC=2;AF=0.863;AN=2;DP=5303;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,128:128:99:5752,386,0:0,0,67,61 chr1 247978996 . A G 1536.86 PASS AC=2;AF=0.905;AN=2;DP=2311;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1473,138,0:0,0,17,29 chr1 248004614 . G A 3268.68 PASS AC=2;AF=0.884;AN=2;DP=5372;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,154:154:99:4851,462,0:0,0,85,69 chr1 248004687 . C G 2723.26 PASS AC=2;AF=0.875;AN=2;DP=6328;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,176:176:99:5236,527,0:0,0,92,84 chr1 248004775 . C T 1653.55 PASS AC=2;AF=0.875;AN=2;DP=5173;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,136:136:99:4156,405,0:0,0,57,79 chr1 248004848 . G C 1453.67 PASS AC=2;AF=0.875;AN=2;DP=3962;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,108:108:99:3378,322,0:0,0,47,61 chr1 248004877 . C T 1720.27 PASS AC=2;AF=0.875;AN=2;DP=3743;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,93:93:99:4130,283,0:0,0,42,51 chr1 248004884 . T C 1661.48 PASS AC=2;AF=0.966;AN=2;DP=3749;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,95:95:99:4155,289,0:0,0,43,52 chr1 248005213 . G C 3151.61 PASS AC=2;AF=0.875;AN=2;DP=4870;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,92:92:99:2945,275,0:0,0,35,57 chr1 248023966 . C T 1518.37 PASS AC=2;AF=0.648;AN=2;DP=1753;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant13-variant18-variant20-variant21-variant23-variant25-variant26-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2063,210,0:0,0,34,36 chr1 248024073 . A C 548.79 PASS AC=2;AF=0.66;AN=2;DP=471;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant18-variant20-variant21-variant23-variant25-variant26-variant28-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:594,54,0:0,0,6,12 chr1 248039713 . A G 3151.37 PASS AC=2;AF=0.744;AN=2;DP=3888;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,99:99:99:3215,296,0:0,0,45,54 chr1 248040018 . A G 9664.93 PASS AC=2;AF=0.591;AN=2;DP=6481;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant9-variant11-variant13-variant20-variant21-variant24-variant25-variant28-variant29-variant31-variant33-variant35-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,263:264:99:8254,746,0:1,0,130,133 chr1 248040293 . T C 3448.83 PASS AC=2;AF=1;AN=2;DP=3759;FS=0;MQ=60;MQRankSum=2.226;ReadPosRankSum=-0.528;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,102:102:99:3506,306,0:0,0,37,65 chr1 248041182 . T G 400.9 PASS AC=2;AF=0.763;AN=2;DP=743;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:351,36,0:0,0,4,8 chr1 248058755 . A G 106.77 PASS AC=2;AF=0.976;AN=2;DP=253;FS=0;MQ=60;MQRankSum=0.922;ReadPosRankSum=0.922;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:267,18,0:0,0,6,0 chr1 248058761 . G C 106.77 PASS AC=1;AF=0.727;AN=2;DP=170;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant11-variant13-variant15-variant16-variant18-variant19-variant23-variant24-variant25-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,4:7:99:156,0,114:3,0,4,0 chr1 248058797 . T G 414.76 PASS AC=2;AF=0.977;AN=2;DP=857;FS=0;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:966,84,0:0,0,21,7 chr1 248058845 . A C 848.32 PASS AC=2;AF=0.977;AN=2;DP=2134;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:1979,186,0:0,0,43,19 chr1 248058879 . A T 1590.41 PASS AC=2;AF=0.977;AN=2;DP=3552;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,98:98:99:3108,294,0:0,0,62,36 chr1 248059423 . C T 6445.63 PASS AC=1;AF=0.636;AN=2;DP=7645;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:154,152:306:99:4089,0,3960:71,83,76,76 chr1 248059456 . G A 2050.05 PASS AC=1;AF=0.633;AN=2;DP=7198;MQ=60;set=variant2-variant3-variant5-variant7-variant8-variant11-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:148,160:308:99:4331,0,3778:71,77,82,78 chr1 248059476 . A C 5891.4 PASS AC=2;AF=0.885;AN=2;DP=9098;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,317:317:99:11714,952,0:0,0,159,158 chr1 248059703 . T A 7532.24 PASS AC=1;AF=0.731;AN=2;DP=7642;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:114,112:226:99:4164,0,5341:52,62,42,70 chr1 248059712 . T C 7372.47 PASS AC=1;AF=0.744;AN=2;DP=7245;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:107,102:209:99:3975,0,5302:49,58,37,65 chr1 248059856 . T C 2717.97 PASS AC=1;AF=0.744;AN=2;DP=4006;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:62,58:120:99:1471,0,1620:26,36,28,30 chr1 248060029 . A G 975.82 PASS AC=2;AF=0.966;AN=2;DP=1166;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:1058,96,0:0,0,13,19 chr1 248084434 . G A 2804.28 PASS AC=2;AF=0.821;AN=2;DP=3686;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,96:96:99:3109,288,0:0,0,31,65 chr1 248084464 . T C 1698.6 PASS AC=2;AF=0.955;AN=2;DP=2892;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,66:66:99:2501,198,0:0,0,16,50 chr1 248084471 . A G 660.67 PASS AC=1;AF=0.567;AN=2;DP=762;set=variant4-variant9-variant10-variant12-variant13-variant15-variant25-variant28-variant29-filterInvariant30-variant31-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,24:61:99:842,0,1451:10,27,4,20 chr1 248084473 . C A 660.67 PASS AC=1;AF=0.577;AN=2;DP=658;FractionInformativeReads=1;set=variant4-variant9-variant10-variant13-variant15-variant28-variant29-filterInvariant30-variant31-variant35-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,24:60:99:842,0,1451:10,26,4,20 chr1 248084511 . T C 1200.5 PASS AC=1;AF=0.591;AN=2;DP=647;FractionInformativeReads=1;set=variant-variant4-variant5-variant6-variant9-variant10-variant13-variant15-variant19-variant20-variant25-variant28-variant29-variant31-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,12:34:99:337,0,557:8,14,0,12 chr1 248084825 . C T 313.46 PASS AC=2;AF=0.853;AN=2;DP=500;FractionInformativeReads=1;set=filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant13-filterInvariant14-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant21-filterInvariant22-filterInvariant23-variant24-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant29-filterInvariant31-filterInvariant32-filterInvariant33-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant39-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:247,30,0:0,0,5,5 chr1 248084980 . G T 93.53 PASS AC=2;AF=0.839;AN=2;DP=180;set=variant2-variant3-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant26-variant27-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:181,15,0:0,0,5,0 chr1 248085108 . C T 1861.97 PASS AC=2;AF=0.837;AN=2;DP=3055;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,63:63:99:2165,188,0:0,0,47,16 chr1 248085341 . T A 2175.71 PASS AC=2;AF=0.884;AN=2;DP=2706;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,64:64:99:2221,192,0:0,0,16,48 chr1 248112627 . T C 7445.38 PASS AC=2;AF=0.692;AN=2;DP=12232;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,322:322:99:10523,964,0:0,0,136,186 chr1 248112745 . G T 6451.64 PASS AC=2;AF=0.818;AN=2;DP=9677;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,204:204:99:6864,611,0:0,0,105,99 chr1 248112762 . T C 8478.52 PASS AC=2;AF=0.807;AN=2;DP=9516;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,217:217:99:9904,658,0:0,0,112,105 chr1 248112763 . G A 8523.52 PASS AC=2;AF=0.807;AN=2;DP=9533;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,218:218:99:10019,667,0:0,0,113,105 chr1 248112771 . C T 8422.94 PASS AC=2;AF=0.807;AN=2;DP=9818;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,213:214:99:9717,649,0:1,0,111,102 chr1 248112809 . A G 6821.24 PASS AC=2;AF=0.965;AN=2;DP=11233;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,292:292:99:9282,875,0:0,0,162,130 chr1 248112836 . A G 6809.8 PASS AC=2;AF=0.966;AN=2;DP=12077;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,313:313:99:9805,938,0:0,0,159,154 chr1 248113026 . T A 3810.96 PASS AC=2;AF=0.966;AN=2;DP=7734;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,205:205:99:6237,611,0:0,0,79,126 chr1 248113040 . A G 3959.03 PASS AC=2;AF=1;AN=2;DP=7366;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,194:195:99:6263,564,0:1,0,70,124 chr1 248113206 . C G 552.37 PASS AC=2;AF=0.966;AN=2;DP=1508;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1141,108,0:0,0,10,26 chr1 248129240 . G A 3577.73 PASS AC=2;AF=0.789;AN=2;DP=4998;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,135:135:99:4278,405,0:0,0,56,79 chr1 248247237 . C A 84.83 PASS AC=1;AF=0.5;AN=2;DP=2468;set=filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant12-filterInvariant14-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant24-filterInvariant26-filterInvariant27-filterInvariant29-filterInvariant30-variant31-variant33-filterInvariant35-filterInvariant42-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:75,22:97:99:289,0,1838:48,27,18,4 chr1 248247308 . A C 1318.98 PASS AC=1;AF=0.5;AN=2;DP=8247;set=filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-variant7-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant13-filterInvariant14-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant29-filterInvariant30-variant31-variant32-filterInvariant33-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant39-filterInvariant40-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:141,93:234:99:1677,0,3355:81,60,58,35 chr1 248247460 . G A 574.65 PASS AC=1;AF=0.5;AN=2;DP=4043;set=variant2-variant3-filterInvariant4-variant6-filterInvariant8-variant9-filterInvariant10-variant11-filterInvariant12-filterInvariant13-variant14-variant16-variant17-variant18-filterInvariant20-variant21-filterInvariant22-variant24-variant26-variant27-variant29-variant30-variant32-variant33-variant34-variant35-filterInvariant40-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:129,26:155:99:703,0,6293:52,77,4,22 chr1 248247461 . G C 574.65 PASS AC=1;AF=0.5;AN=2;DP=3997;set=variant2-variant3-filterInvariant4-variant6-filterInvariant8-variant9-filterInvariant10-variant11-filterInvariant12-filterInvariant13-variant14-variant16-variant17-variant18-filterInvariant20-variant21-filterInvariant22-variant24-variant26-variant27-variant29-variant30-variant32-variant33-variant34-variant35-filterInvariant40-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:128,26:154:99:703,0,6293:51,77,4,22 chr1 248247586 . T G 793.5 PASS AC=1;AF=0.523;AN=2;DP=2055;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:28,42:70:99:1653,0,1387:16,12,27,15 chr1 248247588 . T A 165.24 PASS AC=1;AF=0.5;AN=2;DP=1315;set=variant2-filterInvariant3-variant4-variant6-variant7-variant9-filterInvariant12-variant14-filterInvariant16-filterInvariant17-variant18-variant21-variant22-variant23-variant24-filterInvariant26-variant27-variant28-variant31-variant32-variant34-filterInvariant35-variant36-filterInvariant38-filterInvariant41-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,13:68:99:122,0,2148:36,19,7,6 chr1 248247590 . G A 835.49 PASS AC=1;AF=0.512;AN=2;DP=2130;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,42:70:99:1698,0,1405:16,12,27,15 chr1 248247592 . G C 838.5 PASS AC=1;AF=0.512;AN=2;DP=2161;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,43:72:99:1698,0,1405:16,13,27,16 chr1 248247638 . T C 45.09 PASS AC=1;AF=0.5;AN=2;DP=1188;set=filterInvariant4-filterInvariant6-variant8-variant9-variant10-variant13-variant15-variant17-variant25-filterInvariant28-filterInvariant29-filterInvariant30-variant31-filterInvariant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:82,14:96:99:115,0,1941:41,41,10,4 chr1 248247744 . G T 243.64 PASS AC=1;AF=0.5;AN=2;DP=1336;FractionInformativeReads=1;set=variant4-variant9-variant10-variant13-variant15-variant28-filterInvariant29-variant30-variant31-variant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:79,25:104:99:763,0,3998:44,35,9,16 chr1 248247745 . GC G 145.98 PASS AC=1;AF=0.528;AN=2;DP=1858;set=filterInvariant3-variant4-variant9-variant10-filterInvariant11-variant13-variant15-variant20-variant28-filterInvariant29-variant30-variant31-variant35-filterInvariant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,51:102:99:1865,0,2826:30,21,23,28 chr1 248247747 . C T 155.02 PASS AC=1;AF=0.5;AN=2;DP=462;FractionInformativeReads=1;set=variant3-filterInvariant11-variant13-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:77,26:103:99:713,0,3995:40,37,14,12 chr1 248247784 . C T 505.03 PASS AC=1;AF=0.5;AN=2;DP=684;FractionInformativeReads=1;set=variant3-filterInvariant9-variant25-variant31-filterInvariant35 GT:AD:DP:GQ:PL:SB 0/1:104,15:119:69:69,0,2734:60,44,4,11 chr1 248262644 . A G 1951.95 PASS AC=1;AF=0.5;AN=2;DP=1447;MQ=60;set=variant-variant7-variant10-variant11-variant22-variant31-variant35-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,68:133:99:1685,0,1610:35,30,40,28 chr1 248264018 . C T 9491.88 PASS AC=2;AF=0.763;AN=2;DP=11552;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,277:277:99:8368,831,0:0,0,144,133 chr1 248285809 . A G 3714.42 PASS AC=1;AF=0.5;AN=2;DP=1068;FractionInformativeReads=1;set=variant-variant10-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:170,138:308:99:3715,0,4415:84,86,71,67 chr1 248343543 . C T 2152.62 PASS AC=2;AF=0.737;AN=2;DP=7315;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,223:223:99:7159,667,0:0,0,126,97 chr1 248343945 . C G 2550.77 PASS AC=2;AF=0.737;AN=2;DP=9358;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,213:213:99:6956,638,0:0,0,105,108 chr1 248343990 . T C 2213.09 PASS AC=2;AF=0.737;AN=2;DP=7694;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,175:175:99:5787,524,0:0,0,80,95 chr1 248344442 . C T 94.73 PASS AC=2;AF=0.75;AN=2;DP=270;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:128,9,0:0,0,1,2 chr1 248366702 . G A 5368.43 PASS AC=2;AF=0.705;AN=2;DP=16499;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,460:460:99:13578,1375,0:0,0,251,209 chr1 248367415 . C T 993.15 PASS AC=2;AF=0.802;AN=2;DP=1916;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1516,125,0:0,0,7,35 chr1 248402758 . C T 1201.62 PASS AC=2;AF=0.78;AN=2;DP=4230;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,138:138:99:4458,413,0:0,0,61,77 chr1 248436611 . G A 1195.57 PASS AC=2;AF=0.779;AN=2;DP=5161;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:3,115:118:99:3232,265,0:3,0,68,47 chr1 248436616 . A G 1251.01 PASS AC=2;AF=0.779;AN=2;DP=5354;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,121:121:99:5302,367,0:0,0,70,51 chr1 248436805 . T G 554.62 PASS AC=2;AF=0.739;AN=2;DP=4729;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,106:106:99:3708,318,0:0,0,47,59 chr1 248436809 . G A 883.09 PASS AC=1;AF=0.5;AN=2;DP=4394;set=variant2-variant3-variant4-filterInvariant5-filterInvariant6-filterInvariant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:74,28:102:99:950,0,2988:35,39,9,19 chr1 248436811 . G C 883.09 PASS AC=1;AF=0.5;AN=2;DP=4342;set=variant2-variant3-variant4-filterInvariant5-filterInvariant6-filterInvariant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:74,28:102:99:950,0,2988:34,40,9,19 chr1 248436972 . A G 1199.74 PASS AC=1;AF=0.529;AN=2;DP=1424;set=variant3-variant11-variant12-variant13-variant15-variant16-variant17-variant21-variant23-variant25-variant33-variant35-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:39,51:90:99:1342,0,1027:21,18,29,22 chr1 248437210 . T C 1393.83 PASS AC=1;AF=0.5;AN=2;DP=1024;FractionInformativeReads=1;set=variant3-variant11-variant12-variant13-variant15-variant16-variant17-variant21-variant25-variant33-variant35-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:46,25:71:99:579,0,1282:14,32,9,16 chr1 248437247 . GCCCTAA G 1042.35 PASS AC=2;AF=0.779;AN=2;DP=1639;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1559,108,0:0,0,11,25 chr1 248457979 . C A 3426.87 PASS AC=2;AF=0.774;AN=2;DP=14543;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,326:328:99:11701,934,0:1,1,154,172 chr1 248457993 . C G 4543.49 PASS AC=1;AF=0.538;AN=2;DP=4188;set=variant3-variant8-variant11-variant13-variant15-variant16-variant17-variant25-variant33-variant35-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:159,151:310:99:3676,0,3667:75,84,65,86 chr1 248458571 . T A 94.01 PASS AC=1;AF=0.672;AN=2;DP=553;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant31-variant32-filterInvariant33-variant34-variant35-variant36-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,8:13:99:217,0,152:3,2,3,5 chr1 248458676 . T C 628.02 PASS AC=2;AF=0.744;AN=2;DP=2911;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-filterInvariant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1998,138,0:0,0,31,12 chr1 248458689 . A G 749.11 PASS AC=2;AF=0.744;AN=2;DP=3532;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-filterInvariant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:2273,168,0:0,0,35,21 chr1 248458717 . C G 987.51 PASS AC=2;AF=0.75;AN=2;DP=4673;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,89:89:99:3128,270,0:0,0,51,38 chr1 248458736 . A G 2776.14 PASS AC=1;AF=0.536;AN=2;DP=1780;set=variant3-variant8-variant11-variant13-variant15-variant16-variant17-variant25-variant33-variant34-variant35-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:56,42:98:99:1516,0,2145:29,27,28,14 chr1 248458760 . C A 3334.73 PASS AC=1;AF=0.533;AN=2;DP=2340;set=variant3-variant8-variant11-variant13-variant15-variant16-variant17-variant25-variant33-variant34-variant35-variant39-variant40-filterInvariant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:67,54:121:99:1745,0,2406:32,35,30,24 chr1 248458875 . CT C 3134.22 PASS AC=1;AF=0.538;AN=2;DP=2058;set=variant3-variant8-variant11-variant13-variant15-variant16-variant17-variant25-variant33-variant35-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:61,75:136:99:2600,0,2050:29,32,35,40 chr1 248458974 . T A 374.48 PASS AC=2;AF=0.767;AN=2;DP=2414;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1425,137,0:0,0,15,31 chr1 248486895 . G T 1268.48 PASS AC=2;AF=0.779;AN=2;DP=6591;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,174:174:99:5210,521,0:0,0,105,69 chr1 248486913 . A G 1859.91 PASS AC=2;AF=0.779;AN=2;DP=7850;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,197:197:99:6031,591,0:0,0,118,79 chr1 248487016 . C T 4114.73 PASS AC=1;AF=0.538;AN=2;DP=3345;MQ=60;set=variant3-variant8-variant11-variant13-variant15-variant16-variant17-variant25-variant33-variant35-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:115,131:246:99:3378,0,3190:56,59,63,68 chr1 248487300 . C T 4295.81 PASS AC=1;AF=0.667;AN=2;DP=11759;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:172,208:380:99:5561,0,4612:91,81,97,111 chr1 248487338 . C A 4676.93 PASS AC=2;AF=0.779;AN=2;DP=13757;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,384:384:99:12629,1151,0:0,0,200,184 chr1 248487638 . A G 2425 PASS AC=2;AF=0.779;AN=2;DP=7878;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,203:203:99:7041,609,0:0,0,85,118 chr1 248487768 . A G 4116.89 PASS AC=2;AF=0.779;AN=2;DP=13893;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,343:344:99:11061,986,0:1,0,208,135 chr1 248512064 . T G 743.03 PASS AC=1;AF=0.722;AN=2;DP=2737;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,36:97:99:815,0,1501:34,27,22,14 chr1 248512094 . C T 1044.81 PASS AC=1;AF=0.722;AN=2;DP=3539;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:75,47:122:99:1061,0,2030:44,31,27,20 chr1 248512498 . A G 3032.32 PASS AC=1;AF=0.538;AN=2;DP=2259;MQ=60;set=variant3-variant8-variant11-variant13-variant15-variant16-variant17-variant25-variant33-variant35-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:100,93:193:99:2165,0,2776:43,57,38,55 chr1 248512637 . C T 1707.64 PASS AC=1;AF=0.722;AN=2;DP=4299;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:75,88:163:99:2368,0,1724:39,36,39,49 chr1 248512749 . G A 1104.68 PASS AC=1;AF=0.722;AN=2;DP=3048;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:71,50:121:99:1356,0,1899:33,38,28,22 chr1 248512767 . G T 996.32 PASS AC=1;AF=0.722;AN=2;DP=2964;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:62,52:114:99:1439,0,1680:31,31,30,22 chr1 248513023 . G A 2666.08 PASS AC=1;AF=0.722;AN=2;DP=7753;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:85,107:192:99:2753,0,1888:40,45,48,59 chr1 248513088 . G C 1680.01 PASS AC=1;AF=0.722;AN=2;DP=4560;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,68:118:99:1786,0,1158:18,32,23,45 chr1 248524937 . ATGGGACTCTTCAGACAATCCAAACATCCAATGGCCAATATCACCTGGATGGCCAACCACACTGGATGGTCGGATTTCATCCTGT A 1112.25 PASS AC=1;AF=0.5;AN=2;DP=3344;set=variant3-variant11-filterInvariant15-variant16-variant17-variant25-variant33-variant35-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:250,51:301:99:1304,0,10282:142,108,19,32 chr1 248525053 . A T 1347.63 PASS AC=1;AF=0.5;AN=2;DP=2696;set=variant3-variant11-variant15-variant16-variant17-variant25-variant33-variant35-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:222,41:263:99:1342,0,9376:114,108,9,32 chr1 248525060 . T A 1105.68 PASS AC=1;AF=0.5;AN=2;DP=2730;set=variant3-variant11-variant15-variant16-variant17-variant25-variant33-variant35-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:220,44:264:99:1278,0,9304:114,106,13,31 chr1 248525071 . T C 1171.66 PASS AC=1;AF=0.5;AN=2;DP=2734;set=variant3-variant11-variant15-variant16-variant17-variant25-variant33-variant35-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:204,51:255:99:1366,0,8500:110,94,21,30 chr1 248525146 . C T 2767.74 PASS AC=1;AF=0.5;AN=2;DP=3878;set=variant3-variant11-variant13-variant15-variant16-variant17-filterInvariant25-filterInvariant33-variant35-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:260,68:328:99:877,0,7212:143,117,30,38 chr1 248525193 . C T 1140.84 PASS AC=1;AF=0.5;AN=2;DP=4397;FractionInformativeReads=1;set=variant3-variant11-variant13-variant15-variant16-filterInvariant17-filterInvariant25-filterInvariant33-variant35-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:297,68:365:99:778,0,7855:153,144,36,32 chr1 248525285 . T C 1240.15 PASS AC=1;AF=0.5;AN=2;DP=3624;set=variant3-variant11-variant13-variant15-variant16-variant17-variant25-variant33-variant35-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:272,38:310:99:749,0,12734:116,156,31,7 chr1 248525290 . C T 1342.2 PASS AC=1;AF=0.5;AN=2;DP=3559;FractionInformativeReads=1;set=variant3-variant11-variant13-variant15-variant16-variant17-variant25-variant33-filterInvariant35-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:258,40:298:99:976,0,12603:110,148,35,5 chr1 248525291 . G C 1354.2 PASS AC=1;AF=0.5;AN=2;DP=3561;FractionInformativeReads=1;set=variant3-variant11-variant13-variant15-variant16-variant17-variant25-variant33-filterInvariant35-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:257,42:299:99:994,0,12423:110,147,36,6 chr1 248525328 . C CTA 3228.05 PASS AC=1;AF=0.5;AN=2;DP=3398;set=variant3-variant11-variant13-variant15-variant16-variant17-variant25-variant33-variant35-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:190,77:267:99:2738,0,9578:79,111,53,24 chr1 248525330 . A G 3236.87 PASS AC=1;AF=0.5;AN=2;DP=3409;set=variant3-variant11-variant13-variant15-variant16-variant17-variant25-variant33-variant35-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:191,79:270:99:2738,0,9578:80,111,55,24 chr1 248525638 . CA C 3333.65 PASS AC=1;AF=0.654;AN=2;DP=10718;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:132,113:245:99:3832,0,5187:59,73,51,62 chr1 248525647 . C A 5317.48 PASS AC=1;AF=0.5;AN=2;DP=3090;set=variant3-variant11-variant13-variant15-variant16-variant17-variant25-variant33-variant35-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:117,122:239:99:4762,0,4706:54,63,52,70 chr1 248525650 . C T 5331.36 PASS AC=1;AF=0.5;AN=2;DP=3044;set=variant3-variant11-variant13-variant15-variant16-variant17-variant25-variant33-variant35-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:117,121:238:99:4749,0,4588:52,65,52,69 chr1 248525657 . G A 5040.51 PASS AC=1;AF=0.5;AN=2;DP=2934;set=variant3-variant11-variant13-variant15-variant16-variant17-variant25-variant33-variant35-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:117,116:233:99:4455,0,4612:53,64,51,65 chr1 248525780 . C T 2931.17 PASS AC=1;AF=0.5;AN=2;DP=1944;set=variant3-variant11-variant13-variant15-variant16-variant17-variant25-variant33-variant35-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:60,70:130:99:1902,0,1676:30,30,36,34 chr1 248550894 . T G 1021.13 PASS AC=1;AF=0.5;AN=2;DP=895;FractionInformativeReads=1;MQ=60;set=variant3-variant11-variant13-variant15-variant16-variant17-variant25-variant33-variant35-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:51,34:85:99:809,0,1395:34,17,20,14 chr1 248550970 . A G 2144.89 PASS AC=1;AF=0.5;AN=2;DP=1770;MQ=60;set=variant3-variant11-variant13-variant15-variant16-variant17-variant25-variant33-variant35-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:101,54:155:99:1057,0,2641:59,42,29,25 chr1 248550976 . T G 1616.15 PASS AC=2;AF=0.75;AN=2;DP=6050;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,157:157:99:5534,471,0:0,0,87,70 chr1 248551203 . T C 1473.14 PASS AC=1;AF=0.5;AN=2;DP=1080;FractionInformativeReads=1;MQ=60;set=variant3-variant11-variant13-variant15-variant16-variant17-variant25-variant33-variant35-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:41,45:86:99:1156,0,1251:13,28,19,26 chr1 248551560 . C T 3275.94 PASS AC=1;AF=0.5;AN=2;DP=2776;MQ=60;set=variant3-variant11-variant13-variant15-variant16-variant17-variant25-variant33-variant35-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:133,130:263:99:3104,0,3178:68,65,75,55 chr1 248551636 . T G 2849.97 PASS AC=1;AF=0.5;AN=2;DP=2728;MQ=60;set=variant3-variant11-variant13-variant15-variant16-variant17-variant25-variant33-variant35-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:106,114:220:99:2958,0,2547:47,59,52,62 chr1 248551955 . C A 354.12 PASS AC=1;AF=0.5;AN=2;DP=238;FractionInformativeReads=1;MQ=60;set=variant3-variant11-variant13-variant15-variant16-variant17-variant25-variant33-variant35-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:20,7:27:99:190,0,683:3,17,3,4 chr1 248569282 . A G 882.65 PASS AC=1;AF=0.615;AN=2;DP=2235;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,23:67:99:589,0,1174:29,15,17,6 chr1 248569369 . A G 1955.64 PASS AC=1;AF=0.618;AN=2;DP=5439;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:80,72:152:99:1672,0,1941:47,33,43,29 chr1 248570440 . G A 684.34 PASS AC=2;AF=0.86;AN=2;DP=3269;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:2512,237,0:0,0,30,49 chr1 248570551 . A AGAGT 481.3 PASS AC=1;AF=0.763;AN=2;DP=1056;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,12:25:99:446,0,1213:4,9,1,11 chr1 248570553 . A AT 481.3 PASS AC=1;AF=0.763;AN=2;DP=967;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,10:23:99:446,0,1213:4,9,1,9 chr1 248604452 . A G 644.75 PASS AC=1;AF=0.515;AN=2;DP=1192;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant21-filterInvariant22-variant23-variant24-variant25-variant26-variant27-variant28-filterInvariant29-variant31-variant32-variant34-variant35-variant37-filterInvariant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:15,13:28:99:469,0,609:11,4,10,3 chr1 248604465 . C T 1098.17 PASS AC=1;AF=0.537;AN=2;DP=1608;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-filterInvariant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:16,11:27:99:414,0,598:10,6,8,3 chr1 248604542 . C T 995.3 PASS AC=1;AF=0.565;AN=2;DP=1273;FractionInformativeReads=1;set=variant-variant2-variant3-variant7-variant8-variant9-variant10-variant11-filterInvariant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-filterInvariant25-variant27-variant28-variant30-variant32-variant34-variant35-variant36-variant37-variant38-variant39-filterInvariant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:13,9:22:99:224,0,381:5,8,0,9 chr1 248604559 . T TTC 579.08 PASS AC=2;AF=0.913;AN=2;DP=1076;set=variant2-filterInvariant3-variant4-variant5-variant6-variant8-variant9-filterInvariant10-variant11-variant12-variant13-variant14-variant15-variant16-filterInvariant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:42:613,42,0:0,0,0,13 chr1 248604614 . A T 294.6 PASS AC=1;AF=0.533;AN=2;DP=893;FractionInformativeReads=1;set=variant2-variant4-variant5-variant6-variant8-variant11-filterInvariant12-filterInvariant14-variant15-variant16-filterInvariant17-variant18-variant19-variant22-variant23-variant24-variant25-filterInvariant26-filterInvariant27-variant28-filterInvariant29-variant32-filterInvariant33-variant35-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,16:25:99:384,0,237:2,7,7,9 chr1 248604694 . C T 169.39 PASS AC=1;AF=0.5;AN=2;DP=380;set=filterInvariant2-variant4-variant5-filterInvariant7-variant8-filterInvariant13-filterInvariant24-filterInvariant26-filterInvariant29-variant34-variant35-variant36-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,12:24:99:317,0,270:8,4,8,4 chr1 248604765 . T A 923.37 PASS AC=1;AF=0.709;AN=2;DP=3056;set=variant-variant2-variant3-variant4-filterInvariant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-filterInvariant23-variant24-variant25-filterInvariant26-variant27-variant28-filterInvariant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-filterInvariant37-variant38-variant39-filterInvariant40-variant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:25,49:74:99:1036,0,559:18,7,22,27 chr1 248605395 . T G 1434.62 PASS AC=1;AF=0.5;AN=2;DP=1415;FractionInformativeReads=1;set=variant-variant4-variant8-variant11-variant15-variant17-variant25-variant35-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:64,72:136:99:1882,0,1457:24,40,30,42 chr1 248605436 . C G 2239.47 PASS AC=1;AF=0.692;AN=2;DP=2792;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,28:78:99:1005,0,2030:19,31,7,21 chr1 248605442 . G T 598.84 PASS AC=1;AF=0.688;AN=2;DP=2548;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,26:75:99:944,0,1959:18,31,7,19 chr1 248637046 . G A 526.8 PASS AC=1;AF=0.5;AN=2;DP=2895;set=filterInvariant-filterInvariant3-filterInvariant4-variant7-filterInvariant8-variant9-variant10-filterInvariant15-filterInvariant17-filterInvariant20-filterInvariant22-filterInvariant25-filterInvariant28-filterInvariant30-filterInvariant34-variant35-filterInvariant37-variant38-filterInvariant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:66,52:118:99:998,0,1501:28,38,20,32 chr1 248637362 . C T 1472.62 PASS AC=1;AF=0.5;AN=2;DP=5807;set=variant-variant3-variant4-variant7-variant8-filterInvariant9-filterInvariant10-variant15-variant17-variant20-variant22-variant25-variant28-filterInvariant30-variant34-variant35-variant37-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:195,58:253:99:984,0,5536:103,92,38,20 chr1 248637416 . G C 2062.76 PASS AC=1;AF=0.5;AN=2;DP=3986;set=variant-variant4-variant8-variant15-variant16-variant17-variant25-variant28-filterInvariant33-filterInvariant34-variant35-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:251,113:364:99:3913,0,11688:141,110,68,45 chr1 248637417 . C T 2269.88 PASS AC=1;AF=0.5;AN=2;DP=3990;set=variant-variant4-variant8-variant15-variant16-variant17-variant25-variant28-filterInvariant33-filterInvariant34-variant35-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:248,113:361:99:3913,0,11688:139,109,67,46 chr1 248637543 . C T 1587.17 PASS AC=1;AF=0.5;AN=2;DP=5908;set=variant-variant3-variant4-variant7-variant8-variant9-variant10-variant15-variant17-variant20-variant22-variant25-variant28-variant30-variant34-variant35-variant37-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:262,94:356:99:1647,0,6356:113,149,35,59 chr1 248637685 . T C 183.34 PASS AC=1;AF=0.5;AN=2;DP=580;set=variant-filterInvariant3-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant14-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant20-filterInvariant22-filterInvariant28-filterInvariant30-filterInvariant33-filterInvariant34-filterInvariant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:30,6:36:85:85,0,822:4,26,0,6 chr1 248651927 . A G 126.09 PASS AC=2;AF=0.975;AN=2;DP=74;FS=0;set=variant4-filterInvariant5-filterInvariant8-filterInvariant9-filterInvariant13-filterInvariant16-filterInvariant23-filterInvariant24-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant29-filterInvariant32-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant39-filterInvariant40-filterInvariant42-filterInvariant44 GT:AD:DP:GQ:PL:SB 1/1:1,4:5:5:83,5,0:1,0,2,2 chr1 248685253 . T C 3123.29 PASS AC=2;AF=1;AN=2;DP=7063;FS=0;MQ=60;MQRankSum=0.584;ReadPosRankSum=0.793;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,195:195:99:5879,585,0:0,0,96,99 chr1 248722611 . C G 53.02 PASS AC=1;AF=0.725;AN=2;DP=460;FractionInformativeReads=1;set=filterInvariant-filterInvariant3-variant7-variant8-filterInvariant11-filterInvariant13-variant14-filterInvariant15-variant16-filterInvariant17-variant21-variant22-filterInvariant25-filterInvariant33-filterInvariant35-variant36-filterInvariant39-filterInvariant40-filterInvariant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:4,11:15:99:475,0,161:4,0,7,4 chr1 248722613 . G A 743.77 PASS AC=1;AF=0.5;AN=2;DP=274;FractionInformativeReads=1;set=filterInvariant3-filterInvariant11-filterInvariant13-filterInvariant15-variant16-filterInvariant17-filterInvariant25-filterInvariant33-filterInvariant35-filterInvariant39-filterInvariant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:5,12:17:99:475,0,161:5,0,8,4 chr1 248722671 . T A 296.4 PASS AC=1;AF=0.759;AN=2;DP=1188;set=filterInvariant-variant3-filterInvariant4-variant7-variant8-variant9-filterInvariant10-variant11-variant13-variant14-variant15-variant16-variant17-filterInvariant20-variant21-variant22-filterInvariant25-filterInvariant28-variant33-filterInvariant34-variant35-variant36-filterInvariant37-variant39-variant40-filterInvariant41-filterInvariant42 GT:AD:DP:GQ:PL:SB 0/1:13,30:43:99:598,0,300:13,0,15,15 chr1 248722722 . T C 654.17 PASS AC=1;AF=0.833;AN=2;DP=908;set=variant-variant2-variant3-variant4-filterInvariant5-filterInvariant6-filterInvariant8-variant9-variant10-variant11-filterInvariant12-filterInvariant13-variant15-variant17-filterInvariant18-variant19-filterInvariant20-variant21-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant26-variant27-filterInvariant28-variant29-variant30-filterInvariant31-filterInvariant32-variant33-filterInvariant34-variant35-variant37-filterInvariant38-variant39-variant40-variant41-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,15:43:99:377,0,1070:13,15,15,0 chr1 248722739 . G C 1173.33 PASS AC=1;AF=0.5;AN=2;DP=673;set=variant3-variant11-variant15-variant16-variant17-variant25-variant33-variant35-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:25,25:50:99:859,0,1059:15,10,10,15 chr1 248722752 . A G 994.78 PASS AC=1;AF=0.5;AN=2;DP=722;FractionInformativeReads=1;set=variant3-variant11-variant15-variant16-variant17-variant25-variant33-variant35-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:33,20:53:99:717,0,1367:16,17,9,11 chr1 248722756 . T A 838.05 PASS AC=1;AF=0.5;AN=2;DP=728;FractionInformativeReads=1;set=variant3-variant11-variant15-variant16-variant17-variant25-variant33-variant35-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:35,19:54:99:689,0,1454:16,19,8,11 chr1 248722767 . T C 838.05 PASS AC=1;AF=0.5;AN=2;DP=722;set=variant3-variant11-variant15-filterInvariant16-variant17-variant25-variant33-variant35-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:34,16:50:99:611,0,1376:14,20,6,10 chr1 248722777 . T A 1274.98 PASS AC=1;AF=0.621;AN=2;DP=1980;FractionInformativeReads=1;set=variant-variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant25-variant28-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-filterInvariant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,15:50:99:518,0,1508:15,20,5,10 chr1 248722788 . G T 742.03 PASS AC=1;AF=0.5;AN=2;DP=713;FractionInformativeReads=1;set=variant3-variant11-variant15-filterInvariant16-variant17-variant25-variant33-variant35-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:39,14:53:99:512,0,1582:17,22,4,10 chr1 248722812 . C A 277.19 PASS AC=1;AF=0.5;AN=2;DP=231;FractionInformativeReads=1;set=variant3-filterInvariant33-filterInvariant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:35,3:38:60:60,0,1444:12,23,0,3 chr1 248737095 . T C 31.26 DRAGENHardSNP AC=2;AF=1;AN=2;DP=4;FS=0;FractionInformativeReads=1;SOR=2.303;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:64,6,0:0,0,2,0 chr1 248737167 . G A 53.22 PASS AC=1;AF=0.5;AN=2;DP=8;FS=0;FractionInformativeReads=1;MQ=34.97;MQRankSum=0.322;QD=6.65;ReadPosRankSum=-1.92;SOR=0.368;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:5,3:8:81:81,0,154:5,0,3,0 chr1 248737259 . C G 234.87 PASS AC=2;AF=1;AN=2;DP=1531;FS=0;FractionInformativeReads=1;set=filterInvariant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-filterInvariant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:2028,159,0:0,0,53,0 chr1 248737293 . G A 37.47 PASS AC=1;AF=0.5;AN=2;DP=1774;set=filterInvariant-filterInvariant4-variant7-filterInvariant8-variant14-variant15-variant16-variant17-variant22-filterInvariant25-variant28-variant33-variant34-filterInvariant35-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:123,13:136:99:199,0,5156:94,29,13,0 chr1 248737294 . C G 37.47 PASS AC=1;AF=0.5;AN=2;DP=1807;set=filterInvariant-filterInvariant4-variant7-filterInvariant8-variant14-variant15-variant16-variant17-variant22-filterInvariant25-variant28-variant33-variant34-filterInvariant35-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:125,14:139:99:199,0,5156:96,29,14,0 chr1 248737343 . C T 1126.48 PASS AC=1;AF=0.525;AN=2;DP=3630;FractionInformativeReads=1;set=variant-variant3-variant4-variant7-variant8-variant9-variant10-variant15-variant17-variant20-variant22-variant25-variant28-variant30-variant34-filterInvariant35-variant37-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:240,52:292:99:602,0,9926:150,90,36,16 chr1 248737348 . G A 1166.94 PASS AC=1;AF=0.521;AN=2;DP=5309;set=variant-variant3-variant4-variant7-variant8-variant9-variant10-variant14-variant15-variant16-variant17-variant20-variant22-variant25-variant28-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:251,60:311:99:1582,0,6623:156,95,40,20 chr1 248737595 . A G 1419.43 PASS AC=1;AF=0.542;AN=2;DP=2044;set=variant-variant3-variant4-variant7-variant8-variant9-variant10-variant14-variant15-variant16-variant17-variant20-variant22-variant25-variant28-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:76,40:116:99:1031,0,2456:12,64,3,37 chr1 248738133 . A G 329.2 PASS AC=1;AF=0.515;AN=2;DP=2022;set=variant2-variant3-variant4-variant5-filterInvariant6-variant7-filterInvariant8-variant9-variant10-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,15:69:99:265,0,1640:13,41,4,11 chr1 248789454 . G C 2187.96 PASS AC=2;AF=0.988;AN=2;DP=4658;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,128:128:99:4068,384,0:0,0,80,48 chr1 248789504 . T C 3578.24 PASS AC=2;AF=0.988;AN=2;DP=6829;MQ=60;MQRankSum=1.326;ReadPosRankSum=-1.148;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,207:207:99:6668,620,0:0,0,123,84 chr1 248790075 . A G 2114.34 PASS AC=2;AF=1;AN=2;DP=6588;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,188:188:99:5618,563,0:0,0,96,92 chr1 248801528 . G A 1513.35 PASS AC=2;AF=0.86;AN=2;DP=663;FractionInformativeReads=1;set=variant4-variant6-variant8-variant12-variant13-variant14-variant15-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,30:32:12:1350,12,0:0,2,26,4 chr1 248801538 . G A 1936.26 PASS AC=2;AF=0.86;AN=2;DP=841;FractionInformativeReads=1;set=variant4-variant6-variant8-variant12-variant13-variant14-variant15-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,43:45:48:1890,48,0:0,2,34,9 chr1 248801542 . A G 2146.21 PASS AC=2;AF=0.86;AN=2;DP=910;FractionInformativeReads=1;set=variant4-variant6-variant8-variant12-variant13-variant14-variant15-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,46:48:57:2025,57,0:0,2,35,11 chr1 248801550 . C T 2314.17 PASS AC=2;AF=0.88;AN=2;DP=1071;FractionInformativeReads=1;set=variant4-variant6-variant8-variant12-variant13-variant14-variant15-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,51:53:73:2250,73,0:0,2,39,12 chr1 248801556 . C T 2572.13 PASS AC=2;AF=0.88;AN=2;DP=1215;FS=0;FractionInformativeReads=1;set=variant4-variant6-variant8-variant12-variant13-variant14-variant15-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,62:64:99:2790,109,0:0,2,43,19 chr1 248801566 . T G 3256.77 PASS AC=2;AF=0.9;AN=2;DP=1429;FS=0;FractionInformativeReads=1;set=variant4-variant6-variant8-variant12-variant13-variant14-variant15-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,73:75:99:3240,139,0:0,2,49,24 chr1 248801592 . C T 3796.77 PASS AC=2;AF=0.96;AN=2;DP=1742;FractionInformativeReads=1;set=variant4-variant6-variant8-variant12-variant13-variant14-variant15-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,87:89:99:3870,181,0:0,2,49,38 chr1 248801602 . T TCA 3922.73 PASS AC=2;AF=0.96;AN=2;DP=1749;FractionInformativeReads=1;set=variant4-variant6-variant8-variant12-variant13-variant14-variant15-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,89:90:99:4005,229,0:0,1,47,42 chr1 248801610 . G A 3776.43 PASS AC=2;AF=0.96;AN=2;DP=1743;FractionInformativeReads=1;set=variant4-variant6-variant8-variant12-variant13-variant14-variant15-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,89:90:99:3960,226,0:0,1,46,43 chr1 248801611 . C T 3776.43 PASS AC=2;AF=0.96;AN=2;DP=1746;FractionInformativeReads=1;set=variant4-variant6-variant8-variant12-variant13-variant14-variant15-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,89:90:99:3960,226,0:0,1,46,43 chr1 248801633 . A G 3515.09 PASS AC=2;AF=0.96;AN=2;DP=1703;FractionInformativeReads=1;set=variant4-variant6-variant8-variant12-variant13-variant14-variant15-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,88:88:99:3964,271,0:0,0,40,48 chr1 248801778 . A T 201.26 PASS AC=1;AF=0.866;AN=2;DP=982;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant5-variant6-filterInvariant7-variant8-variant11-variant12-variant13-filterInvariant14-filterInvariant15-variant16-variant17-filterInvariant18-variant19-filterInvariant20-filterInvariant21-variant22-filterInvariant23-variant24-variant25-filterInvariant26-variant27-variant28-variant29-filterInvariant30-variant31-variant32-variant33-filterInvariant34-variant35-variant36-variant37-filterInvariant38-filterInvariant39-filterInvariant40-filterInvariant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,21:30:99:566,0,192:8,1,11,10 chr1 248801897 . G A 1214.52 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=2749;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:287,139:426:99:2233,0,6022:156,131,75,64 chr1 248801944 . TCAGCACG T 2326.05 PASS AC=1;AF=0.89;AN=2;DP=9772;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:138,273:411:99:10825,0,4875:62,76,122,151 chr1 248802249 . T TAGA 97.32 PASS AC=2;AF=1;AN=2;DP=52;FS=0;set=variant-variant3-variant4-variant7-variant8-variant14-variant16-variant17-variant20-variant22-variant25-variant33-variant34-variant35-variant36-variant39-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:12:180,12,0:0,0,3,0 chr1 248813135 . G A 220.3 PASS AC=2;AF=0.964;AN=2;DP=876;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:883,75,0:0,0,20,5 chr1 248813547 . G C 155.83 PASS AC=2;AF=0.959;AN=2;DP=237;FS=0;FractionInformativeReads=1;set=variant-variant2-variant3-variant5-variant6-filterInvariant7-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-filterInvariant38-variant39-variant40-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:365,30,0:0,0,0,10 chr1 248813901 . A T 56.5 PASS AC=1;AF=0.706;AN=2;DP=478;FractionInformativeReads=1;set=variant-filterInvariant2-variant4-filterInvariant7-variant8-variant10-variant13-variant14-variant19-variant24-filterInvariant25-variant28-variant29-variant31-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:2,3:5:34:98,0,34:1,1,3,0 chr1 248814052 . T A 736.97 PASS AC=1;AF=0.524;AN=2;DP=4177;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-filterInvariant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,91:107:75:2391,0,75:8,8,59,32 chr1 248814080 . A C 1679.89 PASS AC=2;AF=0.989;AN=2;DP=5461;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,139:139:99:3723,414,0:0,0,76,63 chr1 248814126 . G A 409.82 PASS AC=1;AF=0.526;AN=2;DP=5178;set=variant-variant2-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,136:155:26:3153,0,26:10,9,61,75 chr1 248814265 . GAAC G 188.63 PASS AC=2;AF=1;AN=2;DP=138;FS=0;set=variant2-variant4-variant6-variant7-variant8-variant10-variant11-variant13-variant15-variant18-variant22-variant24-variant25-variant26-variant28-variant30-variant32-variant35-variant39-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:225,15,0:0,0,0,5 chr1 248814281 . AGTC A 52.73 PASS AC=2;AF=1;AN=2;DP=40;FS=0;FractionInformativeReads=1;set=variant2-variant6-variant10-variant11-variant13-variant15-variant25-variant26-variant30-variant32-variant35-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:180,12,0:0,0,0,4 chr1 248814285 . G A 151.77 PASS AC=2;AF=1;AN=2;DP=37;FS=0;FractionInformativeReads=1;set=variant6-filterInvariant10-filterInvariant11-variant13-filterInvariant15-filterInvariant25-variant26-filterInvariant30-variant32-filterInvariant35-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:180,12,0:0,0,0,4 chr1 248845097 . C T 1031.73 PASS AC=2;AF=0.86;AN=2;DP=9075;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,219:219:99:6435,655,0:0,0,114,105 chr1 248845411 . G A 1293.74 PASS AC=2;AF=0.849;AN=2;DP=7153;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,167:167:99:5156,501,0:0,0,81,86 chr1 248845458 . C T 1225.31 PASS AC=2;AF=0.849;AN=2;DP=6258;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,147:147:99:6370,445,0:0,0,70,77 chr1 248845471 . T C 3429.76 PASS AC=2;AF=0.977;AN=2;DP=6063;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,139:139:99:6086,424,0:0,0,66,73 chr1 248845499 . A G 3284.77 PASS AC=2;AF=0.988;AN=2;DP=6110;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,133:134:99:3961,359,0:1,0,63,70 chr1 249110906 . G C 670.23 PASS AC=1;AF=0.805;AN=2;DP=3287;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,52:102:99:1316,0,1196:23,27,29,23 chr1 249120088 . T C 346.72 PASS AC=1;AF=0.5;AN=2;DP=721;MQ=60;set=variant2-variant3-variant5-variant6-variant7-filterInvariant11-variant13-variant19-variant20-variant23-filterInvariant24-filterInvariant25-variant29-variant31-variant32-filterInvariant35-variant36-variant37-variant39-filterInvariant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:32,20:52:99:418,0,602:5,27,20,0 chr1 249120092 . T C 340.7 PASS AC=1;AF=0.5;AN=2;DP=757;MQ=60;set=variant2-variant3-variant5-variant6-variant7-filterInvariant11-variant13-filterInvariant19-variant20-variant23-filterInvariant24-variant25-variant29-variant31-variant32-variant35-variant36-variant37-variant39-filterInvariant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:38,14:52:99:214,0,2189:10,28,14,0 chr1 249120097 . G C 327.73 PASS AC=1;AF=0.5;AN=2;DP=713;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant11-variant13-variant19-filterInvariant20-variant23-filterInvariant24-variant25-variant29-variant35-variant36-variant37-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:38,12:50:99:211,0,2221:9,29,12,0 chr1 249120099 . A C 327.73 PASS AC=1;AF=0.5;AN=2;DP=492;MQ=60;set=variant2-variant5-variant7-variant13-variant19-variant23-variant24-variant25-variant29-variant35-variant36-filterInvariant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:39,7:46:99:200,0,2204:10,29,7,0 chr1 249120759 . G C 1404.37 PASS AC=1;AF=0.5;AN=2;DP=90;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.32;QD=15.6;ReadPosRankSum=-0.5;SOR=0.62;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:37,53:90:99:1433,0,986:16,21,24,29 chr2 38938 . A C 2779.6 PASS AC=1;AF=0.538;AN=2;DP=3785;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant9-variant11-variant15-variant18-variant20-variant25-variant27-variant33-variant35-variant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:162,128:290:99:3071,0,3970:97,65,78,50 chr2 39356 . C T 135.3 PASS AC=1;AF=0.55;AN=2;DP=110;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant9-variant11-variant15-variant18-variant20-variant25-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:5,8:13:99:277,0,144:2,3,6,2 chr2 45895 . A G 2476.03 PASS AC=2;AF=1;AN=2;DP=3360;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,85:85:99:3120,255,0:0,0,46,39 chr2 218386 . G A 4660.11 PASS AC=1;AF=0.583;AN=2;DP=6008;set=variant-variant3-variant4-variant5-variant8-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant35-variant36-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:145,135:280:99:3739,0,4069:92,53,83,52 chr2 224919 . A G 278.67 PASS AC=1;AF=0.587;AN=2;DP=1426;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant13-variant14-variant15-variant16-variant17-variant18-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant35-variant36-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:41,20:61:99:325,0,970:22,19,11,9 chr2 224970 . C T 252.65 PASS AC=1;AF=0.726;AN=2;DP=2304;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,12:46:99:253,0,890:16,18,4,8 chr2 230912 . A C 582.19 PASS AC=1;AF=0.583;AN=2;DP=886;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant35-variant36-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:26,27:53:99:788,0,596:17,9,19,8 chr2 233416 . G A 186.83 PASS AC=1;AF=0.5;AN=2;DP=338;FractionInformativeReads=1;MQ=60;set=variant8-variant9-variant11-variant15-variant19-variant21-variant25-variant27-variant29-variant33-variant35-variant37-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:17,6:23:99:171,0,654:1,16,0,6 chr2 239969 . C T 311.73 PASS AC=1;AF=0.583;AN=2;DP=1506;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant35-variant36-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:36,40:76:99:1033,0,890:22,14,20,20 chr2 240054 . A G 246.09 PASS AC=1;AF=0.726;AN=2;DP=3172;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,46:101:99:1224,0,1302:26,29,26,20 chr2 240255 . A C 220.43 PASS AC=2;AF=0.909;AN=2;DP=1985;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,69:69:99:2038,205,0:0,0,31,38 chr2 240785 . G A 764.37 PASS AC=1;AF=0.559;AN=2;DP=1317;MQ=60;set=variant8-variant9-variant11-variant15-variant17-variant19-variant21-variant25-variant27-variant29-variant32-variant33-variant34-variant35-variant37-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:35,48:83:99:1211,0,848:15,20,23,25 chr2 242132 . G A 556.45 PASS AC=1;AF=0.583;AN=2;DP=1568;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant35-variant36-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:43,26:69:99:521,0,1052:28,15,17,9 chr2 242732 . T TAAC 361.66 PASS AC=1;AF=0.726;AN=2;DP=1039;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,12:27:99:459,0,618:12,3,7,5 chr2 242793 . G C 453.01 PASS AC=1;AF=0.575;AN=2;DP=1092;MQ=60;set=variant-variant3-variant4-variant8-variant13-variant14-variant16-variant17-variant18-variant23-variant26-variant27-variant29-variant30-variant31-variant35-variant36-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:27,29:56:99:694,0,632:16,11,16,13 chr2 243567 . T TA 701.61 PASS AC=1;AF=0.726;AN=2;DP=3096;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,35:61:99:794,0,552:13,13,20,15 chr2 244568 . AAAAG A,AAAAGAAAG 410.16 PASS AC=0,1;AF=0.098,0.72;AN=2;DP=728;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:24:99:8,4,10,2 chr2 256116 . G T 46.72 PASS AC=1;AF=0.632;AN=2;DP=140;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant8-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant23-variant28-variant30-variant31-variant35-variant36-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:5,3:8:99:111,0,163:4,1,3,0 chr2 260594 . A G 3382.66 PASS AC=2;AF=1;AN=2;DP=4427;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,97:97:99:3240,291,0:0,0,63,34 chr2 262553 . T C 356.03 PASS AC=1;AF=0.726;AN=2;DP=1793;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,29:63:99:611,0,840:21,13,16,13 chr2 263270 . T C 43.64 PASS AC=2;AF=0.909;AN=2;DP=878;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:668,75,0:0,0,14,11 chr2 264019 . C A 1066.81 PASS AC=1;AF=0.583;AN=2;DP=1948;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant35-variant36-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:39,38:77:99:1030,0,998:17,22,15,23 chr2 264227 . G A 274.02 PASS AC=1;AF=0.583;AN=2;DP=533;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant35-variant36-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:24,27:51:99:548,0,593:9,15,12,15 chr2 264895 . G C 5057.32 PASS AC=2;AF=1;AN=2;DP=9392;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,247:247:99:8100,740,0:0,0,146,101 chr2 271797 . G A 469.06 PASS AC=1;AF=0.583;AN=2;DP=788;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant35-variant36-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:18,12:30:99:266,0,505:13,5,7,5 chr2 271998 . CAA CA,CAAA,C 437.47 PASS AC=1,0,0;AF=0.43,0.244,0.07;AN=2;DP=3458;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-filterInvariant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:69:18:5,4,34,26 chr2 272203 . C T 965.19 PASS AC=1;AF=0.587;AN=2;DP=3353;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant13-variant14-variant15-variant16-variant17-variant18-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant35-variant36-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:82,53:135:99:1182,0,2271:37,45,27,26 chr2 272840 . G A 2390.7 PASS AC=1;AF=0.726;AN=2;DP=5597;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:83,64:147:99:1601,0,2380:39,44,25,39 chr2 272926 . A G 2057.02 PASS AC=1;AF=0.726;AN=2;DP=4786;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:79,62:141:99:1555,0,2084:39,40,33,29 chr2 273070 . A G 1232.89 PASS AC=2;AF=0.909;AN=2;DP=4491;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,111:111:99:3332,333,0:0,0,43,68 chr2 277003 . A G 981.35 PASS AC=1;AF=0.583;AN=2;DP=843;set=variant-variant3-variant4-variant5-variant8-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant35-variant36-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:27,21:48:99:751,0,784:20,7,19,2 chr2 277995 . A G 1864.43 PASS AC=1;AF=0.536;AN=2;DP=2273;set=variant8-variant9-variant11-variant15-variant19-variant21-variant25-variant27-variant29-variant33-variant35-variant37-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:90,93:183:99:2198,0,2264:50,40,51,42 chr2 283231 . A AT 133.32 PASS AC=2;AF=0.919;AN=2;DP=1231;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:771,78,0:0,0,4,22 chr2 286756 . C G 147.97 PASS AC=1;AF=0.619;AN=2;DP=181;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant23-variant27-variant28-variant30-variant31-variant35-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:99:112,0,153:4,0,3,1 chr2 286812 . G A 296.33 PASS AC=2;AF=0.909;AN=2;DP=994;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:816,66,0:0,0,15,7 chr2 287448 . TAAAA T,TA,TAA 474.57 PASS AC=0,1,1;AF=0.372,0.512,0.012;AN=2;DP=1721;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 2/3:47:88:1,1,32,13 chr2 672745 . T C 389.81 PASS AC=2;AF=0.595;AN=2;DP=614;FractionInformativeReads=1;MQ=60;set=variant6-variant7-variant8-variant9-variant10-variant11-variant18-variant22-variant23-variant25-variant28-variant29-variant30-variant32-variant33-variant35-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1113,102,0:0,0,23,11 chr2 675831 . G T 1364.59 PASS AC=2;AF=0.685;AN=2;DP=1462;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant18-variant19-variant22-variant23-variant25-variant28-variant29-variant30-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:2356,186,0:0,0,16,46 chr2 676177 . C G,T 6102.17 PASS AC=2,0;AF=0.756,0.026;AN=2;DP=7939;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:DP:GQ:SB 1/1:172:99:0,0,68,104 chr2 676457 . G C 1166.38 PASS AC=2;AF=0.878;AN=2;DP=2484;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:3492,237,0:0,0,55,22 chr2 676478 . T TGTAA 1807.39 PASS AC=2;AF=0.866;AN=2;DP=3595;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,112:112:99:5244,352,0:0,0,79,33 chr2 677213 . G A 898.44 PASS AC=2;AF=0.866;AN=2;DP=1686;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:1479,140,0:0,0,31,16 chr2 905785 . C CAG 160.58 PASS AC=1;AF=0.5;AN=2;DP=81;FractionInformativeReads=1;set=variant8-variant35 GT:AD:DP:GQ:PL:SB 0/1:22,6:28:99:124,0,814:7,15,1,5 chr2 905889 . C G 262.33 PASS AC=2;AF=0.633;AN=2;DP=635;set=variant-variant6-variant8-variant12-variant17-variant20-variant21-variant23-variant25-variant27-variant29-variant32-variant33-variant35-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:643,51,0:0,0,10,7 chr2 905967 . A G 458.14 PASS AC=2;AF=0.75;AN=2;DP=1382;set=variant-variant2-variant4-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,22:24:36:696,36,0:0,2,9,13 chr2 947006 . T C 308.92 PASS AC=2;AF=1;AN=2;DP=282;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:448,42,0:0,0,5,9 chr2 1079130 . G A 2636.32 PASS AC=1;AF=0.757;AN=2;DP=2305;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,34:69:99:1397,0,1987:25,10,22,12 chr2 1079132 . G A 2636.32 PASS AC=1;AF=0.757;AN=2;DP=2382;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,37:73:99:1397,0,1987:26,10,24,13 chr2 1079143 . A G 804.84 PASS AC=1;AF=0.805;AN=2;DP=3028;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,41:81:99:895,0,1024:28,12,24,17 chr2 1079320 . C T 1059.38 PASS AC=1;AF=0.775;AN=2;DP=2683;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,37:72:99:837,0,929:11,24,16,21 chr2 1093965 . G A 3485.21 PASS AC=2;AF=0.724;AN=2;DP=4430;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,127:127:99:3866,381,0:0,0,68,59 chr2 1133188 . G GCACA 929.31 PASS AC=2;AF=0.716;AN=2;DP=1266;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:96:1424,96,0:0,0,26,4 chr2 1241592 . C T 401.36 PASS AC=2;AF=0.989;AN=2;DP=1399;MQ=60;MQRankSum=1.042;ReadPosRankSum=-0.347;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1207,99,0:0,0,27,6 chr2 1426621 . A G 351.75 PASS AC=2;AF=0.721;AN=2;DP=584;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:587,45,0:0,0,13,2 chr2 1426787 . G A 4090.47 PASS AC=1;AF=0.625;AN=2;DP=2625;MQ=60;set=variant4-variant11-variant12-variant14-variant17-variant18-variant19-variant20-variant21-variant24-variant26-variant29-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:83,65:148:99:1594,0,1950:44,39,36,29 chr2 1437410 . C T 255.13 PASS AC=1;AF=0.714;AN=2;DP=1000;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,16:29:99:503,0,443:1,12,3,13 chr2 1442551 . ATTTT ATTT,A,ATT,AT 264.11 PASS AC=1,0,0,0;AF=0.302,0.267,0.012,0.012;AN=2;DP=3817;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:DP:GQ:SB 0/1:81:99:13,7,35,26 chr2 1457364 . A G 1181.28 PASS AC=2;AF=0.955;AN=2;DP=2543;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:1814,171,0:0,0,41,16 chr2 1459806 . A G 434.7 PASS AC=2;AF=0.955;AN=2;DP=1054;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:1088,87,0:0,0,24,5 chr2 1460004 . G T 1975.83 PASS AC=1;AF=0.636;AN=2;DP=3116;MQ=60;set=variant-variant3-variant4-variant9-variant10-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,68:113:99:1676,0,1129:22,23,34,34 chr2 1460140 . A G 1172.29 PASS AC=1;AF=0.636;AN=2;DP=1761;MQ=60;set=variant-variant3-variant4-variant9-variant10-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,42:69:99:1138,0,680:11,16,18,24 chr2 1460220 . C T 183.07 PASS AC=1;AF=0.5;AN=2;DP=79;FractionInformativeReads=1;MQ=60;set=variant30-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:22,10:32:99:232,0,626:7,15,5,5 chr2 1460297 . C T 262.61 PASS AC=2;AF=0.963;AN=2;DP=342;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:334,27,0:0,0,2,7 chr2 1481231 . G C 1196.26 PASS AC=1;AF=0.653;AN=2;DP=2488;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,33:69:99:890,0,928:18,18,13,20 chr2 1488668 . T C 309.61 PASS AC=2;AF=0.635;AN=2;DP=1051;set=variant-variant2-variant3-variant4-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:908,72,0:0,0,5,19 chr2 1491497 . T C 476.5 PASS AC=2;AF=0.614;AN=2;DP=1635;set=variant-variant2-variant3-variant4-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:1769,161,0:0,0,39,15 chr2 1491510 . CA C,CAA 1003.77 PASS AC=1,1;AF=0.318,0.227;AN=2;DP=728;set=variant3-variant20-variant22-variant23-variant25-variant26-variant30-variant34-variant35-variant41-variant44 GT:DP:GQ:SB 1/2:62:99:1,2,38,21 chr2 1497442 . A G 481.1 PASS AC=2;AF=0.609;AN=2;DP=1764;set=variant-variant2-variant3-variant4-variant9-variant11-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:2099,171,0:0,0,40,17 chr2 1497803 . C T 464.73 PASS AC=2;AF=0.589;AN=2;DP=1484;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant9-variant11-variant14-variant15-variant16-variant17-variant18-variant21-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:1707,161,0:0,0,19,35 chr2 1499728 . C T 91.5 PASS AC=1;AF=0.58;AN=2;DP=318;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant9-variant11-variant14-variant15-variant17-variant18-variant21-variant23-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,3:9:67:67,0,239:5,1,2,1 chr2 1499899 . C T 605.83 PASS AC=2;AF=0.578;AN=2;DP=3511;set=variant-variant3-variant4-variant9-variant11-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,111:111:99:3439,333,0:0,0,68,43 chr2 1499927 . A C 785.85 PASS AC=2;AF=0.576;AN=2;DP=4277;MQ=60;set=variant-variant3-variant4-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,139:139:99:4164,417,0:0,0,76,63 chr2 1500665 . C T 689.7 PASS AC=2;AF=0.603;AN=2;DP=1496;MQ=60;set=variant-variant2-variant3-variant4-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:1547,141,0:0,0,19,28 chr2 1520676 . T C 928.2 PASS AC=2;AF=0.689;AN=2;DP=2728;MQ=60;set=variant-variant2-variant4-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,95:95:99:3215,284,0:0,0,64,31 chr2 1544147 . A T 170.69 PASS AC=2;AF=0.712;AN=2;DP=451;FS=0;MQ=60;set=variant-variant3-variant4-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:834,78,0:0,0,17,9 chr2 1544196 . A AAAT 525.17 PASS AC=2;AF=0.691;AN=2;DP=995;set=variant-variant3-variant4-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:2255,154,0:0,0,33,15 chr2 1544617 . G A 2321.05 PASS AC=2;AF=0.611;AN=2;DP=5146;MQ=60;set=variant-variant2-variant3-variant4-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant23-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,176:176:99:5503,526,0:0,0,86,90 chr2 1546297 . G A 3473.16 PASS AC=1;AF=0.5;AN=2;DP=269;FS=1.47;FractionInformativeReads=0.996;MQ=60;MQRankSum=2.646;QD=12.91;ReadPosRankSum=1.251;SOR=0.605;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:126,142:268:99:3501,0,3111:73,53,79,63 chr2 1636938 . CT C,CTTT,CTT,CTTTT 602.4 PASS AC=0,0,1,0;AF=0.174,0.105,0.256,0.012;AN=2;DP=8915;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 0/3:192:99:58,57,36,41 chr2 1637201 . C T 1092.03 PASS AC=1;AF=0.729;AN=2;DP=2994;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,46:89:99:1134,0,1082:19,24,22,24 chr2 1637531 . A G 1103.48 PASS AC=2;AF=0.817;AN=2;DP=3238;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,88:88:99:2754,264,0:0,0,50,38 chr2 1637648 . T C 1905.15 PASS AC=1;AF=0.722;AN=2;DP=4144;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,81:134:99:1998,0,1293:29,24,43,38 chr2 1639060 . A G 85.71 PASS AC=1;AF=0.531;AN=2;DP=505;FractionInformativeReads=1;MQ=60;set=variant2-variant8-variant9-variant10-variant11-variant15-variant16-variant25-variant29-variant30-variant34-variant35-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,7:23:99:228,0,551:13,3,7,0 chr2 1639122 . T C 1251.73 PASS AC=1;AF=0.526;AN=2;DP=1518;MQ=60;set=variant-variant2-variant4-variant8-variant9-variant11-variant15-variant16-variant17-variant25-variant29-variant30-variant31-variant34-variant35-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,39:93:99:924,0,1350:30,24,25,14 chr2 1642537 . T C 2401.77 PASS AC=2;AF=0.884;AN=2;DP=1907;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:2294,154,0:0,0,41,6 chr2 1642539 . C T 2561.5 PASS AC=2;AF=0.884;AN=2;DP=1983;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:2389,163,0:0,0,43,7 chr2 1642544 . C T 837.79 PASS AC=1;AF=0.5;AN=2;DP=422;FractionInformativeReads=1;MQ=60;set=variant8-variant11-variant12-variant16-variant21-variant23-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:26,35:61:99:1147,0,784:22,4,29,6 chr2 1642545 . C G 2749.29 PASS AC=2;AF=0.884;AN=2;DP=2288;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:2686,187,0:0,0,51,11 chr2 1642803 . CGGGTCTCATTTCAAGGTTTCCTGGGTGTGCACCGCCCCTGATGCTCTGAGCT C 88.73 PASS AC=2;AF=0.833;AN=2;DP=2658;set=filterInvariant-filterInvariant2-filterInvariant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-filterInvariant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,84:84:99:664,107,0:0,0,27,57 chr2 1647171 . T C 445.6 PASS AC=2;AF=0.884;AN=2;DP=6111;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,136:136:99:3936,407,0:0,0,76,60 chr2 1652822 . T G 2196.87 PASS AC=2;AF=0.895;AN=2;DP=8688;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,248:248:99:7646,741,0:0,0,117,131 chr2 1657078 . C T 1335.25 PASS AC=1;AF=0.556;AN=2;DP=2224;MQ=60;set=variant5-variant7-variant10-variant11-variant16-variant18-variant23-variant25-variant28-variant29-variant30-variant33-variant34-variant35-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:79,62:141:99:1353,0,2028:35,44,26,36 chr2 1664654 . A G 1171.22 PASS AC=1;AF=0.825;AN=2;DP=3668;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,50:111:99:1361,0,1727:44,17,37,13 chr2 1667267 . C G 1035.41 PASS AC=1;AF=0.545;AN=2;DP=2638;FractionInformativeReads=1;set=variant-variant4-variant5-variant7-variant10-variant11-variant12-variant16-variant18-variant23-variant24-variant25-variant26-variant28-variant29-variant34-variant35-variant36-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:75,67:142:99:1679,0,2011:49,26,43,24 chr2 1667310 . G A 1465.25 PASS AC=1;AF=0.769;AN=2;DP=6856;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:110,83:193:99:1883,0,2887:67,43,48,35 chr2 1683923 . G T 244.58 PASS AC=1;AF=0.5;AN=2;DP=175;MQ=60;set=variant2-variant7-variant21-variant32-variant33-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:11,9:20:99:244,0,378:10,1,7,2 chr2 1747993 . G A 427.08 PASS AC=1;AF=0.611;AN=2;DP=649;MQ=60;set=variant3-variant5-variant8-variant10-variant11-variant12-variant13-variant15-variant18-variant22-variant23-variant25-variant29-variant30-variant33-variant35-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:21,22:43:99:661,0,510:12,9,16,6 chr2 1748429 . T C 193.34 PASS AC=1;AF=0.647;AN=2;DP=192;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant10-variant11-variant12-variant13-variant15-variant18-variant22-variant23-variant25-variant29-variant30-variant33-variant35-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:4,9:13:60:244,0,60:2,2,4,5 chr2 1748463 . G A 132.13 PASS AC=1;AF=0.607;AN=2;DP=135;MQ=60;set=variant3-variant5-variant10-variant12-variant13-variant15-variant22-variant23-variant25-variant29-variant33-variant35-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:4,5:9:99:157,0,112:2,2,1,4 chr2 1793988 . AT A 649.74 PASS AC=2;AF=0.75;AN=2;DP=1330;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:744,78,0:0,0,13,13 chr2 1794410 . C T 362.72 PASS AC=2;AF=0.65;AN=2;DP=1332;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant16-variant18-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1117,102,0:0,0,16,18 chr2 1794468 . G C 354.66 PASS AC=1;AF=0.5;AN=2;DP=26;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=2.41;QD=13.64;ReadPosRankSum=1.487;SOR=0.693;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:13,13:26:99:383,0,399:7,6,7,6 chr2 1813057 . G T 391.39 PASS AC=1;AF=0.525;AN=2;DP=1815;MQ=60;set=variant-variant2-variant4-variant7-variant16-variant18-variant21-variant22-variant23-variant25-variant26-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:54,47:101:99:1127,0,1371:22,32,18,29 chr2 1844676 . CT C,CTT 139.55 PASS AC=1,0;AF=0.433,0.067;AN=2;DP=781;set=variant2-variant4-filterInvariant5-filterInvariant8-filterInvariant15-filterInvariant17-variant19-filterInvariant21-variant31-filterInvariant32-variant35-variant36-filterInvariant37-variant38-filterInvariant42 GT:DP:GQ:SB 0/1:48:99:12,20,5,11 chr2 1890070 . C T 377.99 PASS AC=2;AF=0.907;AN=2;DP=653;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:367,33,0:0,0,8,3 chr2 1926437 . G T 1922.77 PASS AC=2;AF=0.966;AN=2;DP=5998;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,150:150:99:4753,449,0:0,0,81,69 chr2 2334877 . A G 55.93 PASS AC=1;AF=0.5;AN=2;DP=279;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant9-variant12-variant16-variant17-variant23-variant27-variant30-variant31-variant32-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,8:18:99:212,0,277:4,6,2,6 chr2 3192798 . T C 358.5 PASS AC=2;AF=0.898;AN=2;DP=841;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:506,45,0:0,0,10,5 chr2 3193040 . G A 1752.78 PASS AC=1;AF=0.597;AN=2;DP=2864;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,59:114:99:1456,0,1334:31,24,34,25 chr2 3196040 . A G 293.66 PASS AC=2;AF=0.93;AN=2;DP=629;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:462,36,0:0,0,9,3 chr2 3200948 . C A 394.59 PASS AC=2;AF=0.953;AN=2;DP=735;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:551,51,0:0,0,6,11 chr2 3211756 . C T 2741.91 PASS AC=1;AF=0.5;AN=2;DP=208;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.888;QD=13.18;ReadPosRankSum=2.209;SOR=0.665;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:102,106:208:99:2770,0,2713:69,33,71,35 chr2 3211757 . C G 6217.6 PASS AC=2;AF=0.977;AN=2;DP=7427;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,211:211:99:8208,633,0:0,0,142,69 chr2 3211790 . T C 8749.84 PASS AC=2;AF=0.977;AN=2;DP=10226;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,284:284:99:8570,851,0:0,0,168,116 chr2 3212105 . A G 2726.41 PASS AC=2;AF=0.943;AN=2;DP=3819;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,98:98:99:3202,294,0:0,0,43,55 chr2 3212247 . G T 1362.24 PASS AC=1;AF=0.692;AN=2;DP=3382;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,39:79:99:1117,0,1169:20,20,24,15 chr2 3212704 . C A 2758.6 PASS AC=1;AF=0.694;AN=2;DP=3834;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:79,84:163:99:2160,0,2034:29,50,33,51 chr2 3212817 . C T 743.84 PASS AC=1;AF=0.605;AN=2;DP=719;set=variant-variant2-variant3-variant7-variant8-variant11-variant12-variant13-variant15-variant17-variant20-variant25-variant28-variant30-variant31-variant33-variant35-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,32:52:99:875,0,558:5,15,12,20 chr2 3217777 . A C 715.65 PASS AC=2;AF=0.977;AN=2;DP=467;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:492,33,0:0,0,11,0 chr2 3217794 . T C 802.15 PASS AC=2;AF=0.977;AN=2;DP=676;FS=0;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:746,57,0:0,0,17,2 chr2 3217908 . G C 2909.18 PASS AC=2;AF=0.977;AN=2;DP=4046;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,86:86:99:2548,258,0:0,0,45,41 chr2 3260822 . A G 112.39 PASS AC=1;AF=0.735;AN=2;DP=456;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant15-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,6:14:99:181,0,227:4,4,4,2 chr2 3277884 . A G 702.4 PASS AC=1;AF=0.611;AN=2;DP=693;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant28-variant30-variant31-variant33-variant35-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,8:13:99:277,0,105:3,2,4,4 chr2 3277947 . T A 257.27 PASS AC=1;AF=0.684;AN=2;DP=1728;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,15:33:99:352,0,521:13,5,11,4 chr2 3322797 . C A 759.79 PASS AC=1;AF=0.554;AN=2;DP=1696;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant10-variant11-variant12-variant13-variant16-variant17-variant19-variant20-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,24:52:99:626,0,722:9,19,9,15 chr2 3342009 . T C 196.43 PASS AC=1;AF=0.574;AN=2;DP=271;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant10-variant11-variant12-variant13-variant16-variant17-variant19-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,7:10:99:278,0,103:0,3,0,7 chr2 3356849 . A G 539.43 PASS AC=1;AF=0.679;AN=2;DP=1072;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,13:23:99:487,0,280:8,2,13,0 chr2 3356953 . A T 4668.57 PASS AC=2;AF=1;AN=2;DP=6502;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,179:179:99:5238,535,0:0,0,105,74 chr2 3358458 . ATTATGAAGTTAGAT A 2704.93 PASS AC=2;AF=1;AN=2;DP=3092;FS=0;MQRankSum=1.546;ReadPosRankSum=1.023;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:3336,227,0:0,0,25,50 chr2 3381773 . A G 144.49 PASS AC=1;AF=0.5;AN=2;DP=124;FractionInformativeReads=1;MQ=60;set=variant3-variant9-variant11-variant23-variant26-variant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:7,14:21:99:512,0,182:0,7,1,13 chr2 3383538 . C A,G 4311.61 PASS AC=0,1;AF=0.171,0.632;AN=2;DP=5885;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:165:99:48,38,45,34 chr2 3383662 . C T 1021.43 PASS AC=1;AF=0.639;AN=2;DP=2685;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:45,50:95:99:1259,0,1254:14,31,17,33 chr2 3383741 . G A 286.62 PASS AC=1;AF=0.643;AN=2;DP=683;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:15,8:23:99:227,0,420:4,11,0,8 chr2 3392075 . T C 3668.3 PASS AC=1;AF=0.694;AN=2;DP=12412;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:215,221:436:99:5455,0,5300:117,98,105,116 chr2 3392295 . A G 3477.02 PASS AC=1;AF=0.603;AN=2;DP=7944;MQ=60;set=variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:166,142:308:99:3540,0,4122:87,79,76,66 chr2 3392513 . T C 1927.88 PASS AC=1;AF=0.694;AN=2;DP=5168;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:83,70:153:99:2681,0,4637:32,51,30,40 chr2 3392514 . T A 1927.88 PASS AC=1;AF=0.694;AN=2;DP=5113;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:82,71:153:99:2681,0,4637:32,50,30,41 chr2 3393288 . A G 118.65 PASS AC=1;AF=0.7;AN=2;DP=431;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,12:18:99:517,0,323:4,2,9,3 chr2 3393289 . A C 118.65 PASS AC=1;AF=0.7;AN=2;DP=444;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,13:19:99:517,0,323:4,2,10,3 chr2 3393565 . C CAA 2995.93 PASS AC=1;AF=0.621;AN=2;DP=4943;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant34-variant35-variant36-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:106,73:179:99:2708,0,4699:49,57,28,45 chr2 3425514 . G C 1519.09 PASS AC=1;AF=0.689;AN=2;DP=3757;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:66,52:118:99:1335,0,1714:26,40,21,31 chr2 3425948 . T C 309.05 PASS AC=1;AF=0.689;AN=2;DP=1053;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,10:37:99:182,0,812:7,20,4,6 chr2 3461059 . T G 106.72 PASS AC=1;AF=0.5;AN=2;DP=44;FS=43.489;FractionInformativeReads=1;MQ=60;MQRankSum=-1.091;QD=2.43;ReadPosRankSum=-3.722;SOR=4.16;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:37,7:44:99:135,0,1864:31,6,0,7 chr2 3461066 . A G 103.8 PASS AC=1;AF=0.5;AN=2;DP=43;FS=46.838;FractionInformativeReads=1;MQ=60;MQRankSum=-0.484;QD=2.41;ReadPosRankSum=-2.7;SOR=4.395;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:35,8:43:99:132,0,1880:29,6,0,8 chr2 3461070 . T G 142.86 PASS AC=1;AF=0.5;AN=2;DP=42;FS=45.027;FractionInformativeReads=0.976;MQ=60;MQRankSum=0.049;QD=3.4;ReadPosRankSum=-2.451;SOR=4.395;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:33,8:41:99:171,0,1800:27,6,0,8 chr2 3461075 . T TG 153.67 PASS AC=1;AF=0.5;AN=2;DP=46;FS=55.037;FractionInformativeReads=0.978;MQ=60;MQRankSum=-0.938;QD=3.34;ReadPosRankSum=-2.152;SOR=4.97;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:34,11:45:99:191,0,1723:27,7,0,11 chr2 3519616 . A G 1242.81 PASS AC=2;AF=0.697;AN=2;DP=911;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:563,48,0:0,0,14,2 chr2 3519839 . A G 1889.53 PASS AC=2;AF=0.697;AN=2;DP=1992;FractionInformativeReads=1;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1652,159,0:0,0,21,32 chr2 3521051 . C T 659.84 PASS AC=2;AF=0.854;AN=2;DP=1091;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:689,63,0:0,0,10,11 chr2 3523324 . A G 5032.2 PASS AC=2;AF=0.866;AN=2;DP=5693;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,138:138:99:4348,413,0:0,0,74,64 chr2 3579760 . T C 875.16 PASS AC=1;AF=0.645;AN=2;DP=2374;MQ=60;set=variant2-variant3-variant4-variant6-variant10-variant11-variant12-variant14-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:42,38:80:99:1075,0,1140:21,21,25,13 chr2 3597974 . T C 243.14 PASS AC=1;AF=0.645;AN=2;DP=923;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant10-variant11-variant12-variant14-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,18:31:99:434,0,435:12,1,11,7 chr2 3599539 . A G 65.91 PASS AC=1;AF=0.5;AN=2;DP=152;FractionInformativeReads=1;MQ=60;set=variant6-variant10-variant12-variant14-variant22-variant24-variant25-variant31-variant33-variant35-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:99:139,0,148:4,0,4,0 chr2 3599700 . G T 897.57 PASS AC=1;AF=0.73;AN=2;DP=2781;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:44,26:70:99:606,0,1173:25,19,14,12 chr2 3600012 . CCTCT C 529.65 PASS AC=1;AF=0.5;AN=2;DP=473;MQ=60;set=variant6-variant10-variant12-variant14-variant22-variant24-variant25-variant31-variant33-variant35-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:17,19:36:99:748,0,959:6,11,6,13 chr2 3605468 . A G 2208.25 PASS AC=2;AF=0.738;AN=2;DP=6677;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,170:170:99:5156,510,0:0,0,71,99 chr2 3605528 . T G 1345.35 PASS AC=1;AF=0.648;AN=2;DP=2494;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant26-variant27-variant30-variant32-variant35-variant36-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,45:89:99:1086,0,1130:15,29,17,28 chr2 3605538 . A C 1272.96 PASS AC=2;AF=0.667;AN=2;DP=2260;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant26-variant27-variant30-variant32-variant35-variant36-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:2934,231,0:0,0,26,49 chr2 3627648 . G C 1777.87 PASS AC=2;AF=0.814;AN=2;DP=4665;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,130:130:99:3752,390,0:0,0,65,65 chr2 3628383 . C A 303.45 PASS AC=1;AF=0.5;AN=2;DP=172;FractionInformativeReads=1;set=variant6-variant10-variant12-variant22-variant24-variant25-variant31-variant33-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:8,4:12:99:144,0,284:7,1,4,0 chr2 3652616 . G C 2132.13 PASS AC=2;AF=0.692;AN=2;DP=3675;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,97:97:99:2885,291,0:0,0,55,42 chr2 3653279 . C T 543.97 PASS AC=2;AF=0.684;AN=2;DP=748;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:957,81,0:0,0,21,6 chr2 3653576 . A G 3186.37 PASS AC=2;AF=0.684;AN=2;DP=3252;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,90:90:99:3184,269,0:0,0,57,33 chr2 3653844 . T C 4314.7 PASS AC=2;AF=0.7;AN=2;DP=5662;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,146:146:99:4607,437,0:0,0,54,92 chr2 3660752 . T C 1173.47 PASS AC=2;AF=0.692;AN=2;DP=1704;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:1859,162,0:0,0,39,15 chr2 3685046 . T C 1393.42 PASS AC=1;AF=0.845;AN=2;DP=1947;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,25:49:99:669,0,766:20,4,17,8 chr2 3685074 . A G 1976.82 PASS AC=1;AF=0.845;AN=2;DP=2850;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,37:69:99:914,0,957:25,7,22,15 chr2 3721729 . A G 2049.29 PASS AC=1;AF=0.625;AN=2;DP=2388;FractionInformativeReads=1;MQ=60;set=variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,33:86:99:810,0,1338:29,24,17,16 chr2 3726163 . T C 1492.71 PASS AC=1;AF=0.667;AN=2;DP=5100;MQ=60;set=variant2-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:82,80:162:99:2260,0,2014:29,53,23,57 chr2 3729254 . C T 1166.83 PASS AC=1;AF=0.583;AN=2;DP=1859;MQ=60;set=variant5-variant8-variant10-variant11-variant16-variant17-variant18-variant20-variant22-variant24-variant29-variant32-variant33-variant35-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:76,40:116:99:951,0,2036:38,38,19,21 chr2 3749084 . T C 1226.61 PASS AC=1;AF=0.567;AN=2;DP=4628;MQ=60;set=variant2-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant16-variant17-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:94,97:191:99:2504,0,2135:44,50,49,48 chr2 3749151 . GGAA G 1907.69 PASS AC=1;AF=0.652;AN=2;DP=4232;MQ=60;set=variant2-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:66,67:133:99:2580,0,2881:26,40,26,41 chr2 3749267 . G A 320.05 PASS AC=1;AF=0.567;AN=2;DP=734;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant16-variant17-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,16:27:99:471,0,335:2,9,4,12 chr2 3756073 . G A 199.74 PASS AC=1;AF=0.638;AN=2;DP=537;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant16-variant19-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,15:21:99:369,0,166:5,1,9,6 chr2 3774436 . C T 640.97 PASS AC=2;AF=0.989;AN=2;DP=990;FS=0;MQ=60;MQRankSum=-1.707;ReadPosRankSum=0.919;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,16:16:47:511,47,0:0,0,12,4 chr2 3774448 . T C 295.78 PASS AC=1;AF=0.628;AN=2;DP=1030;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,10:19:99:292,0,212:6,3,7,3 chr2 3774519 . T C 2508.99 PASS AC=2;AF=0.977;AN=2;DP=2911;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,74:74:99:2049,221,0:0,0,42,32 chr2 3800383 . C T 4439.52 PASS AC=1;AF=0.708;AN=2;DP=4613;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:72,65:137:99:1543,0,1866:32,40,30,35 chr2 3800496 . C T 2720.63 PASS AC=1;AF=0.708;AN=2;DP=3526;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:48,35:83:99:860,0,1268:21,27,12,23 chr2 3815250 . A G 1355.65 PASS AC=1;AF=0.757;AN=2;DP=1807;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:27,26:53:99:675,0,799:21,6,17,9 chr2 3815532 . A AT 367.48 PASS AC=2;AF=0.721;AN=2;DP=811;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:2,19:21:26:460,26,0:0,2,6,13 chr2 3894606 . A C 46.12 PASS AC=1;AF=0.5;AN=2;DP=58;FractionInformativeReads=1;MQ=60;set=variant5-variant8-variant15-variant22-variant35 GT:AD:DP:GQ:PL:SB 0/1:10,4:14:99:135,0,1194:2,8,4,0 chr2 3894611 . A C 40.1 PASS AC=1;AF=0.5;AN=2;DP=111;MQ=60;set=variant5-variant7-variant8-variant15-variant22-variant26-variant35-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,4:15:99:129,0,1336:3,8,4,0 chr2 3894616 . T C 63.49 PASS AC=1;AF=0.5;AN=2;DP=110;MQ=60;set=variant5-variant7-variant8-variant15-variant22-variant26-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:15,4:19:99:120,0,1548:5,10,4,0 chr2 3894620 . A C 91.72 PASS AC=1;AF=0.5;AN=2;DP=94;FractionInformativeReads=1;MQ=60;set=variant8-variant15-variant22-variant26-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:16,4:20:99:120,0,1548:6,10,4,0 chr2 3894623 . A G 55.83 PASS AC=1;AF=0.5;AN=2;DP=38;FractionInformativeReads=1;MQ=60;set=variant22-variant35 GT:AD:DP:GQ:PL:SB 0/1:16,3:19:99:117,0,1580:6,10,3,0 chr2 4135981 . C T 860.78 PASS AC=2;AF=0.677;AN=2;DP=2013;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant20-variant21-variant22-variant23-variant24-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:2009,225,0:0,0,39,36 chr2 4136145 . A G 399.82 PASS AC=2;AF=0.63;AN=2;DP=585;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant9-variant10-variant11-variant12-variant14-variant15-variant20-variant21-variant22-variant28-variant29-variant32-variant34-variant35-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1022,105,0:0,0,16,19 chr2 5835697 . GTTT GTT,GT,G,GTTTTT 1402.93 PASS AC=1,0,0,0;AF=0.378,0.134,0.11,0.012;AN=2;DP=10498;set=variant-variant2-variant3-variant4-variant5-variant6-filterInvariant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-filterInvariant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:189:99:51,44,25,69 chr2 5837271 . T C 866.01 PASS AC=1;AF=0.605;AN=2;DP=1244;MQ=60;set=variant-variant2-variant4-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant22-variant24-variant28-variant29-variant31-variant35-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:43,50:93:99:1463,0,1017:20,23,23,27 chr2 5838030 . G A 3935.26 PASS AC=1;AF=0.603;AN=2;DP=7717;MQ=60;set=variant-variant2-variant4-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:122,133:255:99:3246,0,3045:62,60,78,55 chr2 5838161 . AT A 4460.6 PASS AC=1;AF=0.603;AN=2;DP=9735;MQ=60;set=variant-variant2-variant4-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:136,163:299:99:3536,0,2721:68,68,87,76 chr2 5838683 . TAAA TAA,TAAAA,T,TA 1600.76 PASS AC=1,0,0,0;AF=0.338,0.095,0.162,0.041;AN=2;DP=4838;set=variant-variant2-variant4-variant5-filterInvariant6-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-filterInvariant21-variant22-filterInvariant23-variant24-variant25-filterInvariant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-filterInvariant37-variant39-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:105:99:29,12,41,23 chr2 5839686 . A G 6296.53 PASS AC=1;AF=0.621;AN=2;DP=10809;MQ=60;set=variant-variant2-variant4-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:218,184:402:99:4330,0,5555:112,106,92,92 chr2 5839841 . CTTTTT C,CTTTT,CT,CTTT,CTTTTTT 4231.49 PASS AC=1,0,0,0,0;AF=0.33,0.216,0.068,0.011,0.011;AN=2;DP=9341;set=Intersection GT:DP:GQ:SB 0/1:172:99:30,58,33,51 chr2 6790537 . A G 3095.41 PASS AC=1;AF=0.643;AN=2;DP=3571;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:77,61:138:99:1530,0,1944:36,41,32,29 chr2 6988669 . T C 2683.49 PASS AC=1;AF=0.791;AN=2;DP=2950;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,18:25:99:551,0,233:2,5,10,8 chr2 7001233 . ACG A 1563.96 PASS AC=2;AF=0.989;AN=2;DP=1308;MQRankSum=1.085;ReadPosRankSum=2.275;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:1220,90,0:0,0,20,10 chr2 7001249 . ACACACACACC A 780.38 PASS AC=2;AF=0.917;AN=2;DP=1536;set=variant-variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1352,103,0:0,0,21,13 chr2 7003879 . G A 587.07 PASS AC=2;AF=1;AN=2;DP=480;FS=0;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:419,33,0:0,0,1,10 chr2 7005069 . C T 3129.09 PASS AC=2;AF=0.989;AN=2;DP=5514;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,128:128:99:3943,383,0:0,0,80,48 chr2 7005369 . A G 4581.57 PASS AC=2;AF=1;AN=2;DP=7405;FS=0;MQ=60;MQRankSum=1.665;ReadPosRankSum=0.977;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,173:173:99:5179,519,0:0,0,85,88 chr2 7005992 . C T 7007.48 PASS AC=2;AF=0.989;AN=2;DP=10448;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,257:258:99:7175,732,0:0,1,128,129 chr2 7017903 . A G 2527.57 PASS AC=2;AF=0.989;AN=2;DP=4289;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,128:128:99:3773,383,0:0,0,64,64 chr2 7019079 . A G 1699.81 PASS AC=2;AF=0.989;AN=2;DP=3337;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,88:88:99:2670,264,0:0,0,53,35 chr2 7027323 . T A 2025.83 PASS AC=2;AF=0.837;AN=2;DP=4033;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,108:108:99:3137,323,0:0,0,46,62 chr2 7036472 . A T 3018.04 PASS AC=2;AF=0.744;AN=2;DP=7660;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,186:186:99:6126,557,0:0,0,92,94 chr2 7036663 . C CTT,CT 3445.28 PASS AC=1,1;AF=0.487,0.256;AN=2;DP=10285;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 2/1:218:99:8,5,81,124 chr2 7036678 . C T 4403.17 PASS AC=2;AF=0.744;AN=2;DP=8534;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,224:224:99:10241,732,0:0,0,93,131 chr2 7036811 . C T 944.51 PASS AC=2;AF=0.711;AN=2;DP=2599;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,73:73:99:2505,218,0:0,0,27,46 chr2 7036838 . G C 766.93 PASS AC=2;AF=0.711;AN=2;DP=2464;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:2301,204,0:0,0,27,41 chr2 7037067 . G T 748.35 PASS AC=2;AF=0.744;AN=2;DP=2378;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:2208,150,0:0,0,27,23 chr2 7037068 . C T 748.35 PASS AC=2;AF=0.744;AN=2;DP=2392;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:2208,150,0:0,0,26,23 chr2 7037174 . A T 907.38 PASS AC=2;AF=0.744;AN=2;DP=2877;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,69:69:99:2015,207,0:0,0,42,27 chr2 7038125 . CAA CA,CAAA,C,CAAAA,CAAAAA 271.14 PASS AC=1,0,0,0,0;AF=0.3,0.129,0.029,0.057,0.014;AN=2;DP=3500;set=variant-variant2-variant3-filterInvariant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant22-filterInvariant23-filterInvariant26-variant27-variant28-variant29-variant32-filterInvariant33-variant34-variant35-variant38-variant40-variant41-filterInvariant42-variant43-variant44 GT:DP:GQ:SB 0/1:92:99:26,23,37,6 chr2 7046272 . TACACACACACACACACAC T,TACACACACACACACAC,TACACACACACAC,TACACACACAC,TACACACACACACAC,TACACAC 792.35 PASS AC=0,0,0,0,2,0;AF=0.221,0.105,0.279,0.012,0.244,0.012;AN=2;DP=1082;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 5/5:19:50:1,0,16,2 chr2 7076975 . AGTGT AGTGTGTGTGTGTGTGT,AGTGTGTGT,AGTGTGT,AGTGTGTGTGTGTGT,AGTGTGTGTGT,AGT,A,AGTGTGTGTGTGT 652.93 PASS AC=0,1,1,0,0,0,0,0;AF=0.036,0.298,0.226,0.071,0.143,0.012,0.012,0.012;AN=2;DP=1412;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:DP:GQ:SB 3/2:22:99:0,0,18,4 chr2 7130516 . TACACACACACACACAC TAC,TACACACACAC,TACAC,T,TACACACACACACACACAC,TACACACACACAC,TACACACAC,TACACACACACACACACACACAC,TACACACACACACACACACAC 466.86 PASS AC=0,0,2,0,0,0,0,0,0;AF=0.08,0.12,0.14,0.04,0.04,0.18,0.06,0.04,0.04;AN=2;DP=571;set=variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant32-variant34-variant35-variant36-variant40-variant42-variant43 GT:DP:GQ:SB 3/3:12:23:1,0,3,8 chr2 7130533 . A G 386.16 PASS AC=1;AF=0.5;AN=2;DP=103;set=variant4-variant11-variant25-variant32-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:3,6:9:50:151,0,50:2,1,2,4 chr2 7136883 . C CA,CAA 252.32 PASS AC=2,0;AF=0.591,0.045;AN=2;DP=134;MQ=60;set=variant2-variant4-variant7-variant10-variant12-variant25-variant32-variant35-variant38-variant42-variant43 GT:DP:GQ:SB 1/1:17:51:0,0,13,4 chr2 7136926 . C A 331.05 PASS AC=2;AF=0.6;AN=2;DP=413;MQ=60;set=variant-variant2-variant4-variant7-variant10-variant11-variant12-variant25-variant28-variant32-variant33-variant35-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:89:966,89,0:0,0,20,10 chr2 7137067 . A G 2900.61 PASS AC=2;AF=0.817;AN=2;DP=3978;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,89:89:99:2562,266,0:0,0,47,42 chr2 7137435 . C T 92.66 PASS AC=2;AF=0.792;AN=2;DP=79;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant7-variant10-variant11-variant12-variant28-variant32-variant33-variant35-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:525,36,0:0,0,0,12 chr2 7154632 . T C 4003.83 PASS AC=2;AF=1;AN=2;DP=7006;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,161:161:99:4745,483,0:0,0,90,71 chr2 7154826 . AT ATT,A 1135.52 PASS AC=2,0;AF=0.556,0.056;AN=2;DP=1593;MQ=60;set=variant-variant2-variant4-variant7-variant10-variant11-variant12-variant13-variant25-variant26-variant28-variant32-variant33-variant35-variant36-variant38-variant42-variant43 GT:DP:GQ:SB 1/1:106:99:2,0,50,54 chr2 7164483 . C T 879.81 PASS AC=1;AF=0.528;AN=2;DP=897;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant6-variant7-variant10-variant13-variant15-variant18-variant19-variant21-variant23-variant28-variant32-variant34-variant35-variant36-variant37-variant42 GT:AD:DP:GQ:PL:SB 0/1:26,25:51:99:642,0,571:14,12,15,10 chr2 7170388 . CTGTGTGTGTGTGTGTG CTGTGTGTGTG,CTGTG,CTGTGTGTGTGTGTGTGTGTGTG,CTGTGTGTG,CTGTGTG,C,CTGTGTGTGTGTGTGTGTGTG,CTGTGTGTGTGTGTGTGTG,CTGTGTGTGTGTGTG,CTGTGTGTGTGTG,CTGTGTGTGTGTGTGTGTGTGTGTGTG 409.88 PASS AC=0,0,0,0,0,0,0,0,0,0,1;AF=0.282,0.09,0.038,0.077,0.038,0.038,0.064,0.038,0.026,0.013,0.013;AN=2;DP=3138;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43 GT:DP:GQ:SB 0/11:25:99:3,8,5,9 chr2 7181486 . A G 7096.89 PASS AC=1;AF=0.605;AN=2;DP=16726;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:208,223:431:99:5327,0,4980:103,105,113,110 chr2 7181560 . G A 5127.35 PASS AC=1;AF=0.569;AN=2;DP=11245;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant18-variant20-variant22-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant35-variant36-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:190,210:400:99:4816,0,4711:78,112,98,112 chr2 7182177 . G A 1318.95 PASS AC=1;AF=0.641;AN=2;DP=3036;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:45,50:95:99:1437,0,1266:24,21,34,16 chr2 7207995 . C T 136.16 PASS AC=1;AF=0.5;AN=2;DP=93;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant7-variant10-variant13-variant17-variant24-variant31-variant32-variant33-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:5,4:9:99:109,0,159:3,2,3,1 chr2 7208060 . C A 412.63 PASS AC=1;AF=0.603;AN=2;DP=832;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,10:19:99:336,0,264:7,2,9,1 chr2 7208324 . G T 1529.08 PASS AC=1;AF=0.5;AN=2;DP=1534;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant7-variant8-variant10-variant13-variant17-variant18-variant24-variant31-variant32-variant33-variant35-variant36-variant37-variant42 GT:AD:DP:GQ:PL:SB 0/1:68,56:124:99:1216,0,1646:31,37,27,29 chr2 7208422 . T C 1002.56 PASS AC=1;AF=0.5;AN=2;DP=885;MQ=60;set=variant4-variant6-variant7-variant8-variant10-variant13-variant17-variant18-variant24-variant31-variant32-variant33-variant35-variant36-variant37-variant42 GT:AD:DP:GQ:PL:SB 0/1:35,29:64:99:804,0,942:10,25,9,20 chr2 7243449 . AGTGTGTGT AGT,AGTGT,AGTGTGT,AGTGTGTGTGT,A 1057.25 PASS AC=2,0,0,0,0;AF=0.593,0.186,0.035,0.012,0.012;AN=2;DP=3079;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:85:99:0,0,57,28 chr2 7386160 . C T 481.42 PASS AC=1;AF=0.5;AN=2;DP=547;MQ=60;set=variant-variant10-variant11-variant15-variant20-variant27-variant31-variant32-variant35 GT:AD:DP:GQ:PL:SB 0/1:27,22:49:99:580,0,770:19,8,17,5 chr2 7386192 . T C 1814.02 PASS AC=1;AF=0.529;AN=2;DP=1755;MQ=60;set=variant3-variant4-variant7-variant8-variant13-variant14-variant17-variant18-variant22-variant25-variant27-variant33-variant34-variant35-variant37-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:42,36:78:99:921,0,1086:28,14,24,12 chr2 7403641 . TACACACACAC TACACACACACACACAC,TACACACACACAC,TACACACACACACAC,T,TACACACACACACACACAC 643.8 PASS AC=1,0,0,0,1;AF=0.293,0.451,0.049,0.012,0.012;AN=2;DP=2256;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43 GT:DP:GQ:SB 1/5:51:99:1,1,32,17 chr2 7421569 . CTG CTGTG,C 315.97 PASS AC=1,0;AF=0.5,0.031;AN=2;DP=598;MQ=60;set=variant2-variant7-variant10-variant11-filterInvariant13-variant14-variant17-variant23-variant24-variant29-variant33-variant34-variant35-variant36-variant39-variant43 GT:DP:GQ:SB 0/1:39:99:20,4,10,5 chr2 7471480 . TCACA TCA,TCTCACACA,TCACACACACACACA,TCACACACACA,TCACACACACACA,TCACACA,TCTCACACACACA,T,TCACACACA 47.12 PASS AC=1,0,0,0,0,0,0,0,0;AF=0.053,0.132,0.013,0.053,0.211,0.066,0.026,0.013,0.039;AN=2;DP=1224;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-filterInvariant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-filterInvariant35-variant36-variant37-variant39-variant40-variant41-variant43 GT:DP:GQ:SB 0/1:37:73:22,9,4,2 chr2 7594516 . G A 6250.85 PASS AC=1;AF=0.545;AN=2;DP=3196;MQ=60;set=variant-variant5-variant9-variant12-variant14-variant15-variant17-variant18-variant22-variant24-variant26-variant27-variant28-variant30-variant32-variant33-variant35-variant37-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:87,73:160:99:1671,0,2178:54,33,41,32 chr2 8178735 . A G 2276.57 PASS AC=1;AF=0.803;AN=2;DP=3055;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,43:90:99:1015,0,1358:22,25,19,24 chr2 8178798 . C T 2261.21 PASS AC=1;AF=0.743;AN=2;DP=2291;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,32:75:99:834,0,1124:19,24,14,18 chr2 8819143 . GCCA G 3553.68 PASS AC=2;AF=0.909;AN=2;DP=4812;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,134:134:99:5694,403,0:0,0,77,57 chr2 8822892 . CAAAAAAAAAAAA CAAAAAAAAAAA,CAAAAAAAAA,C,CAAAAAAAAAA 293.77 PASS AC=1,0,0,0;AF=0.278,0.139,0.083,0.028;AN=2;DP=1589;set=variant-filterInvariant2-variant5-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-filterInvariant44 GT:DP:GQ:SB 0/1:34:99:12,5,16,1 chr2 8822912 . A C,AC 1749.96 PASS AC=2,0;AF=0.891,0.016;AN=2;DP=1874;set=variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:68:99:1,0,48,19 chr2 8824669 . A C 909.93 PASS AC=1;AF=0.611;AN=2;DP=987;set=variant-variant3-variant4-variant5-variant6-variant9-variant11-variant12-variant13-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,14:22:99:292,0,150:0,8,0,14 chr2 8866844 . C G 335.44 PASS AC=1;AF=0.575;AN=2;DP=167;FractionInformativeReads=1;MQ=60;set=variant4-variant7-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant25-variant31-variant35-variant36-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:99:153,0,123:4,0,4,0 chr2 8870814 . A G 3155.51 PASS AC=2;AF=0.989;AN=2;DP=3763;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,90:90:99:3089,269,0:0,0,41,49 chr2 8871342 . C A 1739.66 PASS AC=1;AF=0.575;AN=2;DP=3365;set=variant4-variant5-variant7-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant25-variant31-variant35-variant36-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:83,95:178:99:2438,0,2295:44,39,49,46 chr2 8887910 . A T 68.21 PASS AC=1;AF=0.639;AN=2;DP=496;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,8:14:99:237,0,182:5,1,6,2 chr2 8898036 . A G 386.18 PASS AC=1;AF=0.575;AN=2;DP=370;set=variant4-variant7-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant25-variant31-variant35-variant36-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,13:24:99:416,0,377:2,9,3,10 chr2 8910717 . T C 163.72 PASS AC=1;AF=0.647;AN=2;DP=128;FractionInformativeReads=1;MQ=60;set=variant4-variant7-variant8-variant9-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant25-variant31-variant35-variant36-variant42 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:99:156,0,150:4,0,4,0 chr2 8910736 . GTT GTTT,GT,G 60.73 PASS AC=0,1,0;AF=0.105,0.368,0.026;AN=2;DP=255;MQ=60;set=variant3-variant4-variant7-variant10-variant14-variant15-variant16-variant17-variant19-variant20-variant22-filterInvariant24-variant28-variant33-variant34-variant35-variant36-variant40-variant42 GT:DP:GQ:SB 0/2:16:99:9,1,5,1 chr2 8910987 . A T 1260.94 PASS AC=2;AF=1;AN=2;DP=2385;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1271,117,0:0,0,14,25 chr2 8911010 . T C 427 PASS AC=1;AF=0.649;AN=2;DP=1421;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,11:24:99:285,0,360:3,10,4,7 chr2 8916847 . A T 1863.52 PASS AC=2;AF=0.989;AN=2;DP=2353;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1270,102,0:0,0,27,7 chr2 8943291 . G A 413.33 PASS AC=2;AF=1;AN=2;DP=528;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:670,48,0:0,0,3,13 chr2 8977770 . A C 390.52 PASS AC=1;AF=0.536;AN=2;DP=834;MQ=60;set=variant4-variant9-variant11-variant12-variant14-variant16-variant18-variant22-variant24-variant31-variant35-variant36-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,29:59:99:714,0,890:14,16,15,14 chr2 8996728 . A G 862.65 PASS AC=2;AF=0.771;AN=2;DP=1405;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:1781,143,0:0,0,8,40 chr2 8998624 . A G 3363.17 PASS AC=2;AF=0.989;AN=2;DP=4547;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,110:110:99:3562,330,0:0,0,51,59 chr2 9419411 . G A 4421.13 PASS AC=2;AF=0.833;AN=2;DP=3845;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,83:83:99:3157,255,0:0,0,56,27 chr2 9419415 . C T 4457.88 PASS AC=1;AF=0.737;AN=2;DP=3637;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,50:91:99:1410,0,961:27,14,34,16 chr2 9463454 . C T 3358.72 PASS AC=2;AF=0.769;AN=2;DP=4600;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,111:111:99:3326,333,0:0,0,46,65 chr2 9484542 . C T 546.22 PASS AC=2;AF=0.977;AN=2;DP=565;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:479,39,0:0,0,11,2 chr2 9484561 . TAAAA T 1042.73 PASS AC=2;AF=0.977;AN=2;DP=816;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:982,66,0:0,0,18,4 chr2 9491017 . C T 2381.6 PASS AC=2;AF=0.989;AN=2;DP=2480;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:2383,213,0:0,0,20,51 chr2 9496291 . T C 2164.62 PASS AC=2;AF=0.765;AN=2;DP=5651;set=variant2-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,168:168:99:5201,503,0:0,0,78,90 chr2 9514917 . C T 568.03 PASS AC=2;AF=0.575;AN=2;DP=1093;MQ=60;set=variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant22-variant24-variant25-variant27-variant35-variant37-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:1868,180,0:0,0,38,22 chr2 9544866 . GTT GT,G 210.02 PASS AC=1,0;AF=0.474,0.026;AN=2;DP=8826;set=filterInvariant3-variant14-variant16-filterInvariant17-variant18-filterInvariant19-variant20-variant24-variant27-variant30-variant31-filterInvariant34-filterInvariant35-variant36-filterInvariant37-variant38-variant39-variant40-variant42 GT:DP:GQ:SB 0/1:390:96:158,182,22,28 chr2 9546030 . C T 7208.38 PASS AC=2;AF=0.86;AN=2;DP=8706;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,244:244:99:7202,729,0:0,0,106,138 chr2 9546189 . C A 848.38 PASS AC=1;AF=0.667;AN=2;DP=782;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:16,18:34:99:699,0,1129:3,13,7,11 chr2 9546191 . T G 384.87 PASS AC=1;AF=0.5;AN=2;DP=81;FractionInformativeReads=1;set=variant2-variant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:16,18:34:99:699,0,1129:3,13,7,11 chr2 9546583 . T G 244.99 PASS AC=2;AF=0.7;AN=2;DP=101;FractionInformativeReads=1;set=variant-variant17-variant21-variant24-variant35 GT:AD:DP:GQ:PL:SB 1/1:3,22:25:5:730,5,0:2,1,17,5 chr2 9547171 . G A 1276.48 PASS AC=1;AF=0.712;AN=2;DP=5126;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:103,94:197:99:2271,0,2719:36,67,39,55 chr2 9547363 . C A 503.63 PASS AC=2;AF=0.735;AN=2;DP=1741;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:1554,144,0:0,0,29,19 chr2 9548026 . T TG 168.17 PASS AC=2;AF=0.75;AN=2;DP=319;MQ=60;set=variant3-variant4-variant5-variant7-variant8-variant11-variant12-variant14-variant15-variant16-variant18-variant20-variant22-variant26-variant27-variant29-variant30-variant31-variant32-variant35-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:57:523,57,0:0,0,15,3 chr2 9552379 . C T 312.44 PASS AC=2;AF=0.611;AN=2;DP=641;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant24-variant25-variant27-variant31-variant35-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:78:1124,78,0:0,0,16,9 chr2 9552383 . A AT 512.81 PASS AC=2;AF=0.611;AN=2;DP=685;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant24-variant25-variant27-variant31-variant35-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:1194,87,0:0,0,19,10 chr2 9554075 . T G 235.3 PASS AC=2;AF=0.788;AN=2;DP=262;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:392,30,0:0,0,9,1 chr2 9554255 . G A 2727.78 PASS AC=2;AF=0.77;AN=2;DP=2897;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,83:84:99:2484,224,0:0,1,48,35 chr2 9554280 . A T 1042.97 PASS AC=2;AF=0.611;AN=2;DP=2457;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant24-variant25-variant27-variant31-variant35-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,94:94:99:2867,280,0:0,0,52,42 chr2 9554461 . C A 1971.01 PASS AC=2;AF=0.764;AN=2;DP=1925;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:1712,173,0:0,0,24,34 chr2 9563307 . CGT C 1852.79 PASS AC=2;AF=0.764;AN=2;DP=1363;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1800,120,0:0,0,19,21 chr2 9564196 . G GA 475.55 PASS AC=2;AF=0.611;AN=2;DP=1666;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant24-variant25-variant27-variant31-variant35-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:5,57:62:51:1505,51,0:2,3,27,30 chr2 9565123 . A G 359.61 PASS AC=2;AF=0.767;AN=2;DP=231;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant22-variant24-variant25-variant26-variant28-variant29-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:259,21,0:0,0,1,6 chr2 9569972 . A T 2304.29 PASS AC=2;AF=0.764;AN=2;DP=3059;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:2034,186,0:0,0,40,22 chr2 9571054 . C T 939.86 PASS AC=2;AF=0.764;AN=2;DP=843;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:812,63,0:0,0,3,18 chr2 9572888 . A T 93.19 PASS AC=2;AF=0.654;AN=2;DP=433;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant22-variant24-variant25-variant27-variant31-variant35-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:514,45,0:0,0,4,11 chr2 9572928 . C T 54.21 PASS AC=2;AF=0.66;AN=2;DP=250;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant22-variant24-variant25-variant27-variant31-variant35-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:281,30,0:0,0,3,7 chr2 9576553 . T C 450.21 PASS AC=2;AF=0.764;AN=2;DP=833;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1274,111,0:0,0,11,26 chr2 9580540 . G GT 995.05 PASS AC=2;AF=0.764;AN=2;DP=1060;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:997,84,0:0,0,23,5 chr2 9583922 . A G 930.55 PASS AC=2;AF=0.75;AN=2;DP=1465;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1547,132,0:0,0,11,33 chr2 9597276 . ATGTGTGTGTGTGTG ATGTGTGTGTGTGTGTG,ATGTGTGTGTGTGTGTGTG,ATGTGTGTGTGTG,ATGTGTGTGTG,A,ATGTGTGTGTGTGTGTGTGTGTG,ATGTGTGTGTGTGTGTGTGTGTGTG,ATGTGTGTGTGTGTGTGTGTGTGTGTG,ATGTGTGTGTGTGTGTGTGTG 70.13 PASS AC=0,0,1,0,0,0,0,0,0;AF=0.21,0.081,0.113,0.129,0.016,0.016,0.016,0.016,0.016;AN=2;DP=1176;set=variant-variant2-variant3-variant6-variant9-filterInvariant10-variant13-variant14-variant15-filterInvariant16-variant18-variant19-filterInvariant20-variant21-variant25-variant26-variant28-filterInvariant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/3:9:86:2,2,0,5 chr2 9611632 . C A 1185.8 PASS AC=1;AF=0.5;AN=2;DP=90;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.206;QD=13.18;ReadPosRankSum=-1.239;SOR=0.726;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:46,44:90:99:1214,0,1216:15,31,14,30 chr2 9613289 . T C 4877.43 PASS AC=2;AF=0.75;AN=2;DP=5950;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,172:172:99:5028,514,0:0,0,74,98 chr2 9613328 . G A 3117.63 PASS AC=2;AF=0.736;AN=2;DP=3685;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,103:103:99:3295,307,0:0,0,33,70 chr2 9614523 . G A 1284.69 PASS AC=2;AF=0.768;AN=2;DP=5127;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,123:123:99:3698,368,0:0,0,73,50 chr2 9615556 . T C 903.83 PASS AC=2;AF=0.75;AN=2;DP=652;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:741,57,0:0,0,1,18 chr2 9616035 . A G 1290.19 PASS AC=2;AF=0.729;AN=2;DP=947;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:936,78,0:0,0,21,5 chr2 9616301 . TAGG T 453.73 PASS AC=2;AF=0.758;AN=2;DP=483;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:712,48,0:0,0,3,13 chr2 9624794 . T A 358.73 PASS AC=2;AF=0.636;AN=2;DP=1284;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1477,138,0:0,0,14,32 chr2 9629286 . T TTTG 8638.76 PASS AC=2;AF=0.565;AN=2;DP=3921;MQ=60;set=variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant22-variant24-variant25-variant27-variant35-variant37-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,173:173:99:7759,520,0:0,0,88,85 chr2 9629367 . T G 799.48 PASS AC=2;AF=0.632;AN=2;DP=3425;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,116:116:99:3758,345,0:0,0,39,77 chr2 9629388 . ATTTT ATTT,AT,ATT,ATTTTT,A 126.61 PASS AC=0,1,1,0,0;AF=0.242,0.161,0.194,0.016,0.016;AN=2;DP=2100;set=filterInvariant-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant20-filterInvariant23-variant26-variant27-variant28-variant30-filterInvariant31-filterInvariant32-variant33-filterInvariant34-variant35-variant37-filterInvariant39-filterInvariant40-variant41-variant42-filterInvariant43-variant44 GT:DP:GQ:SB 2/3:37:99:0,0,5,32 chr2 9629854 . CAAAAAAA CAAAAAAAA,CAA,CA,CAAAAAA,CAAAA,CAAAAA,CAAA,C 302.13 PASS AC=0,0,0,1,0,0,1,0;AF=0.014,0.111,0.069,0.083,0.097,0.111,0.111,0.028;AN=2;DP=4219;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant29-variant30-variant31-filterInvariant32-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 7/4:82:99:3,7,56,16 chr2 9629943 . T TA 2214.74 PASS AC=2;AF=0.708;AN=2;DP=8063;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,214:215:99:6056,619,0:0,1,100,114 chr2 9630016 . T C 3563.01 PASS AC=2;AF=0.636;AN=2;DP=8713;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,258:258:99:8172,774,0:0,0,124,134 chr2 9630231 . C T 1895.97 PASS AC=2;AF=0.722;AN=2;DP=6557;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,201:201:99:6522,603,0:0,0,108,93 chr2 9630244 . AT A 2188.41 PASS AC=2;AF=0.708;AN=2;DP=6303;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,198:198:99:7002,595,0:0,0,104,94 chr2 9631340 . T C 412.38 PASS AC=2;AF=0.636;AN=2;DP=1646;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1311,122,0:0,0,13,28 chr2 9633137 . T G 848.43 PASS AC=2;AF=0.722;AN=2;DP=3408;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,107:107:99:3177,321,0:0,0,54,53 chr2 9634856 . A G 1017.85 PASS AC=2;AF=0.722;AN=2;DP=2746;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:2342,225,0:0,0,36,39 chr2 9642478 . C T 129.74 PASS AC=2;AF=0.641;AN=2;DP=541;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:645,54,0:0,0,4,14 chr2 9642521 . C T 193.54 PASS AC=2;AF=0.611;AN=2;DP=157;MQ=60;set=variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant14-variant17-variant18-variant22-variant24-variant25-variant27-variant35-variant37-variant38-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:398,27,0:0,0,1,8 chr2 9650350 . C CATAA 753.27 PASS AC=2;AF=0.632;AN=2;DP=2289;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,72:74:99:3187,170,0:2,0,24,48 chr2 9661184 . T C 344.88 PASS AC=2;AF=0.764;AN=2;DP=652;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:919,72,0:0,0,21,3 chr2 9661969 . T TCTTCCCTGCCTGCCTGCCTGCCTGCCTGCCTGC,TCTTCCCTGCCTGCCTGCCTGCCTGCCTGCCTGCCTGC,TCTTCCCTGCCTGCCTGCCTGCCTGCCTGC,TCTTCCCTGC,TCTTCCCTGCCTGCCTGCCTGCCTGCCTGCCTGCCTGCCTGCCTGCCTGC,TCTTCCCTGCCTGCCTGCCTGCCTGC 3020.68 PASS AC=0,1,1,0,0,0;AF=0.261,0.087,0.152,0.087,0.022,0.022;AN=2;DP=1452;set=variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant22-variant24-variant25-variant27-variant34-variant35-variant37-variant38-variant39-variant41-variant42 GT:DP:GQ:SB 3/2:18:99:0,0,6,12 chr2 9662210 . G A 4177.25 PASS AC=2;AF=0.764;AN=2;DP=10437;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,328:329:99:10205,976,0:1,0,182,146 chr2 9662410 . T C 10524.8 PASS AC=2;AF=0.571;AN=2;DP=5701;MQ=60;set=variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant22-variant24-variant25-variant27-variant35-variant37-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:1,264:265:99:8323,783,0:1,0,105,159 chr2 9695906 . A G 617.1 PASS AC=2;AF=0.77;AN=2;DP=2762;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,78:80:99:2441,190,0:1,1,28,50 chr2 9728574 . A G 964.42 PASS AC=1;AF=0.543;AN=2;DP=1567;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant16-variant17-variant21-variant23-variant24-variant25-variant27-variant29-variant32-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:35,42:77:99:1109,0,859:13,22,13,29 chr2 9770589 . G GCGGGGC 4479.84 PASS AC=1;AF=0.54;AN=2;DP=8130;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant22-variant23-variant24-variant25-variant27-variant33-variant35-variant36-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:135,136:271:99:5268,0,9124:55,80,60,76 chr2 9771200 . C G 1243.13 PASS AC=1;AF=0.574;AN=2;DP=2822;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant12-variant13-variant15-variant16-variant17-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant32-variant33-variant35-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,65:130:99:1503,0,1581:28,37,27,38 chr2 9981672 . T C 281.51 PASS AC=1;AF=0.575;AN=2;DP=768;FractionInformativeReads=1;set=variant-variant2-variant6-variant8-variant12-variant13-variant15-variant18-variant19-variant23-variant24-variant26-variant29-variant30-variant31-variant32-variant35-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,27:47:99:806,0,540:17,3,20,7 chr2 9983591 . A AG 4401.86 PASS AC=2;AF=1;AN=2;DP=6523;FS=0;MQ=60;MQRankSum=-1.241;ReadPosRankSum=-1.05;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,197:197:99:7334,593,0:0,0,84,113 chr2 9983716 . A C 1572.85 PASS AC=2;AF=1;AN=2;DP=2726;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,85:85:99:2572,254,0:0,0,30,55 chr2 9985341 . TC T 1303.54 PASS AC=1;AF=0.563;AN=2;DP=1601;MQ=60;set=variant-variant2-variant6-variant12-variant13-variant15-variant18-variant19-variant23-variant24-variant26-variant29-variant30-variant32-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:48,57:105:99:1719,0,1381:28,20,33,24 chr2 9986102 . ACT A 277.73 PASS AC=1;AF=0.556;AN=2;DP=87;MQ=60;set=variant2-variant6-variant13-variant18-variant23-variant24-variant26-variant29-variant35 GT:AD:DP:GQ:PL:SB 0/1:8,6:14:99:223,0,318:6,2,4,2 chr2 9986162 . C T 608.05 PASS AC=1;AF=0.567;AN=2;DP=516;FractionInformativeReads=1;MQ=60;set=variant6-variant7-variant10-variant11-variant16-variant19-variant20-variant25-variant28-variant31-variant34-variant35-variant37-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:20,17:37:99:454,0,592:14,6,13,4 chr2 9991556 . G A 528.24 PASS AC=2;AF=1;AN=2;DP=538;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.935;ReadPosRankSum=0.668;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:651,48,0:0,0,14,2 chr2 9991867 . G A 691.66 PASS AC=1;AF=0.567;AN=2;DP=534;MQ=60;set=variant6-variant7-variant10-variant11-variant16-variant19-variant20-variant25-variant28-variant31-variant34-variant35-variant37-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:13,13:26:99:402,0,345:3,10,2,11 chr2 10023016 . T C 347.17 PASS AC=1;AF=0.571;AN=2;DP=551;FractionInformativeReads=1;MQ=60;set=variant6-variant7-variant10-variant11-variant16-variant19-variant20-variant25-variant28-variant31-variant34-variant35-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:18,17:35:99:481,0,462:7,11,4,13 chr2 10044875 . A G 143.87 PASS AC=1;AF=0.729;AN=2;DP=522;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,4:12:99:133,0,208:6,2,4,0 chr2 10044941 . G T 964.02 PASS AC=1;AF=0.716;AN=2;DP=2242;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,22:63:99:767,0,1662:27,14,16,6 chr2 10044946 . G T 967.31 PASS AC=1;AF=0.571;AN=2;DP=1350;MQ=60;set=variant-variant6-variant7-variant10-variant11-variant12-variant15-variant16-variant18-variant19-variant20-variant25-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:44,23:67:99:792,0,1723:27,17,17,6 chr2 10045014 . C T 6504.81 PASS AC=1;AF=0.895;AN=2;DP=5567;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:79,52:131:99:1072,0,2018:46,33,28,24 chr2 10045024 . G A 6831.91 PASS AC=2;AF=1;AN=2;DP=5920;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,137:137:99:4924,412,0:0,0,75,62 chr2 10045147 . A G 2799.69 PASS AC=2;AF=1;AN=2;DP=3272;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,90:90:99:2839,270,0:0,0,33,57 chr2 10050947 . T C 2103.79 PASS AC=1;AF=0.716;AN=2;DP=5815;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:85,88:173:99:2254,0,1911:42,43,41,47 chr2 10050960 . A G 2024.11 PASS AC=1;AF=0.716;AN=2;DP=5413;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:79,83:162:99:2090,0,1804:36,43,38,45 chr2 10051053 . G C,A 973.59 PASS AC=1,0;AF=0.716,0.014;AN=2;DP=1543;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:49:99:3,22,6,18 chr2 10051792 . A G 242.76 PASS AC=1;AF=0.579;AN=2;DP=252;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant7-variant10-variant11-variant12-variant15-variant16-variant19-variant20-variant25-variant28-variant31-variant32-variant34-variant35-variant36-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:7,11:18:99:320,0,188:1,6,3,8 chr2 10053412 . C T 1476.19 PASS AC=1;AF=0.716;AN=2;DP=4405;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,55:113:99:1254,0,1476:27,31,24,31 chr2 10059097 . A C 2741.25 PASS AC=1;AF=0.672;AN=2;DP=4319;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant13-variant17-variant18-variant21-variant23-variant24-variant26-variant27-variant29-variant31-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:94,79:173:99:1936,0,2227:53,41,37,42 chr2 10059770 . G T 1023.01 PASS AC=1;AF=0.697;AN=2;DP=2727;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,38:78:99:960,0,966:25,15,22,16 chr2 10085270 . CCTGT C 1384.39 PASS AC=1;AF=0.5;AN=2;DP=411;MQ=60;set=variant2-variant6-variant13-variant18-variant35 GT:AD:DP:GQ:PL:SB 0/1:25,53:78:99:2150,0,1388:18,7,36,17 chr2 10094992 . A G 755.96 PASS AC=1;AF=0.667;AN=2;DP=2479;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,38:69:99:1010,0,865:24,7,22,16 chr2 10183748 . TGCC T,TGCCGCC 578.57 PASS AC=1,0;AF=0.522,0.043;AN=2;DP=954;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant22-variant25-variant31-variant32-variant34-variant35-variant37-variant40-variant43 GT:DP:GQ:SB 0/1:50:99:18,7,18,7 chr2 10183970 . A G 1199.23 PASS AC=1;AF=0.567;AN=2;DP=1743;MQ=60;set=variant-variant5-variant10-variant11-variant13-variant14-variant15-variant18-variant19-variant25-variant31-variant32-variant35-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:75,82:157:99:2081,0,1608:32,43,32,50 chr2 10188649 . A T 3261.47 PASS AC=1;AF=0.795;AN=2;DP=10112;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:140,124:264:99:2889,0,3348:57,83,57,67 chr2 10193069 . A T 5117.52 PASS AC=1;AF=0.563;AN=2;DP=2678;MQ=60;set=variant-variant5-variant11-variant13-variant18-variant31-variant32-variant35 GT:AD:DP:GQ:PL:SB 0/1:192,158:350:99:4023,0,4824:116,76,103,55 chr2 10193274 . GCAATCATTCCTGTCAC G 4985.66 PASS AC=1;AF=0.563;AN=2;DP=1875;MQ=60;set=variant-variant5-variant11-variant13-variant18-variant31-variant32-variant35 GT:AD:DP:GQ:PL:SB 0/1:91,102:193:99:3914,0,4308:30,61,32,70 chr2 10194192 . T C 5757.97 PASS AC=1;AF=0.795;AN=2;DP=15873;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:219,204:423:99:5092,0,5936:111,108,112,92 chr2 10197270 . T A 4605.42 PASS AC=1;AF=0.795;AN=2;DP=11835;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:150,133:283:99:3444,0,3950:53,97,47,86 chr2 10197615 . T C 888.89 PASS AC=1;AF=0.795;AN=2;DP=2280;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:27,23:50:99:668,0,717:15,12,14,9 chr2 10198197 . G C 595.3 PASS AC=1;AF=0.567;AN=2;DP=617;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant10-variant11-variant13-variant14-variant15-variant18-variant19-variant25-variant31-variant32-variant35-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:21,16:37:99:476,0,543:11,10,9,7 chr2 10198262 . G A 624.67 PASS AC=1;AF=0.567;AN=2;DP=794;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant10-variant11-variant13-variant14-variant15-variant18-variant19-variant25-variant31-variant32-variant35-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:30,26:56:99:641,0,791:18,12,16,10 chr2 10220247 . C A 315.63 PASS AC=1;AF=0.5;AN=2;DP=184;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant7-variant26-variant29-variant30-variant32-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:13,9:22:99:144,0,371:7,6,5,4 chr2 10223894 . T G 798.92 PASS AC=1;AF=0.563;AN=2;DP=636;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant11-variant13-variant18-variant31-variant32-variant35 GT:AD:DP:GQ:PL:SB 0/1:44,47:91:99:1145,0,1246:33,11,30,17 chr2 10225241 . C T 1754.28 PASS AC=2;AF=0.898;AN=2;DP=2723;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:2411,229,0:0,0,56,21 chr2 10262920 . T G 2308.65 PASS AC=1;AF=0.798;AN=2;DP=7090;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:104,116:220:99:3185,0,2552:43,61,50,66 chr2 10264057 . T C 1115.05 PASS AC=2;AF=0.821;AN=2;DP=3056;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,99:99:99:2910,296,0:0,0,43,56 chr2 10265144 . A G 277.21 PASS AC=1;AF=0.553;AN=2;DP=252;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant15-variant18-variant19-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,4:9:99:140,0,198:1,4,0,4 chr2 10267211 . T C 1111.24 PASS AC=1;AF=0.5;AN=2;DP=787;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant11-variant17-variant32-variant35-variant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:55,62:117:99:1799,0,1439:22,33,24,38 chr2 10271196 . A G 6291.99 PASS AC=1;AF=0.55;AN=2;DP=9632;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant14-variant15-variant18-variant19-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:225,256:481:99:6455,0,5386:100,125,110,146 chr2 10271564 . CATTTTA C 2237.82 PASS AC=1;AF=0.55;AN=2;DP=2155;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant14-variant15-variant18-variant19-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,46:96:99:1748,0,3216:14,36,17,29 chr2 10281514 . C T 354.59 PASS AC=1;AF=0.5;AN=2;DP=276;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant11-variant17-variant32-variant35-variant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:17,18:35:99:496,0,543:7,10,6,12 chr2 10281903 . G GC 776.77 PASS AC=2;AF=1;AN=2;DP=1960;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1350,114,0:0,0,25,13 chr2 10282147 . T C 1173.28 PASS AC=1;AF=0.756;AN=2;DP=4962;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:66,80:146:99:1945,0,1415:29,37,33,47 chr2 10332539 . A G 309.64 PASS AC=2;AF=0.607;AN=2;DP=880;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant27-variant28-variant29-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1542,126,0:0,0,34,8 chr2 10351014 . G C 633.36 PASS AC=1;AF=0.5;AN=2;DP=41;FS=3.038;FractionInformativeReads=1;MQ=60;MQRankSum=0.565;QD=15.45;ReadPosRankSum=-0.696;SOR=0.301;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:18,23:41:99:662,0,510:14,4,15,8 chr2 10443340 . A G 228.84 PASS AC=2;AF=0.895;AN=2;DP=447;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:341,24,0:0,0,5,3 chr2 10443748 . C CG 3112.73 PASS AC=2;AF=1;AN=2;DP=2760;FS=0;MQ=60;MQRankSum=1.354;ReadPosRankSum=1.354;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,73:73:99:3361,226,0:0,0,49,24 chr2 10443756 . G C 3273.81 PASS AC=2;AF=0.86;AN=2;DP=2958;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:3402,229,0:0,0,50,26 chr2 10443779 . G GC 4139.4 PASS AC=2;AF=1;AN=2;DP=3645;FS=0;MQ=60;MQRankSum=-0.666;ReadPosRankSum=1.679;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,92:92:99:4132,277,0:0,0,57,35 chr2 10443782 . G GC,GT 4206.2 PASS AC=0,2;AF=0.898,0.102;AN=2;DP=3685;FS=0;MQ=60;set=Intersection GT:DP:GQ:SB 2/2:92:99:0,0,57,35 chr2 10443788 . A AG 4255.04 PASS AC=2;AF=1;AN=2;DP=3803;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,94:94:99:4265,292,0:0,0,59,35 chr2 10444031 . G T 704.54 PASS AC=2;AF=0.55;AN=2;DP=740;MQ=60;set=variant6-variant9-variant10-variant11-variant17-variant22-variant31-variant34-variant35-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,80:80:99:2515,240,0:0,0,33,47 chr2 10444122 . C T 99.74 PASS AC=2;AF=0.571;AN=2;DP=196;MQ=60;set=variant6-variant10-variant17-variant31-variant34-variant35-variant42 GT:AD:DP:GQ:PL:SB 1/1:1,20:21:34:535,34,0:0,1,1,19 chr2 10567082 . A G 8886.26 PASS AC=1;AF=0.798;AN=2;DP=13924;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:200,222:422:99:5398,0,4831:97,103,107,115 chr2 10587702 . C T 927.96 PASS AC=1;AF=0.5;AN=2;DP=115;MQ=60;set=variant7-variant35 GT:AD:DP:GQ:PL:SB 0/1:29,16:45:99:362,0,735:16,13,11,5 chr2 10587869 . G A 188.06 PASS AC=1;AF=0.629;AN=2;DP=774;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,10:20:99:299,0,294:2,8,1,9 chr2 10588138 . C T 86.98 PASS AC=1;AF=0.594;AN=2;DP=207;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant7-variant9-variant10-variant12-variant15-variant21-variant22-variant23-variant27-variant29-variant34-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:8,11:19:99:266,0,183:5,3,7,4 chr2 10588552 . C G 1414.45 PASS AC=1;AF=0.622;AN=2;DP=5514;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,94:146:99:2278,0,1092:23,29,38,56 chr2 10710966 . GA G 1630.09 PASS AC=1;AF=0.643;AN=2;DP=910;MQ=60;set=variant-variant9-variant10-variant24-variant29-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:59,47:106:99:938,0,1191:38,21,28,19 chr2 10711197 . A G 1121.6 PASS AC=1;AF=0.571;AN=2;DP=574;MQ=60;set=variant-variant9-variant10-variant24-variant29-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:33,37:70:99:910,0,883:11,22,15,22 chr2 10711446 . T C 44.12 PASS AC=1;AF=0.571;AN=2;DP=252;FractionInformativeReads=1;MQ=60;set=variant-variant9-variant10-variant24-variant29-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:22,21:43:99:531,0,653:10,12,12,9 chr2 10711494 . C T 268.08 PASS AC=1;AF=0.571;AN=2;DP=311;FractionInformativeReads=1;MQ=60;set=variant-variant9-variant10-variant24-variant29-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:27,20:47:99:612,0,803:15,12,13,7 chr2 10711909 . T TAAA 813.89 PASS AC=1;AF=0.571;AN=2;DP=401;MQ=60;set=variant-variant9-variant10-variant24-variant29-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:30,25:55:99:920,0,1185:10,20,9,16 chr2 10711922 . G A 820.33 PASS AC=1;AF=0.571;AN=2;DP=352;FractionInformativeReads=1;MQ=60;set=variant-variant9-variant10-variant24-variant29-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:31,21:52:99:788,0,1238:10,21,9,12 chr2 10711941 . C A 1333.18 PASS AC=2;AF=1;AN=2;DP=2130;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1751,138,0:0,0,18,28 chr2 10711964 . T C 418.93 PASS AC=1;AF=0.571;AN=2;DP=315;MQ=60;set=variant-variant9-variant10-variant24-variant29-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:28,17:45:99:630,0,1096:10,18,8,9 chr2 10711981 . C T 541.18 PASS AC=1;AF=0.571;AN=2;DP=317;FractionInformativeReads=1;MQ=60;set=variant-variant9-variant10-variant24-variant29-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:29,17:46:99:627,0,1167:12,17,10,7 chr2 10711987 . C T 562.93 PASS AC=1;AF=0.571;AN=2;DP=313;FractionInformativeReads=1;MQ=60;set=variant-variant9-variant10-variant24-variant29-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:23,17:40:99:678,0,912:10,13,11,6 chr2 10712278 . C T 945.38 PASS AC=1;AF=0.571;AN=2;DP=709;FractionInformativeReads=1;MQ=60;set=variant-variant9-variant10-variant24-variant29-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:54,56:110:99:1253,0,1211:31,23,28,28 chr2 10717714 . G C 914.07 PASS AC=1;AF=0.565;AN=2;DP=2004;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,32:69:99:753,0,845:22,15,20,12 chr2 10729032 . C T 234.61 PASS AC=1;AF=0.569;AN=2;DP=464;MQ=60;set=variant3-variant4-variant6-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,14:22:99:374,0,203:6,2,11,3 chr2 10729897 . C T 1757.08 PASS AC=2;AF=0.632;AN=2;DP=1702;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,39:40:78:1417,78,0:0,1,6,33 chr2 10740841 . T C 272.66 PASS AC=1;AF=0.571;AN=2;DP=94;FractionInformativeReads=1;MQ=60;set=variant-variant9-variant10-variant24-variant29-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:8,4:12:99:127,0,275:7,1,4,0 chr2 10741141 . A G 404.24 PASS AC=2;AF=0.672;AN=2;DP=213;FS=0;MQ=60;set=variant-variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:177,12,0:0,0,0,4 chr2 10742741 . T C 659.79 PASS AC=1;AF=0.5;AN=2;DP=322;FractionInformativeReads=1;MQ=60;set=variant-variant9-variant10-variant29-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:29,26:55:99:634,0,653:17,12,17,9 chr2 10743153 . C T 688.12 PASS AC=2;AF=0.632;AN=2;DP=1226;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:1548,141,0:0,0,26,21 chr2 10743191 . G A 764.45 PASS AC=2;AF=0.632;AN=2;DP=1510;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1573,153,0:0,0,26,25 chr2 10743319 . T C 156.28 PASS AC=1;AF=0.571;AN=2;DP=359;FractionInformativeReads=1;MQ=60;set=variant-variant9-variant10-variant24-variant29-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:27,31:58:99:793,0,674:11,16,13,18 chr2 10747229 . C T 42.93 PASS AC=2;AF=0.625;AN=2;DP=21;FractionInformativeReads=1;MQ=60;set=variant-variant9-variant10-variant35 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:135,9,0:0,0,3,0 chr2 10747246 . C G 278.54 PASS AC=2;AF=0.667;AN=2;DP=253;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant34-variant35-variant37-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:15:225,15,0:0,0,4,0 chr2 10747271 . A G 648.56 PASS AC=2;AF=0.632;AN=2;DP=588;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:632,48,0:0,0,15,1 chr2 10762302 . TA T 2916.49 PASS AC=2;AF=1;AN=2;DP=4736;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,104:104:99:3856,313,0:0,0,40,64 chr2 10784491 . A G 831.1 PASS AC=1;AF=0.571;AN=2;DP=637;MQ=60;set=variant-variant9-variant10-variant24-variant29-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:57,44:101:99:963,0,1347:29,28,23,21 chr2 10784528 . T C 914.87 PASS AC=1;AF=0.571;AN=2;DP=558;FractionInformativeReads=1;MQ=60;set=variant-variant9-variant10-variant24-variant29-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:40,45:85:99:1053,0,957:20,20,21,24 chr2 10799467 . TGGG T,TG,TGG,TGGGGG 194.27 PASS AC=0,2,0,0;AF=0.379,0.362,0.017,0.034;AN=2;DP=404;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant10-variant11-variant13-variant14-variant16-variant17-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant37-variant38-variant41-variant42-variant44 GT:DP:GQ:SB 2/2:13:37:0,0,3,10 chr2 10808776 . C CAA 2337.18 PASS AC=2;AF=1;AN=2;DP=1916;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1769,120,0:0,0,16,24 chr2 10813782 . T C 1098.41 PASS AC=2;AF=1;AN=2;DP=1287;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:662,63,0:0,0,6,15 chr2 10815833 . A G 175.66 PASS AC=1;AF=0.565;AN=2;DP=477;MQ=60;set=variant-variant4-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant21-variant22-variant23-variant25-variant28-variant32-variant34-variant35-variant37-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,6:17:99:175,0,326:8,3,5,1 chr2 10861696 . T G 152.74 PASS AC=2;AF=0.976;AN=2;DP=283;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:189,18,0:0,0,3,3 chr2 10911891 . T C 3299.1 PASS AC=1;AF=0.849;AN=2;DP=4055;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,64:99:99:1691,0,801:23,12,43,21 chr2 10912092 . C T 2529.83 PASS AC=1;AF=0.538;AN=2;DP=2345;MQ=60;set=variant4-variant9-variant19-variant20-variant23-variant24-variant25-variant26-variant29-variant30-variant34-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:109,80:189:99:1912,0,2851:38,71,28,52 chr2 10912153 . T G 2009.22 PASS AC=1;AF=0.621;AN=2;DP=1919;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant31-variant35-variant37-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:29,31:60:99:985,0,973:4,25,7,24 chr2 10972383 . A G 381.59 PASS AC=2;AF=0.977;AN=2;DP=2492;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:1888,177,0:0,0,35,24 chr2 10972626 . A T 662.37 PASS AC=2;AF=1;AN=2;DP=1254;FS=0;MQ=60;MQRankSum=1.641;ReadPosRankSum=-0.638;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1173,105,0:0,0,13,22 chr2 10978024 . TTGTG TTGTGTG,TTG,T 111.08 PASS AC=1,0,0;AF=0.25,0.143,0.179;AN=2;DP=328;set=variant3-variant4-variant7-variant11-variant12-variant13-variant18-variant27-variant32-variant34-variant35-variant36-variant39-variant41 GT:DP:GQ:SB 0/1:18:99:5,6,1,6 chr2 10978049 . TGCGC TGC,T 85.69 PASS AC=0,1;AF=0.038,0.635;AN=2;DP=419;MQ=60;set=variant-variant2-variant4-variant7-variant8-variant9-variant14-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant40-variant42-variant44 GT:DP:GQ:SB 0/2:20:99:4,9,3,4 chr2 10978051 . C T 298.3 PASS AC=1;AF=0.542;AN=2;DP=206;set=variant3-variant6-variant7-variant11-variant15-variant16-variant18-variant24-variant27-variant32-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:9,9:18:99:351,0,351:4,5,1,8 chr2 10978053 . C T 46.16 PASS AC=1;AF=0.611;AN=2;DP=259;set=variant-variant3-variant6-variant7-variant11-variant12-variant13-variant15-variant16-variant18-variant24-variant27-variant32-variant35-variant36-variant37-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:9,9:18:99:351,0,351:4,5,1,8 chr2 10978056 . G A 94.73 PASS AC=2;AF=0.786;AN=2;DP=472;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:900,60,0:0,0,5,15 chr2 10994418 . T C 948.25 PASS AC=2;AF=1;AN=2;DP=1711;FS=0;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1833,147,0:0,0,41,8 chr2 11052221 . C T 142.9 PASS AC=1;AF=0.5;AN=2;DP=63;FractionInformativeReads=1;MQ=60;set=variant29-variant35 GT:AD:DP:GQ:PL:SB 0/1:25,14:39:99:354,0,595:14,11,3,11 chr2 11053020 . A G 7564.51 PASS AC=2;AF=0.864;AN=2;DP=12418;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,325:325:99:9979,974,0:0,0,144,181 chr2 11053740 . C T 3944.57 PASS AC=1;AF=0.679;AN=2;DP=6479;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:89,102:191:99:2388,0,2402:45,44,51,51 chr2 11264830 . G A 1625.61 PASS AC=2;AF=0.737;AN=2;DP=3299;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:1814,179,0:0,0,33,27 chr2 11273123 . TCACACACACACACACACACACACA TCACACACACACACACACACACA,TCACACACACACACACACACACACACACA,TCACACACACACACACACACACACACA,TCACACACACACACACACA,T,TCACACACACACACACACACACACACACACA,TCACACACACACACACACACA,TCACACACACACACACACACACACACACACACACACA,TCACACACACACACACA 78.78 PASS AC=2,0,0,0,0,0,0,0,0;AF=0.405,0.135,0.095,0.027,0.014,0.014,0.027,0.014,0.014;AN=2;DP=702;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:DP:GQ:SB 1/1:24:72:0,0,14,10 chr2 11273407 . GTC GTCTC,G,GTCTCTC,GTCTCTCTC 604.76 PASS AC=0,1,0,0;AF=0.081,0.267,0.151,0.012;AN=2;DP=5059;set=variant-variant2-variant3-variant4-filterInvariant5-variant6-variant7-filterInvariant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-filterInvariant18-filterInvariant19-variant20-filterInvariant21-variant22-variant23-filterInvariant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-filterInvariant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-filterInvariant44 GT:DP:GQ:SB 0/2:132:99:64,51,9,8 chr2 11284947 . C CT,CTTT 60.25 PASS AC=2,0;AF=0.882,0.026;AN=2;DP=329;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:DP:GQ:SB 1/1:4:12:0,0,2,2 chr2 11295226 . C CG 189.48 PASS AC=2;AF=0.963;AN=2;DP=358;FS=0;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:163,15,0:0,0,5,0 chr2 11295867 . G C 3409.12 PASS AC=2;AF=0.768;AN=2;DP=3829;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,111:112:99:3252,290,0:0,1,45,66 chr2 11300732 . C T 5598.33 PASS AC=1;AF=0.643;AN=2;DP=6171;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:113,84:197:99:1818,0,2886:62,51,45,39 chr2 11300869 . T C 4139.53 PASS AC=2;AF=0.898;AN=2;DP=5113;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,100:100:99:3344,298,0:0,0,38,62 chr2 11300927 . TAAAA TA,T,TAA,TAAA 806.59 PASS AC=0,1,0,0;AF=0.364,0.303,0.015,0.015;AN=2;DP=1462;set=variant-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-filterInvariant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:28:99:3,17,2,6 chr2 11312181 . G A 2351.17 PASS AC=1;AF=0.605;AN=2;DP=2931;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,42:82:99:1120,0,1032:13,27,13,29 chr2 11312224 . C T 1482.96 PASS AC=1;AF=0.61;AN=2;DP=1473;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,21:34:99:776,0,479:0,13,1,20 chr2 11318191 . G GAGA 7340.61 PASS AC=1;AF=0.59;AN=2;DP=11970;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:160,159:319:99:6197,0,6525:74,86,78,81 chr2 11318224 . CCCATTTTGAGG C 11893.7 PASS AC=1;AF=0.571;AN=2;DP=8879;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:131,111:242:99:2536,0,5790:56,75,45,66 chr2 11318457 . G A 2648.36 PASS AC=1;AF=0.628;AN=2;DP=2788;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,42:72:99:1215,0,884:20,10,25,17 chr2 11318477 . C T 3055.36 PASS AC=2;AF=0.852;AN=2;DP=4058;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,100:100:99:3302,299,0:0,0,62,38 chr2 11320877 . C T 15519 PASS AC=1;AF=0.595;AN=2;DP=16448;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:227,226:453:99:5457,0,5695:117,110,115,111 chr2 11322137 . A AAAAAAC 5796.68 PASS AC=1;AF=0.628;AN=2;DP=5074;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,60:116:99:2446,0,3052:37,19,35,25 chr2 11323078 . CTATA CTA,C 3015.38 PASS AC=2,0;AF=0.852,0.023;AN=2;DP=4837;MQ=60;set=Intersection GT:DP:GQ:SB 1/1:71:99:0,1,25,45 chr2 11323276 . T C 2859.59 PASS AC=1;AF=0.595;AN=2;DP=3860;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,59:126:99:1478,0,1693:28,39,25,34 chr2 11333994 . T G 922.37 PASS AC=1;AF=0.5;AN=2;DP=1537;MQ=60;set=variant2-variant3-variant6-variant7-variant9-variant13-variant14-variant15-variant16-variant17-variant18-variant25-variant26-variant27-variant28-variant33-variant35-variant36-variant37-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,34:68:99:811,0,861:12,22,13,21 chr2 11348364 . C CTAACT 409.21 PASS AC=1;AF=0.618;AN=2;DP=562;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,4:14:99:138,0,674:8,2,3,1 chr2 11348609 . CAAAT C 1028.15 PASS AC=1;AF=0.595;AN=2;DP=937;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,10:19:99:393,0,498:3,6,2,8 chr2 11356190 . G A 1101.45 PASS AC=1;AF=0.595;AN=2;DP=1085;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,18:30:99:469,0,305:8,4,12,6 chr2 11359031 . G T 1352.23 PASS AC=2;AF=0.875;AN=2;DP=1453;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1063,107,0:0,0,25,11 chr2 11359120 . G T 3095.96 PASS AC=1;AF=0.615;AN=2;DP=3459;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,40:83:99:954,0,1014:26,17,25,15 chr2 11359399 . A C 181.36 PASS AC=1;AF=0.645;AN=2;DP=239;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant11-variant12-variant13-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,2:3:26:81,0,26:0,1,0,2 chr2 11484462 . A G,AGCCCG 2107.47 PASS AC=0,1;AF=0.061,0.53;AN=2;DP=1345;MQ=60;set=variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant2-variant40-variant42-variant44 GT:DP:GQ:SB 0/2:40:99:10,11,11,8 chr2 11593496 . A G 363.18 PASS AC=2;AF=0.673;AN=2;DP=225;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant12-variant13-variant14-variant15-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant30-variant35-variant36-variant37-variant38-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:167,12,0:0,0,3,1 chr2 11674295 . A C 676.92 PASS AC=1;AF=0.643;AN=2;DP=740;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant32-variant35-variant36-variant37-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,17:25:99:406,0,157:5,3,9,8 chr2 11680896 . CAA C 1717.79 PASS AC=1;AF=0.712;AN=2;DP=1016;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:21,17:38:99:611,0,855:4,17,6,11 chr2 11682754 . C CG 501.78 PASS AC=1;AF=0.816;AN=2;DP=154;MQ=60;set=variant3-variant7-variant9-variant12-variant13-variant15-variant23-variant24-variant26-variant27-variant28-variant30-variant31-variant33-variant35-variant36-variant37-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:8,4:12:88:88,0,212:8,0,3,1 chr2 11682796 . A T 128.27 PASS AC=1;AF=0.712;AN=2;DP=561;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:15,8:23:99:169,0,416:10,5,5,3 chr2 11683074 . T G 61.77 PASS AC=1;AF=0.75;AN=2;DP=179;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:3,7:10:66:169,0,66:1,2,2,5 chr2 11702661 . A C 593.22 PASS AC=1;AF=0.597;AN=2;DP=1584;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:35,21:56:99:475,0,740:15,20,11,10 chr2 11720986 . G A 2157.17 PASS AC=1;AF=0.556;AN=2;DP=1150;set=variant3-variant7-variant8-variant14-variant31-variant33-variant35-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:75,55:130:99:1548,0,2025:32,43,26,29 chr2 11725179 . G GA 754.25 PASS AC=1;AF=0.613;AN=2;DP=2442;MQ=60;set=variant2-variant3-variant4-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,37:97:99:694,0,1366:34,26,25,12 chr2 11725241 . G A 1313.02 PASS AC=1;AF=0.633;AN=2;DP=4444;MQ=60;set=variant2-variant3-variant4-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant35-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:98,72:170:99:1622,0,2365:47,51,41,31 chr2 11725947 . T C 1643.04 PASS AC=1;AF=0.536;AN=2;DP=1873;MQ=60;set=variant3-variant5-variant7-variant8-variant10-variant14-variant15-variant26-variant31-variant32-variant33-variant35-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:74,59:133:99:1523,0,1833:43,31,35,24 chr2 11726061 . G GA 1742.89 PASS AC=1;AF=0.567;AN=2;DP=1605;MQ=60;set=variant3-variant5-variant7-variant8-variant10-variant14-variant15-variant26-variant31-variant32-variant33-variant34-variant35-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:70,58:128:99:1813,0,2207:32,38,27,31 chr2 11727393 . TG T 3087.94 PASS AC=1;AF=0.536;AN=2;DP=1946;MQ=60;set=variant3-variant5-variant7-variant8-variant10-variant14-variant15-variant26-variant31-variant32-variant33-variant35-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:92,72:164:99:2349,0,3196:56,36,44,28 chr2 11727507 . G A 1986.52 PASS AC=2;AF=0.688;AN=2;DP=8499;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,243:244:99:7432,704,0:0,1,113,130 chr2 11727819 . TAACACACACACACA TCACA,TCA,T,TCACACACACA 197.34 PASS AC=1,0,0,0;AF=0.409,0.045,0.045,0.045;AN=2;DP=156;set=variant3-variant5-variant7-variant8-variant10-variant15-variant26-variant31-variant32-variant33-variant35 GT:DP:GQ:SB 0/1:12:99:2,4,3,3 chr2 11727988 . G C 394.5 PASS AC=2;AF=0.688;AN=2;DP=1441;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:957,99,0:0,0,14,19 chr2 11728080 . G A 209.31 PASS AC=1;AF=0.617;AN=2;DP=389;FractionInformativeReads=1;set=variant2-variant3-variant4-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant35-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,7:9:99:264,0,142:1,1,2,5 chr2 11728089 . C T 187.58 PASS AC=1;AF=0.638;AN=2;DP=334;FractionInformativeReads=1;set=variant2-variant4-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant35-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,5:8:99:201,0,191:1,2,1,4 chr2 11728381 . T C 553.45 PASS AC=2;AF=0.688;AN=2;DP=1042;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:1033,84,0:0,0,17,11 chr2 11728388 . T C 589.2 PASS AC=1;AF=0.633;AN=2;DP=850;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant35-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,17:31:99:389,0,241:8,6,10,7 chr2 11729096 . G A 1054.87 PASS AC=1;AF=0.567;AN=2;DP=680;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant7-variant8-variant10-variant14-variant15-variant26-variant31-variant32-variant33-variant34-variant35-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:33,27:60:99:864,0,1024:8,25,4,23 chr2 11731774 . T G 1341.55 PASS AC=2;AF=0.688;AN=2;DP=4188;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,83:83:99:3026,249,0:0,0,53,30 chr2 11731846 . T C 2565.92 PASS AC=2;AF=0.688;AN=2;DP=8237;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,211:211:99:6848,632,0:0,0,132,79 chr2 11733488 . G T 31.75 PASS AC=2;AF=0.672;AN=2;DP=350;MQ=60;set=variant2-variant3-variant4-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant35-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:551,48,0:0,0,4,12 chr2 11736037 . A G 246.04 PASS AC=2;AF=0.675;AN=2;DP=727;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:1002,78,0:0,0,21,5 chr2 11736305 . G A 1809.08 PASS AC=1;AF=0.533;AN=2;DP=2269;MQ=60;set=variant3-variant5-variant7-variant8-variant10-variant14-variant15-variant26-variant31-variant32-variant33-variant34-variant35-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:82,106:188:99:2454,0,1830:33,49,55,51 chr2 11738091 . T C 6729.62 PASS AC=2;AF=0.989;AN=2;DP=11138;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,297:297:99:9097,889,0:0,0,132,165 chr2 11738765 . C T 1148.05 PASS AC=2;AF=0.977;AN=2;DP=1182;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:998,84,0:0,0,23,5 chr2 11741157 . A G 784.21 PASS AC=1;AF=0.6;AN=2;DP=469;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant19-variant22-variant24-variant35-variant37-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:14,14:28:99:503,0,320:5,9,1,13 chr2 11741193 . C A 263.61 PASS AC=2;AF=0.989;AN=2;DP=774;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.371;ReadPosRankSum=-1.66;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:706,57,0:0,0,3,16 chr2 11742458 . A G 707.47 PASS AC=1;AF=0.625;AN=2;DP=785;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,16:27:99:465,0,315:9,2,12,4 chr2 11751166 . C T 3421.52 PASS AC=1;AF=0.6;AN=2;DP=1132;MQ=60;set=variant3-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant19-variant22-variant24-variant35-variant37-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:56,40:96:99:924,0,1503:20,36,15,25 chr2 11752635 . T C 2978.82 PASS AC=2;AF=1;AN=2;DP=3347;FS=0;MQ=60;MQRankSum=1.256;ReadPosRankSum=0.52;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:1713,165,0:0,0,24,31 chr2 11755443 . T G 475.52 PASS AC=1;AF=0.854;AN=2;DP=1075;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,11:24:99:306,0,398:3,10,1,10 chr2 11757009 . A G 1645.34 PASS AC=2;AF=0.989;AN=2;DP=2564;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1642,150,0:0,0,20,30 chr2 11757023 . C T 1466.49 PASS AC=1;AF=0.724;AN=2;DP=2066;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,31:51:99:831,0,489:10,10,11,20 chr2 11757076 . G C 1205.02 PASS AC=1;AF=0.737;AN=2;DP=1414;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,22:37:99:838,0,555:5,10,8,14 chr2 11757086 . G A 1096.77 PASS AC=1;AF=0.737;AN=2;DP=1285;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,20:34:99:798,0,507:5,9,7,13 chr2 11757140 . G A 1059.3 PASS AC=1;AF=0.607;AN=2;DP=257;MQ=60;set=variant3-variant7-variant8-variant9-variant12-variant13-variant14-variant19-variant22-variant24-variant35-variant37-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:8,9:17:99:270,0,228:2,6,2,7 chr2 11758262 . CACTCCTGGGACAGGTCACTCCTGGGATGGGTGACTCCTGGGACAGGTCACTCCTGGGATGGGTG C,CACTCCTGGGACAGGTCACTCCTGGGATGGGTGACTCCTGGGACAGGTCACTCCTGGGATGGGTGACTCCTGGGACAGGTCACTCCTGGGATGGGTG,CACTCCTGGGACAGGTCACTCCTGGGATGGGTG 630.61 PASS AC=0,2,0;AF=0.125,0.25,0.25;AN=2;DP=117;set=variant34-variant35-variant39-variant43 GT:DP:GQ:SB 2/2:0:15:0,0,0,0 chr2 11761309 . T C 1241.95 PASS AC=2;AF=0.977;AN=2;DP=1495;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:1070,87,0:0,0,6,23 chr2 11774324 . G A 2083.55 PASS AC=1;AF=0.614;AN=2;DP=6734;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:124,145:269:99:3475,0,2871:60,64,70,75 chr2 11778184 . G A 712.73 PASS AC=1;AF=0.523;AN=2;DP=1255;MQ=60;set=variant4-variant5-variant8-variant10-variant14-variant16-variant17-variant18-variant20-variant21-variant24-variant25-variant26-variant30-variant32-variant33-variant34-variant35-variant36-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:34,37:71:99:973,0,826:11,23,12,25 chr2 11781268 . G T 901.31 PASS AC=1;AF=0.5;AN=2;DP=429;MQ=60;set=variant6-variant19-variant22-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,23:76:99:822,0,3190:38,15,20,3 chr2 11781279 . T TGG 1027.71 PASS AC=1;AF=0.5;AN=2;DP=447;MQ=60;set=variant6-variant19-variant22-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,22:76:99:975,0,3458:39,15,21,1 chr2 11781282 . C G 1039.38 PASS AC=1;AF=0.5;AN=2;DP=480;MQ=60;set=variant6-variant19-variant22-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,28:85:99:909,0,3422:41,16,24,4 chr2 11781450 . G C 1988.54 PASS AC=1;AF=0.5;AN=2;DP=891;FractionInformativeReads=1;MQ=60;set=variant6-variant19-variant22-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:102,69:171:99:1433,0,2627:41,61,28,41 chr2 11781593 . G GGTTTT,GGTTTTGTTTTGTTTT,GGTTTGGTTTTGTTTT,GGTTTTGTTTT 501.12 PASS AC=0,0,0,1;AF=0.238,0.338,0.013,0.113;AN=2;DP=937;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/4:7:78:0,1,1,5 chr2 11782191 . C A 191.03 PASS AC=1;AF=0.5;AN=2;DP=105;FractionInformativeReads=1;MQ=60;set=variant6-variant19-variant22-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,10:18:99:255,0,201:2,6,6,4 chr2 11782246 . C CT 44.7 PASS AC=1;AF=0.6;AN=2;DP=52;MQ=60;set=variant6-variant19-variant22-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:97:97,0,157:0,4,2,2 chr2 11782258 . G T 50.76 PASS AC=1;AF=0.6;AN=2;DP=36;MQ=60;set=variant6-variant19-variant22-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,5:9:99:161,0,151:0,4,2,3 chr2 11782310 . C T 156.22 PASS AC=2;AF=0.986;AN=2;DP=177;FS=0;MQ=60;MQRankSum=0.358;ReadPosRankSum=1.231;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:180,12,0:0,0,2,2 chr2 11782314 . G A 96.01 PASS AC=2;AF=1;AN=2;DP=9;FS=0;MQ=60;set=variant22-variant35 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:180,12,0:0,0,2,2 chr2 11782785 . A G 1151.43 PASS AC=1;AF=0.5;AN=2;DP=482;FractionInformativeReads=1;MQ=60;set=variant6-variant19-variant22-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,47:93:99:1142,0,1175:32,14,25,22 chr2 11782948 . C T 334.07 PASS AC=1;AF=0.5;AN=2;DP=179;FractionInformativeReads=1;MQ=60;set=variant6-variant19-variant22-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,22:44:99:516,0,639:4,18,8,14 chr2 11810095 . G A 4394.69 PASS AC=2;AF=0.989;AN=2;DP=6292;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,168:168:99:5449,502,0:0,0,74,94 chr2 11810488 . C G 174.68 PASS AC=1;AF=0.536;AN=2;DP=220;MQ=60;set=variant2-variant3-variant10-variant14-variant15-variant16-variant20-variant21-variant23-variant24-variant34-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,11:23:99:342,0,388:2,10,2,9 chr2 11817812 . G C 1074.72 PASS AC=1;AF=0.75;AN=2;DP=5506;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:80,66:146:99:1620,0,2099:47,33,43,23 chr2 11853988 . A T 917.89 PASS AC=1;AF=0.662;AN=2;DP=3291;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,52:94:99:1204,0,962:20,22,31,21 chr2 11854012 . G A 3010.23 PASS AC=1;AF=0.542;AN=2;DP=1084;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant10-variant18-variant19-variant20-variant27-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:47,38:85:99:793,0,1145:27,20,19,19 chr2 11854099 . T C 322.48 PASS AC=1;AF=0.662;AN=2;DP=1407;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,24:39:99:692,0,345:5,10,6,18 chr2 11905636 . GT G 2185.28 PASS AC=2;AF=0.697;AN=2;DP=2839;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant31-variant33-variant35-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,83:84:99:2460,223,0:0,1,48,35 chr2 11905876 . C T 1721.25 PASS AC=2;AF=0.596;AN=2;DP=1264;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant28-variant29-variant31-variant33-variant35-variant36-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1697,153,0:0,0,19,32 chr2 11917278 . T C 1159.01 PASS AC=2;AF=0.596;AN=2;DP=1291;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant28-variant29-variant31-variant33-variant35-variant36-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1667,153,0:0,0,36,15 chr2 11917519 . G A 2921.52 PASS AC=2;AF=0.636;AN=2;DP=3627;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,101:101:99:3185,302,0:0,0,48,53 chr2 11924950 . T C 494.29 PASS AC=2;AF=0.689;AN=2;DP=2713;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,80:80:99:2554,240,0:0,0,49,31 chr2 11931931 . A AT 875.51 PASS AC=2;AF=0.571;AN=2;DP=823;MQ=60;set=variant2-variant4-variant5-variant7-variant9-variant14-variant15-variant16-variant20-variant23-variant28-variant29-variant35-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1512,159,0:0,0,30,23 chr2 11932173 . G T 298.55 PASS AC=2;AF=0.639;AN=2;DP=1210;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1126,108,0:0,0,11,25 chr2 11936798 . A G 346.77 PASS AC=2;AF=0.639;AN=2;DP=1041;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1183,102,0:0,0,24,10 chr2 11945108 . GT GTT,G,GTTT 145.75 PASS AC=0,1,0;AF=0.34,0.14,0.02;AN=2;DP=1666;set=filterInvariant-filterInvariant4-filterInvariant7-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant15-variant17-filterInvariant18-filterInvariant20-filterInvariant21-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant29-filterInvariant30-variant31-filterInvariant35-filterInvariant36-filterInvariant37-variant40-filterInvariant41-variant42-filterInvariant43-filterInvariant44 GT:DP:GQ:SB 0/2:48:99:22,15,5,6 chr2 11965541 . A G 2834.89 PASS AC=1;AF=0.795;AN=2;DP=9848;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:120,110:230:99:2492,0,2964:65,55,58,52 chr2 12164120 . C T 537.64 PASS AC=1;AF=0.5;AN=2;DP=65;FS=3.535;FractionInformativeReads=1;MQ=59.98;MQRankSum=0.432;QD=8.27;ReadPosRankSum=-2.12;SOR=0.839;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:42,23:65:99:566,0,1042:19,23,13,10 chr2 12164189 . C T 581.72 PASS AC=1;AF=0.756;AN=2;DP=2355;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,29:55:99:764,0,628:15,11,13,16 chr2 12857012 . CG CGG,C,CGGG 78.14 PASS AC=1,0,0;AF=0.542,0.042,0.125;AN=2;DP=103;MQ=60;set=variant4-variant5-variant10-variant14-variant17-variant18-variant20-variant22-variant24-variant27-variant29-variant35 GT:DP:GQ:SB 0/1:7:64:2,1,3,1 chr2 12877307 . C G,T 121.62 PASS AC=2,0;AF=0.603,0.147;AN=2;DP=1138;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:48:99:0,0,31,17 chr2 12877501 . G GA 474.32 PASS AC=2;AF=0.769;AN=2;DP=4557;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,140:140:99:5578,421,0:0,0,76,64 chr2 12881778 . T A 3514.58 PASS AC=2;AF=0.656;AN=2;DP=10414;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,348:348:99:10771,1042,0:0,0,152,196 chr2 12882822 . ATC A 39.73 PASS AC=2;AF=0.683;AN=2;DP=404;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant23-variant24-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:445,30,0:0,0,4,6 chr2 15319070 . TA T 489.03 PASS AC=1;AF=0.648;AN=2;DP=1344;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant13-variant14-variant16-variant19-variant20-variant21-variant23-variant24-variant26-variant29-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,16:50:99:276,0,744:21,13,10,6 chr2 15378822 . G GAATT 277.58 PASS AC=2;AF=0.955;AN=2;DP=474;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:405,27,0:0,0,2,7 chr2 15471027 . T C 278.88 PASS AC=1;AF=0.6;AN=2;DP=199;MQ=60;set=variant2-variant6-variant7-variant9-variant11-variant13-variant14-variant16-variant19-variant20-variant23-variant26-variant29-variant30-variant31-variant35-variant36-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,3:5:76:120,0,76:0,2,0,3 chr2 15491994 . GCACACACACACA G,GCA,GCACACACACA,GCACA,GCACACACACACACACACACA,GCACACACA 1434.63 PASS AC=1,1,0,0,0,0;AF=0.186,0.512,0.035,0.012,0.012,0.023;AN=2;DP=2649;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/2:54:87:0,0,36,18 chr2 15493881 . A G 2166.01 PASS AC=2;AF=0.795;AN=2;DP=2678;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:2636,231,0:0,0,24,53 chr2 15519992 . G T 1749.23 PASS AC=2;AF=0.798;AN=2;DP=2123;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1525,149,0:0,0,18,32 chr2 15523266 . A T 340.68 PASS AC=2;AF=0.976;AN=2;DP=724;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:675,72,0:0,0,14,10 chr2 15523307 . TA T 1132.54 PASS AC=2;AF=0.8;AN=2;DP=1398;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-filterInvariant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1181,120,0:0,0,24,16 chr2 15523549 . T C 639.53 PASS AC=2;AF=0.813;AN=2;DP=665;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:775,66,0:0,0,4,18 chr2 15533689 . T C 998.69 PASS AC=2;AF=0.798;AN=2;DP=1430;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:887,84,0:0,0,19,9 chr2 15533734 . G GAAATGAAAGCGTATGTCTACAC 2768.64 PASS AC=2;AF=0.798;AN=2;DP=2571;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:3052,201,0:0,0,39,18 chr2 15533779 . G A 2940.18 PASS AC=2;AF=0.798;AN=2;DP=4941;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,123:123:99:3706,369,0:0,0,67,56 chr2 15533884 . C A 2299.96 PASS AC=2;AF=0.798;AN=2;DP=3046;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:3210,232,0:0,0,30,47 chr2 15533895 . A G 2176.77 PASS AC=2;AF=0.8;AN=2;DP=2438;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:2902,202,0:0,0,22,40 chr2 15533899 . A G 2041.77 PASS AC=2;AF=0.798;AN=2;DP=2381;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:2553,172,0:0,0,17,39 chr2 15564718 . T C 598.24 PASS AC=2;AF=0.786;AN=2;DP=565;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:32:326,32,0:0,0,2,9 chr2 15567649 . T C 588.92 PASS AC=2;AF=0.798;AN=2;DP=905;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1095,99,0:0,0,24,9 chr2 15601287 . A AT 1103.84 PASS AC=2;AF=0.798;AN=2;DP=992;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:818,63,0:0,0,14,7 chr2 15601441 . C T 2027.14 PASS AC=2;AF=0.798;AN=2;DP=3361;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:2099,230,0:0,0,34,43 chr2 15601574 . C T 327.99 PASS AC=2;AF=0.798;AN=2;DP=482;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:250,18,0:0,0,0,6 chr2 15607842 . T C 2265.54 PASS AC=2;AF=0.795;AN=2;DP=3818;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,117:117:99:3434,350,0:0,0,56,61 chr2 15608013 . C A 250.68 PASS AC=2;AF=0.805;AN=2;DP=547;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:437,36,0:0,0,2,10 chr2 15613678 . T C 242.99 PASS AC=2;AF=0.8;AN=2;DP=729;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:510,45,0:0,0,5,10 chr2 15613715 . G A 190.3 PASS AC=2;AF=0.829;AN=2;DP=346;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:178,15,0:0,0,1,4 chr2 15614404 . T C 1239.93 PASS AC=2;AF=0.798;AN=2;DP=3306;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,91:91:99:2751,272,0:0,0,35,56 chr2 15615910 . A G 3120.86 PASS AC=2;AF=0.8;AN=2;DP=4338;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,103:103:99:2942,308,0:0,0,54,49 chr2 15616013 . C G 755.26 PASS AC=2;AF=0.8;AN=2;DP=2019;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1507,152,0:0,0,18,33 chr2 15616030 . C T 554.71 PASS AC=2;AF=0.8;AN=2;DP=1525;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1186,111,0:0,0,11,26 chr2 15618339 . G A 1095.03 PASS AC=2;AF=0.798;AN=2;DP=1735;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1156,108,0:0,0,24,12 chr2 15623608 . C G 745.72 PASS AC=2;AF=0.805;AN=2;DP=595;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:391,33,0:0,0,1,10 chr2 15644107 . C A 761.49 PASS AC=2;AF=0.763;AN=2;DP=742;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:87:1280,87,0:0,0,24,2 chr2 15644111 . C T 798.26 PASS AC=2;AF=0.776;AN=2;DP=830;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:1317,90,0:0,0,28,2 chr2 15644401 . C T 1106.04 PASS AC=2;AF=0.769;AN=2;DP=1509;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1217,99,0:0,0,7,26 chr2 15674686 . T C 2427.06 PASS AC=2;AF=0.788;AN=2;DP=4325;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,87:87:99:2584,261,0:0,0,44,43 chr2 15676686 . G A 1414.57 PASS AC=2;AF=0.798;AN=2;DP=2064;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:1393,139,0:0,0,18,29 chr2 15678368 . C T 242.08 PASS AC=2;AF=0.8;AN=2;DP=753;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,31:31:93:972,93,0:0,0,21,10 chr2 15678482 . T C 1110.97 PASS AC=2;AF=0.8;AN=2;DP=1921;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:1883,174,0:0,0,30,28 chr2 15678501 . GA G 1191.06 PASS AC=2;AF=0.813;AN=2;DP=1933;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1573,159,0:0,0,26,27 chr2 15679609 . A T 131.48 PASS AC=2;AF=0.838;AN=2;DP=231;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:170,12,0:0,0,0,4 chr2 15691886 . G A 560.6 PASS AC=2;AF=0.8;AN=2;DP=761;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:842,63,0:0,0,2,19 chr2 15694164 . T TA 1496.78 PASS AC=2;AF=0.798;AN=2;DP=1715;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1493,111,0:0,0,23,14 chr2 15731583 . C T 1287.11 PASS AC=1;AF=0.567;AN=2;DP=618;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant9-variant10-variant13-variant18-variant21-variant24-variant27-variant32-variant35-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:15,24:39:99:724,0,424:12,3,16,8 chr2 15731605 . C T 1708.91 PASS AC=1;AF=0.692;AN=2;DP=2244;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,33:60:99:951,0,753:21,6,23,10 chr2 15731859 . A C 5555.12 PASS AC=1;AF=0.692;AN=2;DP=7105;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:81,104:185:99:2655,0,1914:37,44,45,59 chr2 15731904 . T C 1705.48 PASS AC=1;AF=0.5;AN=2;DP=453;MQ=60;set=variant-variant18-variant35 GT:AD:DP:GQ:PL:SB 0/1:76,78:154:99:2423,0,2008:38,38,35,43 chr2 15731998 . A G 6690.76 PASS AC=1;AF=0.692;AN=2;DP=7836;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:93,112:205:99:2925,0,2264:58,35,70,42 chr2 15732238 . G C 2604.07 PASS AC=1;AF=0.567;AN=2;DP=980;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant9-variant10-variant13-variant18-variant21-variant24-variant27-variant32-variant35-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:34,40:74:99:1132,0,1004:7,27,8,32 chr2 15737480 . C A 736.1 PASS AC=1;AF=0.567;AN=2;DP=550;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant9-variant10-variant13-variant18-variant21-variant24-variant27-variant32-variant35-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:17,29:46:99:691,0,384:10,7,18,11 chr2 15737698 . G A 127.77 PASS AC=1;AF=0.667;AN=2;DP=327;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant13-variant14-variant18-variant20-variant21-variant23-variant24-variant26-variant27-variant31-variant32-variant34-variant35-variant36-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:4,9:13:99:319,0,144:0,4,1,8 chr2 15744123 . T G 1606.94 PASS AC=1;AF=0.567;AN=2;DP=722;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant9-variant10-variant13-variant18-variant21-variant24-variant27-variant32-variant35-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:21,30:51:99:792,0,446:8,13,10,20 chr2 15747393 . C T 3465.37 PASS AC=1;AF=0.681;AN=2;DP=3730;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,43:91:99:1005,0,1271:16,32,18,25 chr2 15753307 . AT ATT,A 277.84 PASS AC=2,0;AF=0.6,0.033;AN=2;DP=255;MQ=60;set=variant-variant5-variant9-variant10-variant13-variant21-variant24-variant27-variant32-variant34-variant35-variant38-variant40-variant41-variant42 GT:DP:GQ:SB 1/1:20:6:1,1,10,8 chr2 15753482 . C G 1118.89 PASS AC=1;AF=0.571;AN=2;DP=596;MQ=60;set=variant-variant5-variant9-variant10-variant18-variant21-variant24-variant27-variant32-variant35-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:18,19:37:99:457,0,460:9,9,11,8 chr2 15753604 . A G 419.03 PASS AC=1;AF=0.571;AN=2;DP=206;MQ=60;set=variant-variant5-variant9-variant10-variant18-variant21-variant24-variant27-variant32-variant35-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:4,7:11:99:262,0,150:0,4,0,7 chr2 15758293 . T C 2179.28 PASS AC=1;AF=0.567;AN=2;DP=726;MQ=60;set=variant-variant5-variant9-variant10-variant13-variant18-variant21-variant24-variant27-variant32-variant35-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:23,16:39:99:354,0,586:13,10,9,7 chr2 15763788 . C T 205.68 PASS AC=1;AF=0.567;AN=2;DP=155;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant9-variant10-variant13-variant18-variant21-variant24-variant27-variant32-variant35-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:5,3:8:70:70,0,182:0,5,1,2 chr2 15768846 . AT A 3921.52 PASS AC=1;AF=0.567;AN=2;DP=1832;MQ=60;set=variant-variant5-variant9-variant10-variant13-variant18-variant21-variant24-variant27-variant32-variant35-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:47,44:91:99:1065,0,1146:24,23,22,22 chr2 15768981 . C G 524.49 PASS AC=1;AF=0.63;AN=2;DP=1085;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant22-variant25-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,15:22:99:531,0,173:0,7,1,14 chr2 15770061 . G A 973.12 PASS AC=1;AF=0.567;AN=2;DP=332;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant9-variant10-variant13-variant18-variant21-variant24-variant27-variant32-variant35-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:12,12:24:99:375,0,376:9,3,9,3 chr2 15771285 . T C 220.28 PASS AC=1;AF=0.5;AN=2;DP=62;FractionInformativeReads=1;MQ=60;set=variant-variant18-variant35 GT:AD:DP:GQ:PL:SB 0/1:24,12:36:99:341,0,766:4,20,1,11 chr2 15840505 . C A 1152.15 PASS AC=2;AF=0.663;AN=2;DP=3525;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:2355,225,0:0,0,39,36 chr2 15840522 . G T 1197.97 PASS AC=2;AF=0.663;AN=2;DP=3719;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:2239,224,0:0,0,37,38 chr2 15840645 . T C 712.05 PASS AC=2;AF=0.686;AN=2;DP=2436;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,52:52:99:1566,155,0:0,0,19,33 chr2 15841230 . T A 317.15 PASS AC=2;AF=0.675;AN=2;DP=447;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:293,21,0:0,0,7,0 chr2 15841288 . G A 392.67 PASS AC=2;AF=0.663;AN=2;DP=1352;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:725,66,0:0,0,16,6 chr2 15884353 . G C 676.7 PASS AC=1;AF=0.5;AN=2;DP=85;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.726;QD=7.96;ReadPosRankSum=-1.195;SOR=0.61;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:52,33:85:99:705,0,1233:31,21,19,14 chr2 16080813 . A C 141.26 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=485;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:98,27:125:63:63,0,2183:29,69,27,0 chr2 16731572 . CA CAA,C,CAAA 149.3 PASS AC=0,1,0;AF=0.458,0.083,0.021;AN=2;DP=884;set=variant-variant2-variant6-filterInvariant7-variant10-variant11-variant13-variant20-variant21-variant23-variant24-filterInvariant25-variant26-variant28-variant30-variant32-variant34-variant35-variant36-filterInvariant38-variant40-variant41-variant42-variant44 GT:DP:GQ:SB 0/2:41:99:13,18,5,5 chr2 16734295 . A G 986.07 PASS AC=1;AF=0.5;AN=2;DP=753;FractionInformativeReads=1;MQ=60;set=variant5-variant6-variant7-variant8-variant16-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:55,54:109:99:1398,0,1294:23,32,26,28 chr2 16743453 . A C 803.1 PASS AC=1;AF=0.574;AN=2;DP=3303;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,57:105:99:1413,0,1256:20,28,21,36 chr2 16805318 . G A 321.74 PASS AC=1;AF=0.682;AN=2;DP=477;FractionInformativeReads=1;MQ=60;set=variant3-variant8-variant12-variant13-variant16-variant17-variant18-variant21-variant22-variant24-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,8:21:99:297,0,669:3,10,3,5 chr2 16805324 . C A 258.01 PASS AC=1;AF=0.682;AN=2;DP=442;FractionInformativeReads=1;MQ=60;set=variant3-variant8-variant12-variant13-variant16-variant17-variant18-variant21-variant22-variant24-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,8:20:99:300,0,636:3,9,3,5 chr2 16805353 . T G 96.25 PASS AC=1;AF=0.682;AN=2;DP=344;MQ=60;set=variant3-variant8-variant12-variant13-variant16-variant17-variant18-variant21-variant22-variant24-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,8:16:99:190,0,234:2,6,3,5 chr2 17691950 . CA C 2780.24 PASS AC=1;AF=0.684;AN=2;DP=4381;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,51:90:99:1159,0,819:24,15,32,19 chr2 17696573 . C T 3983.54 PASS AC=1;AF=0.684;AN=2;DP=6305;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:116,73:189:99:1679,0,2791:65,51,38,35 chr2 17698678 . A G 1922.25 PASS AC=1;AF=0.711;AN=2;DP=2986;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,51:94:99:1578,0,1277:19,24,18,33 chr2 17722597 . T C 4331.58 PASS AC=2;AF=0.989;AN=2;DP=6274;FS=0;MQ=60;MQRankSum=-0.529;ReadPosRankSum=0.183;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,155:155:99:5096,463,0:0,0,104,51 chr2 17722654 . G A 2184.27 PASS AC=1;AF=0.575;AN=2;DP=4881;MQ=60;set=variant2-variant3-variant9-variant12-variant13-variant14-variant15-variant16-variant20-variant21-variant22-variant24-variant26-variant28-variant31-variant33-variant34-variant35-variant36-variant40 GT:AD:DP:GQ:PL:SB 0/1:142,114:256:99:2667,0,3483:77,65,63,51 chr2 17773524 . G A 694.56 PASS AC=1;AF=0.731;AN=2;DP=1957;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,19:34:99:547,0,374:6,9,6,13 chr2 17836722 . TCACACACACA TCACACACACACACACACACA,TCACACACACACACACACA,TCACACA,TCACACACACACACA,TCACACACA,T,TCACACACACACA,TCACACACACACACACA,TCA 2518.13 PASS AC=0,0,0,1,0,0,1,0,0;AF=0.023,0.081,0.081,0.36,0.058,0.012,0.174,0.035,0.035;AN=2;DP=3671;set=variant-variant2-filterInvariant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 7/4:58:99:4,1,35,18 chr2 17837741 . C T 1800.7 PASS AC=1;AF=0.548;AN=2;DP=1814;MQ=60;set=variant-variant3-variant5-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant23-variant25-variant27-variant28-variant30-variant33-variant34-variant35-variant37-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:52,45:97:99:1425,0,1676:24,28,23,22 chr2 17837992 . A G 3264.92 PASS AC=1;AF=0.548;AN=2;DP=3914;set=variant-variant3-variant5-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant23-variant25-variant27-variant28-variant30-variant33-variant34-variant35-variant37-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:101,97:198:99:2401,0,2587:53,48,50,47 chr2 17845296 . A G 10896.7 PASS AC=1;AF=0.866;AN=2;DP=12972;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:172,157:329:99:3448,0,4003:90,82,77,80 chr2 17846162 . A G 477.66 PASS AC=1;AF=0.545;AN=2;DP=1361;MQ=60;set=variant-variant3-variant5-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant23-variant25-variant27-variant28-variant30-variant33-variant34-variant35-variant37-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:35,39:74:99:1031,0,1051:11,24,18,21 chr2 17846592 . A T 6526.84 PASS AC=1;AF=0.866;AN=2;DP=7630;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:114,78:192:99:1686,0,2854:69,45,46,32 chr2 17883218 . T A 372.72 PASS AC=1;AF=0.55;AN=2;DP=391;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant23-variant25-variant27-variant28-variant30-variant33-variant34-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:7,9:16:99:332,0,219:2,5,2,7 chr2 17884495 . C T 431.09 PASS AC=1;AF=0.548;AN=2;DP=1001;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant23-variant25-variant27-variant28-variant30-variant33-variant34-variant35-variant37-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:23,22:45:99:487,0,497:12,11,12,10 chr2 17888457 . G A 930.6 PASS AC=1;AF=0.643;AN=2;DP=2603;MQ=60;set=variant-variant3-variant5-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant19-variant23-variant24-variant25-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:52,39:91:99:949,0,1215:29,23,25,14 chr2 17897488 . T C 425.59 PASS AC=1;AF=0.5;AN=2;DP=885;MQ=60;set=variant-variant5-variant8-variant11-variant12-variant13-variant14-variant23-variant25-variant27-variant28-variant30-variant33-variant34-variant35-variant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:25,25:50:99:612,0,614:10,15,12,13 chr2 17898326 . C T 909.76 PASS AC=1;AF=0.643;AN=2;DP=2018;MQ=60;set=variant-variant3-variant5-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant19-variant23-variant24-variant25-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:38,29:67:99:643,0,932:23,15,17,12 chr2 17899558 . C G 122.16 PASS AC=1;AF=0.5;AN=2;DP=64;FS=0;FractionInformativeReads=1;MQ=60;set=variant5-variant8-variant11-variant13-variant25-variant27-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:1,3:4:34:116,0,34:0,1,0,3 chr2 17913266 . A C 1647.07 PASS AC=2;AF=1;AN=2;DP=1242;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:1066,84,0:0,0,5,23 chr2 17927275 . C T 276.51 PASS AC=1;AF=0.655;AN=2;DP=541;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant19-variant23-variant24-variant25-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,17:26:99:556,0,288:1,8,3,14 chr2 17934162 . T C 114.72 PASS AC=1;AF=0.588;AN=2;DP=185;MQ=60;set=variant3-variant5-variant8-variant10-variant12-variant13-variant14-variant25-variant27-variant28-variant33-variant35-variant36-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,5:12:99:135,0,200:5,2,3,2 chr2 17934826 . AAGG A 2140.31 PASS AC=1;AF=0.5;AN=2;DP=1114;MQ=60;set=variant5-variant8-variant11-variant13-variant23-variant25-variant27-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:68,76:144:99:2952,0,2895:44,24,51,25 chr2 17941423 . T G 198.72 PASS AC=1;AF=0.756;AN=2;DP=1512;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,23:53:99:705,0,892:8,22,4,19 chr2 17942775 . T A 816.53 PASS AC=1;AF=0.756;AN=2;DP=4027;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,68:113:99:1459,0,906:23,22,33,35 chr2 17954027 . G A 2304 PASS AC=2;AF=1;AN=2;DP=3510;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,86:86:99:2431,257,0:0,0,37,49 chr2 17954140 . A G 304.31 PASS AC=1;AF=0.756;AN=2;DP=998;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,10:19:99:364,0,262:2,7,3,7 chr2 17954421 . C G 1140.69 PASS AC=1;AF=0.756;AN=2;DP=2788;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,27:54:99:675,0,688:13,14,14,13 chr2 17954647 . T G 119.18 PASS AC=1;AF=0.784;AN=2;DP=261;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,5:9:99:154,0,103:1,3,1,4 chr2 17959420 . TAC T,TACAC 188.6 PASS AC=1,1;AF=0.564,0.115;AN=2;DP=796;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/2:17:99:0,2,1,14 chr2 17959441 . GTA G 487.77 PASS AC=1;AF=0.643;AN=2;DP=212;set=variant2-variant9-variant12-variant13-variant16-variant18-variant21-variant24-variant26-variant31-variant35-variant37-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:6,9:15:99:345,0,225:0,6,1,8 chr2 17962450 . A G 1297.68 PASS AC=1;AF=0.714;AN=2;DP=3464;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:63,71:134:99:1762,0,1527:34,29,37,34 chr2 17962518 . C T 1547.34 PASS AC=1;AF=0.756;AN=2;DP=4703;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:63,63:126:99:1599,0,1582:30,33,29,34 chr2 17962993 . CAAGTT C 945.71 PASS AC=1;AF=0.556;AN=2;DP=667;MQ=60;set=variant9-variant12-variant13-variant16-variant21-variant22-variant24-variant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:32,30:62:99:1163,0,1855:15,17,12,18 chr2 17965931 . G A 6569.43 PASS AC=1;AF=0.714;AN=2;DP=13970;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:219,224:443:99:5382,0,5575:124,95,123,101 chr2 17966157 . A G 2410.3 PASS AC=1;AF=0.756;AN=2;DP=5850;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:91,82:173:99:2129,0,2519:26,65,24,58 chr2 17966421 . T G 688.69 PASS AC=1;AF=0.756;AN=2;DP=1637;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,32:52:99:969,0,602:17,3,24,8 chr2 17981258 . C T 390.93 PASS AC=1;AF=0.694;AN=2;DP=773;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,9:18:99:301,0,309:8,1,7,2 chr2 17981308 . G T 753.51 PASS AC=1;AF=0.732;AN=2;DP=1829;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,21:56:99:805,0,1516:24,11,14,7 chr2 17981319 . C A 1557.2 PASS AC=1;AF=0.636;AN=2;DP=1223;FractionInformativeReads=1;MQ=60;set=variant2-variant9-variant10-variant11-variant12-variant13-variant16-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant31-variant32-variant35-variant36-variant37-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:45,25:70:99:865,0,1693:30,15,17,8 chr2 17981360 . G A 1858.14 PASS AC=1;AF=0.732;AN=2;DP=4198;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:71,45:116:99:1007,0,1785:45,26,24,21 chr2 17981399 . A G 2203.28 PASS AC=1;AF=0.756;AN=2;DP=6060;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:100,67:167:99:1549,0,2452:58,42,38,29 chr2 17981589 . G A 637.25 PASS AC=1;AF=0.694;AN=2;DP=1442;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,15:40:99:435,0,867:3,22,3,12 chr2 17997581 . T C 470.6 PASS AC=1;AF=0.568;AN=2;DP=340;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant9-variant10-variant12-variant13-variant15-variant20-variant21-variant22-variant24-variant25-variant26-variant29-variant31-variant33-variant35-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,5:11:99:192,0,157:3,3,5,0 chr2 17998025 . A T 4287.49 PASS AC=1;AF=0.718;AN=2;DP=6087;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:89,89:178:99:2424,0,2272:37,52,40,49 chr2 17998095 . C T 3441.91 PASS AC=1;AF=0.705;AN=2;DP=4676;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:77,73:150:99:1996,0,2000:35,42,36,37 chr2 17998331 . T C 1017.48 PASS AC=1;AF=0.711;AN=2;DP=5671;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:79,75:154:99:1819,0,1771:34,45,35,40 chr2 18059381 . A G 359.52 PASS AC=2;AF=0.952;AN=2;DP=479;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:551,51,0:0,0,6,11 chr2 18059912 . T C 66.22 PASS AC=2;AF=0.94;AN=2;DP=529;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:733,66,0:0,0,18,4 chr2 18098857 . C T 254.23 PASS AC=1;AF=0.614;AN=2;DP=209;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant18-variant19-variant22-variant24-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,12:19:99:421,0,170:5,2,9,3 chr2 18112473 . G A 5902.49 PASS AC=2;AF=1;AN=2;DP=7849;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,218:218:99:6653,652,0:0,0,114,104 chr2 18113623 . A G 1972.33 PASS AC=1;AF=0.72;AN=2;DP=5738;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:76,80:156:99:2216,0,1910:36,40,36,44 chr2 18113789 . G A 2435.54 PASS AC=1;AF=0.673;AN=2;DP=4140;MQ=60;set=variant-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant16-variant18-variant19-variant22-variant23-variant24-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:81,87:168:99:2318,0,2128:47,34,46,41 chr2 18744082 . G A 340.02 PASS AC=1;AF=0.5;AN=2;DP=65;FractionInformativeReads=1;MQ=60;set=variant19-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:14,8:22:99:242,0,474:12,2,7,1 chr2 18744332 . CT C,CTT 217.36 PASS AC=0,1;AF=0.196,0.304;AN=2;DP=4633;MQ=60;set=filterInvariant2-variant7-filterInvariant8-filterInvariant9-variant10-filterInvariant12-filterInvariant13-variant14-variant17-variant19-variant20-filterInvariant22-filterInvariant24-filterInvariant25-variant29-variant31-variant32-variant33-variant35-variant38-variant39-filterInvariant41-variant42 GT:DP:GQ:SB 0/2:161:99:33,59,28,41 chr2 18744758 . C T 2595.23 PASS AC=1;AF=0.5;AN=2;DP=703;FractionInformativeReads=1;MQ=60;set=variant19-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:112,136:248:99:3354,0,2768:60,52,68,68 chr2 18757501 . G C 570.4 PASS AC=1;AF=0.538;AN=2;DP=714;MQ=60;set=variant7-variant10-variant14-variant17-variant19-variant20-variant29-variant31-variant33-variant35-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:26,22:48:99:492,0,683:18,8,13,9 chr2 18765292 . TG T 2228.67 PASS AC=1;AF=0.5;AN=2;DP=168;FS=3.614;FractionInformativeReads=0.994;MQ=60;MQRankSum=-1.3;QD=13.27;ReadPosRankSum=1.387;SOR=0.469;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:93,74:167:99:2266,0,2960:55,38,39,35 chr2 18768850 . A G 1529.1 PASS AC=1;AF=0.538;AN=2;DP=1098;MQ=60;set=variant7-variant10-variant14-variant17-variant19-variant20-variant29-variant31-variant33-variant35-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:40,35:75:99:889,0,1118:13,27,10,25 chr2 18770540 . G C 211.27 PASS AC=1;AF=0.538;AN=2;DP=403;MQ=60;set=variant7-variant10-variant14-variant17-variant19-variant20-variant29-variant31-variant33-variant35-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:15,18:33:99:612,0,480:13,2,15,3 chr2 20101222 . GA G 4685.62 PASS AC=2;AF=0.919;AN=2;DP=4886;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,113:113:99:4000,340,0:0,0,50,63 chr2 20111433 . G A 3865.53 PASS AC=1;AF=0.5;AN=2;DP=325;FS=0.4;FractionInformativeReads=1;MQ=60;MQRankSum=4.016;QD=11.89;ReadPosRankSum=-2.733;SOR=0.669;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:172,153:325:99:3894,0,4681:91,81,80,73 chr2 20131079 . T C 1019.97 PASS AC=2;AF=0.641;AN=2;DP=2424;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:1660,179,0:0,0,28,32 chr2 20131184 . C A 1462.08 PASS AC=2;AF=0.989;AN=2;DP=1510;MQ=60;MQRankSum=0.201;ReadPosRankSum=0.755;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:608,60,0:0,0,7,13 chr2 20232287 . C T 294.86 PASS AC=2;AF=0.716;AN=2;DP=701;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:1090,78,0:0,0,25,1 chr2 20233135 . T C 351.06 PASS AC=2;AF=0.722;AN=2;DP=560;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:325,24,0:0,0,4,4 chr2 20234523 . C T 841.17 PASS AC=2;AF=0.966;AN=2;DP=1284;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:587,57,0:0,0,13,6 chr2 20302442 . AAGAAGG A 423.4 PASS AC=1;AF=0.5;AN=2;DP=99;set=variant10-variant14-variant35 GT:AD:DP:GQ:PL:SB 0/1:5,12:17:99:470,0,181:5,0,10,2 chr2 20302490 . GAGAAGA GAGAAGGAGAAGAAGAAGAAGAAGA,GAGAAGAAGAAGA,GAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGA,GAGAAGAAGA,G,GAGA,GAGAAGGAGAAGGAGAAGGAGAAGAAGA,GAGAAGAAGAAGAAGAAGAAGAAGAAGAAGA,GAGAAGAAGAAGAAGAAGAAGAAGAAGA 578.62 PASS AC=0,0,0,0,0,0,0,1,0;AF=0.033,0.167,0.033,0.067,0.033,0.067,0.033,0.067,0.067;AN=2;DP=793;set=variant-variant4-variant6-variant8-variant14-variant22-filterInvariant23-variant25-variant28-variant34-variant35-variant39-variant43-variant37-variant44 GT:DP:GQ:SB 0/8:45:99:19,11,7,8 chr2 20302569 . C T 844.6 PASS AC=1;AF=0.5;AN=2;DP=249;FractionInformativeReads=1;set=variant-variant29-variant35 GT:AD:DP:GQ:PL:SB 0/1:47,43:90:99:965,0,1080:20,27,20,23 chr2 20317940 . T C 488.17 PASS AC=1;AF=0.5;AN=2;DP=235;FractionInformativeReads=1;set=variant-variant29-variant35 GT:AD:DP:GQ:PL:SB 0/1:50,56:106:99:1362,0,1157:26,24,31,25 chr2 20320479 . AG A 153.84 PASS AC=1;AF=0.563;AN=2;DP=178;set=variant5-variant14-variant15-variant20-variant27-variant29-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:6,9:15:82:132,0,82:4,2,9,0 chr2 20320493 . G A 41.82 PASS AC=1;AF=0.675;AN=2;DP=558;set=filterInvariant-variant5-variant10-variant13-variant14-variant15-variant19-variant20-variant26-variant27-variant30-filterInvariant31-filterInvariant33-variant35-filterInvariant36-variant37-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,4:20:91:91,0,525:14,2,4,0 chr2 20400556 . T C 2701.91 PASS AC=2;AF=0.989;AN=2;DP=4521;MQ=60;MQRankSum=1.265;ReadPosRankSum=-2.706;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,125:125:99:3769,374,0:0,0,77,48 chr2 20400599 . T C 1931.43 PASS AC=1;AF=0.5;AN=2;DP=164;FS=5.729;FractionInformativeReads=1;MQ=60;MQRankSum=0.16;QD=11.78;ReadPosRankSum=-0.745;SOR=1.123;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:90,74:164:99:1960,0,2243:49,41,47,27 chr2 20401858 . TAA TA,T 274.12 PASS AC=1,0;AF=0.529,0.071;AN=2;DP=1373;set=variant-variant2-filterInvariant3-variant4-filterInvariant5-variant6-filterInvariant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant39-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:35:99:7,5,13,10 chr2 20402380 . C G 586.44 PASS AC=1;AF=0.583;AN=2;DP=2064;MQ=60;set=variant-variant3-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:49,40:89:99:929,0,1277:29,20,22,18 chr2 20403794 . A T 6751.11 PASS AC=2;AF=1;AN=2;DP=8927;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,201:201:99:6345,601,0:0,0,97,104 chr2 20403949 . C T 5239.09 PASS AC=1;AF=0.526;AN=2;DP=3370;set=variant2-variant3-variant4-variant5-variant7-variant9-variant12-variant13-variant15-variant17-variant20-variant23-variant25-variant26-variant30-variant34-variant35-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:96,105:201:99:2514,0,2364:40,56,52,53 chr2 20405004 . C T 104.2 PASS AC=1;AF=0.577;AN=2;DP=383;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant12-variant13-variant15-variant17-variant20-variant22-variant23-variant25-variant26-variant29-variant30-variant34-variant35-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,16:26:99:494,0,291:8,2,13,3 chr2 20405050 . A C 911.08 PASS AC=2;AF=1;AN=2;DP=1463;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1415,108,0:0,0,29,7 chr2 20423154 . A G 1394.14 PASS AC=2;AF=1;AN=2;DP=2563;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,81:81:99:2439,243,0:0,0,22,59 chr2 20424364 . G A 276.56 PASS AC=1;AF=0.5;AN=2;DP=46;MQ=60;set=variant10-variant35 GT:AD:DP:GQ:PL:SB 0/1:15,6:21:99:144,0,368:9,6,5,1 chr2 20448561 . A G 1410.97 PASS AC=1;AF=0.5;AN=2;DP=1756;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant9-variant13-variant16-variant20-variant24-variant25-variant29-variant32-variant35-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:60,50:110:99:1256,0,1568:37,23,32,18 chr2 20647241 . C T 3560.04 PASS AC=1;AF=0.5;AN=2;DP=1065;MQ=60;set=variant4-variant6-variant24-variant35 GT:AD:DP:GQ:PL:SB 0/1:117,130:247:99:3070,0,2708:67,50,74,56 chr2 20647430 . C T 2931.26 PASS AC=1;AF=0.5;AN=2;DP=1441;MQ=60;set=variant10-variant18-variant26-variant27-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:131,109:240:99:2707,0,3663:61,70,51,58 chr2 20648211 . G T 1649.99 PASS AC=1;AF=0.578;AN=2;DP=1828;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant24-variant25-variant28-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:45,23:68:99:504,0,1257:18,27,10,13 chr2 20648933 . A AT 5719.06 PASS AC=1;AF=0.609;AN=2;DP=8010;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant24-variant25-variant26-variant28-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:108,88:196:99:1684,0,2215:38,70,28,60 chr2 20649063 . ATTG A 916.67 PASS AC=1;AF=0.5;AN=2;DP=737;MQ=60;set=variant4-variant7-variant8-variant10-variant15-variant18-variant26-variant27-variant28-variant30-variant31-variant32-variant35-variant36-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:15,24:39:99:963,0,675:3,12,3,21 chr2 20699625 . G A 119.97 PASS AC=1;AF=0.625;AN=2;DP=115;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant6-variant9-variant13-variant14-variant16-variant21-variant22-variant24-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:5,10:15:99:261,0,136:4,1,7,3 chr2 20699667 . C G 216.52 PASS AC=1;AF=0.854;AN=2;DP=603;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,12:27:99:294,0,370:10,5,8,4 chr2 20699997 . C T 217.45 PASS AC=1;AF=0.567;AN=2;DP=194;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant6-variant9-variant13-variant14-variant16-variant21-variant22-variant24-variant28-variant33-variant35-variant36-variant41 GT:AD:DP:GQ:PL:SB 0/1:3,4:7:74:159,0,74:1,2,2,2 chr2 20700900 . A G 2461.57 PASS AC=2;AF=1;AN=2;DP=5563;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,123:123:99:3612,368,0:0,0,60,63 chr2 20729143 . C CT,CTT,CTTTTTT,CTTT 143.47 PASS AC=0,2,0,0;AF=0.308,0.487,0.026,0.038;AN=2;DP=479;FS=0;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 2/2:11:33:0,0,6,5 chr2 20817493 . C T 114.14 PASS AC=1;AF=0.563;AN=2;DP=230;set=variant4-variant5-variant6-variant14-variant15-variant20-variant22-variant25-variant26-variant29-variant30-variant31-variant32-variant35-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,7:10:94:244,0,94:3,0,6,1 chr2 20817673 . G A 1634.7 PASS AC=1;AF=0.563;AN=2;DP=2295;MQ=60;set=variant4-variant5-variant6-variant14-variant15-variant20-variant22-variant25-variant26-variant29-variant30-variant31-variant32-variant35-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:76,65:141:99:1509,0,2102:44,32,36,29 chr2 20817777 . C T 1487.63 PASS AC=1;AF=0.579;AN=2;DP=2823;MQ=60;set=variant6-variant7-variant8-variant14-variant16-variant18-variant19-variant21-variant23-variant24-variant26-variant32-variant34-variant35-variant36-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:88,99:187:99:2467,0,2054:37,51,50,49 chr2 20818193 . G A 1293.97 PASS AC=1;AF=0.81;AN=2;DP=2720;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,47:91:99:1247,0,1229:23,21,28,19 chr2 20818286 . A C 1709.23 PASS AC=1;AF=0.81;AN=2;DP=3428;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,65:118:99:1719,0,1230:27,26,32,33 chr2 20818454 . T A 1933.66 PASS AC=1;AF=0.81;AN=2;DP=3992;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,73:121:99:2859,0,2738:25,23,38,35 chr2 20818458 . G A 2274.99 PASS AC=1;AF=0.583;AN=2;DP=1767;MQ=60;set=variant6-variant7-variant8-variant14-variant16-variant18-variant19-variant21-variant23-variant24-variant26-variant32-variant34-variant35-variant36-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:49,70:119:99:2809,0,2744:26,23,37,33 chr2 20818764 . C T 4148.7 PASS AC=1;AF=0.559;AN=2;DP=5128;MQ=60;set=variant4-variant5-variant6-variant14-variant15-variant20-variant22-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:139,169:308:99:3707,0,3364:68,71,81,88 chr2 20822218 . T C 1731.8 PASS AC=2;AF=1;AN=2;DP=2062;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1804,159,0:0,0,28,25 chr2 20822486 . G C 2950.38 PASS AC=1;AF=0.655;AN=2;DP=2042;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:35,22:57:99:625,0,827:16,19,7,15 chr2 20822564 . C T 491.32 PASS AC=1;AF=0.559;AN=2;DP=838;MQ=60;set=variant4-variant5-variant6-variant14-variant15-variant20-variant22-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,13:37:99:339,0,602:11,13,5,8 chr2 20822694 . C T 538.43 PASS AC=1;AF=0.579;AN=2;DP=594;MQ=60;set=variant6-variant7-variant8-variant14-variant16-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant32-variant34-variant35-variant36-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:15,14:29:99:413,0,414:8,7,8,6 chr2 20823252 . A G 1044.44 PASS AC=1;AF=0.81;AN=2;DP=2598;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,48:92:99:1097,0,954:21,23,23,25 chr2 20823286 . T C 815.18 PASS AC=1;AF=0.559;AN=2;DP=1023;MQ=60;set=variant4-variant5-variant6-variant14-variant15-variant20-variant22-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,39:84:99:835,0,1113:22,23,19,20 chr2 20823612 . A G 2007.24 PASS AC=1;AF=0.81;AN=2;DP=2916;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,48:102:99:1060,0,1298:28,26,29,19 chr2 20823724 . T C 3394.59 PASS AC=2;AF=1;AN=2;DP=4321;FS=0;MQRankSum=-0.17;ReadPosRankSum=-0.509;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,106:106:99:3229,317,0:0,0,49,57 chr2 20823816 . G T,A 825.57 PASS AC=1,0;AF=0.537,0.093;AN=2;DP=2069;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant16-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant43 GT:DP:GQ:SB 0/1:77:99:16,21,17,23 chr2 20823850 . T C 2752.22 PASS AC=2;AF=1;AN=2;DP=2637;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:1865,186,0:0,0,27,35 chr2 20824498 . C T 2474.44 PASS AC=1;AF=0.721;AN=2;DP=3463;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,71:117:99:1763,0,1234:29,17,41,30 chr2 20824559 . C T 1126.81 PASS AC=1;AF=0.583;AN=2;DP=2393;MQ=60;set=variant6-variant7-variant8-variant14-variant16-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant32-variant34-variant35-variant36-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:72,80:152:99:1889,0,1748:33,39,44,36 chr2 20824658 . G A 930.57 PASS AC=1;AF=0.579;AN=2;DP=2127;MQ=60;set=variant6-variant7-variant8-variant14-variant16-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant32-variant34-variant35-variant36-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:58,73:131:99:1812,0,1533:24,34,27,46 chr2 20824708 . T C 1110.02 PASS AC=1;AF=0.574;AN=2;DP=2145;MQ=60;set=variant2-variant3-variant6-variant7-variant8-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:42,41:83:99:1080,0,990:20,22,14,27 chr2 20835450 . A G 752.96 PASS AC=1;AF=0.588;AN=2;DP=677;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant6-variant14-variant15-variant20-variant22-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,26:43:99:592,0,481:8,9,12,14 chr2 20836787 . T TG 809.53 PASS AC=1;AF=0.609;AN=2;DP=894;set=variant4-variant6-variant7-variant8-variant14-variant16-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:34,10:44:99:283,0,1192:19,15,1,9 chr2 20836788 . G GGCCC,GGCC,GGC 796.46 PASS AC=0,1,0;AF=0.083,0.167,0.25;AN=2;DP=277;set=variant4-variant7-variant12-variant24-variant34-variant35 GT:DP:GQ:SB 0/2:39:99:7,23,9,0 chr2 20836789 . C G 1129.4 PASS AC=1;AF=0.75;AN=2;DP=1349;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,20:39:99:810,0,684:10,9,6,14 chr2 20836792 . CCG C 772.66 PASS AC=1;AF=0.5;AN=2;DP=925;set=variant2-variant3-variant5-variant6-filterInvariant8-variant11-variant13-filterInvariant14-variant15-variant22-variant25-variant26-variant29-variant30-filterInvariant31-variant33-variant35-variant36-variant37-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,16:41:99:311,0,853:13,12,3,13 chr2 20836794 . G C 174.1 PASS AC=1;AF=0.652;AN=2;DP=1307;set=variant-filterInvariant3-variant4-filterInvariant5-variant6-variant7-variant8-filterInvariant10-variant12-filterInvariant13-variant14-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:22,19:41:99:684,0,809:6,16,10,9 chr2 20836798 . C CA 593.27 PASS AC=1;AF=0.571;AN=2;DP=769;set=variant6-variant7-variant8-variant14-variant16-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:36,10:46:99:277,0,1235:19,17,1,9 chr2 20836803 . G C 171.18 PASS AC=1;AF=0.5;AN=2;DP=825;set=variant-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant7-variant10-filterInvariant12-filterInvariant13-filterInvariant16-filterInvariant17-filterInvariant23-variant24-filterInvariant26-filterInvariant31-variant34-variant35-filterInvariant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,9:41:99:141,0,1246:7,25,9,0 chr2 20836808 . G C 161.2 PASS AC=1;AF=0.5;AN=2;DP=553;set=variant-filterInvariant3-filterInvariant4-filterInvariant5-variant7-variant12-filterInvariant13-variant24-filterInvariant26-variant34-filterInvariant35-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,6:37:81:81,0,1220:7,24,6,0 chr2 20836932 . G T 783.75 PASS AC=2;AF=1;AN=2;DP=2399;FS=0;MQ=60;MQRankSum=0.075;ReadPosRankSum=0.226;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:1619,141,0:0,0,29,18 chr2 20837127 . T C 1646.49 PASS AC=2;AF=1;AN=2;DP=2833;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,74:74:99:2488,222,0:0,0,42,32 chr2 20837292 . G A 1654.31 PASS AC=1;AF=0.591;AN=2;DP=2202;MQ=60;set=variant3-variant5-variant6-variant8-variant9-variant10-variant14-variant15-variant20-variant22-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,64:112:99:1618,0,1360:21,27,31,33 chr2 20837364 . A G 1420.26 PASS AC=1;AF=0.531;AN=2;DP=1382;MQ=60;set=variant5-variant6-variant14-variant15-variant20-variant22-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,59:107:99:1208,0,1145:22,26,26,33 chr2 20837469 . C T 905.6 PASS AC=1;AF=0.575;AN=2;DP=1309;MQ=60;set=variant4-variant7-variant8-variant14-variant16-variant18-variant19-variant21-variant23-variant24-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:33,37:70:99:897,0,865:16,17,16,21 chr2 20837719 . G A 561.61 PASS AC=1;AF=0.543;AN=2;DP=1188;MQ=60;set=variant2-variant4-variant5-variant6-variant12-variant14-variant15-variant20-variant22-variant23-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,36:71:99:842,0,942:20,15,18,18 chr2 20838222 . C T 3898.63 PASS AC=1;AF=0.531;AN=2;DP=1678;MQ=60;set=variant5-variant6-variant14-variant15-variant20-variant22-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,50:110:99:1373,0,1609:28,32,19,31 chr2 20838318 . G A 1381.83 PASS AC=1;AF=0.579;AN=2;DP=2321;MQ=60;set=variant4-variant7-variant8-variant14-variant16-variant18-variant19-variant21-variant23-variant24-variant31-variant32-variant34-variant35-variant36-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:65,60:125:99:1519,0,1657:33,32,31,29 chr2 20839725 . G T 279.76 PASS AC=1;AF=0.567;AN=2;DP=208;FractionInformativeReads=1;MQ=60;set=variant5-variant6-variant14-variant15-variant20-variant22-variant25-variant26-variant29-variant30-variant33-variant35-variant36-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,8:16:99:268,0,230:4,4,3,5 chr2 20841059 . C T 1034.52 PASS AC=1;AF=0.679;AN=2;DP=1142;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,26:45:99:855,0,608:2,17,4,22 chr2 20845041 . G A 304.17 PASS AC=1;AF=0.5;AN=2;DP=137;FractionInformativeReads=1;MQ=60;set=variant16-variant26-variant32-variant35 GT:AD:DP:GQ:PL:SB 0/1:18,22:40:99:583,0,504:14,4,14,8 chr2 20845273 . G A 495.96 PASS AC=2;AF=0.724;AN=2;DP=2180;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,73:73:99:2172,218,0:0,0,28,45 chr2 20866493 . T TGGAGGGCGAGCCCTTCCGCGGCCC 1261.41 PASS AC=2;AF=0.731;AN=2;DP=1758;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1994,133,0:0,0,23,12 chr2 20866720 . G C 2733.32 PASS AC=2;AF=0.75;AN=2;DP=3071;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,66:66:99:2033,198,0:0,0,29,37 chr2 20866888 . CG C 318.96 PASS AC=2;AF=1;AN=2;DP=354;FS=0;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:318,27,0:0,0,6,3 chr2 20867122 . G GGGCGGCGGC,GGGCGGCGGCGGCGGCGGC,GGGCGGCGGCGGCGGC,GGGCGGCGGCGGC 322.17 PASS AC=2,0,0,0;AF=0.765,0.162,0.029,0.029;AN=2;DP=321;FS=0;MQ=60;MQRankSum=0.633;ReadPosRankSum=0.633;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant44 GT:DP:GQ:SB 1/1:12:36:0,0,5,7 chr2 20870579 . G A 2202.29 PASS AC=2;AF=0.732;AN=2;DP=3285;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,112:113:99:3253,325,0:1,0,54,58 chr2 20871190 . A C 4408.58 PASS AC=2;AF=1;AN=2;DP=7071;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,164:164:99:5727,492,0:0,0,71,93 chr2 20871293 . A G 3083.23 PASS AC=2;AF=1;AN=2;DP=5674;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,152:152:99:4780,455,0:0,0,77,75 chr2 20871867 . ACCCCC AC,A,ACC 4105.61 PASS AC=2,0,0;AF=0.716,0.182,0.057;AN=2;DP=2722;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-filterInvariant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:84:99:0,0,38,46 chr2 20871874 . C A 4141.33 PASS AC=2;AF=0.756;AN=2;DP=2477;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,87:87:99:3697,264,0:0,0,39,48 chr2 20871877 . C A 2140.1 PASS AC=2;AF=0.72;AN=2;DP=2355;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,81:81:99:3672,261,0:0,0,37,44 chr2 20871887 . CTT CTTT,CT,CTTTT,C,CTTTTT 310.95 PASS AC=0,1,0,0,0;AF=0.125,0.328,0.047,0.016,0.016;AN=2;DP=1524;set=variant-variant3-variant4-variant5-filterInvariant6-variant7-variant10-variant12-variant13-variant14-variant16-variant17-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant32-variant33-variant34-filterInvariant35-variant36-variant37-variant38-filterInvariant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:54:99:19,19,6,10 chr2 20872960 . A AAT 5786.12 PASS AC=1;AF=0.594;AN=2;DP=7564;set=variant2-variant4-variant6-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:128,99:227:99:2385,0,4788:71,57,58,41 chr2 20872962 . G GA,A 7404.75 PASS AC=1,1;AF=0.194,0.486;AN=2;DP=8968;set=variant12-variant15-variant16-variant17-variant18-variant19-variant4-variant3-variant20-variant21-variant6-variant-variant22-variant23-variant25-variant8-variant14-variant26-variant28-variant29-variant30-variant9-variant31-variant32-variant33-variant34-variant11-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:DP:GQ:SB 1/2:218:99:1,1,123,93 chr2 20873099 . T A 11269.5 PASS AC=1;AF=0.653;AN=2;DP=10782;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:145,123:268:99:3039,0,3459:60,85,50,73 chr2 20873333 . G A 3107.71 PASS AC=1;AF=0.653;AN=2;DP=3235;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,40:73:99:1052,0,780:18,15,21,19 chr2 20873449 . T C 1654.74 PASS AC=1;AF=0.594;AN=2;DP=1249;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant6-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,26:41:99:726,0,330:6,9,8,18 chr2 20884135 . TTTAATC T 4773.31 PASS AC=2;AF=0.625;AN=2;DP=6039;MQ=60;set=variant2-variant4-variant6-variant9-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant23-variant26-variant27-variant33-variant34-variant35-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,233:233:99:10222,703,0:0,0,94,139 chr2 20884262 . G A 1816.67 PASS AC=2;AF=0.683;AN=2;DP=1475;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant26-variant27-variant28-variant33-variant34-variant35-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,50:51:99:1776,142,0:0,1,13,37 chr2 20884546 . A C 1255.33 PASS AC=2;AF=0.625;AN=2;DP=2764;MQ=60;set=variant2-variant4-variant6-variant9-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant23-variant26-variant27-variant33-variant34-variant35-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,127:127:99:3966,381,0:0,0,69,58 chr2 20884586 . G C 1322.5 PASS AC=2;AF=0.625;AN=2;DP=2784;MQ=60;set=variant2-variant4-variant6-variant9-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant23-variant26-variant27-variant33-variant34-variant35-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,138:139:99:4268,406,0:1,0,69,69 chr2 20884973 . A C 6115.87 PASS AC=2;AF=0.683;AN=2;DP=5137;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant26-variant27-variant28-variant33-variant34-variant35-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,193:193:99:5782,578,0:0,0,104,89 chr2 20939706 . T C 1379.67 PASS AC=2;AF=0.704;AN=2;DP=1203;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant6-variant9-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant23-variant25-variant26-variant27-variant28-variant31-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1708,117,0:0,0,32,7 chr2 20939708 . C T 649.9 PASS AC=2;AF=0.781;AN=2;DP=1497;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1708,117,0:0,0,32,7 chr2 21225912 . C T 1796.65 PASS AC=1;AF=0.5;AN=2;DP=186;FS=0.546;FractionInformativeReads=0.995;MQ=60;MQRankSum=0.441;QD=9.66;ReadPosRankSum=1.425;SOR=0.639;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:108,77:185:99:1825,0,2601:49,59,36,41 chr2 21229609 . C T 1826.9 PASS AC=1;AF=0.5;AN=2;DP=161;FS=2.756;FractionInformativeReads=1;MQ=60;MQRankSum=0.655;QD=11.35;ReadPosRankSum=2.423;SOR=0.507;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:85,76:161:99:1855,0,2280:47,38,38,38 chr2 21231524 . G A 1167.69 PASS AC=2;AF=0.536;AN=2;DP=1697;MQ=60;set=variant5-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant29-variant30-variant31-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,125:125:99:4062,374,0:0,0,68,57 chr2 21232803 . T C 4714.59 PASS AC=2;AF=1;AN=2;DP=5520;FS=0;MQ=60;MQRankSum=1.119;ReadPosRankSum=-0.08;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,128:128:99:4055,384,0:0,0,50,78 chr2 21235475 . T C 3349.77 PASS AC=2;AF=1;AN=2;DP=4494;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,107:107:99:3451,321,0:0,0,40,67 chr2 21236482 . A G 1337.74 PASS AC=2;AF=1;AN=2;DP=2004;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:1958,195,0:0,0,26,39 chr2 21237544 . G A 654.38 PASS AC=2;AF=0.536;AN=2;DP=642;FractionInformativeReads=1;MQ=60;set=variant5-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant29-variant30-variant31-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:1856,176,0:0,0,18,41 chr2 21250914 . G A 3368.83 PASS AC=2;AF=0.65;AN=2;DP=2698;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,98:98:99:3006,294,0:0,0,37,61 chr2 21251040 . T G 1559.69 PASS AC=2;AF=0.886;AN=2;DP=1544;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1148,102,0:0,0,20,14 chr2 21252365 . GAGGAAGGAAGGA GAGGAAGGA,GAGGA,G,GAGGAAGGAAGGAAGGA 708.26 PASS AC=2,0,0,0;AF=0.581,0.048,0.016,0.016;AN=2;DP=613;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant39-variant40-variant43-variant44 GT:DP:GQ:SB 1/1:14:42:0,0,12,2 chr2 21255573 . C CCATCT 356.92 PASS AC=2;AF=0.886;AN=2;DP=1244;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1473,102,0:0,0,6,28 chr2 21263639 . T G 270.93 PASS AC=2;AF=0.767;AN=2;DP=750;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:576,45,0:0,0,13,2 chr2 21360583 . A G 1646.76 PASS AC=2;AF=0.537;AN=2;DP=2937;MQ=60;set=variant2-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant21-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,118:118:99:3755,354,0:0,0,55,63 chr2 23608644 . C CG 669.41 PASS AC=2;AF=1;AN=2;DP=932;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:791,66,0:0,0,7,15 chr2 23785517 . A G 262.31 PASS AC=2;AF=0.841;AN=2;DP=819;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1444,99,0:0,0,10,23 chr2 23785524 . C A 217.56 PASS AC=2;AF=0.776;AN=2;DP=688;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1454,102,0:0,0,10,23 chr2 23862187 . C G 1075.51 PASS AC=1;AF=0.621;AN=2;DP=2459;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,36:64:99:883,0,613:14,14,14,22 chr2 23865014 . G A 328.29 PASS AC=1;AF=0.618;AN=2;DP=2184;MQ=60;set=variant-variant3-variant4-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,39:79:99:919,0,994:24,16,23,16 chr2 23865260 . T C 1265.87 PASS AC=1;AF=0.775;AN=2;DP=5723;MQ=60;set=variant-variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:73,63:136:99:1626,0,1840:37,36,30,33 chr2 23865908 . G C 860.51 PASS AC=1;AF=0.618;AN=2;DP=3729;MQ=60;set=variant-variant3-variant4-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,65:121:99:1650,0,1402:28,28,28,37 chr2 23907532 . TCTC T 403.74 PASS AC=2;AF=0.849;AN=2;DP=2401;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:2164,148,0:0,0,26,23 chr2 23919375 . C T 1618.03 PASS AC=2;AF=0.712;AN=2;DP=2295;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,86:86:99:2770,257,0:0,0,44,42 chr2 23919630 . C G 1606.93 PASS AC=2;AF=0.712;AN=2;DP=1705;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:1569,141,0:0,0,26,21 chr2 23920545 . A G 1400.81 PASS AC=2;AF=0.712;AN=2;DP=1955;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1470,132,0:0,0,20,24 chr2 23920609 . G C 1047.47 PASS AC=2;AF=1;AN=2;DP=1748;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1118,108,0:0,0,17,19 chr2 23920632 . C G 1082.37 PASS AC=2;AF=0.813;AN=2;DP=1434;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1047,105,0:0,0,17,18 chr2 23920646 . G C 959.92 PASS AC=2;AF=0.712;AN=2;DP=1103;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:990,96,0:0,0,16,16 chr2 23925980 . T C 1363.76 PASS AC=2;AF=0.712;AN=2;DP=1461;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:1743,178,0:0,0,37,23 chr2 23926659 . T C 5408.35 PASS AC=2;AF=0.667;AN=2;DP=5811;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,187:187:99:5452,560,0:0,0,89,98 chr2 23930714 . A G 178.58 PASS AC=2;AF=0.895;AN=2;DP=1865;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1343,126,0:0,0,24,18 chr2 23931036 . C T 3076.37 PASS AC=2;AF=0.667;AN=2;DP=4003;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,116:117:99:3306,340,0:0,1,51,65 chr2 23973799 . T C 11096.4 PASS AC=2;AF=0.652;AN=2;DP=12515;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,363:363:99:11446,1088,0:0,0,181,182 chr2 24009163 . A G 861.96 PASS AC=2;AF=0.574;AN=2;DP=2158;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:2299,213,0:0,0,22,49 chr2 24042550 . C T 907.81 PASS AC=2;AF=0.966;AN=2;DP=1212;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:706,72,0:0,0,14,10 chr2 24055058 . G C 7125.65 PASS AC=2;AF=0.955;AN=2;DP=8203;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,203:203:99:6104,609,0:0,0,95,108 chr2 24079058 . CA C,CAA,CAAA,CAAAA 128.69 PASS AC=1,0,0,0;AF=0.393,0.036,0.048,0.024;AN=2;DP=1949;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-filterInvariant24-variant25-variant26-variant27-variant28-variant29-filterInvariant30-variant31-variant33-variant34-variant35-filterInvariant36-variant37-variant38-variant39-filterInvariant40-variant41-variant42-filterInvariant43-variant44 GT:DP:GQ:SB 0/1:58:99:23,11,22,2 chr2 24108652 . T C 3670.2 PASS AC=2;AF=1;AN=2;DP=4396;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,114:114:99:3322,341,0:0,0,54,60 chr2 24110911 . G GA 326.58 PASS AC=2;AF=0.667;AN=2;DP=527;set=variant2-variant3-variant4-variant5-variant6-variant8-variant11-variant13-variant14-variant15-variant17-filterInvariant19-variant20-variant21-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:253,27,0:0,0,2,7 chr2 24150503 . A AG,AGG 96.2 PASS AC=0,2;AF=0.091,0.5;AN=2;DP=164;MQ=60;set=variant11-variant12-variant15-variant17-variant18-variant29-variant33-variant34-variant35-variant36-variant41 GT:DP:GQ:SB 2/2:13:43:0,0,9,4 chr2 24163300 . C CCT 3089.99 PASS AC=2;AF=0.672;AN=2;DP=1516;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1920,132,0:0,0,28,15 chr2 24163433 . G A 625.32 PASS AC=2;AF=0.55;AN=2;DP=838;MQ=60;set=variant11-variant17-variant28-variant29-variant33-variant35-variant36-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,86:86:99:2348,253,0:0,0,42,44 chr2 24194314 . C T 545.41 PASS AC=2;AF=0.75;AN=2;DP=877;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:787,75,0:0,0,9,16 chr2 24223954 . C T 319.51 PASS AC=1;AF=0.5;AN=2;DP=28;FS=0;FractionInformativeReads=1;MQ=59.33;MQRankSum=-0.282;QD=11.41;ReadPosRankSum=-1.693;SOR=1.096;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:17,11:28:99:348,0,686:1,16,0,11 chr2 24225621 . T C 598.06 PASS AC=2;AF=0.845;AN=2;DP=852;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:596,60,0:0,0,12,8 chr2 24226593 . CCAAAA CAA,CA,C,CAAA 322.99 PASS AC=1,1,0,0;AF=0.429,0.268,0.054,0.036;AN=2;DP=781;set=variant2-variant3-filterInvariant4-variant5-variant6-filterInvariant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant24-variant25-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant42-variant44 GT:DP:GQ:SB 2/1:16:89:0,1,7,8 chr2 24227107 . C CTG 8473.78 PASS AC=2;AF=0.826;AN=2;DP=7374;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,178:178:99:8055,539,0:0,0,98,80 chr2 24227480 . T C 414.76 PASS AC=2;AF=0.821;AN=2;DP=191;FS=0;FractionInformativeReads=1;set=variant2-variant3-variant4-variant5-variant7-variant8-variant11-variant12-variant15-variant16-variant19-variant20-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:325,24,0:0,0,8,0 chr2 24246175 . C T 2483.98 PASS AC=2;AF=0.826;AN=2;DP=3384;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,78:78:99:2739,233,0:0,0,20,58 chr2 24246679 . A G 2371.08 PASS AC=2;AF=0.826;AN=2;DP=3004;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1816,157,0:0,0,8,45 chr2 24252417 . T C 2570.52 PASS AC=2;AF=0.721;AN=2;DP=3141;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,96:96:99:3234,287,0:0,0,37,59 chr2 24252436 . A G 2278.44 PASS AC=2;AF=0.703;AN=2;DP=2796;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,97:97:99:3358,291,0:0,0,42,55 chr2 24254118 . G A 238.16 PASS AC=1;AF=0.5;AN=2;DP=14;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.936;QD=17.01;ReadPosRankSum=0.421;SOR=0.693;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:7,7:14:99:266,0,269:0,7,0,7 chr2 24255862 . C G 1568.84 PASS AC=2;AF=1;AN=2;DP=1618;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.867;ReadPosRankSum=0.124;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1428,117,0:0,0,11,28 chr2 24262331 . C G 1684.54 PASS AC=1;AF=0.5;AN=2;DP=153;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.208;QD=11.01;ReadPosRankSum=-1.602;SOR=0.638;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:86,67:153:99:1713,0,2423:31,55,25,42 chr2 24338777 . CAAAA CAA,CAAA,CA,C 98.98 PASS AC=0,2,0,0;AF=0.214,0.393,0.071,0.018;AN=2;DP=500;set=variant2-variant3-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant18-variant19-variant20-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant44 GT:DP:GQ:SB 2/2:11:10:0,1,3,7 chr2 24369674 . C T 2616.76 PASS AC=2;AF=0.966;AN=2;DP=3877;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:2444,237,0:0,0,39,40 chr2 24384424 . T C 2155.9 PASS AC=2;AF=0.955;AN=2;DP=2975;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:2458,237,0:0,0,48,31 chr2 24387178 . G GC 1322.19 PASS AC=2;AF=0.989;AN=2;DP=2183;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:2314,187,0:0,0,26,36 chr2 24388096 . G A 370.97 PASS AC=2;AF=0.955;AN=2;DP=1052;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:890,87,0:0,0,19,10 chr2 24390517 . G A 2588.3 PASS AC=2;AF=0.782;AN=2;DP=3198;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:2281,215,0:0,0,38,34 chr2 24395269 . T C 693.41 PASS AC=2;AF=0.955;AN=2;DP=472;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:304,21,0:0,0,6,1 chr2 24395294 . T C 1117.59 PASS AC=2;AF=0.955;AN=2;DP=959;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:460,42,0:0,0,10,4 chr2 24395506 . T C 1247.37 PASS AC=2;AF=0.955;AN=2;DP=1535;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1161,111,0:0,0,13,24 chr2 24397791 . T C 62.98 PASS AC=2;AF=0.963;AN=2;DP=307;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:229,21,0:0,0,4,3 chr2 24397866 . T G 235.43 PASS AC=2;AF=1;AN=2;DP=476;FS=0;MQ=60;MQRankSum=1.085;ReadPosRankSum=0.434;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:317,30,0:0,0,5,5 chr2 24398281 . T G 1376.21 PASS AC=2;AF=0.966;AN=2;DP=1705;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,32:32:95:1037,95,0:0,0,20,12 chr2 24398446 . A T 2518.06 PASS AC=1;AF=0.775;AN=2;DP=3276;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,47:83:99:1143,0,816:18,18,21,26 chr2 24402127 . C CAA 1942.88 PASS AC=2;AF=0.989;AN=2;DP=2049;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:2084,144,0:0,0,19,28 chr2 24414002 . A G 6353.67 PASS AC=2;AF=0.786;AN=2;DP=6906;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,208:208:99:6355,624,0:0,0,108,100 chr2 24432211 . C T 1493.3 PASS AC=2;AF=0.977;AN=2;DP=2156;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:1939,174,0:0,0,14,44 chr2 24432620 . A G 1080.14 PASS AC=2;AF=0.762;AN=2;DP=1464;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1562,135,0:0,0,35,10 chr2 24432667 . C G 2316.73 PASS AC=2;AF=0.977;AN=2;DP=3393;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,86:86:99:2644,257,0:0,0,58,28 chr2 24440997 . A T 556.6 PASS AC=2;AF=0.989;AN=2;DP=1127;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:915,84,0:0,0,9,19 chr2 24443271 . C A 11570.4 PASS AC=2;AF=0.786;AN=2;DP=13105;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,310:310:99:9264,928,0:0,0,164,146 chr2 24443330 . A G 10382.7 PASS AC=2;AF=0.762;AN=2;DP=11380;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,270:270:99:8387,810,0:0,0,124,146 chr2 24475205 . T C 2877.97 PASS AC=2;AF=1;AN=2;DP=3175;FS=0;MQ=60;MQRankSum=1.254;ReadPosRankSum=0.856;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:2393,204,0:0,0,47,21 chr2 24484150 . T C 1319.12 PASS AC=2;AF=0.989;AN=2;DP=1464;MQ=60;MQRankSum=-1.183;ReadPosRankSum=1.25;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:1042,84,0:0,0,5,23 chr2 24498839 . T G 287.46 PASS AC=2;AF=0.989;AN=2;DP=404;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.198;ReadPosRankSum=-0.922;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:517,42,0:0,0,1,13 chr2 24507757 . ATTTT ATT,A,AT,ATTT 392.18 PASS AC=1,0,0,0;AF=0.257,0.1,0.229,0.043;AN=2;DP=1535;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-filterInvariant12-variant14-variant15-variant17-variant18-variant19-variant21-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:11:40:2,1,1,7 chr2 24521493 . C T 1619.58 PASS AC=2;AF=0.989;AN=2;DP=2176;FS=0;MQ=60;MQRankSum=0.991;ReadPosRankSum=-1.664;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,52:52:99:1652,156,0:0,0,34,18 chr2 24521766 . C T 498.96 PASS AC=2;AF=0.989;AN=2;DP=617;FS=0;MQ=60;MQRankSum=0.727;ReadPosRankSum=-0.727;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,20:20:59:579,59,0:0,0,7,13 chr2 24550867 . CAA CA,C 878.68 PASS AC=2,0;AF=0.898,0.08;AN=2;DP=2275;set=Intersection GT:DP:GQ:SB 1/1:48:38:3,1,33,11 chr2 24583108 . G A 111.22 PASS AC=2;AF=0.989;AN=2;DP=811;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1167,114,0:0,0,22,16 chr2 24583119 . G C 275.4 PASS AC=2;AF=0.989;AN=2;DP=918;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1272,126,0:0,0,25,17 chr2 24583198 . T A 1307.3 PASS AC=2;AF=0.989;AN=2;DP=2206;MQ=60;MQRankSum=-2.775;ReadPosRankSum=1.808;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,92:92:99:2664,273,0:0,0,53,39 chr2 24583398 . C T 955.42 PASS AC=2;AF=0.989;AN=2;DP=1551;MQ=60;MQRankSum=0.529;ReadPosRankSum=2.304;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1537,147,0:0,0,23,26 chr2 24583475 . C T 1705 PASS AC=2;AF=0.989;AN=2;DP=2526;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,63:63:99:1855,189,0:0,0,31,32 chr2 24583677 . A G 1178.6 PASS AC=2;AF=0.989;AN=2;DP=1676;MQ=60;MQRankSum=0.568;ReadPosRankSum=0.178;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1239,125,0:0,0,15,27 chr2 24583719 . G C 785.95 PASS AC=2;AF=0.989;AN=2;DP=895;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:611,54,0:0,0,4,14 chr2 24714831 . G T 121.72 PASS AC=2;AF=0.69;AN=2;DP=415;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant10-variant11-variant12-variant15-variant16-variant18-variant21-variant22-variant24-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,17:18:43:428,43,0:0,1,11,6 chr2 24807533 . C T 4308.24 PASS AC=2;AF=0.898;AN=2;DP=4910;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,108:108:99:3464,323,0:0,0,35,73 chr2 24896389 . T G 886.26 PASS AC=2;AF=0.722;AN=2;DP=2129;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:1828,177,0:0,0,21,38 chr2 24905684 . C CA 1256.12 PASS AC=2;AF=0.92;AN=2;DP=858;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,20:20:63:845,63,0:0,0,19,1 chr2 24905927 . G C 5546.63 PASS AC=2;AF=0.884;AN=2;DP=8579;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,193:193:99:5655,578,0:0,0,79,114 chr2 24933689 . A C 713.62 PASS AC=2;AF=0.884;AN=2;DP=1159;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1232,102,0:0,0,28,6 chr2 24952740 . C CT 1067.7 PASS AC=2;AF=0.92;AN=2;DP=2332;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,73:73:99:2946,220,0:0,0,22,51 chr2 24974945 . T G 1930.25 PASS AC=2;AF=0.884;AN=2;DP=3514;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,88:88:99:2560,264,0:0,0,48,40 chr2 24991385 . CAAAA CA,CAAAAAAA,CAA,C,CAAA,CAAAAA 391.35 PASS AC=0,0,0,1,0,0;AF=0.13,0.019,0.13,0.093,0.093,0.037;AN=2;DP=1386;set=variant2-variant3-variant5-variant7-variant8-variant10-variant14-variant16-variant18-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant40-variant41-variant43-variant44 GT:DP:GQ:SB 0/4:54:99:23,15,14,2 chr2 25013062 . T C 2612.09 PASS AC=2;AF=0.617;AN=2;DP=6297;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant10-variant11-variant12-variant15-variant18-variant21-variant22-variant23-variant24-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,240:240:99:7371,719,0:0,0,135,105 chr2 25022442 . TA T 1010.49 PASS AC=2;AF=0.8;AN=2;DP=883;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant22-variant23-variant24-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:59:484,59,0:0,0,14,6 chr2 25037042 . G A 275.88 PASS AC=2;AF=0.712;AN=2;DP=327;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant22-variant24-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:458,42,0:0,0,10,4 chr2 25039804 . G A 1178.11 PASS AC=2;AF=0.92;AN=2;DP=1188;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:691,60,0:0,0,5,15 chr2 25040423 . G A 775.03 PASS AC=2;AF=0.763;AN=2;DP=1900;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1804,150,0:0,0,37,13 chr2 25042625 . C G 2164.74 PASS AC=2;AF=0.895;AN=2;DP=4625;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,124:124:99:3846,372,0:0,0,61,63 chr2 25044754 . A G 982.24 PASS AC=2;AF=0.686;AN=2;DP=2268;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant21-variant22-variant23-variant24-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:3499,235,0:0,0,36,41 chr2 25044755 . C T 982.24 PASS AC=2;AF=0.686;AN=2;DP=2248;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant21-variant22-variant23-variant24-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,78:78:99:3499,235,0:0,0,37,41 chr2 25044763 . A G 862.29 PASS AC=2;AF=0.686;AN=2;DP=2182;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant21-variant22-variant23-variant24-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,73:73:99:3244,220,0:0,0,35,38 chr2 25046090 . T C 821.77 PASS AC=2;AF=0.784;AN=2;DP=1073;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant21-variant22-variant23-variant24-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:962,90,0:0,0,20,10 chr2 25046355 . T C 410.02 PASS AC=2;AF=0.691;AN=2;DP=866;set=variant-variant2-variant3-variant5-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant21-variant22-variant23-variant24-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1226,105,0:0,0,14,21 chr2 25047408 . A G 1089.02 PASS AC=2;AF=0.632;AN=2;DP=5604;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant21-variant22-variant23-variant24-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,192:192:99:5731,574,0:0,0,85,107 chr2 25048847 . A G 976.64 PASS AC=2;AF=0.784;AN=2;DP=2435;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant21-variant22-variant23-variant24-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,63:63:99:2068,189,0:0,0,46,17 chr2 25050977 . T C 1164.96 PASS AC=2;AF=0.784;AN=2;DP=2844;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant21-variant22-variant23-variant24-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,74:74:99:2409,222,0:0,0,31,43 chr2 25057298 . C G 705.22 PASS AC=1;AF=0.667;AN=2;DP=327;MQ=60;set=variant4-variant6-variant11-variant14-variant16-variant20-variant21-variant23-variant25-variant26-variant27-variant29-variant30-variant35-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,7:14:99:182,0,191:5,2,4,3 chr2 25061270 . GGGGTGGGGTGGGTGGGGT GGGGTGGGGT,G 418.87 PASS AC=1,0;AF=0.786,0.024;AN=2;DP=311;MQ=60;set=variant3-variant4-variant6-variant11-variant14-variant16-variant20-variant21-variant23-variant25-variant26-variant29-variant30-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:12:99:3,0,9,0 chr2 25064079 . G A 46.75 PASS AC=1;AF=0.595;AN=2;DP=159;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant7-variant8-variant10-variant13-variant15-variant17-variant18-variant21-variant22-variant24-variant28-variant29-variant35-variant36-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,3:7:94:94,0,106:2,2,3,0 chr2 25064193 . G A 1028.93 PASS AC=1;AF=0.65;AN=2;DP=921;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant10-variant12-variant13-variant15-variant17-variant18-variant21-variant22-variant23-variant24-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:21,15:36:99:392,0,512:13,8,9,6 chr2 25100738 . C A 721.55 PASS AC=1;AF=0.692;AN=2;DP=956;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant12-variant13-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant27-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:15,23:38:99:492,0,381:10,5,14,9 chr2 25100902 . C G 1306.56 PASS AC=1;AF=0.696;AN=2;DP=1567;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant27-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:19,27:46:99:650,0,475:7,12,14,13 chr2 25141434 . G A 856.96 PASS AC=1;AF=0.5;AN=2;DP=951;MQ=60;set=variant2-variant3-variant8-variant11-variant17-variant33-variant35-variant36-variant41 GT:AD:DP:GQ:PL:SB 0/1:65,67:132:99:1882,0,1787:41,24,43,24 chr2 25141538 . A G 2444.45 PASS AC=1;AF=0.683;AN=2;DP=6366;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:123,126:249:99:3160,0,2766:66,57,63,63 chr2 25142806 . T G 131.06 PASS AC=1;AF=0.591;AN=2;DP=123;MQ=60;set=variant2-variant3-variant8-variant11-variant12-variant17-variant19-variant25-variant35-variant36-variant41 GT:AD:DP:GQ:PL:SB 0/1:6,8:14:91:197,0,91:3,3,5,3 chr2 25169200 . A G 641.86 PASS AC=1;AF=0.667;AN=2;DP=1031;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:20,16:36:99:512,0,490:12,8,7,9 chr2 25194741 . G A 3578.25 PASS AC=2;AF=0.814;AN=2;DP=14128;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,354:354:99:10741,1056,0:0,0,150,204 chr2 25264835 . G GGGGGCGGGGCGCA 121.12 PASS AC=2;AF=1;AN=2;DP=53;FS=0;MQ=60;set=variant6-variant7-variant8-variant12-variant16-variant19-variant22-variant33-variant35-variant36-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:12:180,12,0:0,0,2,1 chr2 25353279 . C T 481.66 PASS AC=1;AF=0.5;AN=2;DP=170;FractionInformativeReads=1;MQ=60;set=variant3-variant8-variant33-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:17,18:35:99:607,0,610:16,1,14,4 chr2 25359422 . G A 1476.52 PASS AC=2;AF=0.591;AN=2;DP=3172;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant8-variant10-variant11-variant14-variant18-variant21-variant24-variant28-variant30-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,152:152:99:4280,454,0:0,0,74,78 chr2 25368951 . GTTT G,GTT,GT,GTTTT 408.36 PASS AC=0,1,0,0;AF=0.061,0.197,0.242,0.091;AN=2;DP=1490;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-filterInvariant37-variant38-filterInvariant39-filterInvariant41-variant42-variant44 GT:DP:GQ:SB 0/2:33:19:3,3,13,14 chr2 25369884 . G A 1069.34 PASS AC=1;AF=0.5;AN=2;DP=89;FS=0.793;FractionInformativeReads=1;MQ=60;MQRankSum=0.177;QD=12.02;ReadPosRankSum=0.661;SOR=0.662;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:46,43:89:99:1098,0,1267:22,24,22,21 chr2 25375105 . T C 337.44 PASS AC=2;AF=0.764;AN=2;DP=540;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:640,51,0:0,0,5,12 chr2 25377176 . T C 1988.41 PASS AC=2;AF=0.708;AN=2;DP=7255;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,212:212:99:6647,636,0:0,0,98,114 chr2 25383887 . G A 1227.33 PASS AC=1;AF=0.556;AN=2;DP=2009;MQ=60;set=variant-variant5-variant8-variant10-variant11-variant14-variant18-variant21-variant24-variant28-variant30-variant34-variant35-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:75,63:138:99:1710,0,2040:44,31,41,22 chr2 25387858 . G GACC 322.73 PASS AC=2;AF=0.857;AN=2;DP=590;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:630,42,0:0,0,3,11 chr2 25456647 . CA C 273.12 PASS AC=1;AF=0.629;AN=2;DP=1051;set=variant-variant3-variant4-variant5-variant6-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-filterInvariant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,13:25:99:233,0,242:9,3,9,4 chr2 25458379 . G A 35.5 PASS AC=1;AF=0.636;AN=2;DP=611;MQ=60;set=variant-variant3-variant5-variant6-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,12:26:99:324,0,428:10,4,9,3 chr2 25458546 . C T 617.15 PASS AC=1;AF=0.636;AN=2;DP=3545;MQ=60;set=variant-variant3-variant5-variant6-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:66,45:111:99:1119,0,1689:35,31,24,21 chr2 25462988 . G A 500.81 PASS AC=1;AF=0.5;AN=2;DP=138;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant33-variant34-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:19,5:24:99:140,0,624:16,3,5,0 chr2 25463483 . G A 232.04 PASS AC=1;AF=0.618;AN=2;DP=1993;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,29:68:99:610,0,1110:24,15,18,11 chr2 25466888 . G T 977.59 PASS AC=1;AF=0.733;AN=2;DP=2331;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,27:66:99:596,0,1102:15,24,13,14 chr2 25469913 . C T 691.27 PASS AC=1;AF=0.733;AN=2;DP=2956;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,32:85:99:765,0,1411:32,21,20,12 chr2 25472784 . C T 1222.53 PASS AC=1;AF=0.733;AN=2;DP=1096;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,11:24:99:330,0,370:3,10,3,8 chr2 25497684 . A AC 524.34 PASS AC=2;AF=0.691;AN=2;DP=1028;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1454,108,0:0,0,23,13 chr2 25498283 . A C 198.42 PASS AC=1;AF=0.5;AN=2;DP=1216;set=variant-variant2-filterInvariant3-variant4-variant8-variant9-variant10-filterInvariant11-variant12-variant13-variant15-variant16-filterInvariant17-variant18-filterInvariant19-variant20-filterInvariant22-variant23-filterInvariant24-variant25-filterInvariant27-variant29-variant30-variant31-variant32-variant33-filterInvariant35-variant36-variant37-variant38-filterInvariant39-filterInvariant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,22:44:99:706,0,2488:6,16,22,0 chr2 25498287 . T C 430 PASS AC=1;AF=0.5;AN=2;DP=1384;set=variant-variant2-variant3-variant4-variant7-variant8-variant9-variant10-filterInvariant11-variant12-variant13-variant15-variant16-variant17-filterInvariant18-filterInvariant19-variant20-filterInvariant22-variant23-filterInvariant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-filterInvariant35-variant36-variant37-variant38-filterInvariant39-filterInvariant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,21:50:99:691,0,2683:9,20,21,0 chr2 25498290 . G C 418.43 PASS AC=1;AF=0.5;AN=2;DP=1455;set=variant-variant2-variant3-variant4-variant7-variant8-variant9-variant10-filterInvariant11-variant12-variant13-variant15-variant16-variant17-filterInvariant19-variant20-filterInvariant22-variant23-variant24-filterInvariant25-variant27-variant29-filterInvariant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-filterInvariant39-filterInvariant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,20:52:99:636,0,2689:12,20,20,0 chr2 25498296 . T C 405.44 PASS AC=1;AF=0.5;AN=2;DP=1396;set=variant-filterInvariant3-variant7-variant9-variant12-variant13-variant15-variant16-variant17-filterInvariant19-variant20-variant22-variant24-filterInvariant25-variant27-variant29-filterInvariant30-variant31-filterInvariant32-variant33-variant35-variant36-variant37-variant38-filterInvariant39-variant40-filterInvariant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,14:51:99:146,0,3755:15,22,14,0 chr2 25498298 . A C 55.18 PASS AC=1;AF=0.5;AN=2;DP=1236;set=filterInvariant-filterInvariant3-variant7-variant9-filterInvariant11-variant12-variant13-variant15-variant16-filterInvariant17-filterInvariant19-variant20-variant22-variant24-variant27-variant29-variant31-variant35-variant36-variant37-variant38-filterInvariant39-variant40-filterInvariant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,12:54:99:142,0,3751:18,24,12,0 chr2 25498565 . C G 664.51 PASS AC=1;AF=0.5;AN=2;DP=158;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant35-variant36-variant39 GT:AD:DP:GQ:PL:SB 0/1:12,15:27:99:463,0,338:5,7,4,11 chr2 25551692 . C T 64.44 PASS AC=2;AF=0.647;AN=2;DP=380;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:380,36,0:0,0,4,8 chr2 25602142 . G A 3121.95 PASS AC=1;AF=0.773;AN=2;DP=2661;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant13-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,36:75:99:887,0,973:24,15,24,12 chr2 25602310 . C T 771.46 PASS AC=1;AF=0.556;AN=2;DP=1519;MQ=60;set=variant2-variant3-variant6-variant8-variant9-variant13-variant16-variant19-variant23-variant25-variant28-variant31-variant33-variant35-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:44,42:86:99:1031,0,1141:16,28,19,23 chr2 25610287 . G T 483.18 PASS AC=1;AF=0.528;AN=2;DP=733;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant6-variant8-variant9-variant13-variant16-variant17-variant19-variant23-variant25-variant28-variant31-variant35-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:16,30:46:99:691,0,380:7,9,15,15 chr2 25655446 . T G 350.28 PASS AC=2;AF=0.828;AN=2;DP=541;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:1057,81,0:0,0,25,2 chr2 25655772 . T C 2077.41 PASS AC=1;AF=0.605;AN=2;DP=3080;MQ=60;set=variant5-variant7-variant8-variant9-variant12-variant14-variant15-variant18-variant23-variant26-variant27-variant29-variant30-variant34-variant35-variant36-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:78,106:184:99:2869,0,1852:38,40,51,55 chr2 25656880 . C G 1835.45 PASS AC=2;AF=0.875;AN=2;DP=2055;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,52:52:99:1837,156,0:0,0,19,33 chr2 25656889 . G GT 316.08 PASS AC=1;AF=0.526;AN=2;DP=691;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant10-variant12-variant14-variant15-variant18-variant21-variant23-variant29-variant30-variant35-variant36-variant37-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:24,14:38:99:260,0,553:8,16,3,11 chr2 25754235 . T C 573.32 PASS AC=2;AF=0.588;AN=2;DP=616;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant7-variant8-variant10-variant13-variant14-variant15-variant19-variant29-variant35-variant36-variant37-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1351,129,0:0,0,28,15 chr2 25875401 . T TA,TAA 518.6 PASS AC=1,1;AF=0.313,0.333;AN=2;DP=1072;set=variant3-variant5-variant6-variant8-variant9-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant27-variant30-variant31-variant35-variant36-variant37-variant39-variant41-variant42-variant44 GT:DP:GQ:SB 1/2:39:99:3,0,25,11 chr2 25961583 . A G 1590.69 PASS AC=1;AF=0.5;AN=2;DP=4003;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant10-variant11-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant29-variant31-variant32-variant33-variant35-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:78,78:156:99:1721,0,1917:39,39,38,40 chr2 25962238 . GT GTT,G 1699.51 PASS AC=1,0;AF=0.468,0.032;AN=2;DP=8640;set=variant2-filterInvariant3-variant4-filterInvariant5-variant6-filterInvariant7-filterInvariant8-filterInvariant9-variant10-filterInvariant11-filterInvariant12-filterInvariant14-filterInvariant15-variant19-filterInvariant21-filterInvariant22-filterInvariant25-filterInvariant27-filterInvariant28-filterInvariant30-filterInvariant32-filterInvariant33-filterInvariant34-filterInvariant35-filterInvariant36-variant38-filterInvariant39-filterInvariant40-filterInvariant42-filterInvariant43-filterInvariant44 GT:DP:GQ:SB 0/1:209:89:77,99,18,15 chr2 25965982 . C T 3048.12 PASS AC=1;AF=0.5;AN=2;DP=234;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.087;QD=13.03;ReadPosRankSum=2.138;SOR=0.693;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:117,117:234:99:3076,0,2875:51,66,51,66 chr2 25973309 . C T 388.29 PASS AC=1;AF=0.536;AN=2;DP=859;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant29-variant31-variant32-variant33-variant35-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:16,18:34:99:462,0,376:5,11,7,11 chr2 25990640 . T C 589.9 PASS AC=1;AF=0.5;AN=2;DP=754;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant15-variant17-variant20-variant21-variant23-variant25-variant26-variant29-variant31-variant35-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:20,23:43:99:631,0,526:6,14,9,14 chr2 25994412 . A AG 1223.58 PASS AC=1;AF=0.5;AN=2;DP=3868;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant10-variant11-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant29-variant31-variant32-variant33-variant35-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:58,56:114:99:1436,0,1638:29,29,28,28 chr2 26003068 . C T 281.63 PASS AC=1;AF=0.568;AN=2;DP=219;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant15-variant17-variant18-variant19-variant21-variant24-variant25-variant31-variant33-variant35-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:3,6:9:99:159,0,106:3,0,4,2 chr2 26003230 . A G 234.06 PASS AC=1;AF=0.5;AN=2;DP=522;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant10-variant11-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant29-variant31-variant32-variant33-variant35-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:13,14:27:99:346,0,261:5,8,6,8 chr2 26068509 . C T 309.04 PASS AC=1;AF=0.571;AN=2;DP=95;FractionInformativeReads=1;MQ=60;set=variant4-variant7-variant10-variant11-variant15-variant17-variant19-variant21-variant23-variant26-variant31-variant33-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:4,3:7:99:114,0,120:1,3,1,2 chr2 26082046 . GT G 185.85 PASS AC=1;AF=0.605;AN=2;DP=194;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant10-variant15-variant17-variant20-variant21-variant23-variant24-variant26-variant29-variant31-variant32-variant33-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:6,4:10:99:120,0,194:3,3,1,3 chr2 26082057 . T C 459.21 PASS AC=2;AF=0.878;AN=2;DP=389;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:418,36,0:0,0,5,7 chr2 26101403 . A C 326.24 PASS AC=1;AF=0.5;AN=2;DP=598;MQ=60;set=variant2-variant4-variant5-variant7-variant9-variant10-variant11-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant29-variant31-variant32-variant33-variant35-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:16,14:30:99:339,0,327:6,10,6,8 chr2 26149502 . A G 304.59 PASS AC=2;AF=0.78;AN=2;DP=758;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:411,39,0:0,0,5,8 chr2 26149968 . C T 2048.05 PASS AC=2;AF=1;AN=2;DP=3844;FS=0;MQ=60;MQRankSum=1.643;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,87:87:99:3759,262,0:0,0,49,38 chr2 26149988 . G C 668.06 PASS AC=2;AF=0.768;AN=2;DP=3774;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,93:93:99:3904,279,0:0,0,49,44 chr2 26150589 . G T 10344.9 PASS AC=2;AF=0.872;AN=2;DP=13054;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,284:284:99:8722,850,0:0,0,161,123 chr2 26150773 . T G 9344.7 PASS AC=2;AF=0.872;AN=2;DP=11087;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,255:255:99:7936,763,0:0,0,104,151 chr2 26151206 . T C 1357.46 PASS AC=2;AF=0.953;AN=2;DP=2506;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,73:73:99:2088,218,0:0,0,41,32 chr2 26151643 . A T 758.86 PASS AC=2;AF=0.857;AN=2;DP=1317;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:983,96,0:0,0,15,17 chr2 26161226 . CA CAA,C 214.03 PASS AC=1,0;AF=0.526,0.026;AN=2;DP=982;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-filterInvariant13-variant15-variant16-variant17-filterInvariant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant33-variant34-filterInvariant35-variant37-filterInvariant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:27:93:13,7,4,3 chr2 26203678 . T C 4287.94 PASS AC=2;AF=1;AN=2;DP=8006;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,185:185:99:5900,555,0:0,0,97,88 chr2 26205081 . A T 3274.84 PASS AC=2;AF=1;AN=2;DP=4704;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,110:110:99:3429,328,0:0,0,65,45 chr2 26257249 . C G 7173.16 PASS AC=2;AF=1;AN=2;DP=5774;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,138:138:99:6118,415,0:0,0,54,84 chr2 26257250 . G C 7173.16 PASS AC=2;AF=1;AN=2;DP=5696;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,135:135:99:6118,415,0:0,0,53,82 chr2 26321526 . T C 605.88 PASS AC=1;AF=0.782;AN=2;DP=1841;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,18:40:99:443,0,575:14,8,10,8 chr2 26350136 . G T 1154.69 PASS AC=1;AF=0.782;AN=2;DP=2903;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,32:73:99:757,0,1069:13,28,11,21 chr2 26357748 . G T 825.3 PASS AC=1;AF=0.789;AN=2;DP=2333;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,43:88:99:1084,0,1103:29,16,25,18 chr2 26358110 . G C 1906.01 PASS AC=1;AF=0.797;AN=2;DP=5501;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:79,83:162:99:2134,0,1917:33,46,40,43 chr2 26359128 . T A 2858 PASS AC=1;AF=0.5;AN=2;DP=799;MQ=60;set=variant15-variant16-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:72,98:170:99:2093,0,1786:27,45,38,60 chr2 26359315 . G A 2717.79 PASS AC=1;AF=0.795;AN=2;DP=6902;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:83,74:157:99:1772,0,2065:47,36,40,34 chr2 26399214 . G A 472.82 PASS AC=1;AF=0.75;AN=2;DP=4584;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,81:145:99:1955,0,1627:33,31,41,40 chr2 26403766 . G A 1274.93 PASS AC=1;AF=0.833;AN=2;DP=1800;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,26:45:99:745,0,511:13,6,19,7 chr2 26404221 . C T 2318.02 PASS AC=1;AF=0.833;AN=2;DP=2689;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,48:101:99:1120,0,1308:26,27,24,24 chr2 26404510 . T G 764.93 PASS AC=1;AF=0.5;AN=2;DP=83;FractionInformativeReads=1;MQ=60;set=variant15-variant35 GT:AD:DP:GQ:PL:SB 0/1:14,23:37:99:675,0,339:4,10,8,15 chr2 26405016 . C G 1834.35 PASS AC=1;AF=0.833;AN=2;DP=3463;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,41:95:99:923,0,1477:25,29,21,20 chr2 26405985 . A G 534.3 PASS AC=1;AF=0.833;AN=2;DP=1252;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-filterInvariant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,16:35:99:404,0,612:5,14,6,10 chr2 26408064 . T C 983.58 PASS AC=1;AF=0.955;AN=2;DP=1212;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:19,20:39:99:532,0,395:10,9,9,11 chr2 26410541 . C T 2367.93 PASS AC=1;AF=0.5;AN=2;DP=149;FS=9.31;FractionInformativeReads=0.993;MQ=60;MQRankSum=-1.287;QD=15.89;ReadPosRankSum=0.614;SOR=0.284;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:50,98:148:99:2396,0,1402:17,33,47,51 chr2 26411894 . C T 1800.17 PASS AC=1;AF=0.821;AN=2;DP=3113;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,32:78:99:788,0,1378:23,23,14,18 chr2 26412563 . AAAC A 583.7 PASS AC=1;AF=0.833;AN=2;DP=707;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,11:22:99:429,0,459:2,9,6,5 chr2 26412638 . G T 196.77 PASS AC=1;AF=0.857;AN=2;DP=277;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,9:13:99:201,0,122:1,3,4,5 chr2 26413817 . C T 929.58 PASS AC=1;AF=0.647;AN=2;DP=737;FractionInformativeReads=1;MQ=60;set=variant4-variant8-variant11-variant14-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant28-variant34-variant35-variant37-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:21,24:45:99:685,0,636:8,13,10,14 chr2 26413917 . C T 782.79 PASS AC=1;AF=0.833;AN=2;DP=1031;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,13:29:99:336,0,379:6,10,4,9 chr2 26415088 . TA TAA,T 35.88 PASS AC=0,1;AF=0.083,0.5;AN=2;DP=766;MQ=60;set=filterInvariant2-variant4-filterInvariant5-variant8-filterInvariant9-variant11-variant14-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant44 GT:DP:GQ:SB 0/2:35:99:15,8,8,4 chr2 26415093 . A C 726.96 PASS AC=1;AF=0.5;AN=2;DP=94;MQ=60;set=variant15-variant35 GT:AD:DP:GQ:PL:SB 0/1:14,23:37:99:480,0,398:10,4,15,8 chr2 26415429 . A G 680.97 PASS AC=1;AF=0.833;AN=2;DP=661;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,7:11:99:193,0,139:0,4,2,5 chr2 26416301 . A G 1197.5 PASS AC=1;AF=0.833;AN=2;DP=1879;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,34:58:99:822,0,664:18,6,21,13 chr2 26417533 . C A 553.53 PASS AC=1;AF=0.833;AN=2;DP=638;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,6:15:99:205,0,317:1,8,1,5 chr2 26420708 . T G 2286.71 PASS AC=1;AF=0.833;AN=2;DP=3306;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,38:78:99:856,0,983:20,20,16,22 chr2 26420809 . G C 455.3 PASS AC=1;AF=0.842;AN=2;DP=688;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,4:22:73:73,0,511:5,13,1,3 chr2 26455002 . C G 274.18 PASS AC=1;AF=0.639;AN=2;DP=405;MQ=60;set=variant4-variant8-variant11-variant14-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant28-variant34-variant35-variant37-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:7,11:18:99:391,0,262:7,0,9,2 chr2 26455127 . G A 900.2 PASS AC=1;AF=0.639;AN=2;DP=1749;MQ=60;set=variant4-variant8-variant11-variant14-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant28-variant34-variant35-variant37-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:50,48:98:99:1187,0,1258:25,25,27,21 chr2 26457267 . T G 490.97 PASS AC=1;AF=0.639;AN=2;DP=821;FractionInformativeReads=1;MQ=60;set=variant4-variant8-variant11-variant14-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant28-variant34-variant35-variant37-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:32,26:58:99:668,0,721:14,18,9,17 chr2 26462093 . A T 109.74 PASS AC=1;AF=0.647;AN=2;DP=201;FractionInformativeReads=1;MQ=60;set=variant4-variant8-variant11-variant14-variant17-variant21-variant22-variant23-variant24-variant25-variant28-variant34-variant35-variant37-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:11,5:16:99:161,0,293:3,8,1,4 chr2 26467347 . C A 1035.18 PASS AC=1;AF=0.639;AN=2;DP=1596;MQ=60;set=variant4-variant8-variant11-variant14-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant28-variant34-variant35-variant37-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:46,51:97:99:1479,0,1192:30,16,36,15 chr2 26467653 . C T 1052.62 PASS AC=1;AF=0.639;AN=2;DP=1118;MQ=60;set=variant4-variant8-variant11-variant14-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant28-variant34-variant35-variant37-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:36,38:74:99:1030,0,1008:18,18,22,16 chr2 26476977 . A G 2102.4 PASS AC=1;AF=0.977;AN=2;DP=3188;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:32,39:71:99:1325,0,945:24,8,35,4 chr2 26477125 . G GACT 17279.8 PASS AC=1;AF=0.977;AN=2;DP=15219;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:166,163:329:99:3862,0,7628:81,85,73,90 chr2 26500101 . CTTT CTT,C,CT,CTTTT,CTTTTT 46.22 PASS AC=0,0,1,0,0;AF=0.204,0.056,0.259,0.056,0.019;AN=2;DP=1094;MQ=60;set=filterInvariant2-filterInvariant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-filterInvariant13-variant15-variant17-variant19-variant20-variant21-variant22-variant25-filterInvariant26-variant28-variant33-variant34-variant35-variant37-variant38-variant41-filterInvariant42-filterInvariant44 GT:DP:GQ:SB 0/3:20:99:4,4,3,9 chr2 26501953 . C A 654.67 PASS AC=1;AF=0.639;AN=2;DP=538;MQ=60;set=variant4-variant8-variant11-variant14-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant28-variant34-variant35-variant37-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:22,17:39:99:459,0,708:18,4,13,4 chr2 26502875 . T C 252.46 PASS AC=1;AF=0.632;AN=2;DP=341;FractionInformativeReads=1;MQ=60;set=variant4-variant8-variant11-variant13-variant14-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant28-variant34-variant35-variant37-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:13,9:22:99:258,0,399:10,3,7,2 chr2 26505858 . A G 1229.01 PASS AC=1;AF=0.639;AN=2;DP=1610;MQ=60;set=variant4-variant8-variant11-variant14-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant28-variant34-variant35-variant37-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:56,34:90:99:791,0,1302:29,27,16,18 chr2 26507076 . A T 1253.71 PASS AC=1;AF=0.5;AN=2;DP=265;FractionInformativeReads=1;MQ=60;set=variant15-variant35 GT:AD:DP:GQ:PL:SB 0/1:66,62:128:99:1514,0,1669:34,32,36,26 chr2 26507724 . T C 569.11 PASS AC=1;AF=0.632;AN=2;DP=1111;MQ=60;set=variant4-variant8-variant11-variant13-variant14-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant28-variant34-variant35-variant37-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:41,29:70:99:648,0,999:24,17,16,13 chr2 26508607 . G GTTTTTTT,GTTTTTTTTTTTTTTTTTT,GTTTTTTTTTTTTTTTTT,GTTTTTTTT,GTTTTTTTTT,GTTTTTTTTTTTTT,GTTTTTTTTTTTTTTTTTTTT,GTTTTTTTTTT,GTTTTTT,GTTTTTTTTTTTTTTTTTTT 384.1 PASS AC=0,0,0,0,0,0,0,1,0,0;AF=0.111,0.111,0.111,0.222,0.111,0.056,0.056,0.028,0.111,0.056;AN=2;DP=251;FS=0;MQRankSum=-1.718;ReadPosRankSum=-2.047;set=variant4-variant5-variant6-variant8-variant14-variant17-variant25-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant44 GT:DP:GQ:SB 0/8:12:99:2,4,2,4 chr2 26512733 . T G 1355.81 PASS AC=1;AF=0.632;AN=2;DP=2477;FractionInformativeReads=1;set=variant4-variant8-variant11-variant13-variant14-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant28-variant34-variant35-variant37-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:90,78:168:99:2038,0,2300:50,40,42,36 chr2 26512957 . G C 11413 PASS AC=1;AF=0.977;AN=2;DP=11530;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:130,151:281:99:3963,0,3268:63,67,75,76 chr2 26532491 . G T 1336.53 PASS AC=2;AF=0.732;AN=2;DP=4487;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,125:126:99:3612,335,0:1,0,55,70 chr2 26532735 . G A 882.19 PASS AC=2;AF=0.713;AN=2;DP=2982;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:2444,216,0:0,0,46,26 chr2 26533023 . C T 844.36 PASS AC=2;AF=0.713;AN=2;DP=4320;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,106:106:99:3122,317,0:0,0,49,57 chr2 26534801 . G A 1173.68 PASS AC=2;AF=0.725;AN=2;DP=3146;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:2268,215,0:0,0,36,36 chr2 26536555 . T C 584.33 PASS AC=2;AF=0.744;AN=2;DP=1283;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1311,117,0:0,0,19,20 chr2 26536694 . C T 487.73 PASS AC=2;AF=0.732;AN=2;DP=4005;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,90:90:99:2592,268,0:0,0,46,44 chr2 26536967 . C A 893.43 PASS AC=1;AF=0.5;AN=2;DP=347;FractionInformativeReads=1;MQ=60;set=variant5-variant7-variant9-variant28-variant32-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:26,28:54:99:659,0,711:10,16,13,15 chr2 26537499 . A C 968.27 PASS AC=2;AF=0.966;AN=2;DP=4290;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,106:106:99:3171,318,0:0,0,40,66 chr2 26541158 . G A 145.31 PASS AC=1;AF=0.965;AN=2;DP=272;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,5:10:99:141,0,115:2,3,1,4 chr2 26542143 . A G 184.68 PASS AC=2;AF=0.988;AN=2;DP=281;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.067;ReadPosRankSum=0.572;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:330,24,0:0,0,0,8 chr2 26542155 . C A 91.49 PASS AC=1;AF=0.667;AN=2;DP=126;MQ=60;set=variant-variant7-variant8-variant9-variant10-variant11-variant17-variant21-variant22-variant23-variant25-variant28-variant32-variant34-variant35-variant37-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:5,3:8:94:94,0,189:1,4,0,3 chr2 26587076 . G A 435.78 PASS AC=1;AF=0.636;AN=2;DP=862;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant7-variant8-variant9-filterInvariant14-variant17-variant21-variant22-variant23-variant24-variant25-variant28-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:24,26:50:99:560,0,643:14,10,12,14 chr2 26590084 . T G 1488.55 PASS AC=1;AF=0.636;AN=2;DP=2324;MQ=60;set=variant-variant4-variant5-variant7-variant8-variant9-variant14-variant17-variant21-variant22-variant23-variant24-variant25-variant28-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:43,57:100:99:1356,0,1104:20,23,24,33 chr2 26590118 . C T 1431.57 PASS AC=1;AF=0.636;AN=2;DP=2041;set=variant-variant4-variant5-variant7-variant8-variant9-variant14-variant17-variant21-variant22-variant23-variant24-variant25-variant28-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:40,44:84:99:968,0,956:18,22,18,26 chr2 26606154 . T C 610.47 PASS AC=1;AF=0.5;AN=2;DP=170;FractionInformativeReads=1;MQ=60;set=variant15-variant29-variant35 GT:AD:DP:GQ:PL:SB 0/1:21,20:41:99:527,0,501:13,8,13,7 chr2 26607815 . T C 987.8 PASS AC=1;AF=0.5;AN=2;DP=192;FractionInformativeReads=1;MQ=60;set=variant15-variant29-variant35 GT:AD:DP:GQ:PL:SB 0/1:25,25:50:99:635,0,658:17,8,19,6 chr2 26607992 . T C 2001.51 PASS AC=2;AF=0.966;AN=2;DP=2000;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1279,117,0:0,0,10,29 chr2 26609469 . G A 683.82 PASS AC=1;AF=0.636;AN=2;DP=1063;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant7-variant8-variant9-variant14-variant17-variant21-variant22-variant23-variant24-variant25-variant28-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:25,15:40:99:470,0,772:6,19,3,12 chr2 26613056 . C T 18703.2 PASS AC=2;AF=1;AN=2;DP=21909;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,486:486:99:14832,1456,0:0,0,230,256 chr2 26613329 . A G 5806.89 PASS AC=1;AF=0.636;AN=2;DP=9790;MQ=60;set=variant-variant4-variant5-variant7-variant8-variant9-variant14-variant17-variant21-variant22-variant23-variant24-variant25-variant28-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:253,225:478:99:5512,0,6380:98,155,83,142 chr2 26613943 . ATT A 9392.42 PASS AC=2;AF=1;AN=2;DP=8586;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,211:211:99:9419,635,0:0,0,122,89 chr2 26613974 . C T 7776.14 PASS AC=2;AF=0.966;AN=2;DP=9747;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,254:254:99:7650,758,0:0,0,145,109 chr2 26614583 . T TA 8545.9 PASS AC=2;AF=0.966;AN=2;DP=11077;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,252:252:99:7758,757,0:0,0,154,98 chr2 26616401 . A T 1012.15 PASS AC=2;AF=0.966;AN=2;DP=1443;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:856,87,0:0,0,16,13 chr2 26616624 . G C 804.1 PASS AC=1;AF=0.5;AN=2;DP=144;FractionInformativeReads=1;MQ=60;set=variant15-variant29-variant35 GT:AD:DP:GQ:PL:SB 0/1:21,26:47:99:648,0,526:10,11,14,12 chr2 26647277 . T G 655.8 PASS AC=1;AF=0.93;AN=2;DP=2413;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,22:59:99:503,0,1112:11,26,7,15 chr2 26652671 . A G 907.03 PASS AC=1;AF=0.965;AN=2;DP=1104;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,10:25:99:284,0,463:6,9,2,8 chr2 26663187 . TTG TTGTG,TTGTGTG,T,TTGTGTGTG,TTGTGTGTGTG 159.32 PASS AC=1,0,0,0,0;AF=0.317,0.463,0.073,0.012,0.012;AN=2;DP=408;FS=0;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:13:99:5,1,5,2 chr2 26667615 . T C 4168.54 PASS AC=2;AF=1;AN=2;DP=6645;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,183:183:99:5609,548,0:0,0,105,78 chr2 26671092 . CA CAAAA,CAA,C,CAAA 30.68 PASS AC=0,0,1,0;AF=0.017,0.397,0.086,0.052;AN=2;DP=513;set=variant2-variant3-variant5-variant6-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant24-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-filterInvariant39-variant40-variant43 GT:DP:GQ:SB 0/3:25:99:12,4,6,3 chr2 26671544 . A G 1679.37 PASS AC=1;AF=0.893;AN=2;DP=4339;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,52:104:99:1236,0,1187:26,26,26,26 chr2 26676322 . A G 852.9 PASS AC=2;AF=1;AN=2;DP=2128;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:1893,180,0:0,0,26,34 chr2 26676395 . G T 586.38 PASS AC=1;AF=0.5;AN=2;DP=131;MQ=60;set=variant15-variant29-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:14,18:32:99:508,0,318:6,8,7,11 chr2 26677303 . G T 1109.41 PASS AC=1;AF=0.955;AN=2;DP=1518;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:37,17:54:99:367,0,961:24,13,10,7 chr2 26677810 . A G 171.09 PASS AC=1;AF=0.869;AN=2;DP=1383;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,19:33:99:575,0,410:8,6,11,8 chr2 26678169 . G A 116.96 PASS AC=1;AF=0.5;AN=2;DP=69;FractionInformativeReads=1;MQ=60;set=variant15-variant29-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:13,6:19:99:193,0,446:3,10,0,6 chr2 26684910 . CA C 173.37 PASS AC=1;AF=0.5;AN=2;DP=50;FS=59.617;FractionInformativeReads=0.98;MQ=60;MQRankSum=1.522;QD=3.47;ReadPosRankSum=-1.593;SOR=4.97;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:38,11:49:99:211,0,2477:7,31,11,0 chr2 26684914 . CAGCTCAGT CCTCAGT,C 86.02 PASS AC=0,1;AF=0.125,0.375;AN=2;DP=297;MQ=60;set=filterInvariant3-filterInvariant11-filterInvariant24-variant35 GT:DP:GQ:SB 0/2:60:99:16,33,11,0 chr2 26684926 . T C 68.75 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=208;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:57,9:66:99:152,0,3301:23,34,9,0 chr2 26695143 . A G 88.71 PASS AC=1;AF=0.609;AN=2;DP=640;MQ=60;set=variant-variant4-variant7-variant8-variant9-variant14-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant34-variant35-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,12:24:99:346,0,356:8,4,9,3 chr2 26698682 . G T 331.6 PASS AC=1;AF=0.646;AN=2;DP=1122;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant8-variant9-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant37-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:22,29:51:99:794,0,763:17,5,21,8 chr2 26699126 . C G 327.77 PASS AC=1;AF=0.629;AN=2;DP=2619;MQ=60;set=variant-variant4-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,50:87:99:1240,0,1002:13,24,22,28 chr2 26699855 . G C 695.52 PASS AC=1;AF=0.646;AN=2;DP=1705;MQ=60;set=variant-variant4-variant8-variant9-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant37-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:36,36:72:99:1014,0,1076:20,16,18,18 chr2 26700700 . G A 1140.36 PASS AC=1;AF=0.635;AN=2;DP=3330;MQ=60;set=variant-variant4-variant8-variant9-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:75,62:137:99:1444,0,1960:31,44,32,30 chr2 26700819 . TGG T 1666.74 PASS AC=1;AF=0.629;AN=2;DP=2965;set=variant-variant4-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,60:108:99:2342,0,1751:22,26,30,30 chr2 26700908 . C G 825.24 PASS AC=1;AF=0.629;AN=2;DP=2536;MQ=60;set=variant-variant4-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,57:92:99:1368,0,1230:16,19,24,33 chr2 26700924 . G C 985.37 PASS AC=1;AF=0.5;AN=2;DP=166;FS=0;FractionInformativeReads=1;MQ=60;set=variant6-variant35 GT:AD:DP:GQ:PL:SB 0/1:53,33:86:99:889,0,2130:23,30,14,19 chr2 26702057 . GT G 211.36 PASS AC=1;AF=0.646;AN=2;DP=701;MQ=60;set=variant-variant4-variant8-variant9-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant37-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:15,18:33:99:573,0,455:10,5,12,6 chr2 26717641 . A G 238.34 PASS AC=1;AF=0.641;AN=2;DP=1058;MQ=60;set=variant-variant4-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,16:36:99:373,0,509:12,8,8,8 chr2 26724725 . T G 2376.89 PASS AC=1;AF=0.656;AN=2;DP=3019;set=variant-variant4-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,50:90:99:1190,0,987:15,25,23,27 chr2 26726752 . G A 3431.33 PASS AC=1;AF=0.632;AN=2;DP=3124;MQ=60;set=variant-variant7-variant8-variant9-variant11-variant16-variant17-variant20-variant22-variant23-variant25-variant26-variant28-variant30-variant32-variant34-variant35-variant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:74,82:156:99:1863,0,1826:31,43,36,46 chr2 26733500 . C T 2777.68 PASS AC=1;AF=0.563;AN=2;DP=1805;MQ=60;set=variant-variant3-variant10-variant11-variant14-variant15-variant16-variant17-variant20-variant23-variant26-variant28-variant34-variant35-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:69,65:134:99:1694,0,1770:46,23,46,19 chr2 26739247 . T A 3265.28 PASS AC=1;AF=0.769;AN=2;DP=3658;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,49:95:99:1262,0,1041:28,18,32,17 chr2 26739423 . T C 2928.11 PASS AC=1;AF=0.536;AN=2;DP=1683;MQ=60;set=variant-variant3-variant11-variant16-variant17-variant20-variant23-variant26-variant27-variant28-variant30-variant33-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:65,59:124:99:1608,0,1571:28,37,24,35 chr2 26741961 . G A 1049.87 PASS AC=1;AF=0.621;AN=2;DP=4397;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,63:128:99:1683,0,1725:21,44,24,39 chr2 26750557 . T C 978.83 PASS AC=2;AF=0.977;AN=2;DP=1899;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1600,132,0:0,0,31,13 chr2 26750645 . G A 2927.54 PASS AC=1;AF=0.802;AN=2;DP=4503;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,74:133:99:1724,0,1444:37,22,41,33 chr2 26781685 . CGTGT CGT,C 426.12 PASS AC=2,0;AF=0.895,0.058;AN=2;DP=1487;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:27:81:0,0,7,20 chr2 26794844 . AT A 145.74 PASS AC=1;AF=0.583;AN=2;DP=112;FractionInformativeReads=1;MQ=60;set=variant4-variant12-variant13-variant15-variant22-variant26-variant28-variant33-variant34-variant35-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:2,5:7:50:158,0,50:2,0,4,1 chr2 26795217 . GT G 40.72 PASS AC=1;AF=0.781;AN=2;DP=291;MQ=60;set=variant2-variant3-variant5-variant7-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:1,5:6:2:179,0,2:0,1,1,4 chr2 26795235 . C T 129.39 PASS AC=1;AF=0.591;AN=2;DP=77;FractionInformativeReads=1;MQ=60;set=variant13-variant14-variant16-variant22-variant23-variant26-variant28-variant33-variant35-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:1,5:6:2:179,0,2:0,1,1,4 chr2 26798893 . A T 3719.1 PASS AC=1;AF=0.531;AN=2;DP=4996;MQ=60;set=variant4-variant12-variant13-variant14-variant15-variant16-variant17-variant22-variant23-variant26-variant28-variant33-variant34-variant35-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:162,130:292:99:2813,0,3886:74,88,58,72 chr2 26799031 . G A 1507.62 PASS AC=1;AF=0.531;AN=2;DP=1308;MQ=60;set=variant4-variant12-variant13-variant14-variant15-variant16-variant17-variant22-variant23-variant26-variant28-variant33-variant34-variant35-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:46,34:80:99:943,0,1416:16,30,10,24 chr2 26801795 . C T 1477.72 PASS AC=1;AF=0.556;AN=2;DP=2856;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant13-variant16-variant19-variant20-variant25-variant26-variant30-variant32-variant35-variant37-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:100,80:180:99:1734,0,2463:40,60,36,44 chr2 26802392 . A T 1286.14 PASS AC=1;AF=0.536;AN=2;DP=1815;MQ=60;set=variant4-variant14-variant15-variant16-variant17-variant22-variant23-variant26-variant28-variant33-variant34-variant35-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:94,78:172:99:2049,0,2226:43,51,30,48 chr2 26804122 . T G 582.79 PASS AC=2;AF=0.65;AN=2;DP=2165;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant10-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2152,209,0:0,0,45,25 chr2 26804143 . T C 717.81 PASS AC=2;AF=0.656;AN=2;DP=2674;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,80:80:99:2418,240,0:0,0,44,36 chr2 26804218 . G A 1710.56 PASS AC=2;AF=0.977;AN=2;DP=4860;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,102:102:99:2954,305,0:0,0,53,49 chr2 26804247 . T C 502.05 PASS AC=2;AF=0.607;AN=2;DP=2755;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant30-variant32-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,97:97:99:2987,291,0:0,0,44,53 chr2 26818006 . T C 1624.67 PASS AC=1;AF=0.81;AN=2;DP=7125;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:121,87:208:99:2086,0,2881:61,60,44,43 chr2 26818021 . C T 1497.22 PASS AC=1;AF=0.816;AN=2;DP=6480;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:123,85:208:99:1889,0,3100:59,64,37,48 chr2 26846282 . T C 1116.67 PASS AC=1;AF=0.706;AN=2;DP=2549;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:42,36:78:99:944,0,1045:27,15,26,10 chr2 26915624 . G T 435.19 PASS AC=1;AF=0.75;AN=2;DP=317;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:10,8:18:99:173,0,235:6,4,5,3 chr2 26951449 . G A 1913.24 PASS AC=2;AF=0.989;AN=2;DP=4135;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,113:113:99:3422,337,0:0,0,56,57 chr2 26952703 . C CAA,CA,CAAA 50.53 PASS AC=0,1,0;AF=0.156,0.375,0.031;AN=2;DP=189;set=variant2-variant3-variant9-variant10-variant12-variant13-variant14-variant16-variant17-filterInvariant25-variant27-variant28-variant31-variant34-variant35-variant44 GT:DP:GQ:SB 0/2:8:10:2,0,4,2 chr2 26953354 . G T 2696.29 PASS AC=1;AF=0.686;AN=2;DP=4104;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:83,69:152:99:1598,0,2023:42,41,34,35 chr2 26953540 . A G 3818.36 PASS AC=1;AF=0.686;AN=2;DP=4926;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:73,89:162:99:2111,0,1854:40,33,47,42 chr2 26953582 . T G 4805.9 PASS AC=1;AF=0.686;AN=2;DP=4703;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:78,78:156:99:1955,0,1939:39,39,42,36 chr2 26953591 . G A 4582.02 PASS AC=2;AF=0.989;AN=2;DP=5924;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,151:151:99:5788,454,0:0,0,78,73 chr2 26953671 . G A 2863.68 PASS AC=2;AF=0.989;AN=2;DP=4945;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,123:123:99:3899,366,0:0,0,62,61 chr2 26953747 . A G 2923.86 PASS AC=2;AF=0.989;AN=2;DP=4735;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,118:119:99:3719,346,0:1,0,57,61 chr2 26953850 . C T 2968.94 PASS AC=1;AF=0.686;AN=2;DP=3393;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,44:97:99:1124,0,1529:27,26,21,23 chr2 26954217 . C T 855.39 PASS AC=1;AF=0.65;AN=2;DP=930;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant20-variant21-variant22-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant37-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:17,21:38:99:654,0,574:2,15,7,14 chr2 26954344 . G A 178.65 PASS AC=2;AF=0.985;AN=2;DP=178;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,6:7:11:207,11,0:1,0,1,5 chr2 26955621 . A G 2509.83 PASS AC=1;AF=0.65;AN=2;DP=2437;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant20-variant21-variant22-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant37-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:45,64:109:99:1613,0,995:20,25,31,33 chr2 26956187 . G A 1075.07 PASS AC=2;AF=0.989;AN=2;DP=1730;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1436,129,0:0,0,20,23 chr2 26997031 . G A 2551.95 PASS AC=1;AF=0.667;AN=2;DP=2546;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant20-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:42,70:112:99:1671,0,834:23,19,43,27 chr2 27016988 . C T 4578.22 PASS AC=2;AF=0.943;AN=2;DP=13801;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:2,311:313:99:9950,886,0:1,1,141,170 chr2 27157400 . A G 343.27 PASS AC=2;AF=1;AN=2;DP=475;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:505,39,0:0,0,11,2 chr2 27163044 . T C 4288.97 PASS AC=2;AF=0.7;AN=2;DP=5770;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,159:161:99:5289,433,0:1,1,76,83 chr2 27163284 . G A 275.29 PASS AC=2;AF=0.988;AN=2;DP=347;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.421;ReadPosRankSum=-2.017;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:505,39,0:0,0,1,12 chr2 27164806 . G A 4368.14 PASS AC=2;AF=0.7;AN=2;DP=5400;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,193:193:99:5949,577,0:0,0,120,73 chr2 27167469 . A G 654.88 PASS AC=1;AF=0.5;AN=2;DP=66;FS=0.937;FractionInformativeReads=0.985;MQ=60;MQRankSum=-0.164;QD=9.92;ReadPosRankSum=-1.638;SOR=0.57;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:35,30:65:99:683,0,785:21,14,17,13 chr2 27167617 . G A 981.27 PASS AC=1;AF=0.5;AN=2;DP=330;FractionInformativeReads=1;MQ=60;set=variant14-variant35-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:42,51:93:99:1271,0,974:22,20,26,25 chr2 27169637 . TC T 1334.73 PASS AC=2;AF=0.714;AN=2;DP=1828;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:2205,166,0:0,0,40,15 chr2 27169842 . C A 4434.41 PASS AC=2;AF=0.714;AN=2;DP=8363;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,244:246:99:7058,715,0:0,2,128,116 chr2 27170470 . C CG 2879.49 PASS AC=2;AF=0.714;AN=2;DP=3080;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,89:89:99:2793,270,0:0,0,39,50 chr2 27170941 . CCACACA CCA,CCACA,CCACACACA,C,CCACACACACACACACACACACACACACACACACACACACGCACACA 567.18 PASS AC=1,1,0,0,0;AF=0.143,0.369,0.238,0.036,0.012;AN=2;DP=1248;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-filterInvariant43-variant44 GT:DP:GQ:SB 1/2:21:99:0,0,9,12 chr2 27170982 . C T 1062.45 PASS AC=2;AF=0.714;AN=2;DP=1366;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1913,159,0:0,0,28,23 chr2 27173249 . G A 869.65 PASS AC=2;AF=0.714;AN=2;DP=1266;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1209,110,0:0,0,9,28 chr2 27237614 . A G 635.51 PASS AC=2;AF=0.721;AN=2;DP=887;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1014,106,0:0,0,22,14 chr2 27246285 . C T 4255.29 PASS AC=2;AF=0.932;AN=2;DP=9184;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,223:223:99:6579,666,0:0,0,116,107 chr2 27249245 . A G 3903.66 PASS AC=2;AF=0.721;AN=2;DP=5501;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,179:180:99:5370,500,0:1,0,88,91 chr2 27259794 . G A 2591.51 PASS AC=2;AF=0.706;AN=2;DP=2850;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:2514,230,0:0,0,39,38 chr2 27261329 . A G 1195.68 PASS AC=2;AF=1;AN=2;DP=1960;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1848,167,0:0,0,33,23 chr2 27262763 . GGGA G 1463.65 PASS AC=2;AF=1;AN=2;DP=2996;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:3126,214,0:0,0,19,52 chr2 27263122 . T C 3270.56 PASS AC=2;AF=0.714;AN=2;DP=6623;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,222:222:99:7193,666,0:0,0,104,118 chr2 27276202 . G A 2104.54 PASS AC=2;AF=0.714;AN=2;DP=2297;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:2721,237,0:0,0,48,31 chr2 27279416 . A G 3956.63 PASS AC=2;AF=1;AN=2;DP=3643;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,82:82:99:2584,246,0:0,0,52,30 chr2 27280092 . T A 1853.95 PASS AC=2;AF=0.778;AN=2;DP=1729;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,69:69:99:2110,206,0:0,0,46,23 chr2 27280127 . G A 2286.3 PASS AC=2;AF=0.778;AN=2;DP=2634;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,90:90:99:2729,268,0:0,0,56,34 chr2 27280460 . A G 654.9 PASS AC=2;AF=0.714;AN=2;DP=852;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1258,99,0:0,0,4,29 chr2 27290525 . A G 2475.31 PASS AC=2;AF=0.778;AN=2;DP=4680;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,141:141:99:4382,422,0:0,0,74,67 chr2 27291661 . G A 2551.44 PASS AC=1;AF=0.656;AN=2;DP=2290;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,37:69:99:1023,0,874:11,21,10,27 chr2 27292651 . T C 3108.29 PASS AC=2;AF=0.714;AN=2;DP=3835;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,123:123:99:3926,369,0:0,0,50,73 chr2 27293150 . G T 5936.56 PASS AC=2;AF=0.714;AN=2;DP=6042;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,177:177:99:5486,529,0:0,0,76,101 chr2 27302165 . T C 1969.14 PASS AC=2;AF=0.714;AN=2;DP=2260;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:2412,213,0:0,0,23,48 chr2 27303755 . A G 2329.22 PASS AC=2;AF=1;AN=2;DP=4917;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,149:149:99:4691,446,0:0,0,50,99 chr2 27307769 . G C 4260.56 PASS AC=2;AF=0.722;AN=2;DP=5724;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,167:167:99:5183,500,0:0,0,79,88 chr2 27309659 . A C 1816.24 PASS AC=2;AF=0.714;AN=2;DP=2157;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,85:85:99:2655,255,0:0,0,52,33 chr2 27319826 . A G 3067.75 PASS AC=2;AF=1;AN=2;DP=4598;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,115:115:99:3400,344,0:0,0,53,62 chr2 27321887 . A G 882.5 PASS AC=2;AF=1;AN=2;DP=1505;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1116,102,0:0,0,23,11 chr2 27323468 . A C 9916.31 PASS AC=2;AF=1;AN=2;DP=11993;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,264:264:99:8199,790,0:0,0,144,120 chr2 27323936 . G GC 2284.68 PASS AC=2;AF=0.735;AN=2;DP=2689;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,103:103:99:3533,312,0:0,0,53,50 chr2 27324036 . G A 2297.4 PASS AC=2;AF=0.734;AN=2;DP=2323;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,102:102:99:3302,306,0:0,0,51,51 chr2 27324724 . G C 2515.95 PASS AC=2;AF=0.735;AN=2;DP=4327;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,147:147:99:4775,440,0:0,0,74,73 chr2 27324751 . G T 2359.49 PASS AC=2;AF=0.735;AN=2;DP=4827;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,147:147:99:4869,440,0:0,0,80,67 chr2 27351279 . G A 452.07 PASS AC=2;AF=0.727;AN=2;DP=1092;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1540,145,0:0,0,36,13 chr2 27351948 . T G 1427.29 PASS AC=2;AF=1;AN=2;DP=4528;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,107:107:99:3400,320,0:0,0,58,49 chr2 27354173 . C A 1732.38 PASS AC=2;AF=1;AN=2;DP=3481;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:2410,230,0:0,0,46,31 chr2 27354419 . C T 754.55 PASS AC=1;AF=0.571;AN=2;DP=397;FractionInformativeReads=1;MQ=60;set=variant5-variant7-variant23-variant32-variant34-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,28:53:99:728,0,697:10,15,11,17 chr2 27355454 . A C 928.26 PASS AC=2;AF=1;AN=2;DP=1581;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:1634,144,0:0,0,36,12 chr2 27357038 . C T 640.15 PASS AC=1;AF=0.5;AN=2;DP=199;MQ=60;set=variant7-variant23-variant34-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,17:40:99:515,0,639:15,8,14,3 chr2 27359807 . CA C 945.25 PASS AC=1;AF=0.5;AN=2;DP=246;MQ=60;set=variant7-variant23-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:48,23:71:99:598,0,1545:24,24,13,10 chr2 27359887 . C T 1455.84 PASS AC=1;AF=0.692;AN=2;DP=1335;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant16-variant21-variant22-variant23-variant25-variant27-variant31-variant32-variant34-variant35-variant37-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,42:71:99:1089,0,749:14,15,26,16 chr2 27361418 . G T 968.26 PASS AC=1;AF=0.5;AN=2;DP=457;MQ=60;set=variant14-variant20-variant25-variant29-variant35-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:35,38:73:99:923,0,842:17,18,17,21 chr2 27376376 . C CTCTTT,CTCTTTTCTTTTCTTT,CTCTTTTCTTTTCTTTTCTTT,CTCTTTTCTTT 93.7 PASS AC=1,0,0,0;AF=0.472,0.153,0.181,0.125;AN=2;DP=334;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:5:88:0,2,1,2 chr2 27422605 . C T 1532.85 PASS AC=2;AF=0.942;AN=2;DP=2384;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,47:49:97:1349,97,0:1,1,28,19 chr2 27424496 . G A 2458.86 PASS AC=2;AF=0.942;AN=2;DP=4572;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,116:116:99:3718,346,0:0,0,64,52 chr2 27424636 . G A 3960.28 PASS AC=2;AF=0.757;AN=2;DP=6763;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,216:218:99:6320,596,0:2,0,115,101 chr2 27426514 . G C 955.34 PASS AC=2;AF=0.977;AN=2;DP=2867;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1651,159,0:0,0,31,22 chr2 27426878 . C T 373.44 PASS AC=2;AF=0.764;AN=2;DP=565;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:329,27,0:0,0,2,7 chr2 27428147 . A G 2320.48 PASS AC=2;AF=1;AN=2;DP=2602;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:2383,216,0:0,0,52,20 chr2 27428295 . A G 5604.43 PASS AC=2;AF=1;AN=2;DP=10335;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,274:275:99:7776,813,0:1,0,141,133 chr2 27428702 . A C 317.08 PASS AC=2;AF=0.942;AN=2;DP=472;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:340,24,0:0,0,7,1 chr2 27428815 . C G 2728.66 PASS AC=2;AF=0.942;AN=2;DP=2999;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,67:67:99:2063,201,0:0,0,39,28 chr2 27428877 . C G 3300.39 PASS AC=2;AF=0.942;AN=2;DP=4473;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,119:119:99:3358,352,0:0,0,65,54 chr2 27430781 . A G 464.21 PASS AC=2;AF=0.757;AN=2;DP=433;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:414,33,0:0,0,2,9 chr2 27431413 . T C 455.98 PASS AC=2;AF=0.942;AN=2;DP=1361;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1161,108,0:0,0,21,15 chr2 27435250 . A G 5495.57 PASS AC=2;AF=0.977;AN=2;DP=9111;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,213:213:99:6762,639,0:0,0,118,95 chr2 27435374 . G A 6037.48 PASS AC=2;AF=0.757;AN=2;DP=8738;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,266:266:99:7545,792,0:0,0,120,146 chr2 27440013 . CT C 790.21 PASS AC=2;AF=0.757;AN=2;DP=1492;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,52:52:99:1656,156,0:0,0,17,35 chr2 27440785 . C T 2007.45 PASS AC=2;AF=1;AN=2;DP=5736;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,152:152:99:4600,455,0:0,0,85,67 chr2 27466258 . CTTT C,CT,CTT,CTTTT 342.9 PASS AC=0,0,1,0;AF=0.014,0.171,0.343,0.014;AN=2;DP=3370;set=variant-variant2-variant3-filterInvariant5-variant6-variant7-variant8-variant9-variant10-variant11-filterInvariant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:DP:GQ:SB 0/3:60:99:12,17,11,20 chr2 27477627 . AACACACACACAC AACACACAC,AACACACACACACAC,AACACACACAC,AACACACACACACACACAC,AAC,AACACAC,AACACACACACACACAC,A 1079.07 PASS AC=0,1,0,0,0,0,0,0;AF=0.197,0.132,0.145,0.013,0.026,0.079,0.026,0.013;AN=2;DP=1353;set=variant2-filterInvariant3-variant4-variant6-filterInvariant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-filterInvariant44 GT:DP:GQ:SB 0/2:31:99:13,6,9,3 chr2 27486032 . G C 103.45 PASS AC=1;AF=0.5;AN=2;DP=163;MQ=60;set=variant5-variant8-variant17-filterInvariant24-filterInvariant35 GT:AD:DP:GQ:PL:SB 0/1:27,6:33:94:94,0,1545:8,19,6,0 chr2 27486038 . A C 88.42 PASS AC=1;AF=0.5;AN=2;DP=184;MQ=60;set=variant5-variant8-variant17-filterInvariant24-filterInvariant35 GT:AD:DP:GQ:PL:SB 0/1:32,6:38:85:85,0,1645:13,19,6,0 chr2 27486134 . G A 3205.94 PASS AC=1;AF=0.55;AN=2;DP=2371;MQ=60;set=variant2-variant9-variant10-variant13-variant18-variant20-variant24-variant29-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:148,132:280:99:3160,0,4039:97,51,81,51 chr2 27522543 . CCTATCTATCTAT CCTATCTATCTATCTAT,CCTATCTATCTATCTATCTAT,CCTATCTAT,C 594.56 PASS AC=2,0,0,0;AF=0.474,0.167,0.038,0.013;AN=2;DP=1958;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:38:99:0,0,15,23 chr2 27535311 . T TG 2624.78 PASS AC=2;AF=1;AN=2;DP=6101;FS=0;MQ=60;MQRankSum=1.015;ReadPosRankSum=-0.237;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,152:152:99:5451,460,0:0,0,72,80 chr2 27548038 . A C 52.74 PASS AC=1;AF=0.58;AN=2;DP=182;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant10-variant11-variant14-variant15-variant16-variant17-variant19-variant23-variant27-variant28-variant30-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,6:11:99:211,0,178:1,4,3,3 chr2 27549833 . CA C 539.15 PASS AC=1;AF=0.58;AN=2;DP=2537;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant10-variant11-variant14-variant15-variant16-variant17-variant19-variant23-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,54:83:99:1209,0,528:18,11,24,30 chr2 27550967 . A G 707.59 PASS AC=1;AF=0.574;AN=2;DP=2970;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant10-variant11-variant14-variant15-variant16-variant17-variant19-variant23-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,72:132:99:1632,0,1437:31,29,32,40 chr2 27556721 . G A 1540.23 PASS AC=1;AF=0.603;AN=2;DP=3262;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant10-variant11-variant14-variant15-variant16-variant17-variant19-variant23-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,64:132:99:1602,0,1698:32,36,32,32 chr2 27558252 . A G 981.98 PASS AC=1;AF=0.611;AN=2;DP=1942;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant10-variant11-variant14-variant15-variant16-variant17-variant19-variant23-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,41:71:99:944,0,656:17,13,23,18 chr2 27566520 . T A 945.35 PASS AC=1;AF=0.5;AN=2;DP=1554;MQ=60;set=variant4-variant5-variant7-variant8-variant14-variant15-variant16-variant17-variant19-variant23-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,62:103:99:1349,0,937:17,24,26,36 chr2 27579231 . T C 1696.68 PASS AC=1;AF=0.574;AN=2;DP=3839;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant10-variant11-variant14-variant15-variant16-variant17-variant19-variant23-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,73:140:99:1791,0,1556:37,30,39,34 chr2 27587922 . CTTTT C,CTTT 76.91 PASS AC=0,1;AF=0.022,0.522;AN=2;DP=400;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant10-variant13-variant14-variant15-variant16-variant17-variant19-variant23-variant27-variant28-variant32-variant33-variant35-variant38-variant39-filterInvariant41-variant43 GT:DP:GQ:SB 0/2:14:99:0,6,1,7 chr2 27589810 . T C 1626.39 PASS AC=1;AF=0.571;AN=2;DP=3897;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant23-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,79:135:99:2013,0,1404:25,31,44,35 chr2 27590666 . C T 1032.92 PASS AC=1;AF=0.5;AN=2;DP=151;FractionInformativeReads=1;MQ=60;set=variant29-variant35 GT:AD:DP:GQ:PL:SB 0/1:31,42:73:99:861,0,731:17,14,22,20 chr2 27591804 . T C 1102.64 PASS AC=1;AF=0.52;AN=2;DP=1945;FractionInformativeReads=1;MQ=60;set=variant5-variant7-variant8-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant23-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,52:80:99:1507,0,628:19,9,38,14 chr2 27592423 . C T 1494.82 PASS AC=1;AF=0.577;AN=2;DP=3028;MQ=60;set=variant2-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant23-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:73,58:131:99:1464,0,1767:35,38,29,29 chr2 27595756 . G C 722.68 PASS AC=1;AF=0.593;AN=2;DP=1338;MQ=60;set=variant2-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant23-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:22,22:44:99:630,0,760:11,11,8,14 chr2 27597805 . CTT C 355.44 PASS AC=1;AF=0.596;AN=2;DP=1232;MQ=60;set=variant2-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant23-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:27,30:57:99:1141,0,1169:17,10,19,11 chr2 27598097 . T C 733.61 PASS AC=1;AF=0.632;AN=2;DP=1931;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant23-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:41,35:76:99:1127,0,1238:12,29,5,30 chr2 27599132 . G A 3588.33 PASS AC=1;AF=0.593;AN=2;DP=8767;MQ=60;set=variant2-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant23-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:162,173:335:99:4095,0,3949:79,83,86,87 chr2 27599875 . T G 623.85 PASS AC=1;AF=0.593;AN=2;DP=1742;MQ=60;set=variant2-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant23-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:37,38:75:99:947,0,944:21,16,21,17 chr2 27600239 . G A 2020.23 PASS AC=1;AF=0.596;AN=2;DP=5716;MQ=60;set=variant2-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant23-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:122,103:225:99:2287,0,3281:78,44,63,40 chr2 27603306 . G C 134.09 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=123;FS=106.43;FractionInformativeReads=0.992;MQ=60;MQRankSum=-1.103;QD=1.09;ReadPosRankSum=-4.996;SOR=6.089;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:102,20:122:99:162,0,3646:23,79,20,0 chr2 27604279 . A G 1403.83 PASS AC=1;AF=0.593;AN=2;DP=3426;MQ=60;set=variant2-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant23-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:62,82:144:99:1902,0,1542:30,32,40,42 chr2 27605696 . G GT 37.09 PASS AC=1;AF=0.75;AN=2;DP=87;MQ=60;set=variant5-variant10-variant15-variant27-variant33-variant35-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,6:11:98:123,0,98:1,4,0,6 chr2 27606098 . A G 896.83 PASS AC=2;AF=0.977;AN=2;DP=1618;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1677,153,0:0,0,36,15 chr2 27608115 . C T 598.48 PASS AC=1;AF=0.596;AN=2;DP=858;MQ=60;set=variant2-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant23-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:27,18:45:99:421,0,702:10,17,9,9 chr2 27651054 . A T 3351.98 PASS AC=1;AF=0.596;AN=2;DP=7033;MQ=60;set=variant2-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant23-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:136,139:275:99:3181,0,3280:63,73,69,70 chr2 27651099 . G T 2647.32 PASS AC=1;AF=0.5;AN=2;DP=225;FS=3.003;FractionInformativeReads=0.996;MQ=60;MQRankSum=-2.386;QD=11.77;ReadPosRankSum=0.026;SOR=0.91;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:116,108:224:99:2676,0,2868:53,63,44,64 chr2 27651375 . C T 1369.7 PASS AC=1;AF=0.633;AN=2;DP=4142;set=variant2-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant23-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:83,52:135:99:1174,0,1910:41,42,29,23 chr2 27651693 . T C 122.15 PASS AC=1;AF=0.6;AN=2;DP=296;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant23-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,6:11:99:156,0,140:2,3,2,4 chr2 27656036 . A G 981.9 PASS AC=1;AF=0.596;AN=2;DP=1722;set=variant2-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant23-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:43,27:70:99:669,0,1116:27,16,18,9 chr2 27656822 . G GA 1547.13 PASS AC=1;AF=0.638;AN=2;DP=3479;MQ=60;set=variant2-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant23-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:72,64:136:99:1976,0,2288:35,37,31,33 chr2 27659491 . T C 952.58 PASS AC=1;AF=0.596;AN=2;DP=1818;MQ=60;set=variant2-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant23-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:40,32:72:99:837,0,945:22,18,20,12 chr2 27663215 . T A 1203.53 PASS AC=1;AF=0.596;AN=2;DP=2505;MQ=60;set=variant2-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant23-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:49,43:92:99:978,0,1260:30,19,27,16 chr2 27663416 . G T 1511.31 PASS AC=1;AF=0.596;AN=2;DP=3135;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant23-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:76,56:132:99:1523,0,2254:38,38,29,27 chr2 27665361 . C G 1860.79 PASS AC=1;AF=0.596;AN=2;DP=4603;MQ=60;set=variant2-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant23-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:121,104:225:99:2611,0,3210:60,61,57,47 chr2 27667297 . A G 279.63 PASS AC=1;AF=0.596;AN=2;DP=965;MQ=60;set=variant2-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant23-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:18,11:29:99:228,0,487:12,6,7,4 chr2 27667520 . T TTTTG 238.53 PASS AC=1;AF=0.638;AN=2;DP=415;MQ=60;set=variant2-variant5-variant7-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant23-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,12:16:99:492,0,189:0,4,4,8 chr2 27669341 . AT A 7374.33 PASS AC=1;AF=0.596;AN=2;DP=11511;MQ=60;set=variant2-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant23-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:199,209:408:99:6595,0,6170:85,114,86,123 chr2 27669365 . G GT 3669.48 PASS AC=1;AF=0.596;AN=2;DP=8534;MQ=60;set=variant2-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant23-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:140,127:267:99:2690,0,3145:52,88,51,76 chr2 27670307 . G A 1475.08 PASS AC=1;AF=0.596;AN=2;DP=3061;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant23-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:75,65:140:99:1558,0,1734:43,32,38,27 chr2 27676287 . A T 998.48 PASS AC=1;AF=0.596;AN=2;DP=2153;MQ=60;set=variant2-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant23-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:49,39:88:99:913,0,1178:23,26,21,18 chr2 27677691 . G A 443.14 PASS AC=1;AF=0.596;AN=2;DP=899;MQ=60;set=variant2-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant23-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,15:28:99:450,0,354:4,9,4,11 chr2 27677763 . C T 145.49 PASS AC=1;AF=0.5;AN=2;DP=111;MQ=60;set=variant5-variant7-variant23-variant28-variant32-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:8,5:13:99:137,0,234:2,6,2,3 chr2 27681598 . A C 284.53 PASS AC=1;AF=0.596;AN=2;DP=713;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant23-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:16,13:29:99:376,0,524:13,3,10,3 chr2 27681837 . G A 399.26 PASS AC=1;AF=0.5;AN=2;DP=39;FS=1.39;FractionInformativeReads=1;MQ=60;MQRankSum=0.899;QD=10.24;ReadPosRankSum=0.642;SOR=1.144;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:23,16:39:99:427,0,617:8,15,4,12 chr2 27684734 . A G 577.51 PASS AC=1;AF=0.596;AN=2;DP=1914;set=variant2-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant23-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:40,45:85:99:1089,0,890:18,22,15,30 chr2 27685388 . G A 205.56 PASS AC=1;AF=0.633;AN=2;DP=499;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant23-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,13:18:99:456,0,175:5,0,12,1 chr2 27688601 . C T 857.46 PASS AC=1;AF=0.596;AN=2;DP=2960;MQ=60;set=variant2-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant23-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:61,67:128:99:1575,0,1379:34,27,39,28 chr2 27694905 . CA C 195.42 PASS AC=1;AF=0.583;AN=2;DP=430;MQ=60;set=variant5-variant7-filterInvariant8-variant10-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,7:16:99:119,0,160:6,3,5,2 chr2 27706640 . T C 776.78 PASS AC=1;AF=0.607;AN=2;DP=1774;MQ=60;set=variant2-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant23-variant25-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,20:53:99:556,0,945:20,13,14,6 chr2 27715207 . T A 1249.11 PASS AC=1;AF=0.596;AN=2;DP=2894;MQ=60;set=variant2-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant23-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:67,68:135:99:1685,0,1709:36,31,38,30 chr2 27715416 . C T 1166.73 PASS AC=1;AF=0.596;AN=2;DP=2783;set=variant2-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant23-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:65,60:125:99:1547,0,1472:27,38,22,38 chr2 27716494 . G A 332.65 PASS AC=1;AF=0.604;AN=2;DP=324;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant8-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant23-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:3,12:15:88:411,0,88:0,3,3,9 chr2 27721971 . T C 1371.64 PASS AC=1;AF=0.596;AN=2;DP=3280;MQ=60;set=variant2-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant23-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:68,68:136:99:1705,0,1586:37,31,27,41 chr2 27722416 . G A 739.49 PASS AC=1;AF=0.596;AN=2;DP=1778;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant23-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:25,44:69:99:1253,0,596:10,15,14,30 chr2 27728777 . C G 1409.71 PASS AC=1;AF=0.596;AN=2;DP=3949;MQ=60;set=variant2-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant23-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:70,100:170:99:2577,0,1524:27,43,42,58 chr2 27729480 . G A 2274.97 PASS AC=1;AF=0.596;AN=2;DP=5589;MQ=60;set=variant2-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant23-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:108,108:216:99:2680,0,2729:57,51,61,47 chr2 27730940 . T C 936.02 PASS AC=1;AF=0.647;AN=2;DP=3037;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant23-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:64,37:101:99:1048,0,1902:43,21,23,14 chr2 27731212 . T C 298.29 PASS AC=1;AF=0.5;AN=2;DP=253;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant6-variant7-variant19-variant20-variant35 GT:AD:DP:GQ:PL:SB 0/1:23,20:43:99:611,0,761:3,20,4,16 chr2 27732642 . CAA CA,CAAAA,C,CAAA 245.95 PASS AC=0,1,0,0;AF=0.176,0.324,0.029,0.118;AN=2;DP=306;MQ=60;set=variant-variant3-variant7-variant10-variant12-variant13-variant15-filterInvariant22-variant23-variant25-variant27-variant28-variant31-variant32-variant35-variant39-variant41 GT:DP:GQ:SB 0/2:9:89:0,5,0,4 chr2 27806793 . G GT 555.1 PASS AC=1;AF=0.538;AN=2;DP=197;MQ=60;set=variant2-variant4-variant9-variant14-variant15-variant20-variant24-variant27-variant28-variant29-variant33-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:5,6:11:99:179,0,146:0,5,1,5 chr2 27858167 . CT CTTTTTTT,CTT,CTTTTTTTT,C,CTTTTTTTTT,CTTTTTT,CTTTTTTTTTT 1336.45 PASS AC=0,1,0,0,0,0,0;AF=0.106,0.091,0.212,0.091,0.076,0.03,0.03;AN=2;DP=2295;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-filterInvariant10-variant12-filterInvariant13-filterInvariant15-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42 GT:DP:GQ:SB 0/2:61:99:12,24,12,13 chr2 27861707 . G A 617.11 PASS AC=2;AF=0.683;AN=2;DP=892;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1040,104,0:0,0,23,12 chr2 27873415 . G A 1384.03 PASS AC=2;AF=0.691;AN=2;DP=1986;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1895,168,0:0,0,38,18 chr2 27874332 . A C 5331.76 PASS AC=2;AF=0.691;AN=2;DP=7019;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,221:221:99:6929,662,0:0,0,108,113 chr2 27874563 . G T 11552.6 PASS AC=2;AF=0.691;AN=2;DP=13012;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,410:410:99:12494,1228,0:0,0,219,191 chr2 27875042 . A T 444.91 PASS AC=2;AF=0.957;AN=2;DP=652;FS=0;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:677,60,0:0,0,15,5 chr2 27884878 . C T 18129.5 PASS AC=2;AF=1;AN=2;DP=20856;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,537:537:99:16030,1608,0:0,0,286,251 chr2 27887034 . C A 2405.98 PASS AC=2;AF=0.691;AN=2;DP=3569;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,100:100:99:3045,297,0:0,0,58,42 chr2 27905388 . ATTCTT AT,A,ATT 194.57 PASS AC=2,0,0;AF=0.607,0.179,0.036;AN=2;DP=83;FS=0;set=variant2-variant6-variant8-variant11-variant15-variant16-variant17-variant20-variant27-variant28-variant33-variant35-variant36-variant44 GT:DP:GQ:SB 1/1:6:18:0,0,1,5 chr2 27929616 . CT C 211.99 PASS AC=2;AF=0.932;AN=2;DP=1095;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:663,75,0:0,0,8,17 chr2 27995781 . A C 207.11 PASS AC=2;AF=0.829;AN=2;DP=502;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:631,45,0:0,0,1,14 chr2 28070071 . T A 487.06 PASS AC=1;AF=0.5;AN=2;DP=238;MQ=60;set=variant5-variant6-variant7-variant23-variant28-variant32-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:24,17:41:99:514,0,691:6,18,4,13 chr2 28268467 . C T 305.4 PASS AC=2;AF=0.903;AN=2;DP=234;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant20-variant21-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:403,30,0:0,0,9,1 chr2 28464435 . T C 1335.86 PASS AC=2;AF=1;AN=2;DP=903;FS=0;MQRankSum=0.528;ReadPosRankSum=1.583;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:906,66,0:0,0,3,19 chr2 28638358 . G C 738.64 PASS AC=2;AF=1;AN=2;DP=2063;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:1556,141,0:0,0,16,31 chr2 28639121 . A G 878.66 PASS AC=1;AF=0.5;AN=2;DP=80;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.502;QD=10.98;ReadPosRankSum=-2.548;SOR=0.714;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:43,37:80:99:907,0,960:20,23,17,20 chr2 28639331 . CTTT CT,CTT,C 812.04 PASS AC=1,1,0;AF=0.568,0.386,0.023;AN=2;DP=2275;set=Intersection GT:DP:GQ:SB 1/2:36:88:0,0,18,18 chr2 28639641 . C G 10120.2 PASS AC=2;AF=0.689;AN=2;DP=10325;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,252:252:99:7881,755,0:0,0,147,105 chr2 28639816 . CT C,CTT,CTTTT,CTTTTT 142.46 PASS AC=1,0,0,0;AF=0.338,0.1,0.05,0.025;AN=2;DP=6932;set=filterInvariant-filterInvariant2-filterInvariant3-variant4-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant8-variant9-filterInvariant10-filterInvariant12-filterInvariant14-filterInvariant15-variant16-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-variant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant26-variant27-filterInvariant28-filterInvariant29-variant31-filterInvariant32-variant33-variant34-filterInvariant35-variant36-variant38-filterInvariant39-filterInvariant40-variant41-variant42-filterInvariant43-variant44 GT:DP:GQ:SB 0/1:110:99:28,45,8,29 chr2 28718897 . A G 3297.43 PASS AC=2;AF=1;AN=2;DP=5882;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,134:134:99:3943,401,0:0,0,66,68 chr2 28748857 . T C 5104.34 PASS AC=2;AF=0.989;AN=2;DP=8919;MQ=60;MQRankSum=0.824;ReadPosRankSum=0.724;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,212:212:99:6551,635,0:0,0,98,114 chr2 28748916 . A C 4121.95 PASS AC=2;AF=0.788;AN=2;DP=6578;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,173:173:99:5409,518,0:0,0,63,110 chr2 28752498 . T C 1392.84 PASS AC=2;AF=0.989;AN=2;DP=2215;FS=0;MQ=60;MQRankSum=0.867;ReadPosRankSum=-1.382;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1678,150,0:0,0,30,20 chr2 28752555 . T C 1977.84 PASS AC=2;AF=0.943;AN=2;DP=3140;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,67:67:99:2189,201,0:0,0,38,29 chr2 28752727 . C G 967.44 PASS AC=2;AF=0.989;AN=2;DP=994;FS=0;FractionInformativeReads=1;MQRankSum=-1.848;ReadPosRankSum=2.266;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:993,69,0:0,0,4,19 chr2 28752741 . A G 876.22 PASS AC=2;AF=0.943;AN=2;DP=787;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,20:20:63:927,63,0:0,0,4,16 chr2 28761257 . A G 1680.07 PASS AC=2;AF=0.92;AN=2;DP=2963;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,85:85:99:2495,253,0:0,0,35,50 chr2 28761282 . A G 1268.25 PASS AC=2;AF=0.92;AN=2;DP=2241;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:2232,236,0:0,0,32,47 chr2 28761481 . C T 167.95 PASS AC=2;AF=0.97;AN=2;DP=143;FS=0;MQ=60;MQRankSum=0.736;ReadPosRankSum=0.736;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:180,12,0:0,0,1,3 chr2 28761484 . G A 167.95 PASS AC=2;AF=0.97;AN=2;DP=143;FS=0;MQ=60;MQRankSum=0.736;ReadPosRankSum=0.736;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:180,12,0:0,0,1,3 chr2 28761981 . G C 2253.13 PASS AC=1;AF=0.55;AN=2;DP=4100;MQ=60;set=variant-variant3-variant6-variant7-variant10-variant13-variant16-variant20-variant22-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:108,117:225:99:2776,0,2619:59,49,61,56 chr2 28763374 . G T 1451.88 PASS AC=1;AF=0.645;AN=2;DP=4631;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant32-variant33-variant35-variant37-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:68,71:139:99:1650,0,1713:33,35,33,38 chr2 28771452 . CTA C,CTATATA 1691.59 PASS AC=2,0;AF=0.955,0.023;AN=2;DP=2420;MQ=60;set=Intersection GT:DP:GQ:SB 1/1:54:99:0,0,29,25 chr2 28771579 . C T 907.2 PASS AC=1;AF=0.575;AN=2;DP=1704;MQ=60;set=variant-variant3-variant6-variant7-variant10-variant13-variant16-variant20-variant22-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,51:108:99:1313,0,1426:33,24,31,20 chr2 28771624 . T G 4325.26 PASS AC=2;AF=0.932;AN=2;DP=5223;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,136:136:99:4145,407,0:0,0,76,60 chr2 28771897 . T C 572.23 PASS AC=2;AF=0.756;AN=2;DP=688;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:557,45,0:0,0,2,13 chr2 28785754 . G C 599.08 PASS AC=2;AF=0.977;AN=2;DP=599;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:410,36,0:0,0,8,4 chr2 28788428 . AG A 1634.85 PASS AC=2;AF=0.767;AN=2;DP=2762;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:2166,175,0:0,0,25,33 chr2 28789643 . T C 1617.54 PASS AC=1;AF=0.667;AN=2;DP=8501;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:113,157:270:99:3764,0,2596:62,51,78,79 chr2 28795893 . G A 851.49 PASS AC=1;AF=0.786;AN=2;DP=809;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,16:28:99:644,0,673:11,1,13,3 chr2 28795899 . C T 888.08 PASS AC=1;AF=0.756;AN=2;DP=856;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,19:34:99:710,0,722:12,3,16,3 chr2 28795962 . G A 1941.85 PASS AC=1;AF=0.786;AN=2;DP=2950;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,52:100:99:1356,0,1274:33,15,36,16 chr2 28816814 . CT CTTT,CTTTT,CTT,C 1205.67 PASS AC=0,1,0,0;AF=0.341,0.402,0.012,0.037;AN=2;DP=2049;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-filterInvariant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-filterInvariant37-variant38-variant39-variant40-variant42-variant43-filterInvariant44 GT:DP:GQ:SB 0/2:43:99:18,10,8,7 chr2 28816948 . C T 3075.89 PASS AC=1;AF=0.842;AN=2;DP=3991;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:52,43:95:99:925,0,1373:25,27,21,22 chr2 28817459 . CTG C 2122.79 PASS AC=1;AF=0.757;AN=2;DP=2178;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:35,31:66:99:1192,0,1373:21,14,18,13 chr2 28817870 . C T 175.34 PASS AC=1;AF=0.575;AN=2;DP=941;MQ=60;set=variant6-variant7-variant13-variant14-variant15-variant17-variant19-variant20-variant24-variant25-variant28-variant29-variant30-variant35-variant36-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,16:31:99:374,0,459:7,8,8,8 chr2 28818039 . A G 393.23 PASS AC=1;AF=0.583;AN=2;DP=407;FractionInformativeReads=1;MQ=60;set=variant13-variant14-variant20-variant24-variant28-variant29-variant30-variant35-variant36-variant37-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,10:32:99:225,0,572:11,11,5,5 chr2 28818367 . T G 1296.36 PASS AC=1;AF=0.577;AN=2;DP=1551;FractionInformativeReads=1;MQ=60;set=variant13-variant14-variant20-variant24-variant28-variant29-variant30-variant35-variant36-variant37-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:81,74:155:99:1904,0,1970:48,33,47,27 chr2 28818931 . G A 50.98 PASS AC=1;AF=0.625;AN=2;DP=84;FractionInformativeReads=1;MQ=60;set=variant6-variant14-variant15-variant19-variant24-variant28-variant29-variant30-variant35-variant36-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,4:9:99:126,0,117:2,3,0,4 chr2 28818957 . G T 157.44 PASS AC=2;AF=0.952;AN=2;DP=127;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant14-variant15-variant16-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:90,12,0:0,0,1,3 chr2 28821662 . C T 737.87 PASS AC=1;AF=0.703;AN=2;DP=2844;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,42:86:99:1017,0,1177:14,30,13,29 chr2 28824303 . C G 97.21 PASS AC=1;AF=0.575;AN=2;DP=333;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant7-variant8-variant9-variant13-variant15-variant20-variant25-variant28-variant30-variant32-variant33-variant35-variant36-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,19:26:99:627,0,185:1,6,3,16 chr2 28824793 . C G 1237.72 PASS AC=1;AF=0.703;AN=2;DP=7084;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:122,122:244:99:2869,0,3373:64,58,57,65 chr2 28824940 . G A 320.75 PASS AC=1;AF=0.548;AN=2;DP=889;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant7-variant8-variant9-variant13-variant14-variant15-variant20-variant25-variant28-variant30-variant32-variant33-variant35-variant36-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,21:52:99:635,0,1010:6,25,4,17 chr2 28840344 . G T 540.4 PASS AC=1;AF=0.671;AN=2;DP=860;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,23:46:99:661,0,822:22,1,17,6 chr2 28840678 . C T 1933.59 PASS AC=1;AF=0.5;AN=2;DP=128;FS=1.508;FractionInformativeReads=1;MQ=60;MQRankSum=-1.011;QD=15.11;ReadPosRankSum=-1.286;SOR=0.916;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:54,74:128:99:1962,0,1350:20,34,24,50 chr2 28840691 . C T 1420.59 PASS AC=1;AF=0.524;AN=2;DP=1725;MQ=60;set=variant-variant2-variant5-variant7-variant8-variant9-variant13-variant14-variant15-variant20-variant25-variant28-variant30-variant32-variant33-variant35-variant36-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,55:102:99:1426,0,1244:15,32,17,38 chr2 28841021 . G A 239.14 PASS AC=1;AF=0.676;AN=2;DP=893;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,14:27:99:338,0,296:8,5,10,4 chr2 28841049 . G A 151.61 PASS AC=1;AF=0.609;AN=2;DP=1195;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,21:40:99:603,0,397:11,8,15,6 chr2 28843939 . G C 674.76 PASS AC=1;AF=0.75;AN=2;DP=48;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.449;ReadPosRankSum=0.118;set=variant12-variant35 GT:AD:DP:GQ:PL:SB 0/1:24,7:31:99:208,0,906:3,21,1,6 chr2 28849435 . T C 761.61 PASS AC=1;AF=0.595;AN=2;DP=990;MQ=60;set=variant3-variant5-variant6-variant8-variant11-variant12-variant13-variant16-variant22-variant23-variant27-variant29-variant31-variant32-variant34-variant35-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:37,34:71:99:941,0,1023:12,25,11,23 chr2 28849473 . T C 496.39 PASS AC=1;AF=0.629;AN=2;DP=805;MQ=60;set=variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:21,24:45:99:702,0,617:6,15,6,18 chr2 28855918 . A AG 2451.93 PASS AC=2;AF=1;AN=2;DP=5605;FS=0;MQ=60;MQRankSum=0.818;ReadPosRankSum=0.845;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,109:109:99:3855,328,0:0,0,51,58 chr2 28975107 . G C 2304.86 PASS AC=2;AF=0.782;AN=2;DP=2712;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,82:82:99:2812,246,0:0,0,21,61 chr2 29001691 . A G 1775.43 PASS AC=2;AF=0.75;AN=2;DP=2050;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:1907,180,0:0,0,37,23 chr2 29004923 . G A 457.42 PASS AC=2;AF=1;AN=2;DP=531;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:321,27,0:0,0,3,6 chr2 29023092 . CTTT CTT,CTTTT,C,CT,CTTTTTT,CTTTTTTTTTTTTT 578.73 PASS AC=1,0,0,0,0,0;AF=0.271,0.171,0.043,0.1,0.014,0.014;AN=2;DP=3320;set=variant-variant2-variant3-filterInvariant4-filterInvariant5-variant6-variant7-variant8-filterInvariant9-filterInvariant11-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant22-variant23-variant24-filterInvariant28-variant29-variant30-filterInvariant31-variant32-filterInvariant33-variant34-variant35-variant36-variant37-filterInvariant39-variant41-variant42-filterInvariant43-variant44 GT:DP:GQ:SB 0/1:38:99:5,7,2,24 chr2 29023749 . A G 2973.82 PASS AC=2;AF=0.7;AN=2;DP=5889;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant12-variant13-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,208:208:99:7128,622,0:0,0,84,124 chr2 29025479 . A G 5870.03 PASS AC=2;AF=0.743;AN=2;DP=6501;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,178:178:99:5685,533,0:0,0,88,90 chr2 29041877 . T C 881.05 PASS AC=2;AF=0.707;AN=2;DP=1320;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant12-variant13-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1579,159,0:0,0,32,21 chr2 29045323 . C T 1920.76 PASS AC=2;AF=1;AN=2;DP=2713;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1343,135,0:0,0,19,26 chr2 29052256 . T C 311.99 PASS AC=2;AF=0.907;AN=2;DP=1366;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1351,105,0:0,0,7,28 chr2 29052283 . GT GTT,G 32.03 PASS AC=2,0;AF=0.7,0.02;AN=2;DP=434;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant12-variant13-variant17-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant39-variant44 GT:DP:GQ:SB 1/1:13:16:0,1,3,9 chr2 29063384 . G A 406.23 PASS AC=1;AF=0.5;AN=2;DP=82;FractionInformativeReads=1;MQ=60;set=variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:20,22:42:99:558,0,652:2,18,7,15 chr2 29087799 . C A 482.56 PASS AC=2;AF=0.707;AN=2;DP=765;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant12-variant13-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:917,72,0:0,0,21,3 chr2 29135468 . C G 1863.44 PASS AC=1;AF=0.797;AN=2;DP=5753;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:84,79:163:99:1894,0,2085:44,40,41,38 chr2 29136435 . A G 235.59 PASS AC=1;AF=0.5;AN=2;DP=68;FractionInformativeReads=1;MQ=60;set=variant25-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:11,13:24:99:367,0,286:7,4,10,3 chr2 29145663 . GTT G,GT,GTTTT,GTTTTT,GTTTTTT,GTTT,GTTTTTTT 1161.83 PASS AC=0,1,0,0,0,0,0;AF=0.023,0.186,0.128,0.186,0.163,0.023,0.035;AN=2;DP=2496;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:43:99:18,8,13,4 chr2 29145725 . G T 1761.22 PASS AC=1;AF=0.797;AN=2;DP=4430;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:72,46:118:99:1221,0,2135:37,35,21,25 chr2 29152384 . T G 454.27 PASS AC=1;AF=0.618;AN=2;DP=328;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant7-variant9-variant14-variant15-variant22-variant25-variant31-variant33-variant35-variant36-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:17,7:24:99:109,0,529:13,4,5,2 chr2 29152456 . A G 151.18 PASS AC=2;AF=0.775;AN=2;DP=2422;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:1805,171,0:0,0,35,22 chr2 29161010 . G A 1448.37 PASS AC=2;AF=0.92;AN=2;DP=3861;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,103:103:99:3180,308,0:0,0,42,61 chr2 29161173 . G C 412.06 PASS AC=1;AF=0.633;AN=2;DP=168;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant7-variant9-variant10-variant14-variant15-variant22-variant25-variant31-variant33-variant35-variant36-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,12:18:99:385,0,178:1,5,2,10 chr2 29169612 . T C 1203.92 PASS AC=1;AF=0.789;AN=2;DP=3273;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,32:67:99:1051,0,944:18,17,15,17 chr2 29170720 . A G 323.52 PASS AC=1;AF=0.5;AN=2;DP=138;MQ=60;set=variant25-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:29,27:56:99:715,0,753:17,12,15,12 chr2 29170730 . GTT G,GTTTT,GT,GTTTTT,GTTT,GTTTTTT 54.88 PASS AC=0,0,1,0,0,0;AF=0.214,0.086,0.257,0.057,0.014,0.014;AN=2;DP=1583;set=filterInvariant-variant2-variant3-filterInvariant4-variant5-variant6-filterInvariant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant37-variant38-filterInvariant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/3:34:88:11,10,4,9 chr2 29204055 . T G 202.44 PASS AC=1;AF=0.765;AN=2;DP=104;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant10-variant11-variant14-variant16-variant22-variant25-variant27-variant28-variant33-variant35-variant36-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:3,6:9:99:196,0,105:3,0,4,2 chr2 29222070 . G A 1240.61 PASS AC=1;AF=0.556;AN=2;DP=2401;MQ=60;set=variant2-variant7-variant9-variant10-variant11-variant14-variant15-variant18-variant21-variant22-variant25-variant33-variant35-variant36-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:66,71:137:99:1693,0,1579:31,35,38,33 chr2 29222388 . G C 596.78 PASS AC=1;AF=0.674;AN=2;DP=979;MQ=60;set=variant2-variant7-variant9-variant10-variant11-variant14-variant15-variant16-variant18-variant21-variant22-variant25-variant27-variant28-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:27,30:57:99:872,0,781:7,20,7,23 chr2 29226498 . G A 1071.21 PASS AC=2;AF=0.814;AN=2;DP=4934;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,121:121:99:3423,360,0:0,0,51,70 chr2 29226512 . A G 880 PASS AC=2;AF=0.942;AN=2;DP=4238;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,105:107:99:3313,271,0:1,1,36,69 chr2 29226559 . C T 431.44 PASS AC=2;AF=0.93;AN=2;DP=1896;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1395,107,0:0,0,3,33 chr2 29239942 . T G 911.36 PASS AC=1;AF=0.559;AN=2;DP=1467;MQ=60;set=variant2-variant7-variant9-variant10-variant11-variant14-variant15-variant18-variant22-variant25-variant33-variant35-variant36-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:40,48:88:99:1149,0,900:19,21,26,22 chr2 29240005 . T C 1534.17 PASS AC=1;AF=0.729;AN=2;DP=4301;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,55:111:99:1306,0,1353:24,32,28,27 chr2 29240060 . A G 1039.08 PASS AC=1;AF=0.559;AN=2;DP=1650;MQ=60;set=variant2-variant7-variant9-variant10-variant11-variant14-variant15-variant18-variant22-variant25-variant33-variant35-variant36-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:41,42:83:99:1035,0,989:20,21,15,27 chr2 29240582 . T C 391.5 PASS AC=1;AF=0.559;AN=2;DP=912;MQ=60;set=variant2-variant7-variant9-variant10-variant11-variant14-variant15-variant18-variant22-variant25-variant33-variant35-variant36-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:40,23:63:99:563,0,1087:27,13,16,7 chr2 29240673 . G A 1000.01 PASS AC=1;AF=0.559;AN=2;DP=2354;MQ=60;set=variant2-variant7-variant9-variant10-variant11-variant14-variant15-variant18-variant22-variant25-variant33-variant35-variant36-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:102,58:160:99:1185,0,2311:50,52,33,25 chr2 29240686 . A C 1017.72 PASS AC=1;AF=0.559;AN=2;DP=2534;MQ=60;set=variant2-variant7-variant9-variant10-variant11-variant14-variant15-variant18-variant22-variant25-variant33-variant35-variant36-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:105,65:170:99:1338,0,2297:51,54,33,32 chr2 29240783 . A G 935.12 PASS AC=1;AF=0.64;AN=2;DP=3131;MQ=60;set=variant2-variant3-variant7-variant9-variant10-variant11-variant14-variant15-variant16-variant18-variant21-variant22-variant25-variant27-variant28-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:55,56:111:99:1241,0,1381:18,37,25,31 chr2 29245933 . G A 2311.54 PASS AC=1;AF=0.672;AN=2;DP=5740;MQ=60;set=variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant13-variant16-variant18-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:127,101:228:99:2129,0,3033:66,61,51,50 chr2 29246044 . T C 1913.81 PASS AC=1;AF=0.71;AN=2;DP=4050;MQ=60;set=variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant18-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:74,63:137:99:1476,0,1875:31,43,28,35 chr2 29247304 . C T 1014.82 PASS AC=1;AF=0.62;AN=2;DP=2107;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant12-variant13-variant14-variant16-variant20-variant21-variant23-variant24-variant26-variant30-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,36:85:99:1137,0,1377:19,30,12,24 chr2 29249403 . T A,G 309.4 PASS AC=0,1;AF=0.453,0.234;AN=2;DP=869;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant7-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:DP:GQ:SB 0/2:24:99:6,3,11,4 chr2 29249415 . C T 398.43 PASS AC=1;AF=0.688;AN=2;DP=1047;MQ=60;set=variant-variant2-variant6-variant7-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:10,16:26:99:386,0,244:6,4,11,5 chr2 29249903 . G C 108.35 PASS AC=1;AF=0.5;AN=2;DP=350;MQ=60;set=variant2-variant7-variant9-variant10-variant11-variant15-variant18-variant22-variant25-variant31-variant33-variant35-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:15,18:33:99:470,0,429:3,12,6,12 chr2 29268295 . A C 530.21 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=1262;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:65,21:86:99:209,0,2337:17,48,21,0 chr2 29268300 . A C 505.18 PASS AC=1;AF=0.5;AN=2;DP=1111;set=filterInvariant3-filterInvariant4-variant8-filterInvariant12-filterInvariant13-filterInvariant22-filterInvariant24-filterInvariant33-filterInvariant35-variant36-filterInvariant39-filterInvariant41-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:71,24:95:99:185,0,1333:21,50,24,0 chr2 29275272 . T C 598.01 PASS AC=2;AF=0.743;AN=2;DP=1743;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,67:67:99:1892,201,0:0,0,37,30 chr2 29275318 . T C 777.74 PASS AC=2;AF=0.841;AN=2;DP=2245;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:1917,186,0:0,0,32,30 chr2 29275612 . A G 637.8 PASS AC=2;AF=0.791;AN=2;DP=2580;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,69:69:99:2403,207,0:0,0,32,37 chr2 29275940 . A G 1154.6 PASS AC=2;AF=0.757;AN=2;DP=3053;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,87:87:99:2767,261,0:0,0,41,46 chr2 29275983 . C T 943.56 PASS AC=1;AF=0.5;AN=2;DP=239;FractionInformativeReads=1;MQ=60;set=variant11-variant25-variant35 GT:AD:DP:GQ:PL:SB 0/1:38,29:67:99:680,0,1032:20,18,13,16 chr2 29276010 . G T 333.67 PASS AC=2;AF=0.615;AN=2;DP=1794;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant18-variant20-variant22-variant23-variant25-variant26-variant27-variant30-variant35-variant36-variant37-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:2201,194,0:0,0,32,33 chr2 29276412 . C T 926.59 PASS AC=1;AF=0.5;AN=2;DP=220;FractionInformativeReads=1;MQ=60;set=variant11-variant25-variant35 GT:AD:DP:GQ:PL:SB 0/1:42,30:72:99:674,0,1095:15,27,14,16 chr2 29276630 . T C 39.79 PASS AC=2;AF=0.615;AN=2;DP=829;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant18-variant20-variant22-variant23-variant25-variant26-variant27-variant30-variant35-variant36-variant37-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1417,138,0:0,0,23,23 chr2 29277200 . T C 254.7 PASS AC=2;AF=0.677;AN=2;DP=1034;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:896,90,0:0,0,13,17 chr2 29277355 . C G 229.36 PASS AC=2;AF=0.677;AN=2;DP=500;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:652,48,0:0,0,13,3 chr2 29277387 . G GGAGC 174.54 PASS AC=2;AF=0.75;AN=2;DP=29;FS=0;MQ=60;MQRankSum=0.05;ReadPosRankSum=-0.352;set=variant18-variant35 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:224,24,0:0,0,8,0 chr2 29277391 . C G,T 187.58 PASS AC=2,0;AF=0.536,0.214;AN=2;DP=218;MQ=60;set=variant-variant2-variant3-variant5-variant8-variant9-variant12-variant22-variant24-variant25-variant26-variant30-variant35-variant39 GT:DP:GQ:SB 1/1:8:24:0,0,8,0 chr2 29277403 . T G 216.86 PASS AC=1;AF=0.5;AN=2;DP=236;MQ=60;set=variant-variant3-variant4-filterInvariant7-variant9-variant11-variant12-variant13-variant18-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:8,11:19:99:398,0,317:4,4,10,1 chr2 29277405 . C G 217.85 PASS AC=1;AF=0.5;AN=2;DP=84;MQ=60;set=variant3-variant4-variant12-variant35 GT:AD:DP:GQ:PL:SB 0/1:10,11:21:99:397,0,317:6,4,10,1 chr2 29277730 . G A 86.5 PASS AC=2;AF=1;AN=2;DP=6;FS=0;FractionInformativeReads=1;MQ=60;SOR=1.179;set=variant9-variant35 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:114,9,0:0,0,1,2 chr2 29277731 . T TA 77.26 PASS AC=2;AF=1;AN=2;DP=3;FS=0;FractionInformativeReads=1;MQ=60;QD=25.75;SOR=1.179;set=variant35 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:115,9,0:0,0,1,2 chr2 29277732 . T TA 77.26 PASS AC=2;AF=1;AN=2;DP=2;FS=0;FractionInformativeReads=1;MQ=60;QD=25.97;SOR=2.303;set=variant35 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:9:115,9,0:0,0,0,2 chr2 29277736 . T A 61.77 PASS AC=2;AF=1;AN=2;DP=1;FS=0;FractionInformativeReads=1;MQ=60;QD=30.46;SOR=1.609;set=variant35 GT:AD:DP:GQ:PL:SB 1/1:0,1:1:6:90,6,0:0,0,0,1 chr2 29279251 . A AT 632.14 PASS AC=2;AF=1;AN=2;DP=1506;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:653,69,0:0,0,7,16 chr2 29280153 . G T 49.19 PASS AC=2;AF=0.683;AN=2;DP=1426;FractionInformativeReads=1;MQ=60;set=filterInvariant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant35-variant36-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1661,153,0:0,0,32,19 chr2 29280261 . A G 490.11 PASS AC=2;AF=0.615;AN=2;DP=1933;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant18-variant20-variant22-variant23-variant25-variant26-variant27-variant30-variant35-variant36-variant37-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,66:66:99:2346,198,0:0,0,32,34 chr2 29280745 . G A 435.94 PASS AC=2;AF=0.683;AN=2;DP=1492;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant35-variant36-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1294,120,0:0,0,20,20 chr2 29280761 . C T 380.24 PASS AC=2;AF=0.615;AN=2;DP=1306;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant18-variant20-variant22-variant23-variant25-variant26-variant27-variant30-variant35-variant36-variant37-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1394,129,0:0,0,23,20 chr2 29280791 . G A 375.72 PASS AC=2;AF=0.615;AN=2;DP=1382;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant18-variant20-variant22-variant23-variant25-variant26-variant27-variant30-variant35-variant36-variant37-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1541,150,0:0,0,29,21 chr2 29281458 . G A 382.45 PASS AC=2;AF=1;AN=2;DP=650;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.714;ReadPosRankSum=1.531;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,16:17:40:422,40,0:1,0,9,7 chr2 29281584 . G C 60.2 PASS AC=2;AF=0.615;AN=2;DP=526;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant18-variant20-variant22-variant23-variant25-variant26-variant27-variant30-variant35-variant36-variant37-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:522,51,0:0,0,9,8 chr2 29281796 . T G,TGG 2909.53 PASS AC=0,1;AF=0.167,0.5;AN=2;DP=273;FS=0;set=variant25-filterInvariant35-variant37 GT:DP:GQ:SB 0/2:79:99:57,6,15,1 chr2 29281798 . T TGG 224.59 PASS AC=1;AF=0.525;AN=2;DP=2617;set=filterInvariant-variant3-filterInvariant4-filterInvariant5-variant8-variant9-filterInvariant13-filterInvariant16-variant18-filterInvariant20-variant23-variant26-filterInvariant27-variant30-variant35-variant36-variant37-filterInvariant39-filterInvariant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,46:79:99:546,0,439:25,8,44,2 chr2 29281800 . T G,TGG 5450.61 PASS AC=1,1;AF=0.281,0.359;AN=2;DP=4527;set=variant3-variant8-variant-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant23-filterInvariant24-variant25-variant26-variant27-variant29-variant2-variant4-variant30-variant32-filterInvariant33-variant10-variant35-variant36-variant37-filterInvariant38-variant39-variant41-variant44 GT:DP:GQ:SB 1/2:81:99:1,0,68,12 chr2 29281804 . T G,TGG,TGGGTGG,TGTGG 6417.9 PASS AC=2,0,0,0;AF=0.667,0.25,0.014,0.014;AN=2;DP=5522;set=variant2-variant4-variant5-variant-variant7-variant3-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant44 GT:DP:GQ:SB 1/1:172:99:0,0,106,66 chr2 29281867 . A G 3121.64 PASS AC=2;AF=0.615;AN=2;DP=5314;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant18-variant20-variant22-variant23-variant25-variant26-variant27-variant30-variant35-variant36-variant37-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,229:229:99:7422,686,0:0,0,100,129 chr2 29283072 . C T 346.67 PASS AC=2;AF=0.683;AN=2;DP=1679;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant35-variant36-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:2375,236,0:0,0,41,38 chr2 29283421 . G A 589.29 PASS AC=2;AF=0.683;AN=2;DP=1957;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant35-variant36-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,64:64:99:1978,192,0:0,0,29,35 chr2 29284806 . A G 2414.27 PASS AC=2;AF=0.977;AN=2;DP=4125;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,110:110:99:3341,329,0:0,0,56,54 chr2 29284981 . T C 716.2 PASS AC=2;AF=0.775;AN=2;DP=2401;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:2256,225,0:0,0,28,47 chr2 29285065 . A G 1341.48 PASS AC=2;AF=0.955;AN=2;DP=2313;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,52:52:99:1773,156,0:0,0,22,30 chr2 29285150 . T C 1317.2 PASS AC=2;AF=0.989;AN=2;DP=2886;FS=0;MQ=60;MQRankSum=-0.257;ReadPosRankSum=0.105;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:2409,216,0:0,0,48,24 chr2 29285210 . C T 1914.03 PASS AC=2;AF=0.708;AN=2;DP=3132;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,107:107:99:3335,319,0:0,0,65,42 chr2 29285254 . C T 1020.25 PASS AC=2;AF=0.553;AN=2;DP=2026;MQ=60;set=variant-variant4-variant5-variant8-variant9-variant11-variant12-variant13-variant16-variant20-variant23-variant25-variant26-variant27-variant35-variant36-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,131:131:99:4076,392,0:0,0,77,54 chr2 29285575 . C T 2008.05 PASS AC=2;AF=0.681;AN=2;DP=3440;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,117:117:99:3810,350,0:0,0,42,75 chr2 29285631 . A G 1810.9 PASS AC=2;AF=0.681;AN=2;DP=2648;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,100:100:99:3277,300,0:0,0,39,61 chr2 29285713 . C T 1499.12 PASS AC=2;AF=0.681;AN=2;DP=2100;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,61:61:99:1849,182,0:0,0,28,33 chr2 29286072 . G A 3501.56 PASS AC=2;AF=0.671;AN=2;DP=5561;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,148:148:99:4660,442,0:0,0,67,81 chr2 29286193 . T C 1529.43 PASS AC=2;AF=0.708;AN=2;DP=2610;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2567,210,0:0,0,29,41 chr2 29286364 . C T 427.83 PASS AC=2;AF=0.575;AN=2;DP=1019;set=variant-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant16-variant20-variant23-variant25-variant26-variant27-variant35-variant36-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:1657,161,0:0,0,22,32 chr2 29286509 . T C 227.36 PASS AC=2;AF=0.568;AN=2;DP=647;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant16-variant20-variant21-variant23-variant25-variant26-variant27-variant35-variant36-variant37-variant38-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:792,75,0:0,0,10,15 chr2 29286670 . T C 238.29 PASS AC=2;AF=0.568;AN=2;DP=781;MQ=60;set=variant-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant16-variant20-variant21-variant23-variant25-variant26-variant27-variant35-variant36-variant37-variant38-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:877,81,0:0,0,15,12 chr2 29286905 . G T 436.71 PASS AC=2;AF=0.568;AN=2;DP=1471;MQ=60;set=variant-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant16-variant20-variant21-variant23-variant25-variant26-variant27-variant35-variant36-variant37-variant38-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:2148,204,0:0,0,29,39 chr2 29287192 . G A 438.34 PASS AC=2;AF=0.575;AN=2;DP=843;MQ=60;set=variant-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant16-variant20-variant23-variant25-variant26-variant27-variant35-variant36-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:1476,144,0:0,0,28,20 chr2 29287227 . T C 1015.94 PASS AC=2;AF=0.568;AN=2;DP=1163;MQ=60;set=variant-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant16-variant20-variant21-variant23-variant25-variant26-variant27-variant35-variant36-variant37-variant38-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:2614,178,0:0,0,34,23 chr2 29287229 . A G 1015.94 PASS AC=2;AF=0.604;AN=2;DP=1301;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant20-variant21-variant23-variant25-variant26-variant27-variant35-variant36-variant37-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:2614,178,0:0,0,36,23 chr2 29287708 . C T 493.19 PASS AC=2;AF=0.568;AN=2;DP=1331;MQ=60;set=variant-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant16-variant20-variant21-variant23-variant25-variant26-variant27-variant35-variant36-variant37-variant38-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,73:73:99:2241,219,0:0,0,29,44 chr2 29287926 . C CGCT 837.84 PASS AC=2;AF=0.609;AN=2;DP=2539;MQ=60;set=variant-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant20-variant21-variant23-variant25-variant26-variant27-variant35-variant36-variant37-variant38-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,123:123:99:5594,381,0:0,0,62,61 chr2 29288109 . A G 115.56 PASS AC=2;AF=0.609;AN=2;DP=445;MQ=60;set=variant-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant20-variant21-variant23-variant25-variant26-variant27-variant35-variant36-variant37-variant38-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:1020,72,0:0,0,3,21 chr2 29294629 . C T 1720.47 PASS AC=2;AF=0.575;AN=2;DP=4356;MQ=60;set=variant-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant16-variant20-variant23-variant25-variant26-variant27-variant35-variant36-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,271:271:99:7736,808,0:0,0,130,141 chr2 29294754 . G C 1558.37 PASS AC=2;AF=0.575;AN=2;DP=2897;MQ=60;set=variant-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant16-variant20-variant23-variant25-variant26-variant27-variant35-variant36-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:4,153:157:99:4465,372,0:2,2,70,83 chr2 29295016 . A G 2487.17 PASS AC=2;AF=0.609;AN=2;DP=4511;MQ=60;set=variant-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant20-variant21-variant23-variant25-variant26-variant27-variant35-variant36-variant37-variant38-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:3,229:232:99:6789,603,0:1,2,112,117 chr2 29295676 . G A 1800.93 PASS AC=2;AF=0.609;AN=2;DP=3872;MQ=60;set=variant-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant20-variant21-variant23-variant25-variant26-variant27-variant35-variant36-variant37-variant38-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,187:188:99:5686,551,0:1,0,91,96 chr2 29296870 . C T 3451.09 PASS AC=2;AF=0.575;AN=2;DP=5637;MQ=60;set=variant-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant16-variant20-variant23-variant25-variant26-variant27-variant35-variant36-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,298:300:99:9328,848,0:1,1,141,157 chr2 29297068 . C T 1544.45 PASS AC=2;AF=0.575;AN=2;DP=2448;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant16-variant20-variant23-variant25-variant26-variant27-variant35-variant36-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,103:103:99:3290,309,0:0,0,43,60 chr2 29320512 . T C 393.61 PASS AC=1;AF=0.55;AN=2;DP=307;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant16-variant20-variant23-variant25-variant26-variant30-variant32-variant35-variant36-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,13:18:91:334,0,91:3,2,7,6 chr2 29320680 . G A 448.87 PASS AC=1;AF=0.55;AN=2;DP=584;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant16-variant20-variant23-variant25-variant26-variant30-variant32-variant35-variant36-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,18:27:99:476,0,238:5,4,8,10 chr2 29356669 . A G 1651.49 PASS AC=2;AF=0.683;AN=2;DP=1868;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,66:66:99:2078,198,0:0,0,26,40 chr2 29366875 . C CACAG 615.91 PASS AC=2;AF=0.702;AN=2;DP=2546;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,67:67:99:2993,201,0:0,0,22,45 chr2 29383256 . G T 1408.21 PASS AC=2;AF=0.571;AN=2;DP=1730;MQ=60;set=variant4-variant12-variant16-variant18-variant20-variant21-variant23-variant25-variant26-variant34-variant35-variant36-variant39-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,127:127:99:3889,380,0:0,0,51,76 chr2 29383374 . G A 1067.04 PASS AC=2;AF=0.907;AN=2;DP=1966;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1223,111,0:0,0,11,26 chr2 29390299 . AG A 852.51 PASS AC=2;AF=0.556;AN=2;DP=1486;MQ=60;set=variant4-variant5-variant7-variant11-variant12-variant16-variant18-variant20-variant21-variant23-variant25-variant26-variant32-variant34-variant35-variant36-variant39-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,87:87:99:3485,262,0:0,0,45,42 chr2 29415792 . G A 11423.7 PASS AC=2;AF=1;AN=2;DP=13812;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,327:327:99:10545,981,0:0,0,197,130 chr2 29416572 . T C 3238.45 PASS AC=2;AF=1;AN=2;DP=6578;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,182:182:99:5667,545,0:0,0,91,91 chr2 29419591 . G T 1196.42 PASS AC=2;AF=0.769;AN=2;DP=3038;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,74:74:99:2335,221,0:0,0,47,27 chr2 29444095 . C T 2423.91 PASS AC=2;AF=0.989;AN=2;DP=4515;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,111:111:99:3458,332,0:0,0,45,66 chr2 29449819 . C T 1175.11 PASS AC=1;AF=0.595;AN=2;DP=2013;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant6-variant9-variant10-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant28-variant30-variant34-variant35-variant36-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,53:113:99:1219,0,1485:36,24,31,22 chr2 29451790 . T C 566.19 PASS AC=1;AF=0.5;AN=2;DP=947;set=filterInvariant2-filterInvariant5-variant7-filterInvariant14-filterInvariant15-filterInvariant16-filterInvariant17-variant18-variant19-filterInvariant22-variant23-variant24-variant27-filterInvariant28-filterInvariant31-variant33-variant34-variant35-variant38-variant40-filterInvariant41-filterInvariant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,7:33:99:127,0,3033:5,21,7,0 chr2 29451793 . A C 569.19 PASS AC=1;AF=0.5;AN=2;DP=891;set=filterInvariant2-filterInvariant5-variant7-filterInvariant14-filterInvariant15-filterInvariant16-filterInvariant17-variant18-variant19-filterInvariant22-variant23-variant24-variant27-filterInvariant28-filterInvariant31-variant33-variant34-variant35-variant38-variant40-filterInvariant41-variant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:25,6:31:99:124,0,3124:4,21,6,0 chr2 29451798 . CTCCGAAA C 287.33 PASS AC=1;AF=0.5;AN=2;DP=681;MQ=60;set=variant5-variant14-variant15-variant16-variant17-variant18-variant19-variant23-variant24-variant27-variant28-variant33-variant34-variant35-filterInvariant38-filterInvariant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:28,6:34:99:110,0,3339:6,22,6,0 chr2 29455267 . A G 2055.45 PASS AC=2;AF=0.813;AN=2;DP=4057;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,141:141:99:4282,423,0:0,0,76,65 chr2 29498210 . A G 3049.07 PASS AC=2;AF=0.955;AN=2;DP=3516;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,80:80:99:2975,239,0:0,0,49,31 chr2 29519588 . AGTGT AGT,AGTGTGTGT,A,AGTGTGT 55.54 PASS AC=0,0,0,1;AF=0.045,0.364,0.045,0.045;AN=2;DP=283;MQ=60;set=filterInvariant6-variant10-variant13-variant19-variant21-variant25-variant29-variant30-variant34-variant35-variant42 GT:DP:GQ:SB 0/4:30:99:16,1,10,3 chr2 29519622 . C T 1121.13 PASS AC=2;AF=0.893;AN=2;DP=1976;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1585,158,0:0,0,37,16 chr2 29525341 . A G 643.53 PASS AC=2;AF=0.932;AN=2;DP=842;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:990,66,0:0,0,19,3 chr2 29525345 . T C 103.61 PASS AC=2;AF=0.841;AN=2;DP=878;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:1027,69,0:0,0,20,3 chr2 29525654 . C T 409.51 PASS AC=2;AF=0.798;AN=2;DP=1043;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1453,123,0:0,0,7,34 chr2 29541104 . C T 648.39 PASS AC=2;AF=0.757;AN=2;DP=2323;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1565,150,0:0,0,33,17 chr2 29543663 . T C 2769.5 PASS AC=2;AF=0.864;AN=2;DP=4068;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,98:98:99:3074,294,0:0,0,61,37 chr2 29606824 . G A 590.23 PASS AC=1;AF=0.5;AN=2;DP=396;FractionInformativeReads=1;MQ=60;set=variant9-variant22-variant30-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:48,46:94:99:1184,0,1234:17,31,21,25 chr2 29917940 . C G 552.83 PASS AC=1;AF=0.779;AN=2;DP=2782;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:35,30:65:99:691,0,855:12,23,14,16 chr2 29940529 . A T 1364.21 PASS AC=1;AF=0.779;AN=2;DP=4739;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:86,59:145:99:1210,0,2157:44,42,32,27 chr2 29940820 . C T 321.52 PASS AC=1;AF=0.779;AN=2;DP=722;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,10:15:99:265,0,142:1,4,3,7 chr2 30143499 . G C 1534.43 PASS AC=2;AF=0.955;AN=2;DP=3279;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,93:93:99:3337,279,0:0,0,40,53 chr2 30371358 . T C 426.35 PASS AC=2;AF=0.762;AN=2;DP=760;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:486,45,0:0,0,6,9 chr2 30379362 . A G 5036.57 PASS AC=1;AF=0.556;AN=2;DP=3922;MQ=60;set=variant5-variant12-variant19-variant20-variant22-variant23-variant24-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:202,262:464:99:6578,0,4944:123,79,153,109 chr2 30381505 . T C 4760.04 PASS AC=1;AF=0.633;AN=2;DP=4774;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant21-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:77,73:150:99:1774,0,1912:43,34,37,36 chr2 30457561 . A G 114.18 PASS AC=1;AF=0.618;AN=2;DP=486;MQ=60;set=variant2-variant9-variant12-variant14-variant15-variant18-variant19-variant20-variant22-variant23-variant24-variant28-variant31-variant35-variant36-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,16:35:99:450,0,494:7,12,7,9 chr2 30479545 . C G 110.42 PASS AC=2;AF=0.692;AN=2;DP=515;FractionInformativeReads=1;set=variant-variant2-variant3-variant5-variant7-variant8-variant11-variant12-variant14-variant16-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant39 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:1059,78,0:0,0,25,1 chr2 30479650 . C T 821.69 PASS AC=2;AF=0.692;AN=2;DP=3910;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant11-variant12-variant14-variant16-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant39 GT:AD:DP:GQ:PL:SB 1/1:0,197:197:99:5633,589,0:0,0,111,86 chr2 30482099 . G A 1071.48 PASS AC=1;AF=0.688;AN=2;DP=1972;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant11-variant12-variant14-variant16-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:55,65:120:99:1709,0,1259:26,29,36,29 chr2 30682360 . G A 835.6 PASS AC=1;AF=0.802;AN=2;DP=1852;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,31:56:99:782,0,637:15,10,20,11 chr2 30748321 . A G 1097.67 PASS AC=1;AF=0.798;AN=2;DP=2053;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,29:59:99:956,0,992:25,5,26,3 chr2 30775299 . G A 205.58 PASS AC=1;AF=0.826;AN=2;DP=936;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,9:26:99:226,0,482:11,6,6,3 chr2 30791152 . A G 420.8 PASS AC=1;AF=0.786;AN=2;DP=1158;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,17:38:99:421,0,586:6,15,5,12 chr2 30828792 . G A 438.96 PASS AC=1;AF=0.738;AN=2;DP=2436;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,36:71:99:934,0,884:22,13,22,14 chr2 30830148 . C T 786.9 PASS AC=1;AF=0.667;AN=2;DP=688;FractionInformativeReads=1;set=variant3-variant6-variant7-variant8-variant11-variant12-variant16-variant17-variant19-variant21-variant22-variant24-variant26-variant28-variant31-variant33-variant35-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:16,17:33:99:610,0,541:14,2,16,1 chr2 30864326 . A G 6747.91 PASS AC=1;AF=0.826;AN=2;DP=16125;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:196,185:381:99:4552,0,5134:89,107,94,91 chr2 30864753 . CT C 493.1 PASS AC=1;AF=0.667;AN=2;DP=493;set=variant3-variant7-variant8-variant11-variant12-variant14-variant16-variant17-variant19-variant21-variant22-variant24-variant26-variant28-variant31-variant33-variant35-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:15,6:21:99:193,0,1524:4,11,3,3 chr2 30864768 . T C 443.25 PASS AC=1;AF=0.667;AN=2;DP=382;set=variant3-variant7-variant8-variant11-variant12-variant14-variant16-variant17-variant19-variant21-variant22-variant24-variant26-variant28-variant31-variant33-variant35-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:14,6:20:99:221,0,1597:4,10,3,3 chr2 30864770 . TTTTC T 403.55 PASS AC=1;AF=0.571;AN=2;DP=372;set=variant3-variant7-variant8-variant11-variant12-variant14-variant16-variant17-variant19-variant21-variant22-variant24-variant26-variant28-variant31-variant33-variant35-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:14,6:20:99:197,0,1572:4,10,3,3 chr2 30864976 . C G 745.64 PASS AC=1;AF=0.667;AN=2;DP=864;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant8-variant11-variant12-variant14-variant16-variant17-variant19-variant21-variant22-variant24-variant26-variant28-variant31-variant33-variant35-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:35,19:54:99:692,0,1580:18,17,13,6 chr2 30864980 . A G 534.68 PASS AC=1;AF=0.81;AN=2;DP=1988;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,21:56:99:750,0,1574:18,17,14,7 chr2 30865048 . G A 620.39 PASS AC=1;AF=0.685;AN=2;DP=1579;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant21-variant22-variant24-variant26-variant27-variant28-variant30-variant31-variant33-variant35-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:37,27:64:99:659,0,835:19,18,13,14 chr2 30865266 . CTT C,CT 238.31 PASS AC=1,0;AF=0.762,0.071;AN=2;DP=899;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:13:99:1,3,7,2 chr2 30865273 . T C 247.29 PASS AC=1;AF=0.8;AN=2;DP=875;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,11:15:99:429,0,233:1,3,9,2 chr2 30955528 . C A 272.69 PASS AC=1;AF=0.857;AN=2;DP=936;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,13:28:99:307,0,374:3,12,7,6 chr2 30959262 . G T 3671.58 PASS AC=1;AF=0.838;AN=2;DP=5352;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:87,64:151:99:1355,0,2219:53,34,33,31 chr2 30968517 . G A 510.98 PASS AC=1;AF=0.5;AN=2;DP=60;FractionInformativeReads=1;MQ=60;set=variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:16,18:34:99:539,0,504:10,6,14,4 chr2 30976058 . C T 3408.78 PASS AC=1;AF=0.625;AN=2;DP=3960;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant13-variant15-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:100,74:174:99:1755,0,2443:49,51,36,38 chr2 30977073 . G A 4284.08 PASS AC=1;AF=0.895;AN=2;DP=4961;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,64:102:99:1624,0,1040:27,11,40,24 chr2 30980940 . C T 1517.15 PASS AC=1;AF=0.813;AN=2;DP=2327;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:32,24:56:99:581,0,797:16,16,16,8 chr2 30986853 . A G 566.19 PASS AC=1;AF=0.5;AN=2;DP=365;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant9-variant16-variant29-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:31,20:51:99:500,0,795:16,15,12,8 chr2 30986989 . G T 1958.13 PASS AC=2;AF=0.92;AN=2;DP=5036;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,110:110:99:3305,329,0:0,0,62,48 chr2 30999017 . T A 809.5 PASS AC=1;AF=0.5;AN=2;DP=104;FractionInformativeReads=1;MQ=60;set=variant7-variant35 GT:AD:DP:GQ:PL:SB 0/1:24,29:53:99:766,0,681:5,19,10,19 chr2 30999023 . AT A 297.61 PASS AC=2;AF=0.643;AN=2;DP=1132;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant27-variant28-variant32-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1687,132,0:0,0,11,33 chr2 31009977 . G C 1009.95 PASS AC=2;AF=0.898;AN=2;DP=1298;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:1051,84,0:0,0,23,5 chr2 31030024 . C T 106.77 PASS AC=1;AF=0.8;AN=2;DP=414;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,5:9:99:131,0,110:3,1,4,1 chr2 31133939 . G C 3534.89 PASS AC=1;AF=0.571;AN=2;DP=4252;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant6-variant7-variant8-variant10-variant12-variant17-variant18-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant35-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:97,112:209:99:2831,0,2285:45,52,43,69 chr2 31135184 . G T 1441.58 PASS AC=1;AF=0.548;AN=2;DP=1962;MQ=60;set=variant3-variant5-variant6-variant7-variant8-variant10-variant12-variant17-variant18-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant35-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:46,62:108:99:1570,0,1230:20,26,28,34 chr2 31188957 . C T 452.06 PASS AC=2;AF=0.977;AN=2;DP=1033;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:872,72,0:0,0,20,4 chr2 31348335 . ACC A 1319.53 PASS AC=2;AF=0.845;AN=2;DP=1463;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1853,133,0:0,0,10,34 chr2 31348390 . A G 583.95 PASS AC=2;AF=0.714;AN=2;DP=413;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:524,36,0:0,0,0,12 chr2 31352176 . A T 123.6 PASS AC=1;AF=0.615;AN=2;DP=345;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant10-variant12-variant14-variant15-variant16-variant18-variant20-variant22-variant25-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,9:19:99:248,0,335:8,2,7,2 chr2 31361259 . T TGCCGCCGCC 2396.74 PASS AC=1;AF=0.588;AN=2;DP=2141;set=variant6-variant7-variant8-variant9-variant11-variant12-variant23-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:84,75:159:99:3007,0,5193:45,39,38,37 chr2 31361399 . CGACA C 1996.74 PASS AC=2;AF=0.75;AN=2;DP=5147;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:3,102:105:99:2908,222,0:2,1,42,60 chr2 31397696 . G C 815.68 PASS AC=1;AF=0.525;AN=2;DP=1520;MQ=60;set=variant4-variant5-variant12-variant14-variant16-variant17-variant18-variant19-variant22-variant24-variant25-variant27-variant30-variant32-variant33-variant35-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:29,40:69:99:1087,0,657:14,15,18,22 chr2 31397727 . T C 497.89 PASS AC=1;AF=0.525;AN=2;DP=1089;MQ=60;set=variant4-variant5-variant12-variant14-variant16-variant17-variant18-variant19-variant22-variant24-variant25-variant27-variant30-variant32-variant33-variant35-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:25,36:61:99:1022,0,531:11,14,15,21 chr2 31399358 . T G 575.8 PASS AC=1;AF=0.525;AN=2;DP=1191;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant12-variant14-variant16-variant17-variant18-variant19-variant22-variant24-variant25-variant27-variant30-variant32-variant33-variant35-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:19,29:48:99:791,0,553:13,6,19,10 chr2 31399414 . G C 891.98 PASS AC=1;AF=0.525;AN=2;DP=1506;MQ=60;set=variant4-variant5-variant12-variant14-variant16-variant17-variant18-variant19-variant22-variant24-variant25-variant27-variant30-variant32-variant33-variant35-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:28,41:69:99:1121,0,838:16,12,23,18 chr2 31399659 . T C 819.6 PASS AC=1;AF=0.522;AN=2;DP=1079;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant10-variant12-variant14-variant16-variant17-variant18-variant19-variant22-variant24-variant25-variant27-variant30-variant32-variant33-variant35-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:21,26:47:99:820,0,648:6,15,12,14 chr2 31399751 . T G 619.56 PASS AC=1;AF=0.525;AN=2;DP=589;FractionInformativeReads=1;set=variant4-variant5-variant12-variant14-variant16-variant17-variant18-variant19-variant22-variant24-variant25-variant27-variant30-variant32-variant33-variant35-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:19,16:35:99:519,0,613:14,5,11,5 chr2 31399988 . C T 1349.06 PASS AC=1;AF=0.525;AN=2;DP=2201;MQ=60;set=variant4-variant5-variant12-variant14-variant16-variant17-variant18-variant19-variant22-variant24-variant25-variant27-variant30-variant32-variant33-variant35-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:62,37:99:99:811,0,1524:24,38,15,22 chr2 31400039 . A G 905.38 PASS AC=1;AF=0.525;AN=2;DP=1078;MQ=60;set=variant4-variant5-variant12-variant14-variant16-variant17-variant18-variant19-variant22-variant24-variant25-variant27-variant30-variant32-variant33-variant35-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:31,19:50:99:542,0,934:7,24,6,13 chr2 31400502 . A C 286.62 PASS AC=1;AF=0.523;AN=2;DP=360;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant10-variant12-variant14-variant16-variant17-variant18-variant19-variant22-variant24-variant25-variant27-variant30-variant32-variant33-variant35-variant37-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:17,12:29:99:453,0,1107:13,4,10,2 chr2 31400510 . G A 364.58 PASS AC=1;AF=0.526;AN=2;DP=348;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant12-variant14-variant16-variant17-variant18-variant19-variant22-variant24-variant25-variant27-variant30-variant32-variant33-variant35-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:19,14:33:99:527,0,1174:15,4,12,2 chr2 31400722 . G A 1824.53 PASS AC=1;AF=0.526;AN=2;DP=3294;MQ=60;set=variant4-variant5-variant12-variant14-variant16-variant17-variant18-variant19-variant22-variant24-variant25-variant27-variant30-variant32-variant33-variant35-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:108,98:206:99:2328,0,2602:51,57,56,42 chr2 31400867 . T C 295.38 PASS AC=1;AF=0.526;AN=2;DP=610;MQ=60;set=variant4-variant5-variant12-variant14-variant16-variant17-variant18-variant19-variant22-variant24-variant25-variant27-variant30-variant32-variant33-variant35-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:18,25:43:99:790,0,624:1,17,4,21 chr2 31401188 . A C 539.87 PASS AC=1;AF=0.5;AN=2;DP=343;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant14-variant16-variant17-variant18-variant25-variant32-variant35-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:18,11:29:99:270,0,624:15,3,8,3 chr2 31401290 . A C 2950.69 PASS AC=2;AF=1;AN=2;DP=4633;FS=0;MQ=60;MQRankSum=0.027;ReadPosRankSum=-0.605;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,125:125:99:3719,374,0:0,0,72,53 chr2 31401499 . G A 340.39 PASS AC=1;AF=0.526;AN=2;DP=631;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant12-variant14-variant16-variant17-variant18-variant19-variant22-variant24-variant25-variant27-variant30-variant32-variant33-variant35-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:15,21:36:99:618,0,402:4,11,4,17 chr2 31403947 . G A 289.71 PASS AC=1;AF=0.528;AN=2;DP=456;MQ=60;set=variant5-variant12-variant14-variant16-variant17-variant18-variant19-variant22-variant24-variant25-variant27-variant30-variant32-variant33-variant35-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:18,13:31:99:295,0,553:4,14,5,8 chr2 31409115 . T C 341.27 PASS AC=1;AF=0.528;AN=2;DP=389;MQ=60;set=variant5-variant12-variant14-variant16-variant17-variant18-variant19-variant22-variant24-variant25-variant27-variant30-variant32-variant33-variant35-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:10,17:27:99:556,0,365:10,0,14,3 chr2 31410653 . C T 1659.95 PASS AC=1;AF=0.5;AN=2;DP=1934;MQ=60;set=variant5-variant12-variant14-variant16-variant17-variant18-variant19-variant22-variant25-variant27-variant30-variant32-variant33-variant35-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:60,58:118:99:1434,0,1479:33,27,33,25 chr2 31410708 . C T 4640.73 PASS AC=2;AF=1;AN=2;DP=6174;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,165:165:99:4888,494,0:0,0,82,83 chr2 31410728 . C A 1572.24 PASS AC=1;AF=0.5;AN=2;DP=2281;MQ=60;set=variant5-variant12-variant14-variant16-variant17-variant18-variant19-variant22-variant25-variant27-variant30-variant32-variant33-variant35-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:84,82:166:99:1895,0,2059:39,45,41,41 chr2 31411184 . C A 996.49 PASS AC=1;AF=0.5;AN=2;DP=1509;MQ=60;set=variant5-variant12-variant14-variant16-variant17-variant18-variant19-variant22-variant25-variant27-variant30-variant32-variant33-variant35-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:52,56:108:99:1275,0,1317:30,22,29,27 chr2 31411242 . C A 1066.55 PASS AC=1;AF=0.5;AN=2;DP=1607;MQ=60;set=variant5-variant12-variant14-variant16-variant17-variant18-variant19-variant22-variant25-variant27-variant30-variant32-variant33-variant35-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:62,47:109:99:997,0,1482:33,29,21,26 chr2 31411310 . C T 586.15 PASS AC=1;AF=0.5;AN=2;DP=894;MQ=60;set=variant5-variant12-variant14-variant16-variant17-variant18-variant19-variant22-variant25-variant27-variant30-variant32-variant33-variant35-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:37,22:59:99:556,0,968:16,21,7,15 chr2 31411365 . G A 219.24 PASS AC=1;AF=0.5;AN=2;DP=403;MQ=60;set=variant5-variant12-variant14-variant16-variant17-variant18-variant19-variant22-variant25-variant27-variant30-variant32-variant33-variant35-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:22,12:34:99:307,0,588:7,15,4,8 chr2 31412096 . T C 135.83 PASS AC=1;AF=0.5;AN=2;DP=316;FractionInformativeReads=1;MQ=60;set=variant5-variant12-variant14-variant16-variant17-variant18-variant19-variant22-variant25-variant27-variant30-variant32-variant33-variant35-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:9,12:21:99:362,0,302:8,1,9,3 chr2 31412443 . T C 701.84 PASS AC=1;AF=0.5;AN=2;DP=866;FractionInformativeReads=1;MQ=60;set=variant5-variant12-variant14-variant16-variant17-variant18-variant19-variant22-variant25-variant27-variant30-variant32-variant33-variant35-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:19,23:42:99:688,0,512:9,10,13,10 chr2 31412646 . T C 748.29 PASS AC=1;AF=0.5;AN=2;DP=1310;FractionInformativeReads=1;MQ=60;set=variant5-variant12-variant14-variant16-variant17-variant18-variant19-variant22-variant25-variant27-variant30-variant32-variant33-variant35-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:31,54:85:99:1426,0,721:13,18,22,32 chr2 31412670 . C T 656.42 PASS AC=1;AF=0.5;AN=2;DP=1015;MQ=60;set=variant5-variant12-variant14-variant16-variant17-variant18-variant19-variant22-variant25-variant27-variant30-variant32-variant33-variant35-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:23,40:63:99:1133,0,524:9,14,12,28 chr2 31414223 . G A 806.62 PASS AC=1;AF=0.5;AN=2;DP=1004;FractionInformativeReads=1;MQ=60;set=variant5-variant12-variant14-variant16-variant17-variant18-variant19-variant22-variant25-variant27-variant30-variant32-variant33-variant35-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:37,35:72:99:867,0,1024:13,24,13,22 chr2 31414807 . C G 1799.48 PASS AC=2;AF=0.955;AN=2;DP=4264;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,112:112:99:3365,336,0:0,0,57,55 chr2 31415077 . G A 492.24 PASS AC=1;AF=0.5;AN=2;DP=722;MQ=60;set=variant2-variant5-variant10-variant13-variant14-variant16-variant17-variant18-variant19-variant25-variant27-variant32-variant35-variant37-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:20,22:42:99:518,0,453:8,12,8,14 chr2 31420245 . A G 1478.47 PASS AC=1;AF=0.553;AN=2;DP=2281;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant22-variant25-variant27-variant29-variant32-variant35-variant37-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:68,53:121:99:1406,0,1751:36,32,22,31 chr2 31420383 . G C 343.24 PASS AC=1;AF=0.553;AN=2;DP=916;MQ=60;set=variant2-variant5-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant22-variant25-variant27-variant29-variant32-variant35-variant37-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:45,25:70:99:526,0,1274:15,30,9,16 chr2 31420415 . G A 206.99 PASS AC=1;AF=0.553;AN=2;DP=720;MQ=60;set=variant2-variant5-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant22-variant25-variant27-variant29-variant32-variant35-variant37-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:38,21:59:99:424,0,1125:11,27,7,14 chr2 31420485 . T C 315.48 PASS AC=2;AF=1;AN=2;DP=710;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:821,60,0:0,0,4,16 chr2 31420506 . C A 87.17 PASS AC=1;AF=0.577;AN=2;DP=158;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant10-variant14-variant16-variant17-variant18-variant25-variant32-variant35-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:10,5:15:99:137,0,350:2,8,1,4 chr2 31422452 . T A 1076.83 PASS AC=1;AF=0.553;AN=2;DP=2349;MQ=60;set=variant2-variant5-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant22-variant25-variant27-variant29-variant32-variant35-variant37-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:60,80:140:99:1933,0,1233:26,34,31,49 chr2 31422514 . T A 558.81 PASS AC=1;AF=0.553;AN=2;DP=1313;MQ=60;set=variant2-variant5-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant22-variant25-variant27-variant29-variant32-variant35-variant37-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:29,41:70:99:1178,0,732:10,19,11,30 chr2 31422601 . A T 116.07 PASS AC=1;AF=0.553;AN=2;DP=342;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant22-variant25-variant27-variant29-variant32-variant35-variant37-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:4,7:11:95:233,0,95:2,2,1,6 chr2 31423443 . G A 910.84 PASS AC=1;AF=0.553;AN=2;DP=1885;MQ=60;set=variant2-variant5-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant22-variant25-variant27-variant29-variant32-variant35-variant37-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:44,42:86:99:1027,0,1055:17,27,18,24 chr2 31457154 . GGGGACCCCGGCTT G 687.8 PASS AC=2;AF=0.75;AN=2;DP=1012;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:92:1353,92,0:0,0,19,11 chr2 31457817 . T C 1352.35 PASS AC=2;AF=0.697;AN=2;DP=1902;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:2025,174,0:0,0,22,36 chr2 31457981 . T C 520.43 PASS AC=2;AF=0.789;AN=2;DP=428;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:448,42,0:0,0,3,11 chr2 31467079 . G A 453.27 PASS AC=2;AF=0.676;AN=2;DP=504;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:59:581,59,0:0,0,12,8 chr2 31467351 . T A 2152.78 PASS AC=2;AF=0.705;AN=2;DP=3578;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,96:96:99:2742,287,0:0,0,45,51 chr2 31483890 . T C 677.99 PASS AC=2;AF=0.808;AN=2;DP=1739;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:2108,150,0:0,0,1,49 chr2 31484334 . G A 1367.28 PASS AC=2;AF=0.878;AN=2;DP=2231;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,52:52:99:1625,155,0:0,0,33,19 chr2 31488965 . C T 329.76 PASS AC=2;AF=0.878;AN=2;DP=974;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:953,87,0:0,0,19,10 chr2 31489627 . TACACACACACACAC TACACACACACACACAC,TACACACACACACACACAC,TACACACACACAC,TACACACACACACACACACAC,TACACACACAC,TACACACAC,T 963.84 PASS AC=0,0,1,0,0,0,0;AF=0.051,0.103,0.231,0.077,0.013,0.064,0.013;AN=2;DP=2865;set=variant-variant2-variant3-filterInvariant4-variant5-variant7-variant8-variant9-variant10-filterInvariant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-filterInvariant19-variant20-variant21-variant22-variant23-variant24-variant25-filterInvariant26-filterInvariant27-variant28-variant29-variant30-variant32-variant33-variant34-filterInvariant35-filterInvariant36-variant37-variant39-filterInvariant40-variant41-variant43 GT:DP:GQ:SB 0/3:56:99:22,23,4,7 chr2 31489727 . T C 2533.73 PASS AC=2;AF=0.89;AN=2;DP=3570;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,103:103:99:3395,308,0:0,0,62,41 chr2 31490716 . C G 1476.62 PASS AC=2;AF=0.854;AN=2;DP=3090;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,92:92:99:2918,276,0:0,0,55,37 chr2 31557308 . G A 1864.72 PASS AC=2;AF=0.638;AN=2;DP=2039;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant11-variant12-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,69:69:99:2119,207,0:0,0,39,30 chr2 31558306 . T C 8612.99 PASS AC=2;AF=0.643;AN=2;DP=7706;MQ=60;set=variant2-variant4-variant5-variant7-variant11-variant12-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,277:277:99:8246,830,0:0,0,133,144 chr2 31567743 . T C 2923.84 PASS AC=2;AF=0.977;AN=2;DP=5168;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,133:133:99:4355,398,0:0,0,54,79 chr2 31569471 . A G 1005.13 PASS AC=1;AF=0.718;AN=2;DP=1194;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,21:34:99:626,0,338:10,3,16,5 chr2 31570376 . T C 2273.65 PASS AC=1;AF=0.711;AN=2;DP=2518;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,36:80:99:933,0,1357:32,12,24,12 chr2 31570626 . C T 691.77 PASS AC=1;AF=0.718;AN=2;DP=1260;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,19:34:99:766,0,965:4,11,5,14 chr2 31570631 . A G 691.77 PASS AC=1;AF=0.718;AN=2;DP=1135;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,19:33:99:766,0,965:3,11,4,15 chr2 31571241 . G C 3250.88 PASS AC=1;AF=0.711;AN=2;DP=5062;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:76,76:152:99:1972,0,2061:32,44,32,44 chr2 31571786 . A G 2668.28 PASS AC=1;AF=0.718;AN=2;DP=3241;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,22:80:99:430,0,1500:27,31,11,11 chr2 31572398 . A G 943.21 PASS AC=1;AF=0.7;AN=2;DP=891;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,12:26:99:410,0,435:12,2,11,1 chr2 31572482 . T TG 2570.32 PASS AC=1;AF=0.711;AN=2;DP=3040;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,40:74:99:1081,0,888:20,14,25,15 chr2 31573234 . CTTTTT CTTT,C,CTT,CT,CTTTTTTT 62.43 PASS AC=1,0,0,0,0;AF=0.288,0.019,0.212,0.058,0.019;AN=2;DP=676;set=variant-variant3-variant4-variant5-variant9-variant10-variant16-variant17-variant21-variant22-filterInvariant23-variant24-variant25-variant26-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-filterInvariant43-variant44 GT:DP:GQ:SB 0/1:6:39:0,2,0,4 chr2 31587235 . G A 1414.14 PASS AC=1;AF=0.724;AN=2;DP=1979;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,33:65:99:862,0,732:13,19,9,24 chr2 31588288 . T A 1920.54 PASS AC=1;AF=0.714;AN=2;DP=4318;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,56:117:99:1339,0,1473:31,30,27,29 chr2 31589654 . T C 321.14 PASS AC=1;AF=0.571;AN=2;DP=465;MQ=60;set=variant-variant3-variant5-variant7-variant9-variant10-variant12-filterInvariant13-variant15-variant16-variant17-variant23-variant25-variant26-variant32-variant34-variant35-variant36-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:14,14:28:99:453,0,462:11,3,11,3 chr2 31590759 . C T 633.54 PASS AC=1;AF=0.575;AN=2;DP=1020;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant7-variant9-variant12-variant13-variant15-variant16-variant17-variant23-variant25-variant26-variant32-variant34-variant35-variant36-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:38,31:69:99:895,0,1020:26,12,24,7 chr2 31596955 . G A 566.51 PASS AC=1;AF=0.62;AN=2;DP=1332;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant23-variant25-variant26-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:22,19:41:99:729,0,1126:9,13,4,15 chr2 31596963 . T C 578.51 PASS AC=1;AF=0.62;AN=2;DP=1248;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant23-variant25-variant26-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:21,17:38:99:729,0,1147:7,14,4,13 chr2 31600146 . T C 1102.23 PASS AC=1;AF=0.718;AN=2;DP=1400;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,13:40:99:264,0,865:5,22,4,9 chr2 31606985 . AGTGTGT AGTGTGTGTGT,AGTGTGTGTGTGTGTGT,AGTGTGTGTGTGTGT,AGTGTGTGTGTGTGTGTGT,A,AGTGTGTGTGTGT,AGTGTGTGT 52.37 PASS AC=0,0,0,0,0,2,0;AF=0.067,0.3,0.383,0.05,0.017,0.117,0.017;AN=2;DP=353;FS=0;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant40-variant41-variant42-variant44 GT:DP:GQ:SB 6/6:6:17:0,0,0,6 chr2 31609448 . A C 2980.15 PASS AC=2;AF=1;AN=2;DP=4388;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,105:105:99:2973,314,0:0,0,53,52 chr2 31611029 . G A 342.61 PASS AC=1;AF=0.65;AN=2;DP=868;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant20-variant22-variant23-variant26-variant27-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,20:36:99:581,0,522:12,4,14,6 chr2 31611367 . T C 412.53 PASS AC=1;AF=0.73;AN=2;DP=706;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,8:14:99:231,0,224:0,6,2,6 chr2 31805619 . T C 1068.92 PASS AC=2;AF=1;AN=2;DP=2831;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,66:66:99:2311,197,0:0,0,46,20 chr2 31805675 . A G 2934.18 PASS AC=2;AF=0.77;AN=2;DP=4440;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,142:142:99:4572,426,0:0,0,88,54 chr2 31805706 . G C 4022.12 PASS AC=2;AF=0.816;AN=2;DP=5909;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,186:186:99:5721,557,0:0,0,105,81 chr2 31805880 . A AG 6101.78 PASS AC=2;AF=1;AN=2;DP=9466;FS=0;MQ=60;MQRankSum=-0.767;ReadPosRankSum=-1.498;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,244:244:99:8667,734,0:0,0,109,135 chr2 31806031 . C G 988.28 PASS AC=2;AF=0.77;AN=2;DP=1564;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1798,159,0:0,0,17,36 chr2 32312568 . G A 697.25 PASS AC=1;AF=0.5;AN=2;DP=55;FS=3.798;FractionInformativeReads=0.982;MQ=60;MQRankSum=1.784;QD=12.68;ReadPosRankSum=1.924;SOR=0.453;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:23,31:54:99:725,0,499:9,14,16,15 chr2 32369901 . T C 415.31 PASS AC=2;AF=0.953;AN=2;DP=526;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:529,36,0:0,0,12,0 chr2 32380665 . T G 2123.77 PASS AC=1;AF=0.5;AN=2;DP=214;FS=1.07;FractionInformativeReads=0.995;MQ=60;MQRankSum=-1.689;QD=9.92;ReadPosRankSum=0.775;SOR=0.798;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:121,92:213:99:2152,0,2868:64,57,51,41 chr2 32381106 . TG T 47.34 PASS AC=1;AF=0.5;AN=2;DP=20;FS=0;FractionInformativeReads=0.65;MQ=60;MQRankSum=0.696;QD=2.37;ReadPosRankSum=-1.545;SOR=1.179;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:8,5:13:85:85,0,143:1,7,0,5 chr2 32381109 . G T 185.03 PASS AC=1;AF=0.524;AN=2;DP=318;set=variant7-variant8-variant9-variant12-variant15-variant16-variant17-variant20-variant23-variant26-variant27-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,8:13:85:143,0,85:0,5,1,7 chr2 32381727 . A AAGG 9413.37 PASS AC=2;AF=0.943;AN=2;DP=8118;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,171:171:99:7742,520,0:0,0,89,82 chr2 32402636 . C T 219.12 PASS AC=1;AF=0.571;AN=2;DP=497;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant7-variant12-variant13-variant15-variant16-variant17-variant20-variant23-variant26-variant27-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:25,10:35:99:223,0,557:14,11,7,3 chr2 32418808 . T A 1587.3 PASS AC=2;AF=0.816;AN=2;DP=1663;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1442,129,0:0,0,31,12 chr2 32434701 . A G 820.42 PASS AC=2;AF=0.803;AN=2;DP=612;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:624,57,0:0,0,4,15 chr2 32446613 . A G 848.66 PASS AC=2;AF=0.682;AN=2;DP=3415;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant20-variant22-variant23-variant24-variant26-variant27-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,109:109:99:3310,326,0:0,0,54,55 chr2 32447718 . C T 3172.39 PASS AC=2;AF=0.691;AN=2;DP=7793;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,234:234:99:6839,700,0:0,0,118,116 chr2 32447868 . A G 1964.58 PASS AC=2;AF=0.722;AN=2;DP=3805;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,103:103:99:3428,309,0:0,0,39,64 chr2 32449871 . ATTTTT AT,A 914.62 PASS AC=2,0;AF=0.662,0.015;AN=2;DP=987;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:19:24:0,1,3,15 chr2 32449879 . T A,TAAA 537.73 PASS AC=0,2;AF=0.022,0.652;AN=2;DP=581;MQ=60;set=variant11-variant13-variant15-variant16-variant17-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:DP:GQ:SB 2/2:17:50:0,0,3,14 chr2 32460348 . A G 37.69 PASS AC=2;AF=0.735;AN=2;DP=382;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant20-variant22-variant24-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:257,21,0:0,0,6,1 chr2 32461493 . T TC 227.83 PASS AC=2;AF=0.964;AN=2;DP=394;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:443,33,0:0,0,2,9 chr2 32466029 . A G 1031.5 PASS AC=2;AF=0.722;AN=2;DP=2140;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant20-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:1805,171,0:0,0,34,23 chr2 32475109 . G A 2107.34 PASS AC=2;AF=0.714;AN=2;DP=5833;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant20-variant22-variant23-variant24-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,181:181:99:5409,541,0:0,0,75,106 chr2 32476390 . T G 1806.37 PASS AC=2;AF=0.714;AN=2;DP=5821;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant20-variant22-variant23-variant24-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,198:198:99:5973,594,0:0,0,90,108 chr2 32481793 . AT A 2769.05 PASS AC=2;AF=0.714;AN=2;DP=4079;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant20-variant22-variant23-variant24-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,124:124:99:5629,379,0:0,0,77,47 chr2 32481795 . T A 2778.11 PASS AC=2;AF=0.714;AN=2;DP=4101;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant20-variant22-variant23-variant24-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,126:126:99:5630,379,0:0,0,78,48 chr2 32489851 . T C 598.07 PASS AC=2;AF=0.77;AN=2;DP=1036;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant22-variant23-variant24-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:853,78,0:0,0,13,13 chr2 32531207 . CTT C 231.95 PASS AC=1;AF=0.548;AN=2;DP=244;MQ=60;set=variant5-variant7-variant9-variant11-variant12-variant13-variant15-variant17-variant19-variant26-variant27-variant28-variant31-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,6:16:99:218,0,385:5,5,4,2 chr2 32532997 . CAAA CAA,CA,C,CAAAA,CAAAAAA 49.56 PASS AC=0,0,0,1,0;AF=0.15,0.2,0.05,0.05,0.05;AN=2;DP=143;set=variant9-variant10-variant13-variant19-variant21-variant27-variant31-variant33-variant35-variant43 GT:DP:GQ:SB 0/4:11:36:6,0,2,3 chr2 32534750 . CTTTTTTTTTTTTTTT CTTTTTTTTTTTT,C,CTTTTTTTTTTT,CTTTTTTTTTTTTTT,CTTTTTTTTTTTTT 127.49 PASS AC=0,1,0,0,0;AF=0.032,0.403,0.032,0.032,0.065;AN=2;DP=1246;set=variant2-variant5-variant7-variant8-variant9-filterInvariant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant21-variant24-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-filterInvariant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:27:99:6,7,5,9 chr2 32655873 . CTT CT,C,CTTT 146.79 PASS AC=1,0,1;AF=0.261,0.065,0.196;AN=2;DP=492;set=variant3-variant4-variant5-variant9-variant10-variant11-variant12-variant13-variant15-filterInvariant21-variant22-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant38-variant40-variant44 GT:DP:GQ:SB 1/3:24:80:3,0,18,3 chr2 32667058 . C A 286.77 PASS AC=2;AF=1;AN=2;DP=563;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,14:14:48:679,48,0:0,0,13,1 chr2 32667061 . T A 323.52 PASS AC=2;AF=1;AN=2;DP=604;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:679,48,0:0,0,14,2 chr2 32667182 . G C 2669.71 PASS AC=2;AF=1;AN=2;DP=3244;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,94:94:99:2967,282,0:0,0,56,38 chr2 32688601 . A C 107.98 PASS AC=2;AF=0.773;AN=2;DP=116;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant7-variant8-variant9-variant13-variant14-variant19-variant20-variant26-variant27-variant28-variant30-variant31-variant35-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:135,9,0:0,0,0,3 chr2 32690253 . ATT A,AT 111.14 PASS AC=0,1;AF=0.104,0.396;AN=2;DP=905;MQ=60;set=variant3-variant5-filterInvariant8-variant9-filterInvariant10-variant11-variant12-filterInvariant15-filterInvariant16-variant20-filterInvariant21-filterInvariant22-variant26-filterInvariant27-filterInvariant28-variant30-filterInvariant31-variant33-filterInvariant34-filterInvariant35-variant36-variant37-variant39-variant43 GT:DP:GQ:SB 0/2:25:96:6,9,2,8 chr2 32706579 . T A 792.48 PASS AC=2;AF=1;AN=2;DP=922;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:846,72,0:0,0,5,19 chr2 32712875 . A C 2806.33 PASS AC=2;AF=1;AN=2;DP=3347;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,87:87:99:2655,260,0:0,0,29,58 chr2 32713706 . A T 594.62 PASS AC=1;AF=0.667;AN=2;DP=1903;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,30:63:99:738,0,694:17,16,14,16 chr2 32713844 . G A 142.13 PASS AC=1;AF=0.5;AN=2;DP=14;FS=3.358;FractionInformativeReads=1;MQ=60;MQRankSum=-1.936;QD=10.15;ReadPosRankSum=1.524;SOR=0.061;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:7,7:14:99:170,0,260:0,7,2,5 chr2 32724590 . GTC G 96.82 PASS AC=1;AF=0.5;AN=2;DP=174;MQ=60;set=filterInvariant-filterInvariant5-variant35 GT:AD:DP:GQ:PL:SB 0/1:45,12:57:99:266,0,1385:28,17,8,4 chr2 32733343 . CTTTTTTTTTTT CTTTTTTT,CTTTTTTTTT,CTTTTTTTTTTTTTT,CTTTTTTTTTTTTT,CTTTTTT,CTTTTT,CT,C,CTTTTTTTTTTTT,CTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTT,CTTTTTTTT 383.5 PASS AC=0,0,0,0,0,0,0,0,0,0,1,0;AF=0.074,0.111,0.037,0.037,0.056,0.13,0.019,0.037,0.019,0.019,0.037,0.019;AN=2;DP=1294;set=variant-variant2-variant3-variant6-variant9-variant12-variant14-variant15-variant18-variant19-variant20-filterInvariant21-variant22-variant23-variant24-variant26-variant27-variant29-filterInvariant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant42 GT:DP:GQ:SB 0/11:22:99:0,11,5,6 chr2 32735881 . A G 481.92 PASS AC=1;AF=0.614;AN=2;DP=242;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant8-variant12-variant14-variant15-variant18-variant20-variant22-variant23-variant24-variant26-variant27-variant31-variant32-variant34-variant35-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:99:117,0,119:0,3,0,3 chr2 32749880 . C T 376.77 PASS AC=2;AF=1;AN=2;DP=406;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:315,21,0:0,0,6,1 chr2 32749890 . C T 511.77 PASS AC=2;AF=1;AN=2;DP=495;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:315,21,0:0,0,6,1 chr2 32749893 . A T 511.77 PASS AC=2;AF=1;AN=2;DP=524;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:315,21,0:0,0,6,1 chr2 32749903 . T C 661.7 PASS AC=2;AF=1;AN=2;DP=649;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:364,27,0:0,0,6,3 chr2 32757201 . C CGTGTGTGTGTGTGTGT,CGTGTGTGTGTGTGT,CGTGTGTGTGTGT,CGTGTGTGTGT,CGTGTGTGT,CGTGTGTGTGTGTGTGTGT,CGTGTGT 367.38 PASS AC=0,0,0,0,0,2,0;AF=0.162,0.122,0.27,0.203,0.054,0.108,0.014;AN=2;DP=401;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:DP:GQ:SB 6/6:11:44:0,0,8,3 chr2 32800422 . C G 311.05 PASS AC=1;AF=0.538;AN=2;DP=425;FractionInformativeReads=1;MQ=60;set=variant-variant8-variant12-variant14-variant20-variant26-variant31-variant32-variant35-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,16:30:99:387,0,298:6,8,7,9 chr2 32822729 . A G 49.73 PASS AC=1;AF=0.579;AN=2;DP=170;FractionInformativeReads=1;MQ=60;set=variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant17-variant19-variant26-variant27-variant28-variant31-variant35-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,3:5:22:120,0,22:0,2,3,0 chr2 32822957 . G A 364.01 PASS AC=1;AF=0.565;AN=2;DP=1441;MQ=60;set=variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant17-variant19-variant26-variant27-variant28-variant30-variant31-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,43:79:99:960,0,733:17,19,19,24 chr2 32843294 . TA T 359.47 PASS AC=1;AF=0.52;AN=2;DP=2196;set=variant2-variant3-variant5-variant7-variant9-variant11-variant12-variant13-filterInvariant16-variant17-variant19-variant26-variant27-variant28-filterInvariant29-variant30-variant31-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,24:68:99:400,0,1399:26,18,17,7 chr2 32843743 . A AT 1117.59 PASS AC=1;AF=0.5;AN=2;DP=502;MQ=60;set=variant8-variant12-variant35 GT:AD:DP:GQ:PL:SB 0/1:94,78:172:99:1636,0,2131:47,47,40,38 chr2 32855615 . A G 8927.36 PASS AC=2;AF=0.989;AN=2;DP=10208;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,217:218:99:6295,605,0:0,1,103,114 chr2 32860415 . C T 1772.7 PASS AC=1;AF=0.955;AN=2;DP=2732;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:44,47:91:99:950,0,914:20,24,24,23 chr2 32875420 . CTTTTTT C,CTTT,CTTTTTTT,CTTTT,CTT,CTTTTT 80.17 PASS AC=0,1,0,0,0,0;AF=0.05,0.175,0.025,0.175,0.1,0.05;AN=2;DP=252;MQ=60;set=variant2-variant4-variant5-variant7-variant10-variant11-variant12-variant14-variant18-variant19-variant23-variant26-variant28-variant32-variant35-variant38-variant39-variant41-variant42-variant43 GT:DP:GQ:SB 0/2:9:68:0,6,0,3 chr2 32959024 . T C 1596.57 PASS AC=1;AF=0.625;AN=2;DP=3624;MQ=60;set=variant-variant3-variant5-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:72,59:131:99:1315,0,1700:31,41,24,35 chr2 32961691 . C T 882.2 PASS AC=1;AF=0.615;AN=2;DP=1583;MQ=60;set=variant-variant3-variant5-variant7-variant9-variant11-variant12-variant13-variant18-variant19-variant21-variant23-variant25-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,30:54:99:926,0,699:18,6,21,9 chr2 32961745 . T A 4388.88 PASS AC=2;AF=0.989;AN=2;DP=5620;MQ=60;MQRankSum=-0.479;ReadPosRankSum=0.241;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,140:140:99:4258,418,0:0,0,87,53 chr2 32962066 . T C 275.15 PASS AC=1;AF=0.633;AN=2;DP=310;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant18-variant19-variant21-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,3:5:76:117,0,76:0,2,0,3 chr2 32983526 . C T 1609.27 PASS AC=1;AF=0.611;AN=2;DP=3336;MQ=60;set=variant-variant3-variant5-variant7-variant9-variant11-variant12-variant13-variant18-variant19-variant21-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:70,77:147:99:1858,0,1877:40,30,42,35 chr2 33042654 . T G 1302.19 PASS AC=1;AF=0.5;AN=2;DP=102;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.231;QD=12.77;ReadPosRankSum=-0.06;SOR=0.693;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:51,51:102:99:1330,0,1463:17,34,17,34 chr2 33150389 . C T 1493.41 PASS AC=1;AF=0.763;AN=2;DP=4514;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:66,57:123:99:1310,0,1502:37,29,30,27 chr2 33150678 . C T 117.03 PASS AC=1;AF=0.629;AN=2;DP=2055;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant10-variant12-variant17-variant18-variant19-variant21-variant23-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,34:59:99:832,0,626:10,15,13,21 chr2 33150720 . A G 63.43 PASS AC=1;AF=0.763;AN=2;DP=1636;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,24:43:99:605,0,382:8,11,8,16 chr2 33172136 . C G 387.02 PASS AC=1;AF=0.588;AN=2;DP=383;FractionInformativeReads=1;MQ=60;set=variant5-variant6-variant7-variant12-variant13-variant17-variant18-variant19-filterInvariant23-variant29-variant31-variant35-variant36-variant37-variant38-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:13,9:22:99:162,0,319:7,6,5,4 chr2 33172358 . C A 308.97 PASS AC=1;AF=0.588;AN=2;DP=460;MQ=60;set=variant5-variant6-variant7-variant12-variant13-variant17-variant18-variant19-variant23-variant29-variant31-variant35-variant36-variant37-variant38-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:15,17:32:99:412,0,301:7,8,9,8 chr2 33173552 . C T 112.44 PASS AC=1;AF=0.607;AN=2;DP=153;FractionInformativeReads=1;MQ=60;set=variant5-variant7-variant12-variant17-variant19-variant23-variant29-variant31-variant35-variant36-variant37-variant38-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:5,7:12:99:176,0,161:4,1,5,2 chr2 33173703 . G A 864.15 PASS AC=1;AF=0.594;AN=2;DP=1074;MQ=60;set=variant5-variant6-variant7-variant12-variant17-variant19-variant23-variant29-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:24,37:61:99:976,0,574:13,11,21,16 chr2 33174072 . A C 215.83 PASS AC=1;AF=0.64;AN=2;DP=656;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant9-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant30-variant32-variant34-variant35-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:14,16:30:99:465,0,360:6,8,4,12 chr2 33335508 . C G 888.01 PASS AC=1;AF=0.656;AN=2;DP=1794;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,35:69:99:783,0,847:19,15,22,13 chr2 33335847 . C T 1574.69 PASS AC=1;AF=0.593;AN=2;DP=4788;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant11-variant12-variant13-variant17-variant19-variant20-variant23-variant24-variant25-variant26-variant29-variant30-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:82,99:181:99:2422,0,1862:37,45,45,54 chr2 33359565 . G A 1343.09 PASS AC=1;AF=0.5;AN=2;DP=899;FractionInformativeReads=1;MQ=60;set=variant8-variant15-variant16-variant35-variant36-variant38 GT:AD:DP:GQ:PL:SB 0/1:116,81:197:99:1890,0,2804:57,59,46,35 chr2 33392911 . G A 759.09 PASS AC=1;AF=0.722;AN=2;DP=3937;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:74,63:137:99:1269,0,1863:43,31,33,30 chr2 33407186 . T C 341.67 PASS AC=1;AF=0.667;AN=2;DP=629;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,14:22:99:439,0,196:6,2,11,3 chr2 33407285 . G A 1181.5 PASS AC=1;AF=0.662;AN=2;DP=3035;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:40,39:79:99:943,0,964:23,17,20,19 chr2 33412077 . G A 1342.93 PASS AC=1;AF=0.667;AN=2;DP=3885;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:57,68:125:99:1772,0,1493:22,35,25,43 chr2 33413640 . G T 462.36 PASS AC=1;AF=0.662;AN=2;DP=1812;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:38,34:72:99:936,0,1112:28,10,26,8 chr2 33413949 . G A 608.62 PASS AC=1;AF=0.711;AN=2;DP=2109;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:35,30:65:99:709,0,1058:9,26,11,19 chr2 33414009 . T A 416.68 PASS AC=2;AF=0.942;AN=2;DP=946;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:571,63,0:0,0,5,16 chr2 33442549 . G A 2445.03 PASS AC=1;AF=0.711;AN=2;DP=2501;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:37,48:85:99:1122,0,784:19,18,26,22 chr2 33447202 . C T 4025.89 PASS AC=1;AF=0.679;AN=2;DP=3732;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant18-variant20-variant22-variant24-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:63,52:115:99:1221,0,1668:36,27,28,24 chr2 33477964 . C T 454.8 PASS AC=1;AF=0.605;AN=2;DP=448;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant7-variant8-variant9-variant11-variant14-variant15-variant16-variant19-variant20-variant26-variant27-variant28-variant29-variant33-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:17,16:33:99:580,0,636:0,17,0,16 chr2 33488419 . G A 1743.17 PASS AC=1;AF=0.625;AN=2;DP=2985;MQ=60;set=variant-variant4-variant5-variant7-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant19-variant20-variant26-variant27-variant28-variant29-variant33-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:86,57:143:99:1155,0,2141:47,39,30,27 chr2 33500848 . A G 898.21 PASS AC=1;AF=0.667;AN=2;DP=2120;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant14-variant15-variant16-variant19-variant20-variant26-variant27-variant28-variant29-variant33-variant34-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,36:87:99:846,0,1342:26,25,22,14 chr2 33525382 . A C 583.48 PASS AC=1;AF=0.75;AN=2;DP=727;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,15:27:99:557,0,374:10,2,14,1 chr2 33525407 . A G 627.09 PASS AC=1;AF=0.667;AN=2;DP=936;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant14-variant15-variant16-variant19-variant20-variant26-variant27-variant28-variant29-variant33-variant34-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,25:47:99:605,0,676:17,5,16,9 chr2 33540138 . G A 488.83 PASS AC=2;AF=0.769;AN=2;DP=645;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:180,12,0:0,0,4,0 chr2 33540172 . A AT 308.49 PASS AC=1;AF=0.577;AN=2;DP=780;MQ=60;set=variant-variant2-variant6-variant10-variant12-variant13-variant15-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,8:20:99:183,0,306:9,3,5,3 chr2 33540248 . G A 1929.51 PASS AC=2;AF=0.711;AN=2;DP=3237;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,80:80:99:2402,240,0:0,0,50,30 chr2 33568113 . A G 978 PASS AC=1;AF=0.556;AN=2;DP=1228;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant8-variant9-variant14-variant15-variant16-variant17-variant19-variant23-variant25-variant30-variant31-variant33-variant35-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:39,42:81:99:1444,0,1434:12,27,15,27 chr2 33568137 . G A 520.43 PASS AC=1;AF=0.604;AN=2;DP=1171;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant19-variant23-variant24-variant25-variant30-variant31-variant33-variant35-variant36-variant37-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:24,25:49:99:971,0,1016:10,14,10,15 chr2 33568191 . T C 226.11 PASS AC=2;AF=0.73;AN=2;DP=721;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:762,75,0:0,0,8,17 chr2 33585796 . T C 5874.98 PASS AC=2;AF=1;AN=2;DP=11198;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,220:220:99:6846,659,0:0,0,100,120 chr2 33585993 . A T 1143.18 PASS AC=1;AF=0.5;AN=2;DP=425;FractionInformativeReads=1;MQ=60;set=variant8-variant14-variant15-variant16-variant33-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:21,21:42:99:614,0,668:4,17,4,17 chr2 33586464 . C CT,CTT 375.13 PASS AC=2,0;AF=0.557,0.023;AN=2;DP=1732;set=Intersection GT:DP:GQ:SB 1/1:45:29:2,2,25,16 chr2 33614187 . C T 1206.71 PASS AC=1;AF=0.703;AN=2;DP=1551;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,21:44:99:545,0,605:16,7,13,8 chr2 33623288 . T C 31.43 PASS AC=2;AF=0.708;AN=2;DP=799;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant27-variant29-variant30-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:1341,96,0:0,0,29,3 chr2 33623306 . C T 218.6 PASS AC=1;AF=0.655;AN=2;DP=878;MQ=60;set=variant2-variant3-variant4-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant23-variant24-variant29-variant30-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,27:44:99:874,0,501:14,3,23,4 chr2 33623387 . A G 1261.16 PASS AC=2;AF=0.775;AN=2;DP=3885;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,111:111:99:4995,334,0:0,0,66,45 chr2 33623388 . T C 1261.16 PASS AC=2;AF=0.775;AN=2;DP=3924;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,111:111:99:4995,334,0:0,0,66,45 chr2 33623734 . A G 2200.24 PASS AC=2;AF=0.775;AN=2;DP=6731;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,163:163:99:5285,489,0:0,0,96,67 chr2 33623851 . A G 2510.36 PASS AC=1;AF=0.5;AN=2;DP=1491;MQ=60;set=variant7-variant15-variant16-variant33-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:132,117:249:99:2681,0,3027:61,71,52,65 chr2 33624279 . G A 3761.42 PASS AC=1;AF=0.5;AN=2;DP=1801;MQ=60;set=variant7-variant15-variant16-variant33-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:172,160:332:99:3762,0,4612:80,92,81,79 chr2 33643740 . T G 275.02 PASS AC=1;AF=0.559;AN=2;DP=1825;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant32-variant34-variant35-variant36-variant37-filterInvariant38-filterInvariant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,12:42:99:153,0,857:12,18,3,9 chr2 33701795 . C CCT 79.62 PASS AC=2;AF=0.889;AN=2;DP=181;FS=0;set=variant3-variant5-variant7-variant9-variant11-variant20-variant21-variant22-variant23-variant27-variant29-variant30-variant33-variant35-variant36-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:32:465,32,0:0,0,3,8 chr2 33701825 . CGTGTGTGTGTGTGTGT CGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT,CGTGCGTGTGTGTGTGTGTGTGTGT,CGTGT,CGTGTGTGTGTGTGTGTGT,CGTGTGTGTGTGTGTGTGTGT,CGTGCGTGTGTGTGTGTGTGTGTGTGT,CGTGCGTGTGTGTGTGTGTGTGT,CGTGTGT,CGTGTGTGTGTGTGTGTGTGTGT,CGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT,CGTGTGTGTGTGTGTGTGTGTGTGTGTGT,CGTGTGTGTGTGTGTGTGTGTGTGT,C,CGTGTGTGTGTGT 52.73 PASS AC=0,0,0,0,0,2,0,0,0,0,0,0,0,0;AF=0.043,0.261,0.087,0.043,0.043,0.13,0.043,0.087,0.022,0.043,0.043,0.022,0.022,0.022;AN=2;DP=150;FS=0;set=variant4-variant5-variant6-variant7-variant8-variant10-variant20-variant22-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 6/6:10:23:0,1,2,7 chr2 33736857 . G A 4239.47 PASS AC=2;AF=0.943;AN=2;DP=10858;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,176:176:99:5175,527,0:0,0,84,92 chr2 33736931 . C T 779.89 PASS AC=1;AF=0.5;AN=2;DP=98;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.586;QD=7.96;ReadPosRankSum=1.495;SOR=0.703;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:61,37:98:99:808,0,1512:25,36,15,22 chr2 33744958 . C T 137.2 PASS AC=1;AF=0.692;AN=2;DP=1445;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,10:27:99:247,0,510:11,6,7,3 chr2 33745208 . T C 903.59 PASS AC=1;AF=0.639;AN=2;DP=2771;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,55:94:99:1310,0,933:15,24,25,30 chr2 33745336 . T C 401.26 PASS AC=2;AF=0.779;AN=2;DP=769;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:854,63,0:0,0,8,13 chr2 33745402 . A G 517.45 PASS AC=1;AF=0.6;AN=2;DP=795;set=variant-variant2-variant3-variant4-variant7-variant8-variant9-variant12-variant13-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant38-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:8,19:27:99:542,0,171:5,3,13,6 chr2 33752129 . GC G 409.15 PASS AC=1;AF=0.5;AN=2;DP=239;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant6-variant10-variant17-variant18-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:16,9:25:99:262,0,523:10,6,7,2 chr2 33764286 . T C 1101.21 PASS AC=1;AF=0.613;AN=2;DP=2809;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant38-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:46,52:98:99:1176,0,976:20,26,25,27 chr2 33784135 . A G 1097.17 PASS AC=1;AF=0.5;AN=2;DP=780;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant6-variant10-variant17-variant35-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,45:82:99:1300,0,908:19,18,26,19 chr2 33784161 . G A 686.8 PASS AC=1;AF=0.558;AN=2;DP=2416;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant8-variant10-variant12-variant13-variant14-variant16-variant17-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant38 GT:AD:DP:GQ:PL:SB 0/1:58,35:93:99:806,0,1507:28,30,19,16 chr2 33784371 . G A 284.34 PASS AC=1;AF=0.5;AN=2;DP=161;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant6-variant10-variant17-variant35-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,11:23:99:342,0,312:6,6,2,9 chr2 33784500 . G A 114.91 PASS AC=1;AF=0.565;AN=2;DP=270;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant7-variant8-variant10-variant12-variant13-variant14-variant16-variant17-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:6,11:17:99:328,0,159:5,1,9,2 chr2 33784801 . G A 330.49 PASS AC=1;AF=0.5;AN=2;DP=337;MQ=60;set=variant2-variant4-variant5-variant6-variant10-variant17-variant35-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,17:31:99:433,0,375:5,9,5,12 chr2 33787976 . CCTAA C 8913.87 PASS AC=2;AF=0.955;AN=2;DP=7956;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,163:164:99:7229,449,0:0,1,91,72 chr2 33788060 . CTT C 12404.8 PASS AC=2;AF=0.779;AN=2;DP=10433;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,204:204:99:8680,614,0:0,0,108,96 chr2 33788156 . C T 2939.85 PASS AC=1;AF=0.523;AN=2;DP=4101;MQ=60;set=variant-variant4-variant7-variant9-variant11-variant12-variant14-variant15-variant17-variant18-variant23-variant25-variant27-variant28-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:94,109:203:99:2956,0,2525:43,51,50,59 chr2 33788270 . CTTGTT C 7850.65 PASS AC=2;AF=0.775;AN=2;DP=8068;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,176:176:99:7771,531,0:0,0,89,87 chr2 33788655 . C T 4747.33 PASS AC=1;AF=0.589;AN=2;DP=5538;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant8-variant11-variant12-variant13-variant16-variant17-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:107,92:199:99:3535,0,9565:63,44,54,38 chr2 33788659 . T TAACA 4896.89 PASS AC=1;AF=0.538;AN=2;DP=5160;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant8-variant12-variant13-variant16-variant17-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant32-variant34-variant35-variant36-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:114,92:206:99:3574,0,9608:68,46,55,37 chr2 33789032 . A G 501.78 PASS AC=1;AF=0.5;AN=2;DP=369;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant7-variant17-variant29-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:30,27:57:99:736,0,763:15,15,10,17 chr2 33789068 . C G 506.61 PASS AC=1;AF=0.591;AN=2;DP=1071;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant16-variant17-variant18-variant23-variant27-variant28-variant29-variant35-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:36,21:57:99:590,0,808:18,18,8,13 chr2 33789534 . A G,AAT 5663.48 PASS AC=1,0;AF=0.55,0.075;AN=2;DP=3079;set=variant5-variant7-variant8-variant10-variant16-variant17-variant18-variant23-variant27-variant28-variant29-variant33-variant35-variant37-variant39-variant40-variant41-variant2-variant42-variant43 GT:DP:GQ:SB 0/1:178:99:54,36,53,35 chr2 33809294 . A G 7915.31 PASS AC=2;AF=0.81;AN=2;DP=10215;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,258:258:99:8263,773,0:0,0,120,138 chr2 33811936 . A T 49.73 PASS AC=1;AF=0.6;AN=2;DP=31;FractionInformativeReads=1;MQ=60;set=variant4-variant17-variant35-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:2,2:4:37:78,0,37:1,1,0,2 chr2 33952055 . C G 121.69 PASS AC=1;AF=0.7;AN=2;DP=876;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,10:21:99:343,0,310:8,3,9,1 chr2 33952413 . T C 2220.97 PASS AC=1;AF=0.779;AN=2;DP=9472;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:118,123:241:99:2940,0,2725:64,54,70,53 chr2 33952456 . C G 5937.4 PASS AC=2;AF=1;AN=2;DP=10894;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,263:263:99:7938,786,0:0,0,146,117 chr2 33952621 . G A 5438.6 PASS AC=1;AF=0.578;AN=2;DP=13690;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant25-variant26-variant27-variant29-variant30-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:277,250:527:99:5745,0,6934:155,122,135,115 chr2 35696612 . C T 1645.5 PASS AC=2;AF=1;AN=2;DP=3045;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:2273,230,0:0,0,30,47 chr2 36583461 . G T 413.37 PASS AC=1;AF=0.5;AN=2;DP=329;FractionInformativeReads=1;MQ=60;set=variant2-variant24-variant31-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,32:66:99:725,0,835:21,13,22,10 chr2 36605585 . A G 3455.52 PASS AC=1;AF=0.769;AN=2;DP=3660;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,52:102:99:1465,0,1383:27,23,26,26 chr2 36605676 . A AT 1407.25 PASS AC=1;AF=0.579;AN=2;DP=2548;MQ=60;set=variant-variant2-variant4-variant11-variant12-variant18-variant19-variant24-variant29-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:87,70:157:99:1476,0,1919:50,37,42,28 chr2 36605949 . GT GTT,G,GGTTT,GGTTTT,GTTT,GGTT 76.18 PASS AC=0,1,0,0,0,0;AF=0.077,0.212,0.135,0.038,0.019,0.058;AN=2;DP=1979;set=filterInvariant-filterInvariant3-filterInvariant5-variant6-variant7-variant9-variant10-filterInvariant11-variant14-filterInvariant15-filterInvariant16-variant17-filterInvariant22-variant23-filterInvariant24-filterInvariant26-variant29-variant30-variant32-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant39-variant42-variant43 GT:DP:GQ:SB 0/2:50:99:12,20,2,16 chr2 36668395 . T A 2630.99 PASS AC=1;AF=0.567;AN=2;DP=1599;MQ=60;set=variant2-variant6-variant8-variant11-variant12-variant14-variant18-variant24-variant25-variant31-variant33-variant35-variant37-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:53,57:110:99:1376,0,1376:27,26,35,22 chr2 36668846 . G A 810.14 PASS AC=1;AF=0.567;AN=2;DP=366;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant8-variant11-variant12-variant14-variant18-variant24-variant25-variant31-variant33-variant35-variant37-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:14,9:23:99:203,0,390:5,9,4,5 chr2 36669645 . T C 3859.97 PASS AC=1;AF=0.563;AN=2;DP=2042;MQ=60;set=variant2-variant6-variant8-variant11-variant12-variant14-variant18-variant21-variant24-variant25-variant31-variant33-variant35-variant37-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:63,64:127:99:1584,0,1472:36,27,35,29 chr2 36669670 . C A 4420.39 PASS AC=1;AF=0.567;AN=2;DP=2147;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant8-variant11-variant12-variant14-variant18-variant24-variant25-variant31-variant33-variant35-variant37-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:75,67:142:99:1712,0,1718:43,32,37,30 chr2 36704144 . C T 722.77 PASS AC=1;AF=0.779;AN=2;DP=3059;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,34:85:99:850,0,1351:24,27,16,18 chr2 36706511 . G C 248.2 PASS AC=1;AF=0.529;AN=2;DP=265;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant9-variant11-variant13-variant17-variant20-variant24-variant25-variant29-variant31-variant35-variant37-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:7,8:15:99:297,0,229:5,2,8,0 chr2 36739553 . T C 508.61 PASS AC=1;AF=0.857;AN=2;DP=1684;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,22:49:99:591,0,701:11,16,6,16 chr2 36756288 . T C 996.81 PASS AC=1;AF=0.849;AN=2;DP=4035;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,60:97:99:1422,0,799:19,18,27,33 chr2 36775410 . CTT CT,CTTT,CTTTTT,CTTTT,C,CTTTTTT 230.62 PASS AC=1,0,0,0,0,0;AF=0.227,0.182,0.015,0.091,0.03,0.015;AN=2;DP=2185;set=variant-variant2-variant3-variant4-variant6-variant7-variant9-variant12-variant13-filterInvariant14-variant16-variant17-variant18-variant19-filterInvariant20-variant21-variant23-variant24-variant25-variant26-variant27-filterInvariant29-variant33-variant34-filterInvariant35-variant36-variant37-variant39-variant40-variant41-variant42-filterInvariant43-variant44 GT:DP:GQ:SB 0/1:74:99:29,27,6,12 chr2 36777184 . ATGTGTGTGTGTG ATGTGTGTGTG,A,ATGTGTGTGTGTGTG 117.7 PASS AC=1,0,0;AF=0.333,0.056,0.111;AN=2;DP=1138;set=variant-variant2-filterInvariant3-variant5-variant8-variant9-variant13-filterInvariant15-filterInvariant21-variant27-variant28-variant29-variant33-filterInvariant35-variant37-variant41-variant43-filterInvariant44 GT:DP:GQ:SB 0/1:48:77:24,17,2,5 chr2 36777377 . ATT AT,A 2564.51 PASS AC=1,0;AF=0.432,0.114;AN=2;DP=14734;set=Intersection GT:DP:GQ:SB 0/1:284:99:93,70,59,62 chr2 36824956 . G GC 148.48 PASS AC=2;AF=1;AN=2;DP=1019;FS=0;MQ=60;MQRankSum=1.22;ReadPosRankSum=1.605;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,22:22:69:838,69,0:0,0,14,8 chr2 36825330 . C CG,CGGCCCAGCCCG 645.07 PASS AC=2,0;AF=0.92,0.068;AN=2;DP=935;MQRankSum=0.693;ReadPosRankSum=-0.945;set=Intersection GT:DP:GQ:SB 1/1:22:66:0,0,9,13 chr2 36923898 . G T 1969.37 PASS AC=2;AF=0.989;AN=2;DP=2257;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,50:51:99:1583,141,0:1,0,35,15 chr2 36924177 . C T 1058.62 PASS AC=2;AF=0.989;AN=2;DP=1053;FS=0;MQ=60;MQRankSum=-1.01;ReadPosRankSum=-0.818;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:1105,78,0:0,0,1,25 chr2 36943338 . C G 508.65 PASS AC=2;AF=0.989;AN=2;DP=1260;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.692;ReadPosRankSum=0.361;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1252,114,0:0,0,29,9 chr2 36943419 . T C 2814.43 PASS AC=2;AF=0.989;AN=2;DP=4098;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,114:114:99:3314,341,0:0,0,62,52 chr2 36986549 . A G 5079.56 PASS AC=2;AF=1;AN=2;DP=7320;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:2,181:183:99:5398,499,0:1,1,75,106 chr2 37000797 . C G 156.22 PASS AC=2;AF=0.929;AN=2;DP=63;FS=0;FractionInformativeReads=1;MQ=60;set=variant5-variant11-variant12-variant16-variant17-variant21-variant24-variant26-variant27-variant28-variant29-variant35-variant37-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:135,9,0:0,0,2,1 chr2 37000877 . A T 204.17 PASS AC=1;AF=0.625;AN=2;DP=128;FractionInformativeReads=1;MQ=60;set=variant5-variant8-variant12-variant14-variant15-variant17-variant22-variant25-variant27-variant28-variant31-variant35-variant38-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,5:11:99:124,0,109:3,3,3,2 chr2 37001570 . C T 1738.09 PASS AC=2;AF=0.977;AN=2;DP=1685;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1606,159,0:0,0,22,31 chr2 37010574 . G A 1494.5 PASS AC=2;AF=0.808;AN=2;DP=5138;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,158:158:99:4774,473,0:0,0,81,77 chr2 37032451 . GA GAA,G 48 PASS AC=1,0;AF=0.462,0.077;AN=2;DP=147;MQ=60;set=variant2-variant4-variant6-variant12-variant13-variant21-variant27-variant28-variant32-variant34-variant35-variant38-variant40 GT:DP:GQ:SB 0/1:11:19:3,0,7,1 chr2 37072266 . C G 8607.69 PASS AC=2;AF=0.919;AN=2;DP=11870;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,251:251:99:7948,751,0:0,0,134,117 chr2 37073027 . AACACACACACACACACACACACGCATGCATGCACACACAC AACACACACACACACACACACGCATGCATGCACACACAC,AACACACAC,AACACACACACACACACACGCATGCATGCACACACAC,A,AACACAC 97.04 PASS AC=2,0,0,0,0;AF=0.662,0.088,0.015,0.029,0.059;AN=2;DP=410;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant42-variant44 GT:DP:GQ:SB 1/1:9:27:0,0,2,7 chr2 37073058 . GCACACACACACA GCACACA,G,GCACA,GCACACACA,GCA 216.31 PASS AC=0,0,0,0,1;AF=0.604,0.083,0.063,0.042,0.021;AN=2;DP=243;set=variant3-variant5-variant6-variant7-variant8-variant10-variant11-variant14-variant15-variant16-variant17-variant21-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant40-variant44 GT:DP:GQ:SB 0/5:4:3:0,1,2,1 chr2 37073172 . AT ATT,A 230.62 PASS AC=2,0;AF=0.91,0.013;AN=2;DP=520;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43 GT:DP:GQ:SB 1/1:12:36:0,0,8,4 chr2 37073809 . T C 12371.9 PASS AC=2;AF=0.989;AN=2;DP=17416;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,405:405:99:11783,1213,0:0,0,212,193 chr2 37074951 . G A 12707.1 PASS AC=2;AF=0.919;AN=2;DP=18839;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,396:396:99:11850,1186,0:0,0,166,230 chr2 37075397 . T G 6727.2 PASS AC=2;AF=0.919;AN=2;DP=7614;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,201:201:99:6381,602,0:0,0,123,78 chr2 37075870 . T G 2762.06 PASS AC=1;AF=0.5;AN=2;DP=232;FS=0.475;FractionInformativeReads=1;MQ=60;MQRankSum=1.139;QD=11.91;ReadPosRankSum=-0.297;SOR=0.695;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:119,113:232:99:2790,0,2941:59,60,57,56 chr2 37077015 . C A 193.47 PASS AC=2;AF=1;AN=2;DP=541;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:647,51,0:0,0,4,13 chr2 37078095 . A ATT,AT 252.89 PASS AC=0,1;AF=0.378,0.451;AN=2;DP=590;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:18:9:2,1,12,3 chr2 37094945 . A G 1880.62 PASS AC=2;AF=0.966;AN=2;DP=2637;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:1580,165,0:0,0,30,25 chr2 37096970 . C T 328.4 PASS AC=2;AF=0.939;AN=2;DP=322;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:184,15,0:0,0,1,4 chr2 37105262 . G A 307.52 PASS AC=1;AF=0.5;AN=2;DP=43;FS=0;FractionInformativeReads=1;MQ=60;set=variant14-variant35 GT:AD:DP:GQ:PL:SB 0/1:16,3:19:74:74,0,609:1,15,0,3 chr2 37111045 . T A 592.47 PASS AC=2;AF=0.688;AN=2;DP=1194;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1241,114,0:0,0,25,13 chr2 37129618 . A ATAAT 131.34 PASS AC=2;AF=1;AN=2;DP=70;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant7-variant10-variant11-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:135,9,0:0,0,3,0 chr2 37193647 . AGCGGAGGCAACAGCG A 505.04 PASS AC=1;AF=0.5;AN=2;DP=38;FS=8.008;FractionInformativeReads=0.868;MQ=60;MQRankSum=1.79;QD=13.29;ReadPosRankSum=1.609;SOR=1.861;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:18,15:33:99:542,0,2650:10,8,4,11 chr2 37292890 . T G 1109.12 PASS AC=1;AF=0.523;AN=2;DP=1600;MQ=60;set=variant3-variant4-variant5-variant7-variant9-variant11-variant15-variant16-variant17-variant19-variant21-variant24-variant25-variant29-variant30-variant31-variant35-variant36-variant37-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:29,39:68:99:1064,0,709:16,13,25,14 chr2 37297329 . C G 862.41 PASS AC=1;AF=0.523;AN=2;DP=1046;MQ=60;set=variant3-variant4-variant5-variant7-variant9-variant11-variant15-variant16-variant17-variant19-variant21-variant24-variant25-variant29-variant30-variant31-variant35-variant36-variant37-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:22,14:36:99:392,0,656:16,6,11,3 chr2 37299145 . G A 559.62 PASS AC=1;AF=0.583;AN=2;DP=889;FractionInformativeReads=1;set=variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant19-variant21-variant24-variant25-variant27-variant29-variant30-variant31-variant35-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:24,18:42:99:488,0,824:20,4,14,4 chr2 37302556 . GA G 910.68 PASS AC=2;AF=0.989;AN=2;DP=1688;MQ=60;MQRankSum=0.161;ReadPosRankSum=-0.023;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1169,117,0:0,0,27,12 chr2 37306151 . G A 1061.39 PASS AC=1;AF=0.528;AN=2;DP=1265;set=variant4-variant5-variant7-variant11-variant15-variant16-variant17-variant19-variant21-variant24-variant25-variant29-variant30-variant31-variant35-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:19,31:50:99:836,0,501:12,7,19,12 chr2 37306343 . G A 1638.48 PASS AC=2;AF=0.989;AN=2;DP=2258;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:1778,171,0:0,0,26,31 chr2 37317869 . C T 1573.73 PASS AC=2;AF=0.989;AN=2;DP=2152;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1550,147,0:0,0,21,28 chr2 37318041 . A G 151.77 PASS AC=2;AF=0.811;AN=2;DP=213;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:135,9,0:0,0,0,3 chr2 37319211 . A G 1923.2 PASS AC=1;AF=0.5;AN=2;DP=971;FractionInformativeReads=1;MQ=60;set=variant4-variant11-variant19-variant21-variant25-variant31-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:49,50:99:99:1173,0,1208:26,23,29,21 chr2 37324096 . T TC 6232.56 PASS AC=2;AF=0.966;AN=2;DP=9025;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,219:219:99:7124,662,0:0,0,130,89 chr2 37325108 . T C 484.08 PASS AC=1;AF=0.686;AN=2;DP=679;FractionInformativeReads=1;set=variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,15:19:42:402,0,42:2,2,5,10 chr2 37325495 . GTA G 471.24 PASS AC=2;AF=0.68;AN=2;DP=335;set=variant-variant4-variant5-variant6-variant7-variant8-variant10-variant16-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:515,45,0:0,0,13,2 chr2 37325510 . T G 183.1 PASS AC=1;AF=0.5;AN=2;DP=421;set=variant-variant4-variant6-variant8-variant13-variant16-variant25-variant26-variant28-variant31-variant34-variant35-variant36-variant42 GT:AD:DP:GQ:PL:SB 0/1:15,9:24:99:175,0,358:12,3,8,1 chr2 37325512 . T G 1357.29 PASS AC=2;AF=0.7;AN=2;DP=771;set=variant-variant4-variant6-variant8-variant9-variant10-variant13-variant16-variant17-variant21-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:1194,96,0:0,0,26,6 chr2 37325780 . A G 1567.42 PASS AC=2;AF=0.66;AN=2;DP=1513;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant14-variant16-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,57:59:99:1976,127,0:1,1,18,39 chr2 37327244 . A G 1334.04 PASS AC=2;AF=0.817;AN=2;DP=2557;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:2120,215,0:0,0,43,29 chr2 37327684 . A C 12726.2 PASS AC=2;AF=0.821;AN=2;DP=15464;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,363:363:99:10996,1088,0:0,0,173,190 chr2 37327806 . C T 5766.65 PASS AC=2;AF=0.625;AN=2;DP=3718;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant14-variant16-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant34-variant35-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,170:172:99:5384,465,0:1,1,59,111 chr2 37328362 . G T 11472.9 PASS AC=2;AF=0.989;AN=2;DP=12368;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,302:302:99:9336,904,0:0,0,165,137 chr2 37329534 . A C 11878.6 PASS AC=2;AF=0.966;AN=2;DP=16627;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,374:374:99:11529,1120,0:0,0,186,188 chr2 37331841 . CT C 329.91 PASS AC=1;AF=0.5;AN=2;DP=12128;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant8-variant9-filterInvariant10-filterInvariant13-filterInvariant14-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant21-filterInvariant22-filterInvariant24-filterInvariant26-filterInvariant28-filterInvariant30-filterInvariant31-filterInvariant33-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant38-filterInvariant39-filterInvariant40-filterInvariant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:297,57:354:99:159,0,6505:142,155,26,31 chr2 37333711 . CT CTT,C 427.69 PASS AC=0,1;AF=0.293,0.207;AN=2;DP=11656;set=filterInvariant-variant2-filterInvariant3-variant4-variant5-filterInvariant6-variant7-filterInvariant8-filterInvariant9-variant10-variant11-variant12-filterInvariant13-filterInvariant14-variant15-variant16-variant17-filterInvariant18-variant19-filterInvariant20-variant21-filterInvariant22-variant24-variant25-filterInvariant26-filterInvariant28-variant29-variant30-variant31-filterInvariant32-filterInvariant33-variant35-filterInvariant36-filterInvariant37-filterInvariant38-variant39-filterInvariant40-filterInvariant41-filterInvariant42-variant43-filterInvariant44 GT:DP:GQ:SB 0/2:265:99:65,89,43,68 chr2 37342456 . T C 247.45 PASS AC=2;AF=0.977;AN=2;DP=1411;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1119,108,0:0,0,20,16 chr2 37373982 . A AT 5011.96 PASS AC=2;AF=0.977;AN=2;DP=4178;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,83:84:99:3275,215,0:1,0,45,38 chr2 37375932 . G A 2723.23 PASS AC=1;AF=0.641;AN=2;DP=2508;MQ=60;set=variant-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,28:67:99:778,0,1024:23,16,17,11 chr2 37376291 . G A 3613.16 PASS AC=1;AF=0.591;AN=2;DP=4476;MQ=60;set=variant-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,77:137:99:1935,0,1349:28,32,45,32 chr2 37384283 . A G 681.13 PASS AC=1;AF=0.641;AN=2;DP=1102;MQ=60;set=variant-variant5-variant6-variant7-variant8-variant9-variant10-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-filterInvariant30-variant31-variant32-variant33-variant34-variant35-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,21:50:99:499,0,1028:9,20,6,15 chr2 37384296 . A C 1352.31 PASS AC=1;AF=0.75;AN=2;DP=483;MQ=60;set=variant2-variant3-variant4-variant9-variant11-variant13-variant19-variant21-variant25-variant29-variant31-variant35-variant36-variant37-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:16,21:37:99:684,0,569:3,13,5,16 chr2 37402270 . C G 1453.69 PASS AC=1;AF=0.621;AN=2;DP=1277;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,34:45:99:843,0,179:7,4,20,14 chr2 37402373 . A G 1744.72 PASS AC=1;AF=0.621;AN=2;DP=1815;MQ=60;set=variant-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,35:64:99:825,0,589:15,14,16,19 chr2 37406644 . A G 872.16 PASS AC=1;AF=0.679;AN=2;DP=1447;MQ=60;set=variant2-variant3-variant4-variant11-variant13-variant15-variant19-variant25-variant29-variant30-variant35-variant36-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:60,36:96:99:746,0,1408:29,31,20,16 chr2 37406680 . C G 839.75 PASS AC=1;AF=0.679;AN=2;DP=1383;MQ=60;set=variant2-variant3-variant4-variant11-variant13-variant15-variant19-variant25-variant29-variant30-variant35-variant36-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:61,38:99:99:850,0,1500:28,33,19,19 chr2 37406761 . T C 249.41 PASS AC=1;AF=0.679;AN=2;DP=631;MQ=60;set=variant2-variant3-variant4-variant11-variant13-variant15-variant19-variant25-variant29-variant30-variant35-variant36-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:30,26:56:99:679,0,743:11,19,8,18 chr2 37406807 . A G 132.56 PASS AC=1;AF=0.692;AN=2;DP=283;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant11-variant15-variant19-variant25-variant29-variant30-variant35-variant36-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,13:26:99:336,0,453:5,8,4,9 chr2 37410537 . C T 2329.48 PASS AC=1;AF=0.706;AN=2;DP=1843;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,38:71:99:1001,0,830:22,11,25,13 chr2 37414431 . A C 2316.12 PASS AC=1;AF=0.617;AN=2;DP=2010;MQ=60;set=variant-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,28:68:99:596,0,1004:21,19,17,11 chr2 37415496 . G C 1457.72 PASS AC=2;AF=0.81;AN=2;DP=1575;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1211,111,0:0,0,25,12 chr2 37425629 . A G 292.45 PASS AC=1;AF=0.609;AN=2;DP=818;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,12:37:99:301,0,620:15,10,9,3 chr2 37428743 . C T 3911.16 PASS AC=1;AF=0.786;AN=2;DP=4678;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,59:124:99:1320,0,1608:33,32,31,28 chr2 37429382 . GT G,GTT 258.74 PASS AC=1,0;AF=0.417,0.083;AN=2;DP=6157;set=filterInvariant-filterInvariant2-filterInvariant5-filterInvariant6-filterInvariant9-filterInvariant12-filterInvariant22-filterInvariant23-filterInvariant27-filterInvariant29-filterInvariant33-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant39-variant40-variant42 GT:DP:GQ:SB 0/1:325:99:121,149,27,28 chr2 37431420 . ATTT ATT,AT,A 111.29 PASS AC=0,1,0;AF=0.4,0.233,0.033;AN=2;DP=210;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant14-variant15-variant17-variant31-variant35-variant40-variant42 GT:DP:GQ:SB 0/2:9:23:0,2,0,7 chr2 37431640 . TG T 592.73 PASS AC=1;AF=0.606;AN=2;DP=583;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,5:10:99:192,0,378:4,1,4,1 chr2 37431646 . C G 638.22 PASS AC=1;AF=0.606;AN=2;DP=640;FractionInformativeReads=1;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,6:12:99:225,0,375:5,1,5,1 chr2 37438274 . T C 522.86 PASS AC=1;AF=0.5;AN=2;DP=168;FractionInformativeReads=1;MQ=60;set=variant5-variant14-variant15-variant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:11,19:30:99:507,0,268:3,8,6,13 chr2 37438993 . G A 1694.48 PASS AC=1;AF=0.621;AN=2;DP=1501;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,13:33:99:429,0,560:14,6,10,3 chr2 37455232 . C A 1341.78 PASS AC=1;AF=0.5;AN=2;DP=134;FS=0.654;FractionInformativeReads=1;MQ=60;MQRankSum=-0.752;QD=10.01;ReadPosRankSum=-2.059;SOR=0.631;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:76,58:134:99:1370,0,2035:29,47,23,35 chr2 37456032 . C T 4529.06 PASS AC=2;AF=0.955;AN=2;DP=4956;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,109:109:99:3350,326,0:0,0,63,46 chr2 37458711 . G A 1803.5 PASS AC=1;AF=0.617;AN=2;DP=4641;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:100,84:184:99:2141,0,2521:48,52,41,43 chr2 37475976 . G C 907.08 PASS AC=1;AF=0.694;AN=2;DP=768;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,8:19:99:291,0,370:10,1,6,2 chr2 37476057 . C CA 2089.39 PASS AC=1;AF=0.689;AN=2;DP=2817;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:36,47:83:99:1056,0,746:22,14,31,16 chr2 37477794 . C A 5605.71 PASS AC=1;AF=0.78;AN=2;DP=6379;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:82,68:150:99:1534,0,1944:48,34,38,30 chr2 37479756 . C T 7229.12 PASS AC=1;AF=0.6;AN=2;DP=6037;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:91,116:207:99:3040,0,2401:50,41,61,55 chr2 37479862 . C T 7830.01 PASS AC=1;AF=0.78;AN=2;DP=9145;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:106,120:226:99:2662,0,2351:43,63,48,72 chr2 37479959 . A C 2175.84 PASS AC=1;AF=0.78;AN=2;DP=2148;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:29,23:52:99:681,0,850:7,22,4,19 chr2 37480249 . A G 12743.7 PASS AC=1;AF=0.583;AN=2;DP=8582;MQ=60;set=variant-variant5-variant6-variant8-variant10-variant12-variant14-variant15-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:184,158:342:99:3828,0,5161:87,97,76,82 chr2 37518045 . G C 4231.07 PASS AC=1;AF=0.6;AN=2;DP=4397;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:56,90:146:99:2164,0,1157:30,26,45,45 chr2 37545203 . T G 370.77 PASS AC=1;AF=0.589;AN=2;DP=326;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant10-variant11-variant12-variant14-variant15-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:6,7:13:99:211,0,232:0,6,1,6 chr2 37571752 . G A 2637.77 PASS AC=2;AF=1;AN=2;DP=4691;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,131:131:99:3963,390,0:0,0,80,51 chr2 37586681 . A G 738.87 PASS AC=1;AF=0.64;AN=2;DP=865;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant7-variant9-variant10-variant13-variant15-variant16-variant18-variant20-variant21-variant24-variant26-variant27-variant29-variant30-variant32-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:17,9:26:99:246,0,425:11,6,7,2 chr2 37600292 . C A 11926.6 PASS AC=2;AF=0.955;AN=2;DP=17208;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,389:389:99:11582,1164,0:0,0,190,199 chr2 37869039 . AT A,ATT 2376.33 PASS AC=1,0;AF=0.474,0.105;AN=2;DP=5261;MQ=60;set=variant2-variant4-variant6-variant9-variant10-variant13-variant15-variant18-variant21-variant22-variant25-variant26-variant29-variant35-variant36-variant37-variant38-variant39-variant42 GT:DP:GQ:SB 0/1:269:99:57,51,93,68 chr2 37869494 . G T 954.59 PASS AC=1;AF=0.6;AN=2;DP=1488;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant7-variant9-variant10-variant13-variant18-variant21-variant22-variant25-variant26-variant29-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:36,42:78:99:1165,0,1192:18,18,18,24 chr2 37870508 . C G 874.64 PASS AC=1;AF=0.6;AN=2;DP=1164;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant7-variant9-variant10-variant13-variant18-variant21-variant22-variant25-variant26-variant29-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:32,23:55:99:585,0,941:21,11,14,9 chr2 37870937 . C G 1087.34 PASS AC=1;AF=0.6;AN=2;DP=1715;MQ=60;set=variant2-variant4-variant7-variant9-variant10-variant13-variant18-variant21-variant22-variant25-variant26-variant29-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:40,24:64:99:674,0,1071:17,23,8,16 chr2 37871116 . ATTTTTT ATTTTT,AT,ATT,A 62.14 PASS AC=0,1,0,0;AF=0.1,0.233,0.267,0.033;AN=2;DP=168;MQ=60;set=variant7-variant8-variant9-variant10-variant13-variant14-variant22-variant25-variant26-variant29-variant31-variant35-variant36-variant37-variant42 GT:DP:GQ:SB 0/2:6:99:1,2,1,2 chr2 37871277 . C T 350.8 PASS AC=1;AF=0.5;AN=2;DP=24;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.193;QD=14.62;ReadPosRankSum=0.537;SOR=0.883;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:9,15:24:99:379,0,214:5,4,9,6 chr2 37871663 . C T 1061.21 PASS AC=1;AF=0.5;AN=2;DP=890;MQ=60;set=variant2-variant9-variant13-variant18-variant29-variant35-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:64,59:123:99:1405,0,1749:38,26,36,23 chr2 37871766 . TAA TA,T 823.93 PASS AC=1,0;AF=0.5,0.023;AN=2;DP=8893;set=Intersection GT:DP:GQ:SB 0/1:184:99:33,29,75,47 chr2 37872139 . G A 3624.02 PASS AC=1;AF=0.563;AN=2;DP=5452;MQ=60;set=variant2-variant4-variant9-variant10-variant13-variant18-variant21-variant22-variant25-variant26-variant29-variant35-variant36-variant37-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:196,153:349:99:3723,0,4828:96,100,73,80 chr2 37872508 . G A 1845.49 PASS AC=1;AF=0.563;AN=2;DP=2954;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant9-variant10-variant13-variant18-variant21-variant22-variant25-variant26-variant29-variant35-variant36-variant37-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:74,69:143:99:1596,0,1823:43,31,35,34 chr2 37872871 . C T 7145.31 PASS AC=1;AF=0.5;AN=2;DP=4055;MQ=60;set=variant2-variant9-variant13-variant18-variant29-variant35-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:313,233:546:99:5268,0,7710:177,136,127,106 chr2 37898963 . CG CAG,CGGG,C 682.73 PASS AC=2,0,0;AF=0.864,0.068,0.011;AN=2;DP=1169;MQ=60;set=Intersection GT:DP:GQ:SB 1/1:29:90:0,0,17,12 chr2 37898965 . G GGGT 263.23 PASS AC=2;AF=0.737;AN=2;DP=1015;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:1329,90,0:0,0,18,12 chr2 37899310 . A G 357.16 PASS AC=2;AF=0.718;AN=2;DP=2641;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:2104,216,0:0,0,28,44 chr2 37899418 . A G 377.44 PASS AC=2;AF=0.939;AN=2;DP=537;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:663,54,0:0,0,5,13 chr2 38152509 . G C 1411.82 PASS AC=1;AF=0.614;AN=2;DP=2668;MQ=60;set=variant2-variant3-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:85,72:157:99:1595,0,2048:46,39,38,34 chr2 38156133 . G A 3561.5 PASS AC=2;AF=0.966;AN=2;DP=4410;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,106:106:99:4080,317,0:0,0,8,98 chr2 38177525 . A C 1655.5 PASS AC=1;AF=0.65;AN=2;DP=1204;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant9-variant11-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant35-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,18:46:99:426,0,723:18,10,13,5 chr2 38178406 . A G 2336.49 PASS AC=1;AF=0.633;AN=2;DP=2130;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant9-variant11-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant35-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,31:81:99:764,0,1167:30,20,20,11 chr2 38179134 . G A 3462.36 PASS AC=2;AF=1;AN=2;DP=5065;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,116:116:99:3581,345,0:0,0,59,57 chr2 38179414 . CTG C 11420.8 PASS AC=1;AF=0.643;AN=2;DP=6183;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant9-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant35-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:119,123:242:99:4803,0,4751:65,54,68,55 chr2 38179773 . A G 10535.6 PASS AC=2;AF=0.884;AN=2;DP=13513;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,315:315:99:9795,944,0:0,0,143,172 chr2 38180069 . G C 1219.77 PASS AC=2;AF=0.893;AN=2;DP=1609;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:1016,90,0:0,0,17,13 chr2 38180088 . G A 1287.68 PASS AC=2;AF=0.784;AN=2;DP=1577;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1365,108,0:0,0,20,16 chr2 38180091 . A G 1093.82 PASS AC=1;AF=0.579;AN=2;DP=796;MQ=60;set=variant3-variant6-variant7-variant8-variant10-variant13-variant14-variant15-variant16-variant18-variant19-variant25-variant29-variant31-variant32-variant33-variant34-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:21,15:36:99:423,0,620:11,10,9,6 chr2 38208233 . T C 1017.38 PASS AC=1;AF=0.655;AN=2;DP=718;MQ=60;set=variant3-variant5-variant6-variant7-variant8-variant10-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:8,8:16:99:297,0,254:7,1,8,0 chr2 38208606 . A T 387.56 PASS AC=1;AF=0.583;AN=2;DP=288;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant7-variant8-variant10-variant15-variant16-variant18-variant19-variant25-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:8,5:13:99:141,0,284:1,7,1,4 chr2 38216766 . C CT 134.72 PASS AC=1;AF=0.5;AN=2;DP=460;MQ=60;set=variant8-variant9-variant11-variant17-variant20-variant22-variant26-variant30-variant31-variant32-variant33-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,14:27:99:254,0,265:4,9,5,9 chr2 38218470 . TA T 786.58 PASS AC=1;AF=0.556;AN=2;DP=290;MQ=60;set=variant3-variant13-variant15-variant29-variant31-variant33-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:16,12:28:99:381,0,543:4,12,3,9 chr2 38244826 . A G 4474.84 PASS AC=1;AF=0.556;AN=2;DP=2780;FractionInformativeReads=1;set=variant3-variant13-variant15-variant29-variant31-variant33-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:144,129:273:99:2832,0,3340:68,76,64,65 chr2 38295456 . T A 2091.51 PASS AC=1;AF=0.531;AN=2;DP=2513;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant15-variant16-variant20-variant24-variant25-variant28-variant35-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:90,73:163:99:1907,0,2483:30,60,25,48 chr2 38296890 . T C 11715.8 PASS AC=1;AF=0.694;AN=2;DP=10235;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:156,148:304:99:3740,0,3761:75,81,71,77 chr2 38297170 . C A 14299.9 PASS AC=2;AF=0.829;AN=2;DP=16794;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,431:432:99:13408,1284,0:0,1,207,224 chr2 38297399 . C T 2949.37 PASS AC=1;AF=0.5;AN=2;DP=237;FS=0.996;FractionInformativeReads=1;MQ=60;MQRankSum=-0.365;QD=12.44;ReadPosRankSum=1.269;SOR=0.617;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:120,117:237:99:2978,0,3076:54,66,55,62 chr2 38297515 . G T 8591.83 PASS AC=2;AF=0.805;AN=2;DP=9037;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,194:194:99:6024,580,0:0,0,94,100 chr2 38297654 . C CA 4797.15 PASS AC=1;AF=0.647;AN=2;DP=5854;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:89,87:176:99:2115,0,2191:44,45,42,45 chr2 38298139 . T C 1795.49 PASS AC=1;AF=0.533;AN=2;DP=1820;FractionInformativeReads=1;MQ=60;set=variant6-variant7-variant8-variant9-variant14-variant17-variant19-variant20-variant22-variant26-variant30-variant33-variant34-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:64,61:125:99:1674,0,1576:30,34,31,30 chr2 38298150 . A G 3178.86 PASS AC=2;AF=0.708;AN=2;DP=4408;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,126:126:99:4002,378,0:0,0,63,63 chr2 38298203 . C G 3331.67 PASS AC=2;AF=0.708;AN=2;DP=4601;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,126:126:99:3757,377,0:0,0,66,60 chr2 38303017 . A AG 3660.55 PASS AC=2;AF=1;AN=2;DP=5130;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,113:113:99:4229,343,0:0,0,60,53 chr2 38522143 . GC G 74.02 PASS AC=1;AF=0.5;AN=2;DP=844;MQ=60;set=filterInvariant4-variant5-variant7-variant8-variant9-variant16-variant17-variant19-variant21-variant28-variant29-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:10,56:66:29:1744,0,29:10,0,49,7 chr2 38522152 . G C 1178.02 PASS AC=1;AF=0.5;AN=2;DP=93;FS=0;FractionInformativeReads=0.968;MQ=60;MQRankSum=-0.74;QD=12.67;ReadPosRankSum=3.166;SOR=0.605;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:42,48:90:99:1206,0,1114:34,8,38,10 chr2 38522260 . A T 4121.76 PASS AC=2;AF=0.579;AN=2;DP=4259;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant16-variant17-variant19-variant21-variant28-variant29-variant31-variant35-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,217:217:99:6404,647,0:0,0,95,122 chr2 38522643 . G T 6502.56 PASS AC=2;AF=0.583;AN=2;DP=8818;MQ=60;set=variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant16-variant17-variant19-variant21-variant28-variant29-variant31-variant35-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,511:512:99:15312,1496,0:1,0,243,268 chr2 38526324 . A T 51.2 PASS AC=2;AF=0.667;AN=2;DP=49;FS=0;FractionInformativeReads=1;MQ=60;set=variant4-variant9-variant10-variant15-variant16-variant29-variant31-variant35-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:76,9,0:0,0,2,1 chr2 38526547 . G A 382.32 PASS AC=2;AF=0.607;AN=2;DP=264;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant6-variant8-variant9-variant16-variant17-variant19-variant21-variant23-variant28-variant29-variant35-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:868,90,0:0,0,13,17 chr2 38536626 . T G 1148.39 PASS AC=2;AF=0.583;AN=2;DP=1435;MQ=60;set=variant4-variant5-variant6-variant7-variant8-variant9-variant16-variant17-variant19-variant21-variant23-variant28-variant29-variant31-variant35-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,81:81:99:2459,243,0:0,0,32,49 chr2 38537626 . A C 753.33 PASS AC=2;AF=0.591;AN=2;DP=843;MQ=60;set=variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant15-variant16-variant17-variant19-variant21-variant23-variant24-variant28-variant29-variant31-variant35-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1524,129,0:0,0,13,30 chr2 38541581 . C CTAT 112.63 PASS AC=2;AF=0.583;AN=2;DP=199;MQ=60;set=variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant16-variant17-variant19-variant21-variant23-variant28-variant29-variant31-variant35-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:540,36,0:0,0,11,1 chr2 38542573 . T C 495.84 PASS AC=2;AF=0.591;AN=2;DP=689;MQ=60;set=variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant15-variant16-variant17-variant19-variant21-variant23-variant24-variant28-variant29-variant31-variant35-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:876,72,0:0,0,5,19 chr2 38570291 . TAAAAAAAAAAAAA TA,T 75.19 PASS AC=0,2;AF=0.25,0.375;AN=2;DP=21;FS=0;set=variant6-variant21-variant23-variant35 GT:DP:GQ:SB 2/2:8:24:0,0,7,1 chr2 38604351 . A G 1812.03 PASS AC=2;AF=0.583;AN=2;DP=2730;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant15-variant16-variant17-variant19-variant21-variant23-variant24-variant28-variant29-variant30-variant31-variant35-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,135:135:99:3873,404,0:0,0,69,66 chr2 38604505 . TCTCCGCCTGTATCTCCTCGCC T,TCTCCGCCTGTATCTCCTCGCCCTCCGCCTGTATCTCCTCGCC 378.79 PASS AC=1,0;AF=0.4,0.1;AN=2;DP=182;set=variant16-variant23-variant28-variant35-variant37 GT:DP:GQ:SB 0/1:17:99:3,7,1,6 chr2 38796893 . G A 65.21 PASS AC=1;AF=0.5;AN=2;DP=42;FractionInformativeReads=1;MQ=60;set=variant5-variant7-variant19-variant27-variant35 GT:AD:DP:GQ:PL:SB 0/1:3,5:8:67:160,0,67:2,1,4,1 chr2 38893184 . G A 567.59 PASS AC=1;AF=0.591;AN=2;DP=425;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant10-variant16-variant20-variant21-variant22-variant25-variant27-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:17,23:40:99:647,0,473:9,8,11,12 chr2 38903022 . T A 711.73 PASS AC=1;AF=0.563;AN=2;DP=835;MQ=60;set=variant-variant4-variant10-variant16-variant25-variant29-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:48,59:107:99:1614,0,1178:32,16,38,21 chr2 38907001 . G C 285.48 PASS AC=1;AF=0.6;AN=2;DP=41;FS=0;FractionInformativeReads=1;MQ=60;set=variant4-variant10-variant16-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:2,6:8:58:202,0,58:2,0,5,1 chr2 38916970 . A T 1322.62 PASS AC=1;AF=0.5;AN=2;DP=961;MQ=60;set=variant-variant4-variant10-variant16-variant25-variant29-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:63,42:105:99:927,0,1564:33,30,24,18 chr2 38956947 . A G 2846.29 PASS AC=2;AF=0.676;AN=2;DP=3690;MQ=60;set=variant-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,99:99:99:3151,296,0:0,0,36,63 chr2 38957055 . T C 799.48 PASS AC=2;AF=0.989;AN=2;DP=1231;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:825,66,0:0,0,4,18 chr2 38960927 . G A 2316.02 PASS AC=2;AF=0.689;AN=2;DP=3069;MQ=60;set=variant-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,74:74:99:2217,221,0:0,0,35,39 chr2 38961832 . G GA 1340.67 PASS AC=1;AF=0.5;AN=2;DP=5797;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:30,92:122:99:1501,0,319:17,13,48,44 chr2 38968123 . CAAA CAA,CA,C 43.86 PASS AC=2,0,0;AF=0.571,0.071,0.071;AN=2;DP=40;FS=0;MQ=60;set=variant16-variant25-variant26-variant27-variant33-variant34-variant35 GT:DP:GQ:SB 1/1:3:9:0,0,1,2 chr2 38971040 . GT GTT,G,GTTT 3166.29 PASS AC=1,0,0;AF=0.5,0.026,0.092;AN=2;DP=6713;set=variant-filterInvariant2-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-filterInvariant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:DP:GQ:SB 0/1:143:99:15,16,56,56 chr2 38971641 . T TCA 12414.1 PASS AC=2;AF=0.966;AN=2;DP=11250;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,229:229:99:10299,689,0:0,0,111,118 chr2 38977371 . C T 2270.14 PASS AC=2;AF=0.738;AN=2;DP=2787;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:1983,162,0:0,0,17,37 chr2 38977402 . T C 1697.06 PASS AC=2;AF=0.738;AN=2;DP=1748;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:1150,96,0:0,0,10,22 chr2 38978727 . C A 1406.26 PASS AC=1;AF=0.5;AN=2;DP=115;FS=0.699;FractionInformativeReads=0.991;MQ=60;MQRankSum=-2.087;QD=12.23;ReadPosRankSum=2.761;SOR=0.604;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:50,64:114:99:1434,0,1164:23,27,31,33 chr2 38978764 . T C 1525.77 PASS AC=2;AF=0.738;AN=2;DP=3111;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,102:102:99:3210,306,0:0,0,48,54 chr2 39005205 . T C 251.35 PASS AC=2;AF=0.764;AN=2;DP=430;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:207,27,0:0,0,5,4 chr2 39006603 . T G 2484.13 PASS AC=2;AF=1;AN=2;DP=4274;FS=0;MQ=60;MQRankSum=1.225;ReadPosRankSum=-1.479;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,98:98:99:2979,294,0:0,0,55,43 chr2 39008949 . G A 1303.85 PASS AC=1;AF=0.5;AN=2;DP=975;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant10-variant15-variant16-variant25-variant35-variant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:53,56:109:99:1350,0,1379:27,26,27,29 chr2 39025043 . GA GAA,G 414.04 PASS AC=2,0;AF=0.511,0.375;AN=2;DP=1472;set=Intersection GT:DP:GQ:SB 1/1:21:12:1,1,13,6 chr2 39025555 . G A 5013.23 PASS AC=2;AF=0.73;AN=2;DP=5710;MQ=60;set=variant-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,161:161:99:4993,483,0:0,0,64,97 chr2 39025632 . A G 3103.78 PASS AC=2;AF=0.73;AN=2;DP=2900;MQ=60;set=variant-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,69:69:99:2287,207,0:0,0,19,50 chr2 39030074 . C T 2429.7 PASS AC=2;AF=0.703;AN=2;DP=3393;MQ=60;set=variant-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,113:114:99:3317,331,0:0,1,54,59 chr2 39042639 . G A 3100.03 PASS AC=2;AF=0.989;AN=2;DP=3042;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:2146,216,0:0,0,42,30 chr2 39045885 . C T 604.21 PASS AC=2;AF=0.73;AN=2;DP=985;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,31:31:93:1015,93,0:0,0,19,12 chr2 39050019 . G T 808.14 PASS AC=2;AF=1;AN=2;DP=1238;FS=0;MQ=60;MQRankSum=-0.657;ReadPosRankSum=0.06;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1252,119,0:0,0,25,15 chr2 39050061 . AT A 1186.56 PASS AC=2;AF=1;AN=2;DP=2137;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:2082,178,0:0,0,38,21 chr2 39050141 . A C 2000.21 PASS AC=2;AF=0.724;AN=2;DP=3875;MQ=60;set=variant-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,112:113:99:3209,328,0:1,0,63,49 chr2 39064753 . C CAAAA,CAAAAAAAAAAAAAAAA,CAAAAAAAAAAAAAAAAAAAA,CAAAAAAAAAAAAAAAAA,CAAAAAAAAAAAAAAA,CAAAAAAAAAAAAAAAAAAA,CAAAAAAAAAAAAAAAAAAAAAA 373.74 PASS AC=0,0,0,2,0,0,0;AF=0.25,0.125,0.063,0.313,0.125,0.063,0.063;AN=2;DP=63;FS=0;set=variant5-variant7-variant8-variant9-variant14-variant24-variant25-variant28-variant31-variant32-variant33-variant35-variant36-variant38-variant40-variant44 GT:DP:GQ:SB 4/4:2:18:0,0,1,1 chr2 39065729 . C A 687.33 PASS AC=2;AF=0.73;AN=2;DP=684;MQ=60;set=variant-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:638,57,0:0,0,13,6 chr2 39075356 . A C 436.33 PASS AC=2;AF=0.73;AN=2;DP=509;MQ=60;set=variant-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:488,36,0:0,0,11,1 chr2 39082344 . T C 5773.31 PASS AC=2;AF=0.724;AN=2;DP=7520;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,209:209:99:6198,625,0:0,0,91,118 chr2 39090696 . T C 2367.78 PASS AC=2;AF=1;AN=2;DP=2549;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:2333,204,0:0,0,18,50 chr2 39103032 . G GC 3970.16 PASS AC=2;AF=1;AN=2;DP=5474;FS=0;MQ=60;MQRankSum=-1.051;ReadPosRankSum=0.015;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,96:96:99:3435,292,0:0,0,44,52 chr2 39108773 . A G 807.34 PASS AC=1;AF=0.62;AN=2;DP=406;FractionInformativeReads=1;set=variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant12-variant16-variant17-variant19-variant21-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,11:19:99:353,0,220:2,6,2,9 chr2 39109935 . A AT,ATT 329.64 PASS AC=1,0;AF=0.45,0.113;AN=2;DP=1839;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:38:99:0,16,1,21 chr2 39117117 . G A 3636.86 PASS AC=1;AF=0.714;AN=2;DP=4716;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:76,72:148:99:1592,0,1717:36,40,37,35 chr2 39117285 . T G 910.44 PASS AC=1;AF=0.661;AN=2;DP=693;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant16-variant17-variant19-variant21-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant38-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,12:20:99:387,0,297:1,7,2,10 chr2 39122900 . T G 1325.83 PASS AC=2;AF=0.966;AN=2;DP=2580;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:2,55:57:99:1284,117,0:2,0,33,22 chr2 39122941 . A C 2139.37 PASS AC=2;AF=0.768;AN=2;DP=3069;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:2269,230,0:0,0,39,38 chr2 39148393 . G A 772.4 PASS AC=1;AF=0.5;AN=2;DP=439;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant7-variant10-variant15-variant16-variant25-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:25,24:49:99:611,0,705:19,6,17,7 chr2 39184964 . A G 160.85 PASS AC=1;AF=0.662;AN=2;DP=622;MQ=60;set=variant-variant3-variant6-variant8-variant9-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,7:15:99:157,0,171:6,2,5,2 chr2 39185048 . C T 1060.48 PASS AC=1;AF=0.909;AN=2;DP=2824;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:43,36:79:99:792,0,1013:26,17,23,13 chr2 39187190 . T C 2228.45 PASS AC=1;AF=0.92;AN=2;DP=6366;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:69,91:160:99:2292,0,1720:40,29,47,44 chr2 39187519 . A G 170.08 PASS AC=1;AF=0.92;AN=2;DP=2012;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:25,25:50:99:728,0,635:7,18,6,19 chr2 39198966 . A G 844.31 PASS AC=1;AF=0.92;AN=2;DP=1812;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:19,27:46:99:672,0,523:15,4,17,10 chr2 39208512 . A AG 1611.4 PASS AC=1;AF=0.92;AN=2;DP=4126;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:54,39:93:99:1136,0,1642:30,24,21,18 chr2 39209047 . A G 1350.68 PASS AC=1;AF=0.909;AN=2;DP=4021;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:46,60:106:99:1645,0,1340:13,33,21,39 chr2 39209426 . A G 1797.55 PASS AC=1;AF=0.909;AN=2;DP=6236;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:71,91:162:99:2370,0,1747:36,35,40,51 chr2 39210398 . A T 7839.98 PASS AC=1;AF=0.92;AN=2;DP=22235;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:266,222:488:99:5138,0,6972:114,152,96,126 chr2 39210719 . T TTA 608.05 PASS AC=1;AF=0.909;AN=2;DP=1334;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:14,16:30:99:619,0,522:6,8,4,12 chr2 39211121 . T C 3654.87 PASS AC=1;AF=0.909;AN=2;DP=12672;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:96,144:240:99:3741,0,2433:49,47,78,66 chr2 39211358 . TA T 4859.46 PASS AC=1;AF=0.92;AN=2;DP=12246;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:122,129:251:99:3826,0,3583:63,59,68,61 chr2 39212565 . T TTG 1839.79 PASS AC=1;AF=0.909;AN=2;DP=5479;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:61,53:114:99:2083,0,2324:35,26,29,24 chr2 39212637 . T C 1511.29 PASS AC=1;AF=0.731;AN=2;DP=5341;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:77,55:132:99:1223,0,1654:36,41,27,28 chr2 39214821 . A C 154.46 PASS AC=1;AF=0.929;AN=2;DP=454;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,6:13:99:179,0,193:2,5,1,5 chr2 39224351 . G T 482.27 PASS AC=1;AF=0.92;AN=2;DP=1124;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:10,10:20:99:268,0,332:9,1,7,3 chr2 39224615 . G GT 466.71 PASS AC=1;AF=0.92;AN=2;DP=1679;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:22,13:35:99:291,0,784:6,16,4,9 chr2 39224637 . G A 58.52 PASS AC=1;AF=0.5;AN=2;DP=86;FractionInformativeReads=1;MQ=60;set=variant4-variant10-variant23-variant35 GT:AD:DP:GQ:PL:SB 0/1:13,15:28:99:425,0,481:3,10,4,11 chr2 39233500 . G A 128.41 PASS AC=1;AF=0.93;AN=2;DP=823;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,15:29:99:490,0,343:9,5,13,2 chr2 39251375 . T TCAC 346.36 PASS AC=1;AF=0.932;AN=2;DP=714;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:6,7:13:99:276,0,267:1,5,2,5 chr2 39262068 . C T 545.31 PASS AC=1;AF=0.92;AN=2;DP=1866;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:21,17:38:99:526,0,661:4,17,2,15 chr2 39281730 . G C 152.82 PASS AC=1;AF=0.909;AN=2;DP=506;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:6,5:11:99:111,0,228:6,0,3,2 chr2 39347388 . GC G 1053.55 PASS AC=1;AF=0.5;AN=2;DP=222;FractionInformativeReads=1;MQ=60;set=variant6-variant14-variant23-variant35 GT:AD:DP:GQ:PL:SB 0/1:25,30:55:99:880,0,725:18,7,19,11 chr2 39348031 . CGGGGCGGAGCT C 1021.84 PASS AC=1;AF=0.5;AN=2;DP=455;MQ=60;set=variant-variant3-variant10-variant13-variant23-variant35-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:45,25:70:99:889,0,3095:28,17,19,6 chr2 39348346 . G A 159.26 PASS AC=1;AF=0.5;AN=2;DP=109;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant10-variant13-variant23-variant35-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:7,11:18:99:264,0,183:3,4,4,7 chr2 39402978 . A AG 7469.99 PASS AC=1;AF=0.92;AN=2;DP=15860;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:169,167:336:99:5690,0,5744:91,78,95,72 chr2 39403006 . G C 4992.85 PASS AC=1;AF=0.5;AN=2;DP=2895;MQ=60;set=variant-variant3-variant10-variant20-variant35-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:179,188:367:99:4607,0,4424:93,86,94,94 chr2 39406572 . C A 444.25 PASS AC=1;AF=0.898;AN=2;DP=1086;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:9,12:21:99:386,0,313:2,7,2,10 chr2 39440727 . G C 304.5 PASS AC=1;AF=0.89;AN=2;DP=1377;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,19:32:99:493,0,285:5,8,8,11 chr2 39452861 . C T 1326.16 PASS AC=1;AF=0.895;AN=2;DP=2503;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,37:71:99:879,0,839:15,19,22,15 chr2 39476482 . T C 2460.87 PASS AC=1;AF=0.897;AN=2;DP=2589;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,38:69:99:1103,0,845:22,9,25,13 chr2 39477170 . T C 4186.78 PASS AC=1;AF=0.897;AN=2;DP=6276;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:63,87:150:99:2475,0,1636:21,42,31,56 chr2 39494197 . C T 343.89 PASS AC=1;AF=0.897;AN=2;DP=735;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,9:26:99:283,0,462:11,6,7,2 chr2 39494469 . C G 237.59 PASS AC=1;AF=0.917;AN=2;DP=408;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,2:6:72:72,0,151:1,3,1,1 chr2 39507417 . T A 838.37 PASS AC=1;AF=0.888;AN=2;DP=3134;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,45:78:99:1016,0,600:17,16,25,20 chr2 39514136 . T C 557.11 PASS AC=1;AF=0.888;AN=2;DP=1503;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,28:53:99:648,0,589:8,17,11,17 chr2 39514204 . G C 148.54 PASS AC=1;AF=0.897;AN=2;DP=426;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,11:17:99:274,0,210:0,6,4,7 chr2 39526842 . A C 1148.2 PASS AC=2;AF=1;AN=2;DP=1964;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1351,120,0:0,0,28,12 chr2 39536689 . ATT ATTT,ATTTT,ATTTTT,AT,A 60.34 PASS AC=0,0,0,0,1;AF=0.233,0.2,0.1,0.017,0.017;AN=2;DP=1462;set=filterInvariant-variant2-filterInvariant3-variant4-variant5-variant7-variant8-variant9-filterInvariant10-variant11-variant12-variant13-variant15-filterInvariant16-variant17-filterInvariant20-variant22-variant23-variant25-variant26-variant28-variant29-variant32-variant33-filterInvariant35-variant36-filterInvariant38-variant39-variant43-variant44 GT:DP:GQ:SB 0/5:17:92:3,8,0,6 chr2 39553271 . A G 2452.21 PASS AC=1;AF=0.905;AN=2;DP=3852;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,40:72:99:1043,0,765:19,13,22,18 chr2 39558928 . G A 3143.46 PASS AC=1;AF=0.905;AN=2;DP=4863;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,59:120:99:1483,0,1631:27,34,27,32 chr2 39563988 . T C 540.36 PASS AC=1;AF=0.5;AN=2;DP=88;FractionInformativeReads=1;MQ=60;set=variant3-variant10-variant20-variant35 GT:AD:DP:GQ:PL:SB 0/1:8,7:15:99:210,0,237:6,2,6,1 chr2 39564620 . C A 751.96 PASS AC=1;AF=0.907;AN=2;DP=2305;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,14:45:99:370,0,855:19,12,9,5 chr2 39570427 . T C 1034 PASS AC=1;AF=0.905;AN=2;DP=1117;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,13:25:99:406,0,333:9,3,11,2 chr2 39583344 . G T 679.84 PASS AC=1;AF=0.5;AN=2;DP=46;FS=9.751;FractionInformativeReads=1;MQ=60;MQRankSum=-2.271;QD=14.78;ReadPosRankSum=0.986;SOR=0.111;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:20,26:46:99:708,0,625:17,3,16,10 chr2 39583446 . A G 3211.29 PASS AC=1;AF=0.905;AN=2;DP=4007;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,47:89:99:1154,0,997:18,24,19,28 chr2 39664535 . C T 112.93 PASS AC=1;AF=0.5;AN=2;DP=34;FS=0;FractionInformativeReads=1;MQ=60;set=variant23-variant35 GT:AD:DP:GQ:PL:SB 0/1:9,14:23:99:380,0,223:2,7,3,11 chr2 39944055 . G A 32.47 PASS AC=1;AF=0.683;AN=2;DP=379;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,8:13:99:272,0,136:5,0,8,0 chr2 39963667 . A G 1184.81 PASS AC=2;AF=0.686;AN=2;DP=3906;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,116:116:99:3531,347,0:0,0,51,65 chr2 39982898 . G GAGTAT 124.57 PASS AC=2;AF=0.708;AN=2;DP=172;MQ=60;set=variant2-variant6-variant7-variant10-variant11-variant12-variant13-variant15-variant17-variant19-variant21-variant25-variant26-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:315,21,0:0,0,7,0 chr2 39993167 . T C 1261.98 PASS AC=2;AF=0.661;AN=2;DP=3263;MQ=60;set=variant2-variant3-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant21-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,129:129:99:3612,385,0:0,0,71,58 chr2 39995885 . C T 280.43 PASS AC=2;AF=0.688;AN=2;DP=1216;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1468,126,0:0,0,14,28 chr2 39995908 . A G 99.12 PASS AC=2;AF=0.69;AN=2;DP=856;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant21-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:1132,96,0:0,0,14,18 chr2 40006430 . A C 539.13 PASS AC=2;AF=0.679;AN=2;DP=1016;MQ=60;set=variant2-variant3-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant21-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1869,129,0:0,0,9,34 chr2 40006442 . C T 472.49 PASS AC=2;AF=0.679;AN=2;DP=767;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant21-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1743,117,0:0,0,7,31 chr2 40006488 . A AGGGAGAGGGAGAGGGAGAGG 48.14 PASS AC=2;AF=0.792;AN=2;DP=150;set=variant3-variant6-variant7-variant11-variant15-variant17-variant18-variant25-variant31-variant34-variant35-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:12:166,12,0:0,0,2,3 chr2 40339478 . GCC GC,G 4722.76 PASS AC=0,2;AF=0.682,0.307;AN=2;DP=9869;MQ=60;set=Intersection GT:DP:GQ:SB 2/2:222:99:0,0,109,113 chr2 40339798 . CA C,CAAA,CAAAA,CAA 1312.99 PASS AC=0,2,0,0;AF=0.129,0.419,0.016,0.065;AN=2;DP=5271;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant30-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:DP:GQ:SB 2/2:129:99:1,1,65,62 chr2 40339986 . T C 4023.85 PASS AC=2;AF=0.629;AN=2;DP=10127;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant30-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,332:332:99:10367,994,0:0,0,169,163 chr2 40340671 . CA C 3301.37 PASS AC=2;AF=0.648;AN=2;DP=3941;MQ=60;set=variant-variant2-variant5-variant7-variant10-variant12-variant13-variant15-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant30-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,119:119:99:4442,358,0:0,0,58,61 chr2 40341388 . T C 1944.47 PASS AC=1;AF=0.536;AN=2;DP=1696;MQ=60;set=variant10-variant12-variant13-variant15-variant20-variant21-variant22-variant23-variant35-variant36-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:56,65:121:99:1884,0,1584:19,37,23,42 chr2 40341605 . G A 499.16 PASS AC=1;AF=0.563;AN=2;DP=954;MQ=60;set=variant2-variant10-variant12-variant13-variant15-variant20-variant21-variant22-variant23-variant35-variant36-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:23,32:55:99:832,0,552:13,10,15,17 chr2 40341660 . C T 461.77 PASS AC=2;AF=0.648;AN=2;DP=1743;MQ=60;set=variant-variant2-variant5-variant7-variant10-variant12-variant13-variant15-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant30-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:2069,180,0:0,0,33,27 chr2 40341847 . C T 1743.09 PASS AC=1;AF=0.536;AN=2;DP=1994;MQ=60;set=variant10-variant12-variant13-variant15-variant20-variant21-variant22-variant23-variant35-variant36-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:78,91:169:99:2427,0,1871:41,37,45,46 chr2 40366301 . G A 136.46 PASS AC=2;AF=0.638;AN=2;DP=633;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant30-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1115,111,0:0,0,23,14 chr2 40392313 . G C 844.77 PASS AC=2;AF=0.966;AN=2;DP=1123;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:604,48,0:0,0,2,14 chr2 40403104 . A G 2498.41 PASS AC=2;AF=0.893;AN=2;DP=3443;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,66:66:99:2124,198,0:0,0,42,24 chr2 40404839 . C T 691.11 PASS AC=2;AF=0.786;AN=2;DP=2651;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1616,138,0:0,0,35,11 chr2 40655563 . CCACACACACACACACA CCACACACACACA,CCACACACACACACA,CCACACA,CCACACACACA,C,CCACACACACACACACACA 1935.28 PASS AC=1,0,0,0,0,1;AF=0.58,0.159,0.136,0.057,0.011,0.011;AN=2;DP=2244;set=Intersection GT:DP:GQ:SB 1/6:40:99:1,0,28,11 chr2 42164619 . TACAC TAC,TACACAC,T 63 PASS AC=1,0,0;AF=0.318,0.167,0.03;AN=2;DP=1070;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-filterInvariant23-variant24-variant25-variant26-variant27-filterInvariant29-variant30-variant31-variant35-variant36-filterInvariant37-variant38-variant40-variant42-filterInvariant44 GT:DP:GQ:SB 0/1:26:99:13,6,5,2 chr2 42280335 . A C 178.89 PASS AC=1;AF=0.5;AN=2;DP=357;MQ=60;set=variant2-filterInvariant4-variant5-variant6-variant18-variant20-variant26-variant33-variant35-variant36-variant37-variant38-filterInvariant39 GT:AD:DP:GQ:PL:SB 0/1:13,6:19:92:92,0,665:1,12,6,0 chr2 42280341 . A C 163.83 PASS AC=1;AF=0.5;AN=2;DP=497;MQ=60;set=variant2-variant4-variant5-variant6-filterInvariant18-variant19-variant20-filterInvariant21-variant26-filterInvariant31-variant33-variant35-variant37-variant38-filterInvariant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:16,5:21:83:83,0,752:3,13,5,0 chr2 42396722 . A G 6018.09 PASS AC=2;AF=0.718;AN=2;DP=8759;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,261:262:99:8345,779,0:1,0,143,118 chr2 42483860 . C G 381.09 PASS AC=1;AF=0.5;AN=2;DP=32;FractionInformativeReads=1;MQ=60;set=variant15-variant35 GT:AD:DP:GQ:PL:SB 0/1:4,10:14:99:272,0,137:1,3,4,6 chr2 42492238 . C CT 150.54 PASS AC=1;AF=0.5;AN=2;DP=334;MQ=60;set=variant4-variant6-variant7-variant10-variant11-variant12-variant15-variant29-variant35-variant36-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,8:17:99:174,0,203:1,8,1,7 chr2 42510018 . A G 3356.25 PASS AC=2;AF=1;AN=2;DP=4934;FS=0;MQ=60;MQRankSum=-0.835;ReadPosRankSum=0.402;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,119:119:99:3474,355,0:0,0,68,51 chr2 42513582 . C T 496.86 PASS AC=1;AF=0.5;AN=2;DP=388;FractionInformativeReads=1;MQ=60;set=variant4-variant7-variant10-variant12-variant15-variant29-variant35-variant36-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,22:37:99:697,0,388:5,10,4,18 chr2 42515388 . A G 2318.96 PASS AC=2;AF=0.943;AN=2;DP=3397;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,87:87:99:2615,260,0:0,0,53,34 chr2 42530186 . C T 422.01 PASS AC=1;AF=0.5;AN=2;DP=29;FS=1.862;FractionInformativeReads=1;MQ=60;MQRankSum=1.68;QD=14.55;ReadPosRankSum=-0.982;SOR=1.449;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:15,14:29:99:450,0,460:11,4,12,2 chr2 42557759 . CT C 1331.12 PASS AC=1;AF=0.5;AN=2;DP=18486;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-filterInvariant17-variant18-filterInvariant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:251,109:360:99:1322,0,4664:121,130,42,67 chr2 42588856 . T A 1877.34 PASS AC=1;AF=0.542;AN=2;DP=1327;MQ=60;set=variant4-variant6-variant7-variant10-variant12-variant15-variant16-variant24-variant29-variant35-variant36-variant41 GT:AD:DP:GQ:PL:SB 0/1:50,43:93:99:990,0,1279:25,25,19,24 chr2 42670398 . A T 5607.57 PASS AC=2;AF=0.58;AN=2;DP=10807;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant15-variant16-variant19-variant23-variant24-variant26-variant29-variant31-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,469:470:99:14076,1393,0:1,0,243,226 chr2 42719847 . T TG 5343.58 PASS AC=2;AF=1;AN=2;DP=6655;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,175:175:99:8049,545,0:0,0,127,48 chr2 42719860 . G GC 6182.35 PASS AC=2;AF=1;AN=2;DP=7844;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,206:206:99:9051,626,0:0,0,143,63 chr2 42721773 . T C 1328.48 PASS AC=2;AF=0.77;AN=2;DP=4658;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,168:168:99:5084,503,0:0,0,102,66 chr2 42722048 . A G 433.64 PASS AC=2;AF=0.77;AN=2;DP=2115;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:2147,174,0:0,0,20,38 chr2 42722369 . T C 189.54 PASS AC=1;AF=0.533;AN=2;DP=344;MQ=60;set=variant-variant2-variant6-variant7-variant10-variant19-variant22-variant26-variant29-variant31-variant35-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,10:20:99:249,0,220:5,5,2,8 chr2 42722410 . T A 101.97 PASS AC=2;AF=0.77;AN=2;DP=607;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:415,39,0:0,0,4,9 chr2 42795716 . A C 231.01 PASS AC=2;AF=0.988;AN=2;DP=455;FS=0;MQ=60;MQRankSum=0.736;ReadPosRankSum=0.736;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:36:540,36,0:0,0,7,3 chr2 42795719 . A C 276.01 PASS AC=2;AF=0.988;AN=2;DP=491;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:42:630,42,0:0,0,10,3 chr2 42795727 . T C 278.33 PASS AC=2;AF=1;AN=2;DP=562;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:655,45,0:0,0,11,4 chr2 42795954 . T C 2610.68 PASS AC=2;AF=1;AN=2;DP=5724;FS=0;MQRankSum=0.144;ReadPosRankSum=0.808;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,152:152:99:4548,454,0:0,0,64,88 chr2 42806441 . A G 2026.49 PASS AC=1;AF=0.5;AN=2;DP=423;MQ=60;set=variant4-variant19-variant21-variant35 GT:AD:DP:GQ:PL:SB 0/1:38,51:89:99:1319,0,1039:9,29,18,33 chr2 42836516 . A G 841.27 PASS AC=2;AF=0.816;AN=2;DP=867;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:880,72,0:0,0,19,5 chr2 42922888 . AT A 449.39 PASS AC=1;AF=0.63;AN=2;DP=1303;MQ=60;set=variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant27-variant29-variant32-variant33-variant35-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,25:39:99:527,0,229:8,6,14,11 chr2 42925079 . TTTC T 325.67 PASS AC=1;AF=0.583;AN=2;DP=130;MQ=60;set=variant2-variant6-variant14-variant26-variant29-variant31-variant34-variant35-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,5:8:99:201,0,130:1,2,0,5 chr2 42931217 . A C 236.14 PASS AC=2;AF=0.771;AN=2;DP=653;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:543,45,0:0,0,13,2 chr2 42935961 . C T 527.89 PASS AC=2;AF=0.743;AN=2;DP=2556;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:2413,231,0:0,0,46,31 chr2 42935979 . C T 617.89 PASS AC=2;AF=0.743;AN=2;DP=2839;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,92:92:99:2870,275,0:0,0,58,34 chr2 42936419 . G GA 2088.9 PASS AC=2;AF=0.757;AN=2;DP=7767;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:3,158:161:99:4274,402,0:1,2,70,88 chr2 42936547 . A C 3820.91 PASS AC=2;AF=0.757;AN=2;DP=7688;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,209:210:99:6570,582,0:1,0,110,99 chr2 42945897 . C T 117.15 PASS AC=1;AF=0.643;AN=2;DP=54;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant26-variant29-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:1,2:3:37:81,0,37:1,0,2,0 chr2 42981239 . A G 992.1 PASS AC=1;AF=0.587;AN=2;DP=1299;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant9-variant10-variant11-variant15-variant17-variant18-variant20-variant21-variant22-variant24-variant27-variant29-variant31-variant33-variant35-variant37-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:30,31:61:99:783,0,765:18,12,16,15 chr2 42981990 . C T 1595.19 PASS AC=1;AF=0.652;AN=2;DP=2877;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,47:89:99:1276,0,1068:21,21,26,21 chr2 42982169 . G A 1384 PASS AC=1;AF=0.587;AN=2;DP=2475;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant9-variant10-variant11-variant15-variant17-variant18-variant20-variant21-variant22-variant24-variant27-variant29-variant31-variant33-variant35-variant37-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:69,74:143:99:2769,0,3300:33,36,34,40 chr2 42982175 . G A 1417.71 PASS AC=1;AF=0.587;AN=2;DP=2414;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant9-variant10-variant11-variant15-variant17-variant18-variant20-variant21-variant22-variant24-variant27-variant29-variant31-variant33-variant35-variant37-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:64,73:137:99:2763,0,3199:30,34,34,39 chr2 42983004 . T C 1769.49 PASS AC=1;AF=0.652;AN=2;DP=3048;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,59:110:99:1488,0,1364:22,29,30,29 chr2 42989744 . G C 1240.22 PASS AC=1;AF=0.652;AN=2;DP=3198;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,44:102:99:1016,0,1440:33,25,26,18 chr2 42990336 . T G 1418.96 PASS AC=1;AF=0.652;AN=2;DP=4554;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:75,78:153:99:2078,0,2022:41,34,42,36 chr2 42994484 . G T 1505.99 PASS AC=1;AF=0.571;AN=2;DP=679;FractionInformativeReads=1;MQ=60;set=variant4-variant7-variant16-variant19-variant22-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,49:108:99:1168,0,1455:30,29,25,24 chr2 42996709 . ATGTGTGTGTGTG A,ATG,ATGTG,ATGTGTGTGTGTGTG,ATGTGTGTGTGTGTGTGTGTGTG,ATGTGTG,ATGTGTGTGTGTGTGTG 392.62 PASS AC=1,0,0,0,0,0,0;AF=0.244,0.195,0.293,0.037,0.012,0.012,0.024;AN=2;DP=1120;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:DP:GQ:SB 0/1:33:99:11,6,11,5 chr2 42996759 . AAGAG A 481.76 PASS AC=1;AF=0.789;AN=2;DP=1681;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,27:55:99:1006,0,1160:17,11,17,10 chr2 42996819 . G A 518.09 PASS AC=1;AF=0.563;AN=2;DP=1231;MQ=60;set=variant-variant4-variant6-variant7-variant10-variant11-variant12-variant19-variant21-variant29-variant35-variant37-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,55:99:99:1268,0,1227:24,20,29,26 chr2 42997614 . G A 828.48 PASS AC=1;AF=0.638;AN=2;DP=2727;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant23-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,56:106:99:1279,0,1271:29,21,33,23 chr2 43011169 . G T 329.82 PASS AC=2;AF=0.729;AN=2;DP=1324;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1323,125,0:0,0,14,28 chr2 43015612 . G T 921.96 PASS AC=2;AF=0.817;AN=2;DP=2653;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,74:74:99:2205,220,0:0,0,48,26 chr2 43015719 . T C 2030.08 PASS AC=2;AF=0.817;AN=2;DP=5771;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,150:150:99:4379,449,0:0,0,75,75 chr2 43015757 . G A 2165.81 PASS AC=2;AF=0.817;AN=2;DP=5058;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,123:123:99:3743,369,0:0,0,53,70 chr2 43015902 . G A 322.92 PASS AC=2;AF=0.817;AN=2;DP=751;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:685,54,0:0,0,3,15 chr2 43019347 . G C 928.19 PASS AC=2;AF=0.817;AN=2;DP=970;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:1014,75,0:0,0,20,5 chr2 43019364 . G C 1230.02 PASS AC=2;AF=0.817;AN=2;DP=1274;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1350,108,0:0,0,27,9 chr2 43019730 . A G 3543.61 PASS AC=2;AF=0.81;AN=2;DP=4965;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,118:118:99:3770,354,0:0,0,44,74 chr2 43451130 . GT G,GTTT 393.63 PASS AC=1,0;AF=0.489,0.011;AN=2;DP=5708;set=variant-variant2-variant3-variant4-variant5-filterInvariant6-variant7-variant8-variant9-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant13-variant14-variant15-filterInvariant16-filterInvariant17-filterInvariant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-filterInvariant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-filterInvariant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:101:99:36,43,11,11 chr2 43452183 . A G 5412.89 PASS AC=1;AF=0.609;AN=2;DP=4240;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant30-variant34-variant35-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:98,98:196:99:2588,0,2412:52,46,53,45 chr2 43514036 . G A 2155.17 PASS AC=1;AF=0.587;AN=2;DP=1801;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant30-variant34-variant35-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:47,36:83:99:919,0,1234:28,19,23,13 chr2 43518932 . AC A 905.46 PASS AC=1;AF=0.5;AN=2;DP=155;MQ=60;set=variant2-variant5-variant35 GT:AD:DP:GQ:PL:SB 0/1:33,21:54:99:602,0,1164:11,22,6,15 chr2 43625078 . T C 512.17 PASS AC=1;AF=0.64;AN=2;DP=735;MQ=60;set=variant-variant2-variant3-variant8-variant10-variant11-variant13-variant14-variant15-variant19-variant21-variant22-variant23-variant25-variant29-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,14:29:99:397,0,402:11,4,11,3 chr2 43625184 . T A 1160.22 PASS AC=1;AF=0.609;AN=2;DP=1867;MQ=60;set=variant-variant2-variant8-variant10-variant11-variant13-variant14-variant15-variant21-variant22-variant23-variant25-variant29-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,44:92:99:1024,0,1180:27,21,28,16 chr2 43657510 . T A 137.68 PASS AC=1;AF=0.64;AN=2;DP=418;MQ=60;set=variant-variant2-variant3-variant8-variant10-variant11-variant13-variant14-variant15-variant19-variant21-variant22-variant23-variant25-variant29-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,8:13:99:205,0,189:1,4,1,7 chr2 43732958 . C T 106.61 PASS AC=1;AF=0.591;AN=2;DP=309;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant8-variant11-variant14-variant15-variant21-variant22-variant23-variant25-variant28-variant29-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,11:26:99:327,0,464:3,12,3,8 chr2 43754992 . C T 424.42 PASS AC=1;AF=0.529;AN=2;DP=1272;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant12-variant15-variant17-variant19-variant20-variant22-variant23-variant24-variant26-variant33-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:29,40:69:99:1063,0,691:18,11,24,16 chr2 43778857 . GA G 68.39 PASS AC=1;AF=0.553;AN=2;DP=318;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant12-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant34-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:5,9:14:99:203,0,99:4,1,6,3 chr2 43783141 . A G 165.07 PASS AC=2;AF=0.875;AN=2;DP=35;FS=0;FractionInformativeReads=1;MQ=60;set=variant17-variant19-variant21-variant23-variant24-variant34-variant35-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:90,6,0:0,0,1,1 chr2 43783294 . A T 248.51 PASS AC=1;AF=0.55;AN=2;DP=586;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant12-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant34-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:17,7:24:99:186,0,534:13,4,5,2 chr2 43787576 . G A 334.43 PASS AC=1;AF=0.556;AN=2;DP=465;set=variant2-variant3-variant4-variant5-variant7-variant8-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant34-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:6,19:25:99:598,0,192:0,6,3,16 chr2 43789786 . C G 481.23 PASS AC=1;AF=0.575;AN=2;DP=722;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant12-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant34-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:19,28:47:99:866,0,480:13,6,20,8 chr2 43790259 . T C 2442.96 PASS AC=1;AF=0.571;AN=2;DP=4712;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant12-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant34-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:115,123:238:99:3000,0,2852:57,58,63,60 chr2 43790347 . A T 2510.2 PASS AC=1;AF=0.575;AN=2;DP=4576;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant12-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant34-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:134,112:246:99:2867,0,3272:61,73,52,60 chr2 43790448 . A C 2426.69 PASS AC=1;AF=0.531;AN=2;DP=3050;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant12-variant15-variant17-variant19-variant20-variant22-variant23-variant24-variant26-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:112,118:230:99:3230,0,2873:52,60,66,52 chr2 43791363 . C T 2349.19 PASS AC=2;AF=0.721;AN=2;DP=5523;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,142:142:99:4743,426,0:0,0,56,86 chr2 43791563 . T C 1361.28 PASS AC=1;AF=0.571;AN=2;DP=2478;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant12-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant34-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:67,69:136:99:1845,0,1671:43,24,42,27 chr2 43791766 . A G 1986.79 PASS AC=1;AF=0.575;AN=2;DP=3590;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant12-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant34-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:96,84:180:99:2192,0,2622:40,56,33,51 chr2 43792538 . C T 147.72 PASS AC=1;AF=0.579;AN=2;DP=282;FractionInformativeReads=1;set=variant2-variant3-variant4-variant5-variant7-variant8-variant12-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant34-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:5,8:13:99:298,0,187:5,0,8,0 chr2 43792570 . CA C,CAA 366.94 PASS AC=1,0;AF=0.422,0.078;AN=2;DP=1288;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-filterInvariant11-filterInvariant13-variant14-variant16-variant19-variant22-variant23-filterInvariant25-variant26-variant27-variant28-variant29-variant31-variant32-filterInvariant34-filterInvariant35-variant36-variant37-variant39-variant40-variant41-variant43-filterInvariant44 GT:DP:GQ:SB 0/1:32:99:16,5,10,1 chr2 43793222 . G C 407.71 PASS AC=1;AF=0.553;AN=2;DP=385;set=variant2-variant3-variant4-variant5-variant7-variant8-variant12-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant34-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:10,12:22:99:410,0,323:7,3,11,1 chr2 43793275 . CA C 629.3 PASS AC=1;AF=0.553;AN=2;DP=1124;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant12-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant34-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:32,39:71:99:904,0,677:21,11,28,11 chr2 43793725 . G A 810.59 PASS AC=1;AF=0.553;AN=2;DP=1639;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant12-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant34-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:37,45:82:99:1117,0,796:19,18,22,23 chr2 43793963 . TA TAAA,T,TAA 109.36 PASS AC=1,0,0;AF=0.475,0.05,0.025;AN=2;DP=415;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant12-variant15-variant17-variant19-filterInvariant20-variant21-variant23-variant24-variant26-variant34-variant35-variant37-variant40 GT:DP:GQ:SB 0/1:15:99:3,7,0,5 chr2 43797619 . C T 975.72 PASS AC=1;AF=0.531;AN=2;DP=1408;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant12-variant15-variant17-variant19-variant20-variant22-variant23-variant24-variant26-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:51,40:91:99:830,0,1136:26,25,19,21 chr2 43797710 . G A 336 PASS AC=1;AF=0.553;AN=2;DP=860;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant12-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant34-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:29,18:47:99:386,0,744:11,18,8,10 chr2 43798792 . G A 594.64 PASS AC=1;AF=0.553;AN=2;DP=1322;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant12-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant34-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:40,27:67:99:594,0,980:22,18,16,11 chr2 43799070 . C T 148.53 PASS AC=2;AF=0.917;AN=2;DP=168;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant31-variant32-variant34-variant35-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:90,6,0:0,0,0,2 chr2 43800174 . A G 823.9 PASS AC=1;AF=0.575;AN=2;DP=1620;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant12-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant34-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:45,38:83:99:993,0,1112:19,26,11,27 chr2 43801712 . A G 944.33 PASS AC=1;AF=0.575;AN=2;DP=1822;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant12-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant34-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:40,47:87:99:1169,0,1053:20,20,24,23 chr2 43802261 . C A 235.31 PASS AC=2;AF=1;AN=2;DP=318;FS=0;MQ=60;MQRankSum=0.731;ReadPosRankSum=0.731;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:180,12,0:0,0,1,3 chr2 43804229 . T C 1335.5 PASS AC=1;AF=0.575;AN=2;DP=1796;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant12-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant34-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:46,67:113:99:1682,0,1218:23,23,33,34 chr2 43804334 . C T 331.29 PASS AC=1;AF=0.5;AN=2;DP=131;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant35 GT:AD:DP:GQ:PL:SB 0/1:18,35:53:99:913,0,494:3,15,13,22 chr2 43817783 . CAAA C,CAA,CA 35.67 PASS AC=0,1,0;AF=0.143,0.357,0.071;AN=2;DP=50;set=variant3-variant11-variant12-variant25-variant26-variant35-variant44 GT:DP:GQ:SB 0/2:11:64:3,2,6,0 chr2 43817950 . CT C 852.9 PASS AC=1;AF=0.531;AN=2;DP=1360;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant12-variant15-variant17-variant19-variant20-variant22-variant23-variant24-variant26-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:34,42:76:99:1065,0,820:16,18,17,25 chr2 43820201 . T C 636.09 PASS AC=1;AF=0.595;AN=2;DP=672;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant8-variant9-variant11-variant13-variant15-variant21-variant25-variant28-variant29-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,13:38:99:298,0,688:10,15,5,8 chr2 43864526 . A G 1061.41 PASS AC=1;AF=0.757;AN=2;DP=2413;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,47:104:99:1122,0,1394:25,32,22,25 chr2 43864555 . T C 706.65 PASS AC=1;AF=0.757;AN=2;DP=2002;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,45:89:99:1041,0,1040:20,24,19,26 chr2 43871983 . T C 1573.86 PASS AC=1;AF=0.757;AN=2;DP=2139;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,31:53:99:748,0,569:6,16,11,20 chr2 43872032 . A G 180.02 PASS AC=1;AF=0.583;AN=2;DP=582;MQ=60;set=variant-variant2-variant4-variant13-variant15-variant17-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,14:24:99:474,0,343:1,9,2,12 chr2 43902511 . G C 2120.68 PASS AC=1;AF=0.78;AN=2;DP=2308;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,34:67:99:836,0,866:22,11,21,13 chr2 43903066 . A G 3874.81 PASS AC=1;AF=0.78;AN=2;DP=4997;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,56:123:99:1426,0,1762:30,37,23,33 chr2 43903354 . T C 5603.01 PASS AC=1;AF=0.768;AN=2;DP=6587;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:79,82:161:99:1734,0,1911:43,36,43,39 chr2 43903483 . T C 2633.33 PASS AC=1;AF=0.78;AN=2;DP=3620;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,42:90:99:1233,0,1310:17,31,12,30 chr2 43905898 . G GAGGTGGAGGTGC 235.58 PASS AC=1;AF=0.606;AN=2;DP=597;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,8:21:99:276,0,1359:7,6,4,4 chr2 43921489 . A T 488.03 PASS AC=1;AF=0.662;AN=2;DP=939;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,13:29:99:451,0,477:12,4,12,1 chr2 43926943 . T A 1424.45 PASS AC=1;AF=0.662;AN=2;DP=4440;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,77:130:99:2081,0,1406:28,25,40,37 chr2 43931176 . T C 1474.32 PASS AC=1;AF=0.662;AN=2;DP=3392;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,53:113:99:1313,0,1418:31,29,28,25 chr2 43931321 . G A 533.84 PASS AC=1;AF=0.662;AN=2;DP=1157;set=variant-variant2-variant4-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,19:37:99:638,0,503:4,14,2,17 chr2 43937723 . CTTTTT CTTTT,CTTTTTTT,CTTTTTT,CTTTTTTTT,CTTT,C 137.46 PASS AC=0,0,1,0,0,0;AF=0.188,0.063,0.234,0.031,0.016,0.016;AN=2;DP=1797;set=variant-variant2-variant4-filterInvariant7-filterInvariant8-variant9-filterInvariant10-variant11-variant12-filterInvariant13-variant14-variant15-filterInvariant16-variant19-filterInvariant20-variant21-filterInvariant22-variant23-variant26-variant27-filterInvariant28-filterInvariant29-filterInvariant31-variant32-variant33-filterInvariant34-filterInvariant35-variant38-variant39-filterInvariant40-variant42-variant44 GT:DP:GQ:SB 0/3:27:90:5,12,3,7 chr2 43991357 . A C 686.62 PASS AC=2;AF=0.791;AN=2;DP=1259;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:928,75,0:0,0,21,4 chr2 44055446 . G A 174.84 PASS AC=1;AF=0.574;AN=2;DP=545;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant12-variant13-variant16-variant19-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,9:24:99:167,0,390:6,9,5,4 chr2 44055527 . T C 45.63 PASS AC=1;AF=0.661;AN=2;DP=262;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant16-variant19-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant32-variant34-variant35-variant37-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,5:14:99:102,0,193:4,5,3,2 chr2 44066174 . T G 920.6 PASS AC=1;AF=0.545;AN=2;DP=1844;FractionInformativeReads=1;set=variant2-variant4-variant5-variant7-variant8-variant12-variant13-variant17-variant19-variant23-variant24-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,55:109:99:1472,0,1477:26,28,27,28 chr2 44071625 . C A 993.84 PASS AC=1;AF=0.6;AN=2;DP=2590;MQ=60;set=variant2-variant4-variant5-variant8-variant12-variant13-variant17-variant19-variant23-variant24-variant27-variant30-variant31-variant32-variant34-variant35-variant37-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:79,74:153:99:1778,0,1827:36,43,35,39 chr2 44071639 . C T 847.8 PASS AC=1;AF=0.625;AN=2;DP=2519;MQ=60;set=variant2-variant4-variant5-variant8-variant12-variant13-variant17-variant19-variant23-variant24-variant27-variant30-variant31-variant32-variant34-variant35-variant37-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:78,72:150:99:1673,0,1884:33,45,32,40 chr2 44071743 . A G 454.91 PASS AC=1;AF=0.6;AN=2;DP=1342;MQ=60;set=variant2-variant4-variant5-variant8-variant12-variant13-variant17-variant19-variant23-variant24-variant27-variant30-variant31-variant32-variant34-variant35-variant37-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,33:66:99:795,0,778:14,19,12,21 chr2 44071833 . A C 139.66 PASS AC=1;AF=0.625;AN=2;DP=356;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant8-variant12-variant13-variant17-variant19-variant23-variant24-variant27-variant30-variant31-variant32-variant34-variant35-variant37-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,4:12:99:144,0,272:1,7,1,3 chr2 44079004 . T C 239.53 PASS AC=2;AF=0.676;AN=2;DP=2189;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,63:63:99:2225,189,0:0,0,14,49 chr2 44080185 . G A 204.57 PASS AC=1;AF=0.5;AN=2;DP=118;FractionInformativeReads=1;MQ=60;set=variant-variant33-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:26,18:44:99:475,0,695:10,16,5,13 chr2 44101214 . CA C 1285.91 PASS AC=2;AF=0.895;AN=2;DP=1589;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1628,123,0:0,0,9,32 chr2 44101394 . A G 163.44 PASS AC=2;AF=0.838;AN=2;DP=297;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:125,9,0:0,0,2,1 chr2 44101430 . T G 153.33 PASS AC=2;AF=0.757;AN=2;DP=564;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:276,24,0:0,0,5,3 chr2 44101649 . G GC,GCCC,GCC 1292.76 PASS AC=2,0,0;AF=0.476,0.226,0.119;AN=2;DP=2017;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:52:99:0,0,15,37 chr2 44101711 . T C 157.44 PASS AC=1;AF=0.545;AN=2;DP=419;MQ=60;set=variant2-variant4-variant5-variant9-variant10-variant11-variant14-variant16-variant18-variant21-variant25-variant26-variant28-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,12:22:99:365,0,256:2,8,2,10 chr2 44104925 . T C 7565.61 PASS AC=1;AF=0.826;AN=2;DP=10669;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:140,150:290:99:3546,0,3232:69,71,74,76 chr2 44114282 . CAAAAA CAAAAAAAAAAAAAAA,CAAAAAAAAAAAAAAAAAAA,CAAAAAAAAAAAAAAAAA,CAAAAAAAAAAAAAAAA,CAAAAAAAAAAAAAA,CAAA,C,CAAAA,CAA,CAAAAAAAAAA 85.69 PASS AC=2,0,0,0,0,0,0,0,0,0;AF=0.143,0.071,0.036,0.071,0.071,0.071,0.036,0.143,0.036,0.071;AN=2;DP=90;set=variant5-variant7-variant13-variant16-variant21-variant23-variant25-variant26-variant27-variant31-variant32-variant35-variant39-variant40 GT:DP:GQ:SB 1/1:3:12:0,0,3,0 chr2 44114304 . G A 49.72 PASS AC=1;AF=0.5;AN=2;DP=12;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.537;QD=4.14;ReadPosRankSum=2.041;SOR=0.039;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:10,2:12:78:78,0,307:9,1,1,1 chr2 44115183 . T A 132.16 PASS AC=1;AF=0.542;AN=2;DP=492;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant10-variant17-variant21-variant25-variant32-variant33-variant34-variant35-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:28,23:51:99:626,0,666:15,13,12,11 chr2 44116836 . C T 1801.87 PASS AC=1;AF=0.683;AN=2;DP=3123;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant9-variant10-variant14-variant15-variant17-variant18-variant21-variant22-variant23-variant25-variant26-variant27-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,50:106:99:1163,0,1402:30,26,26,24 chr2 44117563 . A C 1130.82 PASS AC=1;AF=0.545;AN=2;DP=548;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant10-variant21-variant25-variant32-variant33-variant34-variant35-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:15,27:42:99:977,0,413:2,13,2,25 chr2 44121928 . T C 201.22 PASS AC=1;AF=0.563;AN=2;DP=56;FS=0;FractionInformativeReads=1;MQ=60;set=variant17-variant21-variant25-variant32-variant34-variant35-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:1,5:6:24:204,0,24:0,1,0,5 chr2 44123758 . G A 974.72 PASS AC=1;AF=0.542;AN=2;DP=924;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant10-variant17-variant21-variant25-variant32-variant33-variant34-variant35-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:22,44:66:99:980,0,500:13,9,23,21 chr2 44152058 . A G 676.99 PASS AC=1;AF=0.545;AN=2;DP=685;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant10-variant21-variant25-variant32-variant33-variant34-variant35-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:45,50:95:99:1186,0,1066:27,18,30,20 chr2 44152180 . G A 2885.92 PASS AC=1;AF=0.717;AN=2;DP=3055;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant9-variant10-variant14-variant15-variant17-variant18-variant21-variant22-variant23-variant25-variant26-variant27-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,66:121:99:1663,0,1322:25,30,32,34 chr2 44152995 . C G 1909.5 PASS AC=1;AF=0.545;AN=2;DP=1466;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant10-variant21-variant25-variant32-variant33-variant34-variant35-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:68,72:140:99:1684,0,1659:34,34,34,38 chr2 44187652 . A G 1203.6 PASS AC=1;AF=0.545;AN=2;DP=1223;MQ=60;set=variant-variant5-variant10-variant21-variant25-variant32-variant33-variant34-variant35-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:40,58:98:99:1428,0,862:22,18,33,25 chr2 44187829 . A C 432.64 PASS AC=2;AF=0.807;AN=2;DP=2201;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1476,138,0:0,0,14,32 chr2 44204017 . C G 211.45 PASS AC=1;AF=0.545;AN=2;DP=146;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant10-variant21-variant25-variant32-variant33-variant34-variant35-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:8,9:17:99:297,0,264:6,2,8,1 chr2 44209477 . C T 818.13 PASS AC=2;AF=0.807;AN=2;DP=2931;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,89:89:99:2532,267,0:0,0,43,46 chr2 44222881 . C A 215.22 PASS AC=1;AF=0.556;AN=2;DP=131;FractionInformativeReads=1;MQ=60;set=variant5-variant10-variant21-variant25-variant32-variant33-variant35-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:5,10:15:99:257,0,129:3,2,6,4 chr2 44223131 . C T 860.08 PASS AC=1;AF=0.5;AN=2;DP=823;MQ=60;set=variant-variant5-variant21-variant25-variant32-variant33-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:84,47:131:99:925,0,2066:43,41,21,26 chr2 44396235 . T G 3526.53 PASS AC=1;AF=0.864;AN=2;DP=4903;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:40,54:94:99:1586,0,969:18,22,27,27 chr2 44396279 . C CCGGAGGCGG 3952.54 PASS AC=1;AF=0.864;AN=2;DP=4352;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:46,52:98:99:2128,0,2130:25,21,27,25 chr2 44502788 . A C 4137.5 PASS AC=2;AF=0.821;AN=2;DP=8919;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,206:206:99:5884,618,0:0,0,105,101 chr2 44508835 . G A 526.57 PASS AC=2;AF=0.786;AN=2;DP=422;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:386,30,0:0,0,2,8 chr2 44512797 . T C 821.71 PASS AC=1;AF=0.5;AN=2;DP=191;FractionInformativeReads=1;MQ=60;set=variant14-variant35 GT:AD:DP:GQ:PL:SB 0/1:44,50:94:99:1169,0,1078:22,22,27,23 chr2 44512971 . G A 3208.95 PASS AC=2;AF=0.811;AN=2;DP=2520;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:2101,179,0:0,0,33,27 chr2 44531081 . G T 190.65 PASS AC=2;AF=0.8;AN=2;DP=701;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:1005,78,0:0,0,22,4 chr2 44531484 . C T 308.47 PASS AC=2;AF=0.797;AN=2;DP=1592;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:1706,141,0:0,0,7,40 chr2 44541706 . G C 1922.28 PASS AC=2;AF=0.813;AN=2;DP=4369;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,135:135:99:5499,406,0:0,0,61,74 chr2 44541725 . C T 1871.62 PASS AC=2;AF=0.797;AN=2;DP=3314;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,107:107:99:4896,328,0:0,0,47,60 chr2 44541731 . C CCA 934.16 PASS AC=2;AF=0.662;AN=2;DP=3063;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,70:72:99:2444,142,0:1,1,28,42 chr2 44541917 . AAT A 1654.87 PASS AC=2;AF=0.797;AN=2;DP=3009;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,88:88:99:3622,265,0:0,0,45,43 chr2 44542061 . ATT ATTT,ATTTT,AT,A 107.94 PASS AC=1,0,0,0;AF=0.348,0.13,0.022,0.022;AN=2;DP=993;set=variant-filterInvariant2-variant3-variant4-variant7-variant8-filterInvariant11-variant13-filterInvariant19-filterInvariant20-variant22-filterInvariant26-variant27-variant30-variant31-variant35-variant36-filterInvariant37-variant38-variant39-filterInvariant40-filterInvariant41-variant42 GT:DP:GQ:SB 0/1:20:51:0,6,3,11 chr2 44544955 . G A 166.1 PASS AC=2;AF=0.797;AN=2;DP=1448;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1362,135,0:0,0,22,23 chr2 44545234 . GTTT GTT,GT,G,GTTTT 463.84 PASS AC=2,0,0,0;AF=0.663,0.013,0.075,0.013;AN=2;DP=4472;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:84:99:2,3,27,52 chr2 44545576 . T C 2375.56 PASS AC=2;AF=0.797;AN=2;DP=6528;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,180:180:99:5545,539,0:0,0,110,70 chr2 44545739 . GAAATGATACA G 3321.96 PASS AC=1;AF=0.5;AN=2;DP=8856;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,162:193:99:6274,0,2859:19,12,73,89 chr2 44545751 . TCTG T 3375.94 PASS AC=1;AF=0.513;AN=2;DP=7576;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,149:163:99:6316,0,2288:9,5,61,88 chr2 44545758 . C A 3269.68 PASS AC=1;AF=0.575;AN=2;DP=7164;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,145:152:99:6229,0,1667:4,3,60,85 chr2 44545761 . T G 3158.76 PASS AC=1;AF=0.625;AN=2;DP=7031;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,146:153:99:6151,0,1442:4,3,63,83 chr2 44545764 . A ACAG 2975.76 PASS AC=1;AF=0.625;AN=2;DP=6901;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,144:151:99:6235,0,1436:4,3,63,81 chr2 44545766 . A ATGTATCATTT 2977.56 PASS AC=1;AF=0.625;AN=2;DP=6729;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,142:149:99:6319,0,1430:4,3,63,79 chr2 44546016 . C T 1256.34 PASS AC=2;AF=0.813;AN=2;DP=3987;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:2581,216,0:0,0,49,23 chr2 44546741 . T C 2800.52 PASS AC=2;AF=0.797;AN=2;DP=7172;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,197:197:99:6343,590,0:0,0,103,94 chr2 44547131 . A G 3844.28 PASS AC=2;AF=0.797;AN=2;DP=12655;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,358:358:99:10000,1070,0:0,0,177,181 chr2 44547574 . G A 2331.79 PASS AC=2;AF=0.797;AN=2;DP=4442;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,123:123:99:4079,369,0:0,0,61,62 chr2 44547909 . T C 3005.72 PASS AC=2;AF=0.797;AN=2;DP=8226;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,217:217:99:6756,649,0:0,0,99,118 chr2 44548282 . T C 514.42 PASS AC=2;AF=0.818;AN=2;DP=1510;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1400,114,0:0,0,20,18 chr2 44548613 . T C 1188.75 PASS AC=2;AF=0.797;AN=2;DP=2093;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:2316,224,0:0,0,33,42 chr2 44556298 . T C 398.92 PASS AC=2;AF=0.813;AN=2;DP=804;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,31:31:93:1084,93,0:0,0,7,24 chr2 44565447 . A T 323.09 PASS AC=2;AF=0.784;AN=2;DP=1010;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1100,99,0:0,0,24,9 chr2 44569474 . G A 94.47 PASS AC=2;AF=0.774;AN=2;DP=842;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:960,75,0:0,0,21,4 chr2 44569700 . AAAT A 737.18 PASS AC=2;AF=0.784;AN=2;DP=2005;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1746,118,0:0,0,21,18 chr2 44569739 . T TA 146.81 PASS AC=1;AF=0.605;AN=2;DP=1161;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-filterInvariant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,19:24:41:381,0,41:1,4,4,15 chr2 44570776 . C T 567.13 PASS AC=2;AF=0.784;AN=2;DP=2263;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1537,135,0:0,0,33,12 chr2 44570804 . C A 753.97 PASS AC=2;AF=0.784;AN=2;DP=3227;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,66:66:99:2110,197,0:0,0,45,21 chr2 44573624 . G A 257.58 PASS AC=2;AF=0.774;AN=2;DP=778;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:624,48,0:0,0,2,14 chr2 44573658 . T C 121.67 PASS AC=2;AF=0.803;AN=2;DP=341;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:266,21,0:0,0,1,6 chr2 44573671 . G T 115.73 PASS AC=2;AF=0.838;AN=2;DP=240;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:225,15,0:0,0,0,5 chr2 44587790 . G T 278.86 PASS AC=1;AF=0.5;AN=2;DP=21;FS=1.808;FractionInformativeReads=1;MQ=60;MQRankSum=0.106;QD=13.28;ReadPosRankSum=1.021;SOR=1.276;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:10,11:21:99:307,0,268:4,6,3,8 chr2 44588941 . G A 839.14 PASS AC=2;AF=0.784;AN=2;DP=3651;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,109:109:99:3498,326,0:0,0,62,47 chr2 44617324 . T A 662.58 PASS AC=2;AF=0.813;AN=2;DP=2204;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:1776,171,0:0,0,38,19 chr2 44622256 . A C 370.16 PASS AC=2;AF=0.833;AN=2;DP=371;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:383,36,0:0,0,3,9 chr2 44858687 . T C 650.99 PASS AC=1;AF=0.764;AN=2;DP=1665;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant33-variant34-variant35-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,27:52:99:603,0,598:16,9,18,9 chr2 44942384 . C G 385.11 PASS AC=1;AF=0.684;AN=2;DP=1742;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,16:39:99:351,0,553:13,10,11,5 chr2 44981119 . T G 457.79 PASS AC=1;AF=0.5;AN=2;DP=950;MQ=60;set=variant-variant7-variant11-variant14-variant19-variant24-variant25-variant26-variant28-variant34-variant35-variant36-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,34:67:99:801,0,905:22,11,18,16 chr2 44999603 . AT A,ATT 1014.3 PASS AC=1,0;AF=0.489,0.011;AN=2;DP=14333;set=variant-variant2-filterInvariant3-variant4-variant5-variant6-filterInvariant7-variant8-filterInvariant9-filterInvariant10-variant11-filterInvariant12-filterInvariant13-filterInvariant14-filterInvariant15-filterInvariant16-variant17-filterInvariant18-variant19-variant20-filterInvariant21-variant22-variant23-variant24-filterInvariant25-filterInvariant26-filterInvariant27-variant28-filterInvariant29-filterInvariant30-variant31-filterInvariant32-variant33-variant34-variant35-variant36-filterInvariant37-variant38-filterInvariant39-variant40-filterInvariant41-filterInvariant42-variant43-variant44 GT:DP:GQ:SB 0/1:353:99:134,126,41,52 chr2 45171842 . A G 5168.89 PASS AC=2;AF=0.953;AN=2;DP=10168;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,259:259:99:7736,776,0:0,0,126,133 chr2 45172449 . TAAAAA TAA,T,TAAAA,TAAA,TA 165.18 PASS AC=1,0,0,0,0;AF=0.3,0.12,0.08,0.08,0.1;AN=2;DP=268;set=variant-variant2-variant6-variant8-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant38-variant41-variant43 GT:DP:GQ:SB 0/1:9:92:5,0,4,0 chr2 45172925 . G A 1500.28 PASS AC=1;AF=0.553;AN=2;DP=2834;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant9-variant15-variant16-variant22-variant24-variant26-variant29-variant30-variant32-variant33-variant35-variant36-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:92,92:184:99:2055,0,2460:37,55,37,55 chr2 45232686 . A C 427.01 PASS AC=2;AF=0.852;AN=2;DP=1324;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:795,78,0:0,0,9,17 chr2 45640334 . T C 917.6 PASS AC=2;AF=0.536;AN=2;DP=1167;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant10-variant16-variant23-variant27-variant31-variant32-variant33-variant35-variant36-variant37-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,91:91:99:2709,273,0:0,0,50,41 chr2 45647071 . A G 593.52 PASS AC=1;AF=0.5;AN=2;DP=160;MQ=60;set=variant16-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:37,31:68:99:798,0,1168:9,28,9,22 chr2 45774548 . A C 2346.2 PASS AC=2;AF=0.857;AN=2;DP=2823;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:2205,236,0:0,0,42,37 chr2 45778459 . C T 451.37 PASS AC=2;AF=0.538;AN=2;DP=308;FractionInformativeReads=1;set=variant-variant3-variant4-variant13-variant16-variant27-variant28-variant31-variant32-variant33-variant35-variant36-variant37 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:900,81,0:0,0,6,21 chr2 45812666 . A G 1008.09 PASS AC=2;AF=0.531;AN=2;DP=913;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant10-variant13-variant16-variant23-variant27-variant28-variant31-variant32-variant33-variant35-variant36-variant37-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:2065,213,0:0,0,40,31 chr2 45826526 . CT C 3234.74 PASS AC=2;AF=0.778;AN=2;DP=3078;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,83:83:99:3310,249,0:0,0,61,22 chr2 45829286 . A C 478.21 PASS AC=2;AF=0.55;AN=2;DP=423;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant10-variant13-variant16-variant19-variant20-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:445,33,0:0,0,2,9 chr2 45838565 . C CG 175.11 PASS AC=2;AF=0.6;AN=2;DP=177;MQ=60;set=variant4-variant5-variant7-variant14-variant16-variant22-variant32-variant34-variant35-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,12:13:9:384,9,0:0,1,5,7 chr2 45879610 . A G 441.08 PASS AC=2;AF=0.864;AN=2;DP=742;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:595,48,0:0,0,2,14 chr2 46203796 . G C,A 2418.97 PASS AC=1,0;AF=0.449,0.256;AN=2;DP=2485;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43 GT:DP:GQ:SB 0/1:62:99:9,25,8,20 chr2 46228166 . C T 55.49 PASS AC=1;AF=0.5;AN=2;DP=82;FractionInformativeReads=1;MQ=60;set=variant21-variant22-variant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:11,6:17:99:129,0,280:4,7,2,4 chr2 46231942 . C T 260.13 PASS AC=1;AF=0.5;AN=2;DP=126;FractionInformativeReads=1;MQ=60;set=variant21-variant22-variant35 GT:AD:DP:GQ:PL:SB 0/1:25,25:50:99:711,0,649:8,17,7,18 chr2 46232042 . A C 193.52 PASS AC=1;AF=0.8;AN=2;DP=338;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,3:12:58:58,0,240:3,6,1,2 chr2 46234568 . A G 1065.32 PASS AC=1;AF=0.6;AN=2;DP=2413;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant11-variant12-variant15-variant16-variant19-variant26-variant27-variant32-variant33-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:77,69:146:99:1667,0,1790:42,35,43,26 chr2 46237446 . C A 634.59 PASS AC=1;AF=0.575;AN=2;DP=1445;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant10-variant13-variant14-variant15-variant17-variant21-variant22-variant24-variant28-variant31-variant32-variant34-variant35-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:38,38:76:99:965,0,999:25,13,24,14 chr2 46238244 . A G 1757.73 PASS AC=2;AF=0.93;AN=2;DP=1271;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1549,125,0:0,0,4,38 chr2 46378419 . TACACACAC TACACACACAC,TACACAC,TACAC,TAC,TACACACACACAC,TACACACACACACAC,T,TACACACACACACACAC 491.57 PASS AC=0,0,0,0,2,0,0,0;AF=0.288,0.063,0.2,0.088,0.05,0.038,0.075,0.013;AN=2;DP=1964;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-filterInvariant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 5/5:13:32:0,1,5,7 chr2 46583235 . C A 123.2 PASS AC=1;AF=0.703;AN=2;DP=331;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:6,7:13:99:157,0,151:3,3,5,2 chr2 46583281 . C CCT,T,CT 598.88 PASS AC=0,0,1;AF=0.023,0.545,0.091;AN=2;DP=383;MQ=60;set=variant15-variant18-variant19-variant20-variant21-variant22-variant2-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant42 GT:DP:GQ:SB 0/3:15:99:3,4,4,4 chr2 46584059 . T G 272.24 PASS AC=1;AF=0.5;AN=2;DP=187;FractionInformativeReads=1;MQ=60;set=variant4-variant8-variant14-variant15-variant24-variant35-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:10,8:18:99:246,0,357:1,9,1,7 chr2 46602678 . C A 202.45 PASS AC=1;AF=0.696;AN=2;DP=353;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant9-variant11-variant13-variant14-variant16-variant17-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,11:15:80:320,0,80:3,1,7,4 chr2 46602722 . T C 410.25 PASS AC=1;AF=0.672;AN=2;DP=696;MQ=60;set=variant-variant2-variant4-variant5-variant9-variant10-variant11-variant13-variant14-variant16-variant17-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,16:29:99:380,0,352:9,4,10,6 chr2 46603671 . C G 2475.81 PASS AC=1;AF=0.667;AN=2;DP=3936;MQ=60;set=variant-variant2-variant4-variant5-variant9-variant10-variant11-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:83,40:123:99:986,0,2267:44,39,20,20 chr2 46605659 . A G 798.43 PASS AC=1;AF=0.75;AN=2;DP=516;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,5:17:99:171,0,489:12,0,5,0 chr2 46605954 . G C 2044.17 PASS AC=1;AF=0.682;AN=2;DP=2517;MQ=60;set=variant-variant2-variant4-variant5-variant9-variant10-variant11-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,41:86:99:977,0,1370:10,35,13,28 chr2 46608542 . C G 199.22 PASS AC=1;AF=0.71;AN=2;DP=630;MQ=60;set=variant-variant2-variant4-variant5-variant9-variant10-variant11-variant13-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,17:32:99:602,0,414:11,4,16,1 chr2 46612326 . GTT G,GT 10765.4 PASS AC=2,0;AF=0.683,0.134;AN=2;DP=16130;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:360:99:11,2,169,178 chr2 46707378 . C G 274.36 PASS AC=1;AF=0.5;AN=2;DP=38;FractionInformativeReads=1;MQ=60;set=variant15-variant35 GT:AD:DP:GQ:PL:SB 0/1:11,11:22:99:338,0,311:7,4,7,4 chr2 46746682 . A G 8460.03 PASS AC=2;AF=0.93;AN=2;DP=7418;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,208:208:99:6342,622,0:0,0,118,90 chr2 46746745 . G A 11580.4 PASS AC=2;AF=0.672;AN=2;DP=8437;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant9-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,308:308:99:9390,922,0:0,0,173,135 chr2 46763587 . G A 258.91 PASS AC=2;AF=0.815;AN=2;DP=187;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant25-variant27-variant28-variant30-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:177,18,0:0,0,3,3 chr2 46768543 . A C 722.33 PASS AC=2;AF=0.893;AN=2;DP=2312;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,59:60:99:1617,169,0:0,1,32,27 chr2 46768559 . G A 389.92 PASS AC=2;AF=0.667;AN=2;DP=1195;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant14-variant15-variant17-variant18-variant19-variant25-variant30-variant33-variant35-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,64:64:99:1830,192,0:0,0,34,30 chr2 46769334 . ATTT ATTTTT,AT,ATT,A,ATTTT,ATTTTTT 145.78 PASS AC=0,0,1,0,0,0;AF=0.173,0.077,0.385,0.019,0.019,0.019;AN=2;DP=386;set=variant8-variant9-variant11-variant13-variant14-filterInvariant15-variant16-variant17-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant39-variant41-variant43-variant44 GT:DP:GQ:SB 0/3:17:99:5,4,5,3 chr2 46771134 . G C 1177.9 PASS AC=2;AF=0.857;AN=2;DP=1735;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1888,147,0:0,0,6,43 chr2 46815289 . A G 998.25 PASS AC=1;AF=0.5;AN=2;DP=76;FS=0.886;FractionInformativeReads=1;MQ=60;MQRankSum=-0.99;QD=13.13;ReadPosRankSum=-1.772;SOR=0.843;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:35,41:76:99:1026,0,861:14,21,15,26 chr2 46844082 . A AG 896.71 PASS AC=2;AF=1;AN=2;DP=1698;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1695,126,0:0,0,32,10 chr2 46844219 . C CG 2799.65 PASS AC=2;AF=1;AN=2;DP=3988;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,104:104:99:3858,313,0:0,0,56,48 chr2 46852120 . CT C,CTT 2003.78 PASS AC=1,0;AF=0.477,0.023;AN=2;DP=15054;set=Intersection GT:DP:GQ:SB 0/1:314:99:73,88,71,82 chr2 46852210 . GTT GT,G 539.83 PASS AC=1,0;AF=0.456,0.044;AN=2;DP=4717;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant12-variant13-filterInvariant15-filterInvariant16-filterInvariant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-filterInvariant29-variant31-variant32-variant33-variant34-filterInvariant35-variant36-variant37-variant40-variant41-variant43-variant44 GT:DP:GQ:SB 0/1:110:99:29,47,4,30 chr2 46852514 . CTTTTT CT,C,CTT,CTTT,CTTTT 59.04 PASS AC=0,0,0,0,2;AF=0.063,0.063,0.125,0.188,0.125;AN=2;DP=101;MQ=60;set=variant10-variant16-variant20-variant23-variant28-variant33-variant35-variant42 GT:DP:GQ:SB 5/5:7:20:0,0,3,4 chr2 46926064 . C G 287.2 PASS AC=1;AF=0.662;AN=2;DP=552;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant8-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,4:17:80:80,0,414:9,4,3,1 chr2 46987139 . G A 1022.29 PASS AC=1;AF=0.5;AN=2;DP=800;MQ=60;set=variant10-variant15-variant25-variant29-variant35-variant36-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:64,57:121:99:1377,0,1678:26,38,22,35 chr2 46987300 . T G 493.51 PASS AC=1;AF=0.613;AN=2;DP=531;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,3:11:99:102,0,192:3,5,0,3 chr2 46987935 . T G 11097.7 PASS AC=1;AF=0.567;AN=2;DP=9572;set=variant-variant2-variant4-variant5-variant7-variant8-variant10-variant12-variant15-variant16-variant17-variant18-variant20-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:172,157:329:99:3543,0,4020:91,81,85,72 chr2 47045267 . G A 1257.66 PASS AC=2;AF=0.671;AN=2;DP=1490;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:1920,176,0:0,0,43,16 chr2 47048969 . T C 329.76 PASS AC=2;AF=0.714;AN=2;DP=417;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant35-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:412,36,0:0,0,9,3 chr2 47048980 . A T 290.05 PASS AC=2;AF=0.583;AN=2;DP=174;FractionInformativeReads=1;MQ=60;set=variant3-variant9-variant10-variant13-variant14-variant15-variant23-variant30-variant32-variant35-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:519,51,0:0,0,12,5 chr2 47049453 . A G 2094.06 PASS AC=2;AF=0.692;AN=2;DP=3088;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,96:96:99:2837,287,0:0,0,46,50 chr2 47081092 . C T 894.82 PASS AC=1;AF=0.786;AN=2;DP=5155;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:82,68:150:99:1466,0,2032:34,48,31,37 chr2 47083030 . ATG A 232.73 PASS AC=1;AF=0.824;AN=2;DP=308;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,3:11:99:145,0,569:4,4,3,0 chr2 47083044 . A T 586.27 PASS AC=1;AF=0.861;AN=2;DP=524;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,7:20:99:200,0,708:8,5,6,1 chr2 47083252 . G T 766.42 PASS AC=1;AF=0.6;AN=2;DP=1296;MQ=60;set=variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant24-variant25-variant31-variant32-variant33-variant35-variant37-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,30:54:99:754,0,600:9,15,12,18 chr2 47085398 . C T 223.27 PASS AC=1;AF=0.781;AN=2;DP=557;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,12:24:99:352,0,309:6,6,2,10 chr2 47132834 . TAAA TAA,TAAAA,TAAAAA,TAAAAAA,T 390.36 PASS AC=1,0,0,0,0;AF=0.19,0.119,0.131,0.119,0.036;AN=2;DP=4679;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-filterInvariant11-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:73:99:26,24,15,8 chr2 47132945 . G T 2501.98 PASS AC=1;AF=0.625;AN=2;DP=5743;MQ=60;set=variant2-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant26-variant27-variant28-variant33-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:111,101:212:99:2354,0,2737:56,55,53,48 chr2 47177787 . G T 773.91 PASS AC=1;AF=0.577;AN=2;DP=646;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant6-variant7-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant25-variant26-variant27-variant28-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,16:30:99:514,0,481:1,13,1,15 chr2 47183650 . T C 43.48 PASS AC=2;AF=0.838;AN=2;DP=382;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:341,27,0:0,0,8,1 chr2 47185438 . G A 1238.86 PASS AC=1;AF=0.553;AN=2;DP=1936;MQ=60;set=variant4-variant6-variant10-variant12-variant13-variant14-variant18-variant19-variant22-variant23-variant24-variant25-variant27-variant30-variant34-variant35-variant37-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:55,52:107:99:1356,0,1606:42,13,39,13 chr2 47201797 . A T 599.09 PASS AC=2;AF=0.821;AN=2;DP=2472;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:1477,173,0:0,0,32,26 chr2 47201991 . CT C 717.83 PASS AC=1;AF=0.62;AN=2;DP=397;MQ=60;set=variant3-variant4-variant6-variant8-variant10-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant30-variant32-variant34-variant35-variant37-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:16,7:23:99:207,0,572:4,12,2,5 chr2 47202314 . C T 1297.5 PASS AC=1;AF=0.55;AN=2;DP=1124;MQ=60;set=variant5-variant10-variant14-variant28-variant33-variant35-variant37-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:73,40:113:99:850,0,1818:33,40,21,19 chr2 47220285 . T G 127.41 PASS AC=1;AF=0.625;AN=2;DP=195;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant7-variant8-variant11-variant14-variant15-variant17-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant35-variant36-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,6:11:99:196,0,146:4,1,4,2 chr2 47220414 . T A 836.39 PASS AC=1;AF=0.5;AN=2;DP=288;FractionInformativeReads=1;MQ=60;set=variant14-variant35-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:37,35:72:99:896,0,857:23,14,20,15 chr2 47222001 . T C 51.2 PASS AC=1;AF=0.625;AN=2;DP=187;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant11-variant15-variant17-variant18-variant23-variant25-variant26-variant29-variant31-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,3:9:99:105,0,163:4,2,2,1 chr2 47251469 . G C 1139.32 PASS AC=1;AF=0.542;AN=2;DP=1719;MQ=60;set=variant12-variant14-variant18-variant23-variant25-variant30-variant34-variant35-variant37-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:83,74:157:99:1810,0,2222:48,35,38,36 chr2 47251634 . T C 1454.14 PASS AC=1;AF=0.632;AN=2;DP=3488;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant21-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,57:105:99:1473,0,1307:14,34,22,35 chr2 47256297 . C T 279.85 PASS AC=1;AF=0.536;AN=2;DP=400;FractionInformativeReads=1;MQ=60;set=variant11-variant12-variant14-variant16-variant18-variant23-variant25-variant30-variant34-variant35-variant37-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:16,10:26:99:229,0,410:8,8,7,3 chr2 47256618 . A G 416.54 PASS AC=1;AF=0.545;AN=2;DP=659;FractionInformativeReads=1;MQ=60;set=variant5-variant9-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant23-variant24-variant25-variant26-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:15,26:41:99:694,0,411:4,11,8,18 chr2 47273668 . G A 512.49 PASS AC=1;AF=0.56;AN=2;DP=789;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant11-variant12-variant13-variant14-variant16-variant18-variant21-variant23-variant24-variant25-variant26-variant30-variant31-variant35-variant36-variant37-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,17:30:99:358,0,305:4,9,6,11 chr2 47277043 . C G 490.74 PASS AC=1;AF=0.568;AN=2;DP=1009;FractionInformativeReads=1;MQ=60;set=variant5-variant6-variant9-variant11-variant12-variant13-variant14-variant16-variant18-variant21-variant23-variant24-variant25-variant26-variant30-variant31-variant35-variant36-variant37-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:23,29:52:99:946,0,624:16,7,24,5 chr2 47277207 . C A 1502.72 PASS AC=1;AF=0.625;AN=2;DP=4672;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:78,68:146:99:2549,0,3876:38,40,29,39 chr2 47277208 . A G 1502.72 PASS AC=1;AF=0.625;AN=2;DP=4625;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:78,66:144:99:2549,0,3876:38,40,27,39 chr2 47278823 . C T 44.99 PASS AC=1;AF=0.588;AN=2;DP=176;FractionInformativeReads=1;MQ=60;set=variant6-variant9-variant11-variant12-variant13-variant18-variant21-variant24-variant25-variant26-variant30-variant31-variant35-variant36-variant37-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:7,5:12:99:165,0,227:4,3,3,2 chr2 47301386 . A G 2741.19 PASS AC=2;AF=1;AN=2;DP=3959;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,130:130:99:4156,390,0:0,0,62,68 chr2 47301624 . T TTGGGGCCTC 2690.3 PASS AC=2;AF=0.838;AN=2;DP=2490;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,73:73:99:3265,225,0:0,0,33,40 chr2 47301744 . T C 2659.31 PASS AC=2;AF=0.833;AN=2;DP=3928;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,126:126:99:3663,378,0:0,0,61,65 chr2 47302095 . T C 3824.36 PASS AC=2;AF=0.805;AN=2;DP=4704;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,119:119:99:3762,357,0:0,0,54,65 chr2 47302829 . C G 3237.32 PASS AC=2;AF=0.841;AN=2;DP=3429;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,97:97:99:3037,291,0:0,0,45,52 chr2 47314052 . T C 1321.99 PASS AC=2;AF=0.93;AN=2;DP=1384;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:921,81,0:0,0,19,8 chr2 47348347 . C T 3276.35 PASS AC=2;AF=0.826;AN=2;DP=5659;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,147:147:99:4163,439,0:0,0,76,71 chr2 47357458 . A G 1952.46 PASS AC=2;AF=0.849;AN=2;DP=3566;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,87:87:99:2647,261,0:0,0,33,54 chr2 47357564 . A T 297.18 PASS AC=1;AF=0.779;AN=2;DP=393;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant22-variant23-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,10:14:99:344,0,130:0,4,1,9 chr2 47380145 . T C 1170.4 PASS AC=1;AF=0.5;AN=2;DP=588;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant13-variant15-variant19-variant24-variant27-variant29-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:20,12:32:99:241,0,517:8,12,6,6 chr2 47380203 . T C 1472.2 PASS AC=1;AF=0.802;AN=2;DP=1897;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,14:28:99:334,0,299:7,7,5,9 chr2 47382214 . C G 2567.71 PASS AC=2;AF=0.989;AN=2;DP=3435;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:2233,204,0:0,0,45,23 chr2 47382606 . T A 499.66 PASS AC=2;AF=0.738;AN=2;DP=984;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:743,66,0:0,0,6,16 chr2 47387187 . T C 2196.59 PASS AC=1;AF=0.5;AN=2;DP=1626;MQ=60;set=variant3-variant6-variant13-variant14-variant15-variant19-variant24-variant27-variant29-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:77,65:142:99:1577,0,1869:45,32,38,27 chr2 47390026 . C T 193.54 PASS AC=1;AF=0.78;AN=2;DP=152;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant10-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,4:10:98:98,0,202:1,5,1,3 chr2 47399601 . A G 758.57 PASS AC=1;AF=0.5;AN=2;DP=635;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant13-variant15-variant19-variant24-variant27-variant29-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:32,20:52:99:472,0,873:11,21,7,13 chr2 47403383 . G T 170.35 PASS AC=1;AF=0.5;AN=2;DP=219;MQ=60;set=variant3-variant6-variant13-variant15-variant19-variant24-variant27-variant29-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:10,18:28:99:504,0,332:7,3,11,7 chr2 47601106 . T C 2991.84 PASS AC=1;AF=0.704;AN=2;DP=3395;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant10-variant12-variant15-variant17-variant18-variant23-variant25-variant26-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,73:129:99:1910,0,1418:33,23,33,40 chr2 47605097 . C T 65.72 PASS AC=1;AF=0.625;AN=2;DP=151;FractionInformativeReads=1;set=variant-variant2-variant4-variant5-variant7-variant12-variant15-variant17-variant26-variant30-variant33-variant34-variant35-variant36-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:7,5:12:99:108,0,177:2,5,2,3 chr2 47612224 . C T 376.47 PASS AC=1;AF=0.614;AN=2;DP=935;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant10-variant12-variant13-variant15-variant17-variant26-variant28-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:25,19:44:99:396,0,543:15,10,11,8 chr2 47630550 . C G 1273.69 PASS AC=1;AF=0.673;AN=2;DP=1600;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant10-variant12-variant15-variant17-variant18-variant23-variant25-variant26-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,33:76:99:679,0,1046:17,26,12,21 chr2 47641559 . TAAAAAA TAAA,TAAAAA,T,TAAAA,TA,TAA 280.44 PASS AC=0,0,0,0,0,1;AF=0.155,0.052,0.034,0.19,0.086,0.138;AN=2;DP=1123;set=variant-variant2-variant3-variant7-variant8-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:DP:GQ:SB 0/6:25:99:4,12,2,7 chr2 47656871 . T C 228.4 PASS AC=1;AF=0.5;AN=2;DP=18;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.53;QD=12.69;ReadPosRankSum=-0.177;SOR=1.201;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:9,9:18:99:257,0,232:6,3,7,2 chr2 47672569 . G A 770.47 PASS AC=2;AF=0.757;AN=2;DP=596;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:669,51,0:0,0,16,1 chr2 47690404 . T C 739.62 PASS AC=1;AF=0.63;AN=2;DP=969;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant10-variant12-variant13-variant15-variant17-variant23-variant25-variant26-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,18:39:99:669,0,1702:8,13,7,11 chr2 47690408 . A G 742.62 PASS AC=1;AF=0.619;AN=2;DP=724;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant10-variant12-variant15-variant17-variant26-variant28-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:20,16:36:99:647,0,1705:8,12,6,10 chr2 47690411 . T C 646.46 PASS AC=1;AF=0.63;AN=2;DP=897;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant10-variant12-variant13-variant15-variant17-variant23-variant25-variant26-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,16:34:99:615,0,1623:7,11,6,10 chr2 47693706 . G T 251.06 PASS AC=1;AF=0.636;AN=2;DP=512;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant10-variant12-variant13-variant15-variant17-variant26-variant28-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:19,7:26:99:229,0,603:15,4,6,1 chr2 47693959 . G A 401.51 PASS AC=1;AF=0.643;AN=2;DP=387;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant10-variant12-variant13-variant15-variant17-variant26-variant28-variant30-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,10:22:99:340,0,395:2,10,1,9 chr2 47698308 . A G 1146.65 PASS AC=1;AF=0.636;AN=2;DP=1779;set=variant-variant2-variant4-variant5-variant7-variant10-variant12-variant13-variant15-variant17-variant26-variant28-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:35,38:73:99:1079,0,1014:17,18,13,25 chr2 47698384 . G A 786.36 PASS AC=1;AF=0.64;AN=2;DP=1540;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant10-variant12-variant13-variant15-variant17-variant23-variant25-variant26-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,25:66:99:603,0,1044:17,24,13,12 chr2 47703379 . C T 585.83 PASS AC=2;AF=0.989;AN=2;DP=511;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.37;ReadPosRankSum=-1.664;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:546,39,0:0,0,12,1 chr2 47703500 . T C 1290.63 PASS AC=1;AF=0.5;AN=2;DP=561;MQ=60;set=variant-variant17-variant26-variant33-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:29,72:101:99:2017,0,637:19,10,46,26 chr2 47709807 . T A 31.98 PASS AC=1;AF=0.5;AN=2;DP=58;MQ=60;set=variant7-variant16-variant22-variant23-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:3,7:10:79:158,0,79:3,0,6,1 chr2 47739551 . A G 1176.22 PASS AC=2;AF=0.7;AN=2;DP=3212;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant10-variant12-variant13-variant15-variant16-variant17-variant21-variant22-variant23-variant26-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,118:118:99:3713,354,0:0,0,50,68 chr2 47740198 . G T 132.55 PASS AC=2;AF=0.694;AN=2;DP=1027;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant10-variant12-variant13-variant15-variant16-variant17-variant21-variant22-variant23-variant25-variant26-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1400,126,0:0,0,19,23 chr2 47748292 . A G 6293.49 PASS AC=2;AF=0.717;AN=2;DP=5041;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant26-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,217:217:99:6889,650,0:0,0,107,110 chr2 47798037 . A G 656.51 PASS AC=1;AF=0.658;AN=2;DP=2085;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,42:84:99:999,0,1133:18,24,16,26 chr2 47888040 . A C 854.97 PASS AC=1;AF=0.5;AN=2;DP=258;FractionInformativeReads=1;MQ=60;set=variant9-variant21-variant22-variant35 GT:AD:DP:GQ:PL:SB 0/1:42,23:65:99:614,0,1120:19,23,11,12 chr2 48010558 . C A 2898.27 PASS AC=1;AF=0.55;AN=2;DP=1411;MQ=60;set=variant3-variant7-variant25-variant26-variant27-variant33-variant35-variant36-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:82,66:148:99:1535,0,1886:33,49,23,43 chr2 48010654 . C G 1029.19 PASS AC=1;AF=0.545;AN=2;DP=560;MQ=60;set=variant3-variant7-variant18-variant25-variant26-variant27-variant33-variant35-variant36-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,18:41:99:367,0,619:7,16,7,11 chr2 48016314 . T C 394.37 PASS AC=1;AF=0.63;AN=2;DP=601;set=variant3-variant6-variant7-variant9-variant12-variant15-variant19-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,13:34:99:389,0,515:14,7,9,4 chr2 48016353 . G A 480.22 PASS AC=1;AF=0.55;AN=2;DP=418;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant25-variant26-variant27-variant33-variant35-variant36-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,18:47:99:539,0,732:18,11,12,6 chr2 48018081 . A G 2070.65 PASS AC=1;AF=0.55;AN=2;DP=1256;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant25-variant26-variant27-variant33-variant35-variant36-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,56:117:99:1448,0,1596:32,29,32,24 chr2 48018314 . T A 518.92 PASS AC=1;AF=0.636;AN=2;DP=559;set=variant3-variant6-variant7-variant9-variant12-variant15-variant19-variant22-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,10:20:99:254,0,310:1,9,3,7 chr2 48022900 . A G 34.46 PASS AC=1;AF=0.821;AN=2;DP=368;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,7:10:65:197,0,65:2,1,5,2 chr2 48023115 . T C 1257.01 PASS AC=1;AF=0.595;AN=2;DP=1142;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant6-variant7-variant12-variant18-variant19-variant22-variant23-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant35-variant36-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,30:55:99:732,0,532:11,14,14,16 chr2 48030458 . G C 497.3 PASS AC=1;AF=0.774;AN=2;DP=1660;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,14:37:99:348,0,626:17,6,9,5 chr2 48030838 . A T 1459.99 PASS AC=1;AF=0.54;AN=2;DP=2127;MQ=60;set=variant3-variant5-variant7-variant8-variant13-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant35-variant36-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,27:77:99:663,0,1332:19,31,12,15 chr2 48032874 . ACTAT A 1073.15 PASS AC=1;AF=0.738;AN=2;DP=2321;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,27:47:99:1033,0,822:7,13,13,14 chr2 48032937 . T C 410.43 PASS AC=1;AF=0.762;AN=2;DP=908;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,9:14:99:332,0,145:1,4,0,9 chr2 48033551 . C G 1714.99 PASS AC=1;AF=0.774;AN=2;DP=5220;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,50:118:99:1284,0,1968:32,36,21,29 chr2 48033890 . CTTT CTT,CTTCTTTT,CT,C 367.34 PASS AC=1,0,0,0;AF=0.446,0.014,0.095,0.027;AN=2;DP=1624;set=variant-variant2-filterInvariant3-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant13-filterInvariant14-variant15-variant16-variant19-filterInvariant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-filterInvariant44 GT:DP:GQ:SB 0/1:28:99:7,6,8,7 chr2 48034806 . TA T 778.96 PASS AC=1;AF=0.726;AN=2;DP=3626;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,37:72:99:814,0,688:14,21,11,26 chr2 48040904 . G GA 1724.48 PASS AC=2;AF=0.966;AN=2;DP=3270;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:2329,225,0:0,0,45,30 chr2 48046012 . TA T 217.92 PASS AC=1;AF=0.5;AN=2;DP=1118;MQ=60;set=variant2-filterInvariant3-filterInvariant4-variant6-variant8-filterInvariant9-variant10-variant11-filterInvariant12-filterInvariant14-variant16-variant18-filterInvariant19-filterInvariant20-variant23-variant25-variant27-filterInvariant29-filterInvariant31-variant33-variant34-variant35-variant36-filterInvariant40-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:33,11:44:99:156,0,564:22,11,6,5 chr2 48059471 . AAAAT A 1564.95 PASS AC=1;AF=0.548;AN=2;DP=1501;MQ=60;set=variant-variant2-variant4-variant6-variant8-variant9-variant10-variant13-variant14-variant16-variant17-variant19-variant20-variant27-variant28-variant33-variant35-variant37-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:43,46:89:99:1802,0,2468:25,18,30,16 chr2 48066232 . CT C 35.43 PASS AC=1;AF=0.5;AN=2;DP=43;FS=0;MQ=60;set=variant3-variant26-variant35-variant36-variant41 GT:AD:DP:GQ:PL:SB 0/1:3,4:7:63:92,0,63:0,3,0,4 chr2 48555621 . C T 163.62 PASS AC=1;AF=0.605;AN=2;DP=254;FractionInformativeReads=1;MQ=60;set=variant7-variant8-variant12-variant18-variant19-variant20-variant23-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,5:12:99:108,0,143:4,3,3,2 chr2 48573875 . A G 1353.81 PASS AC=1;AF=0.5;AN=2;DP=68;FS=3.73;FractionInformativeReads=1;MQ=60;MQRankSum=-0.525;QD=19.91;ReadPosRankSum=-1.229;SOR=1.244;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:30,38:68:99:1382,0,1692:10,20,9,29 chr2 48573895 . G C 671.94 PASS AC=1;AF=0.556;AN=2;DP=478;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant25-variant26-variant33-variant34-variant35-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:23,29:52:99:1135,0,1535:6,17,6,23 chr2 48586140 . G C 336.54 PASS AC=1;AF=0.5;AN=2;DP=43;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.79;QD=7.83;ReadPosRankSum=-0.972;SOR=0.902;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:29,14:43:99:365,0,800:19,10,10,4 chr2 48602252 . C T 2193.99 PASS AC=1;AF=0.604;AN=2;DP=3477;MQ=60;set=variant7-variant8-variant9-variant12-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:90,65:155:99:1636,0,2559:39,51,30,35 chr2 48603483 . A C 2652.52 PASS AC=2;AF=0.611;AN=2;DP=6652;MQ=60;set=variant6-variant7-variant8-variant9-variant12-variant13-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,257:257:99:7583,770,0:0,0,114,143 chr2 48604978 . C T 6089.18 PASS AC=1;AF=0.6;AN=2;DP=10494;MQ=60;set=variant7-variant8-variant9-variant12-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:246,223:469:99:5780,0,6230:107,139,95,128 chr2 48605827 . AT A 258.11 PASS AC=1;AF=0.5;AN=2;DP=7764;set=filterInvariant-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant7-variant9-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant13-filterInvariant15-filterInvariant16-variant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant24-variant25-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant32-variant33-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant37-variant38-filterInvariant39-filterInvariant40-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:139,26:165:99:160,0,2821:60,79,11,15 chr2 48688258 . AT A,ATT 133.84 PASS AC=1,0;AF=0.455,0.045;AN=2;DP=1532;MQ=60;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant4-variant11-filterInvariant12-variant13-filterInvariant15-filterInvariant16-filterInvariant22-filterInvariant25-filterInvariant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant34-filterInvariant35-filterInvariant37-filterInvariant39-variant40-filterInvariant41-variant43 GT:DP:GQ:SB 0/1:68:99:27,27,6,8 chr2 48701728 . T G 51.68 PASS AC=1;AF=0.5;AN=2;DP=5;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.358;QD=10.34;ReadPosRankSum=1.231;SOR=1.179;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:2,3:5:20:80,0,20:1,1,2,1 chr2 48713729 . T C 302.09 PASS AC=1;AF=0.563;AN=2;DP=483;FractionInformativeReads=1;MQ=60;set=variant8-variant9-variant12-variant17-variant20-variant29-variant30-variant31-variant32-variant34-variant35-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,18:33:99:501,0,412:9,6,14,4 chr2 48722755 . T C 474.9 PASS AC=1;AF=0.622;AN=2;DP=946;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,22:33:99:508,0,271:8,3,12,10 chr2 48725610 . C T 428.25 PASS AC=1;AF=0.647;AN=2;DP=1174;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant24-variant25-variant26-variant28-variant29-variant30-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,10:19:99:305,0,229:6,3,8,2 chr2 48734576 . G A 3573.46 PASS AC=2;AF=1;AN=2;DP=5858;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,128:128:99:4012,384,0:0,0,45,83 chr2 48738687 . G C 987.81 PASS AC=1;AF=0.821;AN=2;DP=1103;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,8:20:99:246,0,401:2,10,1,7 chr2 48742355 . TTCTC TTCTCTCTCTCTCTCTCTCTCTC,TTCTCTCTCTCTCTC,TTCTCTCTCTCTCTCTCTCTC,TTCTCTCTCTCTC,TTCTCTCTCTCTCTCTCTC,TTC,T,TTCTCTCTC,TTCTCTCTCTCTCTCTC 303.54 PASS AC=0,2,0,0,0,0,0,0,0;AF=0.05,0.263,0.038,0.275,0.138,0.138,0.013,0.013,0.038;AN=2;DP=801;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 2/2:4:11:0,0,1,3 chr2 48756682 . C G 130.47 PASS AC=1;AF=0.559;AN=2;DP=448;FractionInformativeReads=1;MQ=60;set=variant8-variant9-variant12-variant13-variant17-variant20-variant23-variant30-variant31-variant32-variant33-filterInvariant34-variant35-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,21:36:99:473,0,328:5,10,9,12 chr2 48757823 . T C 401.52 PASS AC=1;AF=0.553;AN=2;DP=730;FractionInformativeReads=1;MQ=60;set=variant6-variant8-variant9-variant12-variant13-variant17-variant20-variant23-variant25-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,24:49:99:629,0,697:11,14,11,13 chr2 48807593 . GT G 69.95 PASS AC=1;AF=0.635;AN=2;DP=434;MQ=60;set=variant-variant2-variant3-variant4-variant8-variant11-variant12-variant16-variant19-variant20-variant21-variant23-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,8:18:99:175,0,232:10,0,8,0 chr2 48807796 . A C 2439.65 PASS AC=1;AF=0.621;AN=2;DP=5865;MQ=60;set=variant-variant2-variant3-variant4-variant8-variant9-variant11-variant12-variant13-variant16-variant18-variant19-variant20-variant21-variant23-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:84,114:198:99:2932,0,1992:41,43,58,56 chr2 48807976 . T C 2625.24 PASS AC=1;AF=0.613;AN=2;DP=4951;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant11-variant12-variant13-variant16-variant18-variant19-variant20-variant21-variant23-variant25-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:85,100:185:99:2387,0,1976:43,42,48,52 chr2 48808152 . G C 2115.77 PASS AC=1;AF=0.629;AN=2;DP=5804;MQ=60;set=variant-variant2-variant3-variant4-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant21-variant23-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:98,106:204:99:2702,0,2457:48,50,56,50 chr2 48808594 . C T 3029.91 PASS AC=1;AF=0.689;AN=2;DP=6069;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:110,92:202:99:2204,0,2805:53,57,44,48 chr2 48808882 . T A 1216.77 PASS AC=1;AF=0.621;AN=2;DP=2058;MQ=60;set=variant-variant2-variant3-variant4-variant8-variant9-variant11-variant12-variant13-variant16-variant18-variant19-variant20-variant21-variant23-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,31:57:99:891,0,764:10,16,12,19 chr2 48808898 . C T 1161.64 PASS AC=1;AF=0.621;AN=2;DP=1907;MQ=60;set=variant-variant2-variant3-variant4-variant8-variant9-variant11-variant12-variant13-variant16-variant18-variant19-variant20-variant21-variant23-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,30:52:99:869,0,635:9,13,10,20 chr2 48809593 . G T 1297.05 PASS AC=1;AF=0.679;AN=2;DP=4238;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:63,69:132:99:1637,0,1467:33,30,36,33 chr2 48809756 . T C 908.43 PASS AC=1;AF=0.645;AN=2;DP=2405;MQ=60;set=variant-variant2-variant3-variant4-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant21-variant23-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,41:81:99:1057,0,982:19,21,17,24 chr2 48809873 . T C 388.27 PASS AC=1;AF=0.621;AN=2;DP=832;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant8-variant9-variant11-variant12-variant13-variant16-variant18-variant19-variant20-variant21-variant23-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,11:25:99:297,0,389:4,10,2,9 chr2 48819197 . A G 1444.97 PASS AC=1;AF=0.583;AN=2;DP=892;MQ=60;set=variant3-variant4-variant8-variant9-variant11-variant12-variant13-variant16-variant19-variant20-variant21-variant23-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,21:39:99:600,0,435:7,11,7,14 chr2 48822381 . G A 3083.26 PASS AC=1;AF=0.7;AN=2;DP=3236;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,50:97:99:1283,0,1088:23,24,32,18 chr2 48822540 . T C 4208.97 PASS AC=1;AF=0.538;AN=2;DP=2735;MQ=60;set=variant3-variant4-variant9-variant12-variant13-variant20-variant23-variant29-variant30-variant33-variant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:121,66:187:99:1504,0,3236:62,59,38,28 chr2 48824960 . G A 1219.28 PASS AC=1;AF=0.542;AN=2;DP=888;MQ=60;set=variant-variant7-variant8-variant9-variant18-variant22-variant26-variant27-variant33-variant35-variant36-variant42 GT:AD:DP:GQ:PL:SB 0/1:45,45:90:99:1184,0,1243:17,28,21,24 chr2 48825109 . A G 625.46 PASS AC=1;AF=0.542;AN=2;DP=571;MQ=60;set=variant3-variant4-variant9-variant12-variant20-variant23-variant29-variant30-variant33-variant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,28:51:99:817,0,667:12,11,17,11 chr2 48825650 . C G 2039.25 PASS AC=1;AF=0.708;AN=2;DP=1776;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:26,26:52:99:784,0,877:3,23,5,21 chr2 48829370 . G C 295.36 PASS AC=1;AF=0.5;AN=2;DP=26;FS=0;FractionInformativeReads=1;MQ=60;set=variant7-variant35 GT:AD:DP:GQ:PL:SB 0/1:4,5:9:99:157,0,110:2,2,2,3 chr2 48844707 . C G 152.52 PASS AC=1;AF=0.5;AN=2;DP=24;FractionInformativeReads=1;MQ=60;set=variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:5,9:14:99:282,0,183:5,0,7,2 chr2 48844968 . C G 4131.71 PASS AC=2;AF=0.798;AN=2;DP=6225;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,181:181:99:5369,542,0:0,0,97,84 chr2 48847918 . GAATA G,GAATAAATA 37.81 PASS AC=0,2;AF=0.35,0.4;AN=2;DP=37;FS=0;MQ=60;set=variant2-variant3-variant7-variant11-variant16-variant21-variant27-variant31-variant35-variant42 GT:DP:GQ:SB 2/2:2:9:0,0,2,0 chr2 48848515 . G C 222.67 PASS AC=1;AF=0.536;AN=2;DP=197;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant9-variant12-variant20-variant23-variant29-variant30-variant33-variant34-variant35-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,3:11:99:102,0,278:1,7,0,3 chr2 48873978 . A G 3803.74 PASS AC=1;AF=0.643;AN=2;DP=2673;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant15-variant17-variant18-variant21-variant22-variant26-variant27-variant28-variant33-variant35-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:69,65:134:99:1504,0,1525:35,34,32,33 chr2 48898798 . T A 5296.32 PASS AC=2;AF=0.966;AN=2;DP=6359;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,170:170:99:4760,508,0:0,0,81,89 chr2 48906625 . T C 6068.09 PASS AC=2;AF=0.966;AN=2;DP=7615;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,139:139:99:4288,417,0:0,0,66,73 chr2 48915871 . A G 4141.44 PASS AC=2;AF=0.789;AN=2;DP=4793;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,99:99:99:3069,297,0:0,0,43,56 chr2 48921375 . T C 2119.41 PASS AC=2;AF=0.789;AN=2;DP=2980;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,61:61:99:2013,183,0:0,0,35,26 chr2 48925746 . C T 1328.99 PASS AC=1;AF=0.857;AN=2;DP=2311;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,30:63:99:759,0,770:17,16,18,12 chr2 48925986 . ATT AT,A 102.15 PASS AC=2,0;AF=0.963,0.024;AN=2;DP=614;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:15:45:0,0,6,9 chr2 48948707 . A C 4666.41 PASS AC=1;AF=0.621;AN=2;DP=10170;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:156,138:294:99:3526,0,4075:76,80,70,68 chr2 48952701 . C G 452.97 PASS AC=2;AF=1;AN=2;DP=423;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:434,30,0:0,0,9,1 chr2 48956431 . T A 811.46 PASS AC=1;AF=0.567;AN=2;DP=1713;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant27-variant28-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,38:66:99:915,0,725:12,16,13,25 chr2 48956475 . C T 559.66 PASS AC=1;AF=0.529;AN=2;DP=606;MQ=60;set=variant4-variant5-variant7-variant8-variant10-variant13-variant14-variant18-variant20-variant31-variant34-variant35-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,22:35:99:511,0,311:4,9,9,13 chr2 48956512 . A G 475.24 PASS AC=1;AF=0.559;AN=2;DP=358;MQ=60;set=variant4-variant5-variant7-variant8-variant10-variant13-variant14-variant18-variant20-variant31-variant34-variant35-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,8:16:99:188,0,214:2,6,3,5 chr2 48960032 . G A 1757.17 PASS AC=1;AF=0.5;AN=2;DP=1483;MQ=60;set=variant4-variant5-variant7-variant8-variant18-variant20-variant31-variant34-variant35-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,55:122:99:1407,0,1531:37,30,36,19 chr2 48982485 . T C 1065.91 PASS AC=1;AF=0.571;AN=2;DP=923;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant18-variant19-variant20-variant29-variant31-variant33-variant34-variant35-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,33:52:99:954,0,461:11,8,21,12 chr2 48982622 . C G 1119.32 PASS AC=1;AF=0.5;AN=2;DP=935;MQ=60;set=variant4-variant5-variant7-variant18-variant20-variant31-variant34-variant35-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,42:95:99:1045,0,1277:28,25,19,23 chr2 49003623 . T G 797.52 PASS AC=1;AF=0.553;AN=2;DP=1011;MQ=60;set=variant4-variant5-variant7-variant8-variant10-variant13-variant18-variant20-variant25-variant30-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,31:50:99:742,0,464:5,14,12,19 chr2 49189921 . C T 2176.63 PASS AC=1;AF=0.629;AN=2;DP=5266;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:86,86:172:99:2101,0,2064:38,48,35,51 chr2 49191041 . C T 901.78 PASS AC=1;AF=0.632;AN=2;DP=2200;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,27:71:99:714,0,1156:15,29,9,18 chr2 49210366 . A G 916.4 PASS AC=1;AF=0.5;AN=2;DP=89;FS=1.767;FractionInformativeReads=1;MQ=60;MQRankSum=0.656;QD=10.3;ReadPosRankSum=0.999;SOR=0.493;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:53,36:89:99:945,0,1413:22,31,17,19 chr2 49215977 . G A 533.84 PASS AC=2;AF=0.774;AN=2;DP=1256;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:1058,87,0:0,0,22,7 chr2 49216284 . C T 230.15 PASS AC=2;AF=0.762;AN=2;DP=787;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:924,69,0:0,0,1,22 chr2 49217916 . T G 198.42 PASS AC=1;AF=0.638;AN=2;DP=442;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant17-variant18-variant20-variant21-variant22-variant25-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant37-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,7:20:99:207,0,414:2,11,1,6 chr2 49241849 . G A 435.87 PASS AC=1;AF=0.667;AN=2;DP=798;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,14:27:99:356,0,370:10,3,10,4 chr2 49509859 . C CT 153.76 PASS AC=1;AF=0.56;AN=2;DP=657;MQ=60;set=variant-variant2-variant5-variant8-variant11-variant12-variant15-variant16-variant17-variant19-variant20-variant23-variant27-variant29-variant30-variant31-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:16,12:28:99:284,0,426:12,4,8,4 chr2 49510173 . A C 1368.24 PASS AC=1;AF=0.58;AN=2;DP=2273;MQ=60;set=variant-variant2-variant5-variant8-variant11-variant12-variant15-variant16-variant17-variant19-variant20-variant23-variant27-variant29-variant30-variant31-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,48:113:99:1290,0,1785:32,33,24,24 chr2 50145690 . A ATTGTC 1116.07 PASS AC=1;AF=0.5;AN=2;DP=64;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.877;QD=17.44;ReadPosRankSum=-0.067;SOR=0.566;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:35,29:64:99:1153,0,2293:24,11,19,10 chr2 50147171 . C A 1407.3 PASS AC=1;AF=0.611;AN=2;DP=1842;MQ=60;set=variant-variant2-variant8-variant9-variant14-variant15-variant18-variant20-variant26-variant29-variant33-variant35-variant36-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:62,36:98:99:885,0,1669:28,34,13,23 chr2 50147755 . G C 3716.46 PASS AC=1;AF=0.563;AN=2;DP=4062;set=variant-variant2-variant8-variant9-variant14-variant15-variant18-variant20-variant29-variant33-variant35-variant36-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:121,152:273:99:4153,0,3110:52,69,59,93 chr2 50147835 . CGTGTGTGTGTGTGTGTGT CGTGTGTGT,CGTGTGTGTGTGT,CGTGTGTGTGTGTGTGT,CGTGTGTGTGT,CGTGTGTGTGTGTGT,C,CGTGTGT,CGTGTGTGTGTGTGTGTGTGTGT,CGT 2706.54 PASS AC=1,0,0,1,0,0,0,0,0;AF=0.205,0.159,0.114,0.159,0.057,0.125,0.08,0.011,0.011;AN=2;DP=6065;set=Intersection GT:DP:GQ:SB 1/4:83:99:0,4,45,34 chr2 50148111 . A AAAGT 2571.18 PASS AC=1;AF=0.633;AN=2;DP=4237;MQ=60;set=variant-variant2-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant26-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:76,75:151:99:3081,0,3621:42,34,42,33 chr2 50170729 . G C 287.13 PASS AC=1;AF=0.588;AN=2;DP=303;MQ=60;set=variant-variant2-variant8-variant9-variant14-variant15-variant18-variant20-variant29-variant33-variant35-variant36-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:15,13:28:99:360,0,335:9,6,9,4 chr2 50201110 . A G 865.02 PASS AC=1;AF=0.864;AN=2;DP=4277;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:53,42:95:99:1043,0,1370:31,22,27,15 chr2 50280283 . T C 500.47 PASS AC=1;AF=0.808;AN=2;DP=543;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,5:12:99:182,0,238:4,3,5,0 chr2 50280338 . G A 1185.33 PASS AC=1;AF=0.784;AN=2;DP=1441;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,26:49:99:719,0,612:15,8,18,8 chr2 50434759 . C G 656.74 PASS AC=1;AF=0.895;AN=2;DP=2454;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,36:66:99:728,0,602:18,12,19,17 chr2 50574485 . A G 2153.32 PASS AC=1;AF=0.605;AN=2;DP=2426;FractionInformativeReads=1;MQ=60;set=variant5-variant6-variant9-variant12-variant17-variant19-variant20-variant21-variant23-variant27-variant28-variant30-variant31-variant35-variant36-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:81,71:152:99:1811,0,2092:37,44,35,36 chr2 50692560 . A G 1617.3 PASS AC=1;AF=0.595;AN=2;DP=3560;MQ=60;set=variant-variant3-variant5-variant8-variant11-variant12-variant14-variant17-variant19-variant23-variant24-variant27-variant28-variant34-variant35-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:85,83:168:99:1906,0,2047:47,38,41,42 chr2 50692819 . T G 817.74 PASS AC=2;AF=0.92;AN=2;DP=1480;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1359,135,0:0,0,17,28 chr2 50693504 . AAC A 785.21 PASS AC=1;AF=0.705;AN=2;DP=2810;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,44:81:99:1736,0,1499:19,18,25,19 chr2 50699305 . T A 380.51 PASS AC=1;AF=0.684;AN=2;DP=769;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,12:24:99:377,0,376:10,2,11,1 chr2 50733860 . A G 612.33 PASS AC=2;AF=0.989;AN=2;DP=1766;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1365,134,0:0,0,16,29 chr2 50758657 . T C 390.13 PASS AC=1;AF=0.837;AN=2;DP=1215;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,10:25:99:301,0,548:2,13,1,9 chr2 50858107 . T A 1313.63 PASS AC=1;AF=0.738;AN=2;DP=1764;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:18,27:45:99:675,0,478:11,7,17,10 chr2 50966161 . G A 1448.7 PASS AC=2;AF=0.909;AN=2;DP=1919;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,31:31:93:1062,93,0:0,0,21,10 chr2 50966283 . C T 3906.35 PASS AC=1;AF=0.849;AN=2;DP=4764;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,43:89:99:1121,0,1260:29,17,25,18 chr2 51125707 . C G 712.35 PASS AC=1;AF=0.545;AN=2;DP=819;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant8-variant16-variant21-variant24-variant26-variant27-variant35-variant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:21,39:60:99:1010,0,422:10,11,15,24 chr2 51144368 . T G 1612.13 PASS AC=1;AF=0.595;AN=2;DP=3157;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant9-variant11-variant14-variant18-variant21-variant23-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:81,64:145:99:1571,0,2013:36,45,35,29 chr2 51146150 . A AG 14735.5 PASS AC=1;AF=0.7;AN=2;DP=17078;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:205,210:415:99:6196,0,6035:91,114,95,115 chr2 51148872 . T A 640.49 PASS AC=1;AF=0.625;AN=2;DP=492;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant11-variant14-variant18-variant21-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant35-variant38-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,10:11:13:255,0,13:1,0,5,5 chr2 51206342 . C G 626.97 PASS AC=1;AF=0.636;AN=2;DP=1417;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant9-variant10-variant11-variant14-variant15-variant16-variant18-variant20-variant23-variant24-variant26-variant27-variant30-variant32-variant33-variant35-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:33,28:61:99:714,0,1019:26,7,20,8 chr2 51254478 . G A 191.94 PASS AC=1;AF=0.615;AN=2;DP=921;MQ=60;set=variant-variant2-variant5-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant18-variant20-variant23-variant24-variant26-variant27-variant30-variant32-variant33-variant35-variant36-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,18:34:99:461,0,476:13,3,11,7 chr2 51255604 . G A 601.49 PASS AC=1;AF=0.5;AN=2;DP=32;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.436;QD=18.8;ReadPosRankSum=-0.873;SOR=0.665;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:11,21:32:99:630,0,276:7,4,13,8 chr2 51255692 . A G 287.5 PASS AC=1;AF=0.62;AN=2;DP=1048;MQ=60;set=variant-variant2-variant5-variant7-variant9-variant10-variant11-variant14-variant15-variant16-variant18-variant20-variant23-variant24-variant26-variant27-variant30-variant32-variant33-variant35-variant36-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,23:59:99:534,0,902:19,17,13,10 chr2 51255832 . T G 478.15 PASS AC=1;AF=0.62;AN=2;DP=1068;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant7-variant9-variant10-variant11-variant14-variant15-variant16-variant18-variant20-variant23-variant24-variant26-variant27-variant30-variant32-variant33-variant35-variant36-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,18:50:99:409,0,778:18,14,10,8 chr2 51259644 . AAGAAAGAGAGAGAGAGAGAGAGAGAGAG AAGAGAGAGAGAG,AAGAGAGAGAGAGAG,A,AAGAGAGAGAGAGAGAG 241.12 PASS AC=1,0,0,0;AF=0.389,0.222,0.028,0.028;AN=2;DP=302;set=variant-variant5-variant7-variant9-variant10-variant11-variant14-variant16-variant18-variant20-variant23-variant24-variant26-variant32-variant33-variant35-variant41-variant43 GT:DP:GQ:SB 0/1:21:99:5,9,3,4 chr2 51259648 . AAGAGAGAGAGAGAGAGAGAG AAGAGAGAGAGAGAGAGAGAGAG,AAGAGAGAGAGAGAGAGAGAGAGAG,AAGAGAGAG,AAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG,AAGAGAGAGAGAGAGAG,AAGAGAGAGAGAG,A,AAGAGAGAGAGAGAG 96.51 PASS AC=0,0,0,0,0,0,1,0;AF=0.15,0.1,0.125,0.025,0.075,0.025,0.125,0.075;AN=2;DP=250;set=variant3-variant4-variant6-variant8-variant13-variant15-variant16-variant17-variant19-variant24-variant27-variant28-variant30-variant32-variant35-variant36-variant37-variant39-variant42-variant43 GT:DP:GQ:SB 0/7:17:99:3,4,3,7 chr2 52929596 . C G 93.53 PASS AC=1;AF=0.75;AN=2;DP=80;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant16-variant17-variant18-variant24-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:2,4:6:73:147,0,73:2,0,4,0 chr2 52929680 . T C 655.65 PASS AC=1;AF=0.614;AN=2;DP=525;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant8-variant12-variant16-variant17-variant18-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,14:22:99:402,0,210:6,2,8,6 chr2 52929780 . T G 946.32 PASS AC=1;AF=0.667;AN=2;DP=976;MQ=60;set=variant-variant2-variant3-variant4-variant8-variant12-variant15-variant16-variant17-variant18-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:18,25:43:99:545,0,401:8,10,10,15 chr2 52929844 . G A 655.13 PASS AC=1;AF=0.619;AN=2;DP=448;MQ=60;set=variant-variant2-variant3-variant4-variant12-variant16-variant17-variant18-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,12:25:99:262,0,309:5,8,5,7 chr2 53990532 . C T 1094.55 PASS AC=1;AF=0.5;AN=2;DP=570;MQ=60;set=variant6-variant19-variant20-variant26-variant35-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,30:67:99:769,0,970:23,14,19,11 chr2 53994867 . T C 635.76 PASS AC=1;AF=0.5;AN=2;DP=157;FractionInformativeReads=1;MQ=60;set=variant6-variant19-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,14:35:99:389,0,573:14,7,11,3 chr2 54013527 . C T 914.64 PASS AC=1;AF=0.5;AN=2;DP=588;FractionInformativeReads=1;MQ=60;set=variant6-variant19-variant20-variant26-variant35-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,38:61:99:896,0,507:12,11,20,18 chr2 54013544 . T C 705.89 PASS AC=1;AF=0.617;AN=2;DP=2540;MQ=60;set=variant-variant4-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant31-variant32-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,39:60:99:1045,0,464:10,11,19,20 chr2 54014303 . A G 1465.23 PASS AC=1;AF=0.5;AN=2;DP=740;MQ=60;set=variant6-variant19-variant26-variant35-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:78,80:158:99:2307,0,2069:45,33,42,38 chr2 54023247 . GT G 302.68 PASS AC=1;AF=0.63;AN=2;DP=678;MQ=60;set=variant4-variant6-variant7-variant9-variant10-variant13-variant14-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant31-variant32-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,11:24:99:240,0,260:5,8,3,8 chr2 54024626 . C T 223.93 PASS AC=1;AF=0.625;AN=2;DP=1146;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant27-variant31-variant32-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,22:47:99:513,0,560:14,11,13,9 chr2 54041983 . G T 1182.9 PASS AC=1;AF=0.621;AN=2;DP=2852;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant27-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,66:133:99:1560,0,1523:39,28,41,25 chr2 54042132 . CTTTTTTTTTT CTTTTTTTT,CTTTTTTTTT,C,CTTTTTTT 99.16 PASS AC=0,0,1,0;AF=0.192,0.154,0.096,0.135;AN=2;DP=718;set=variant-filterInvariant3-variant6-variant7-variant9-variant10-filterInvariant11-variant12-filterInvariant14-filterInvariant15-variant18-variant19-variant20-variant24-variant25-variant27-filterInvariant29-variant32-variant34-variant35-variant36-variant37-variant40-variant41-variant43-variant44 GT:DP:GQ:SB 0/3:32:99:3,8,3,18 chr2 54081548 . C T 1268.95 PASS AC=1;AF=0.5;AN=2;DP=603;FractionInformativeReads=1;MQ=60;set=variant10-variant17-variant21-variant28-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:67,62:129:99:1398,0,1689:39,28,31,31 chr2 54091748 . T C 3334.67 PASS AC=1;AF=0.583;AN=2;DP=1446;MQ=60;set=variant6-variant19-variant35-variant36-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:118,100:218:99:2399,0,2963:51,67,43,57 chr2 54093956 . G A 1115.18 PASS AC=1;AF=0.583;AN=2;DP=609;FractionInformativeReads=1;MQ=60;set=variant6-variant19-variant35-variant36-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,48:104:99:1149,0,1313:28,28,25,23 chr2 54101772 . C T 488.27 PASS AC=1;AF=0.6;AN=2;DP=91;FractionInformativeReads=1;MQ=60;set=variant6-variant19-variant35-variant36-variant42 GT:AD:DP:GQ:PL:SB 0/1:12,12:24:99:421,0,417:1,11,1,11 chr2 54115813 . C T 982.43 PASS AC=1;AF=0.583;AN=2;DP=341;FractionInformativeReads=1;MQ=60;set=variant6-variant19-variant35-variant36-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,30:61:99:678,0,806:19,12,17,13 chr2 54120820 . G A 1496.13 PASS AC=1;AF=0.62;AN=2;DP=2303;MQ=60;set=variant-variant4-variant6-variant7-variant10-variant12-variant13-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant31-variant32-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,47:98:99:1167,0,1289:21,30,22,25 chr2 54121960 . C A 161.45 PASS AC=1;AF=0.583;AN=2;DP=84;FractionInformativeReads=1;MQ=60;set=variant6-variant19-variant35-variant36-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,12:20:99:467,0,284:7,1,12,0 chr2 54122956 . A G 419.99 PASS AC=2;AF=0.711;AN=2;DP=1264;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:903,78,0:0,0,6,20 chr2 54125258 . T C 103.63 PASS AC=1;AF=0.603;AN=2;DP=393;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant27-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,3:5:76:117,0,76:0,2,1,2 chr2 54127041 . C T 2250.34 PASS AC=1;AF=0.6;AN=2;DP=3215;MQ=60;set=variant-variant4-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,46:106:99:1039,0,1431:28,32,22,24 chr2 54131093 . C T 302.24 PASS AC=1;AF=0.583;AN=2;DP=154;FS=0;FractionInformativeReads=1;MQ=60;set=variant6-variant19-variant35-variant36-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,12:23:99:422,0,338:10,1,11,1 chr2 54133638 . G A 254.59 PASS AC=1;AF=0.583;AN=2;DP=107;FractionInformativeReads=1;MQ=60;set=variant6-variant19-variant35-variant36-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,9:23:99:214,0,382:10,4,4,5 chr2 54148331 . C A 211.3 PASS AC=1;AF=0.63;AN=2;DP=309;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant6-variant7-variant10-variant12-variant13-variant14-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,8:15:99:271,0,223:1,6,1,7 chr2 54159999 . G A 644.72 PASS AC=1;AF=0.563;AN=2;DP=312;FractionInformativeReads=1;MQ=60;set=variant6-variant19-variant23-variant26-variant35-variant36-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,27:45:99:705,0,456:7,11,9,18 chr2 54343012 . C A 351.52 PASS AC=1;AF=0.621;AN=2;DP=1298;set=variant4-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,20:39:99:539,0,558:6,13,8,12 chr2 54362437 . T C 280.34 PASS AC=1;AF=0.63;AN=2;DP=480;MQ=60;set=variant6-variant7-variant10-variant12-variant14-variant18-variant19-variant20-variant22-variant24-variant25-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,5:13:99:105,0,243:6,2,3,2 chr2 54369120 . TTGTG TTGTGTG,TTGTGTGTGTGTG,T,TTG 139.61 PASS AC=1,0,0,0;AF=0.25,0.188,0.125,0.063;AN=2;DP=66;FS=0;MQ=60;set=variant2-variant8-variant13-variant16-variant35-variant37-variant38-variant41 GT:DP:GQ:SB 0/1:5:51:2,0,1,2 chr2 54480332 . G A 1637.41 PASS AC=1;AF=0.609;AN=2;DP=2101;MQ=60;set=variant3-variant4-variant7-variant10-variant13-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,34:73:99:892,0,1051:26,13,23,11 chr2 54480369 . C A 2099.61 PASS AC=1;AF=0.643;AN=2;DP=3943;MQ=60;set=variant3-variant4-variant6-variant7-variant10-variant13-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:75,63:138:99:1533,0,1919:43,32,38,25 chr2 54481592 . C G 808.66 PASS AC=1;AF=0.638;AN=2;DP=1410;MQ=60;set=variant3-variant4-variant6-variant7-variant10-variant13-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,12:35:99:343,0,692:9,14,6,6 chr2 54482964 . C T 3235.72 PASS AC=1;AF=0.587;AN=2;DP=5007;MQ=60;set=variant3-variant4-variant7-variant10-variant13-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:133,95:228:99:2645,0,3745:70,63,54,41 chr2 54483272 . C A 4752.05 PASS AC=1;AF=0.542;AN=2;DP=2289;set=variant5-variant8-variant11-variant12-variant14-variant15-variant24-variant31-variant34-variant35-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:139,113:252:99:2536,0,3384:66,73,52,61 chr2 54483443 . T C 720.17 PASS AC=1;AF=0.617;AN=2;DP=1448;MQ=60;set=variant3-variant4-variant6-variant7-variant10-variant13-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,36:64:99:935,0,766:8,20,14,22 chr2 54494370 . A G 727.63 PASS AC=2;AF=0.989;AN=2;DP=1318;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.506;ReadPosRankSum=-0.811;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1494,138,0:0,0,34,12 chr2 54587378 . C G 937.13 PASS AC=1;AF=0.542;AN=2;DP=1289;MQ=60;set=variant12-variant14-variant15-variant18-variant24-variant25-variant31-variant32-variant35-variant37-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:72,36:108:99:789,0,1903:37,35,17,19 chr2 54683711 . T C 81.17 PASS AC=1;AF=0.818;AN=2;DP=389;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,4:16:91:91,0,291:6,6,3,1 chr2 54756740 . C T 1932.23 PASS AC=2;AF=0.782;AN=2;DP=4919;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,151:151:99:4442,452,0:0,0,82,69 chr2 54839276 . A G 7478.51 PASS AC=2;AF=0.8;AN=2;DP=11711;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,319:319:99:9450,954,0:0,0,159,160 chr2 54844911 . G A 450.2 PASS AC=2;AF=0.611;AN=2;DP=632;MQ=60;set=variant2-variant4-variant5-variant7-variant9-variant12-variant14-variant17-variant19-variant25-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:1491,141,0:0,0,15,32 chr2 54855137 . T C 3845.99 PASS AC=2;AF=0.8;AN=2;DP=3998;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,107:107:99:3550,321,0:0,0,74,33 chr2 54856640 . C G 1266.98 PASS AC=1;AF=0.5;AN=2;DP=133;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.45;QD=9.53;ReadPosRankSum=-2.319;SOR=0.698;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:78,55:133:99:1295,0,1853:37,41,26,29 chr2 54858511 . C T 1387.3 PASS AC=2;AF=0.588;AN=2;DP=2501;MQ=60;set=variant2-variant4-variant7-variant9-variant12-variant14-variant17-variant19-variant25-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,160:160:99:4975,480,0:0,0,87,73 chr2 54876143 . A C 1480.78 PASS AC=1;AF=0.5;AN=2;DP=131;FS=0.654;FractionInformativeReads=1;MQ=60;MQRankSum=-0.025;QD=11.3;ReadPosRankSum=-3.338;SOR=0.582;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:71,60:131:99:1509,0,1652:31,40,28,32 chr2 54886347 . G A 974.26 PASS AC=2;AF=0.575;AN=2;DP=1367;MQ=60;set=variant2-variant4-variant5-variant7-variant9-variant12-variant14-variant17-variant18-variant19-variant25-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,61:61:99:1949,183,0:0,0,23,38 chr2 54888497 . C T 14921.9 PASS AC=2;AF=0.808;AN=2;DP=15082;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,389:389:99:11857,1164,0:0,0,202,187 chr2 54888533 . T C 14918 PASS AC=2;AF=0.808;AN=2;DP=14836;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,380:380:99:12116,1138,0:0,0,186,194 chr2 54889136 . G A 9250.81 PASS AC=2;AF=0.808;AN=2;DP=9262;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,258:258:99:8090,774,0:0,0,125,133 chr2 54889390 . C T 1465.05 PASS AC=2;AF=0.808;AN=2;DP=1771;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,52:52:99:1648,156,0:0,0,18,34 chr2 54893237 . C T 375.8 PASS AC=2;AF=0.583;AN=2;DP=379;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant12-variant14-variant17-variant19-variant25-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:851,72,0:0,0,6,18 chr2 54895817 . AT A 598.24 PASS AC=1;AF=0.5;AN=2;DP=938;set=variant3-filterInvariant5-variant7-variant8-filterInvariant9-variant13-variant15-variant16-filterInvariant17-variant21-variant24-variant27-variant28-variant29-variant31-variant33-filterInvariant35-filterInvariant37-variant38-filterInvariant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,6:25:82:82,0,353:10,9,3,3 chr2 54896377 . A AT,ATTTT,ATT,ATTT,ATTTTT 3316.09 PASS AC=0,1,0,1,0;AF=0.364,0.205,0.125,0.284,0.011;AN=2;DP=6478;set=Intersection GT:DP:GQ:SB 4/2:113:99:0,0,67,46 chr2 54951888 . C A 966.14 PASS AC=2;AF=0.661;AN=2;DP=3215;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant12-variant14-variant17-variant18-variant19-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,120:121:99:3433,351,0:1,0,48,72 chr2 55040426 . A G 6406.02 PASS AC=1;AF=0.884;AN=2;DP=8202;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:88,92:180:99:2150,0,2158:40,48,46,46 chr2 55071101 . TTGTG TTGTGTGTGTGTGTG,TTGTGTGTGTGTG,TTG,TTGTGTGTGTGTGTGTGTG,T,TTGTGTGTGTG,TTGTGTGTGTGTGTGTG,TTGTGTGTGTGTGTGTGTGTG,TTGTGTG,TTGTGTGTG 1208.79 PASS AC=0,1,1,0,0,0,0,0,0,0;AF=0.114,0.239,0.25,0.023,0.023,0.114,0.045,0.023,0.034,0.045;AN=2;DP=2158;set=Intersection GT:DP:GQ:SB 3/2:43:99:0,0,31,12 chr2 55074429 . C A 43.71 PASS AC=1;AF=0.648;AN=2;DP=332;MQ=60;set=variant2-variant5-variant6-variant8-variant10-variant15-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,5:11:99:189,0,233:6,0,5,0 chr2 55077061 . A G 866.53 PASS AC=1;AF=0.662;AN=2;DP=746;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,9:20:99:327,0,416:11,0,9,0 chr2 55091029 . C T 859.12 PASS AC=1;AF=0.605;AN=2;DP=1690;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant8-variant10-variant14-variant15-variant16-variant18-variant19-variant22-variant29-variant31-variant32-variant34-variant35-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,31:86:99:618,0,1539:24,31,15,16 chr2 55093784 . T A 156.89 PASS AC=1;AF=0.588;AN=2;DP=311;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant8-variant15-variant16-variant18-variant19-variant22-variant29-variant31-variant32-variant34-variant35-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,6:14:99:171,0,217:6,2,5,1 chr2 55121851 . T A 85.7 PASS AC=1;AF=0.615;AN=2;DP=312;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant14-variant15-variant18-variant20-variant26-variant27-variant29-variant30-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:9,10:19:99:292,0,291:8,1,8,2 chr2 55121930 . C G 570.94 PASS AC=1;AF=0.667;AN=2;DP=1674;MQ=60;set=variant2-variant3-variant5-variant7-variant8-variant10-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant25-variant26-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,23:45:99:723,0,586:16,6,18,5 chr2 55122589 . A G 903.68 PASS AC=1;AF=0.633;AN=2;DP=2546;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant18-variant20-variant23-variant26-variant27-variant29-variant30-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:44,29:73:99:711,0,1195:20,24,11,18 chr2 55138272 . G A 554.2 PASS AC=1;AF=0.704;AN=2;DP=314;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant9-variant10-variant11-variant12-variant15-variant19-variant20-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:4,3:7:99:114,0,149:1,3,0,3 chr2 55155672 . A G 1373.83 PASS AC=1;AF=0.654;AN=2;DP=4107;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant15-variant18-variant20-variant23-variant26-variant27-variant30-variant32-variant33-variant35-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:88,93:181:99:2589,0,2373:49,39,52,41 chr2 55155957 . C T 704.61 PASS AC=1;AF=0.563;AN=2;DP=1138;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant9-variant10-variant12-variant18-variant20-variant23-variant27-variant30-variant33-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:25,29:54:99:831,0,542:11,14,8,21 chr2 55176112 . C T 1046.15 PASS AC=1;AF=0.583;AN=2;DP=3030;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant20-variant21-variant22-variant23-variant27-variant30-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:65,65:130:99:1664,0,1759:37,28,38,27 chr2 55177822 . T C 1210.21 PASS AC=1;AF=0.5;AN=2;DP=494;FractionInformativeReads=1;MQ=60;set=variant4-variant12-variant30-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:60,54:114:99:1351,0,1287:32,28,29,25 chr2 55180965 . G A 88.71 PASS AC=2;AF=0.943;AN=2;DP=692;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:631,48,0:0,0,14,2 chr2 55181022 . TA T,TAA 270.68 PASS AC=1,0;AF=0.4,0.1;AN=2;DP=2044;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-filterInvariant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-filterInvariant23-variant24-filterInvariant25-variant27-variant28-variant29-variant30-variant32-filterInvariant33-variant34-variant35-variant36-variant37-filterInvariant38-variant39-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:44:99:21,8,9,6 chr2 55186229 . T C 2627.07 PASS AC=2;AF=0.811;AN=2;DP=3360;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:2176,203,0:0,0,35,33 chr2 55186394 . A C 2143.67 PASS AC=2;AF=0.811;AN=2;DP=2755;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,86:88:99:2475,182,0:2,0,37,49 chr2 55187297 . A AG 2507.14 PASS AC=2;AF=1;AN=2;DP=4606;FS=0;MQ=60;MQRankSum=-0.765;ReadPosRankSum=1.75;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,114:114:99:3725,348,0:0,0,64,50 chr2 55197882 . A T 1122.04 PASS AC=1;AF=0.722;AN=2;DP=1966;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,34:61:99:1218,0,868:5,22,13,21 chr2 55198385 . G T 2440.11 PASS AC=1;AF=0.571;AN=2;DP=4001;MQ=60;set=variant3-variant4-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant16-variant20-variant21-variant23-variant27-variant30-variant32-variant33-variant35-variant36-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:109,81:190:99:1795,0,2779:55,54,39,42 chr2 55198399 . G A 2315.92 PASS AC=1;AF=0.563;AN=2;DP=4656;MQ=60;set=variant3-variant4-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant16-variant18-variant20-variant21-variant22-variant23-variant25-variant27-variant30-variant32-variant33-variant35-variant36-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:104,80:184:99:1825,0,2646:49,55,37,43 chr2 55198661 . G C 1897.91 PASS AC=1;AF=0.526;AN=2;DP=2252;MQ=60;set=variant3-variant4-variant6-variant7-variant9-variant10-variant11-variant12-variant16-variant20-variant23-variant27-variant30-variant32-variant33-variant35-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:63,74:137:99:1782,0,1449:31,32,42,32 chr2 55198795 . A G 2210.86 PASS AC=1;AF=0.5;AN=2;DP=117;FS=1.504;FractionInformativeReads=1;MQ=60;MQRankSum=-1.23;QD=18.9;ReadPosRankSum=2.213;SOR=0.559;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:46,71:117:99:2239,0,1256:27,19,39,32 chr2 55199068 . A G 2034.68 PASS AC=1;AF=0.568;AN=2;DP=1746;MQ=60;set=variant3-variant4-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant16-variant20-variant21-variant23-variant27-variant30-variant32-variant33-variant35-variant36-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:43,49:92:99:1502,0,1097:18,25,17,32 chr2 55199248 . C T 1382.85 PASS AC=1;AF=0.656;AN=2;DP=2580;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,42:82:99:1192,0,1229:25,15,28,14 chr2 55199557 . A ATGT 8184.64 PASS AC=2;AF=0.672;AN=2;DP=12539;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,374:374:99:16945,1143,0:0,0,193,181 chr2 55199931 . CT C,CTT 550.76 PASS AC=1,0;AF=0.405,0.095;AN=2;DP=13121;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant5-variant6-filterInvariant7-filterInvariant8-variant9-variant10-variant12-filterInvariant13-variant14-filterInvariant15-filterInvariant16-variant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-variant24-filterInvariant25-filterInvariant26-filterInvariant27-variant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant32-variant33-filterInvariant34-filterInvariant35-filterInvariant37-filterInvariant38-filterInvariant39-filterInvariant40-variant41-variant42-variant43-filterInvariant44 GT:DP:GQ:SB 0/1:280:99:105,114,27,34 chr2 55200038 . CAGAT C 4545.18 PASS AC=1;AF=0.676;AN=2;DP=8237;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:146,110:256:99:4157,0,7102:73,73,62,48 chr2 55200800 . T G 1002.28 PASS AC=1;AF=0.656;AN=2;DP=1681;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,46:69:99:1393,0,553:12,11,23,23 chr2 55201038 . C T 787.03 PASS AC=2;AF=0.895;AN=2;DP=2638;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2205,209,0:0,0,25,45 chr2 55214618 . A C 162.77 PASS AC=2;AF=0.821;AN=2;DP=1927;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1383,120,0:0,0,28,12 chr2 55214912 . C G 296.95 PASS AC=2;AF=0.915;AN=2;DP=436;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:347,24,0:0,0,0,8 chr2 55277953 . T TG 1455.31 PASS AC=2;AF=0.932;AN=2;DP=3377;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:3555,238,0:0,0,37,42 chr2 55277956 . C G 1464.36 PASS AC=2;AF=0.932;AN=2;DP=3337;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,80:80:99:3589,241,0:0,0,38,42 chr2 55404794 . G A 861.83 PASS AC=2;AF=0.683;AN=2;DP=1712;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1187,114,0:0,0,23,15 chr2 55407754 . C T 4533.6 PASS AC=2;AF=0.989;AN=2;DP=6639;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,175:175:99:5203,524,0:0,0,91,84 chr2 55407935 . G A 638.95 PASS AC=2;AF=0.977;AN=2;DP=1078;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:958,72,0:0,0,2,22 chr2 55439963 . C A 3038.73 PASS AC=2;AF=0.989;AN=2;DP=2870;FS=0;MQ=60;MQRankSum=-1.55;ReadPosRankSum=0.941;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,63:63:99:1996,189,0:0,0,22,41 chr2 55445120 . G C 241.65 PASS AC=1;AF=0.5;AN=2;DP=23;FS=9.132;FractionInformativeReads=1;MQ=60;MQRankSum=-0.226;QD=10.51;ReadPosRankSum=0.42;SOR=3.223;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:15,8:23:99:270,0,379:5,10,0,8 chr2 55449318 . T C 162.35 PASS AC=1;AF=0.605;AN=2;DP=267;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant10-variant11-variant13-variant16-variant17-variant21-variant22-variant26-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,5:15:99:180,0,347:9,1,5,0 chr2 55449464 . T C 1270.32 PASS AC=1;AF=0.605;AN=2;DP=2035;MQ=60;set=variant-variant5-variant10-variant11-variant13-variant16-variant17-variant21-variant22-variant26-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,61:112:99:1687,0,1322:28,23,39,22 chr2 55459094 . C G 464.47 PASS AC=2;AF=0.989;AN=2;DP=1236;FS=0;MQ=60;MQRankSum=-0.373;ReadPosRankSum=1.002;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,18:18:53:521,53,0:0,0,11,7 chr2 55459373 . T G 678.15 PASS AC=1;AF=0.577;AN=2;DP=985;MQ=60;set=variant5-variant10-variant11-variant16-variant21-variant22-variant23-variant30-variant32-variant34-variant35-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,48:91:99:1213,0,1024:20,23,24,24 chr2 55461053 . A G 49.73 PASS AC=1;AF=0.714;AN=2;DP=30;FS=0;FractionInformativeReads=1;MQ=60;set=variant5-variant10-variant16-variant21-variant23-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:2,7:9:22:166,0,22:1,1,3,4 chr2 55461823 . T A 1797.88 PASS AC=1;AF=0.917;AN=2;DP=2277;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,26:45:99:743,0,411:14,5,19,7 chr2 55463576 . A C 1003.42 PASS AC=1;AF=0.594;AN=2;DP=1107;MQ=60;set=variant-variant5-variant11-variant13-variant17-variant21-variant22-variant26-variant28-variant34-variant35-variant36-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,37:76:99:1117,0,1174:30,9,30,7 chr2 55470115 . C T 590.27 PASS AC=1;AF=0.829;AN=2;DP=1113;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,6:19:91:91,0,400:8,5,3,3 chr2 55471382 . T C 984.05 PASS AC=1;AF=0.643;AN=2;DP=550;MQ=60;set=variant5-variant11-variant21-variant22-variant34-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,53:88:99:1345,0,790:17,18,24,29 chr2 55471407 . T C 3334.01 PASS AC=2;AF=0.989;AN=2;DP=3310;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,87:87:99:3379,262,0:0,0,43,44 chr2 55473371 . A G 472.77 PASS AC=1;AF=0.677;AN=2;DP=748;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:20,7:27:99:219,0,597:15,5,7,0 chr2 55473386 . CAT C 679.99 PASS AC=1;AF=0.829;AN=2;DP=1305;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:26,10:36:99:342,0,1166:20,6,8,2 chr2 55473681 . A C 689.76 PASS AC=2;AF=0.989;AN=2;DP=522;MQ=60;MQRankSum=1.683;ReadPosRankSum=-0.248;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:348,27,0:0,0,1,8 chr2 55476591 . G A 2168.8 PASS AC=1;AF=0.571;AN=2;DP=544;MQ=60;set=variant2-variant8-variant17-variant25-variant35-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:47,48:95:99:1061,0,1096:26,21,27,21 chr2 55489629 . T C 145.21 PASS AC=1;AF=0.838;AN=2;DP=516;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,15:23:99:509,0,257:1,7,3,12 chr2 55490819 . G T 782.41 PASS AC=1;AF=0.829;AN=2;DP=3151;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:50,34:84:99:846,0,1216:26,24,22,12 chr2 55494904 . C G 278.84 PASS AC=1;AF=0.531;AN=2;DP=317;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant11-variant17-variant21-variant22-variant26-variant28-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,11:19:99:431,0,291:0,8,0,11 chr2 55496529 . G GTGGC 714.89 PASS AC=1;AF=0.538;AN=2;DP=642;MQ=60;set=variant-variant5-variant11-variant17-variant21-variant22-variant26-variant28-variant34-variant35-variant36-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,23:42:99:908,0,1030:5,14,8,15 chr2 55516323 . T G 3453.21 PASS AC=2;AF=0.93;AN=2;DP=4572;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,91:91:99:3241,272,0:0,0,46,45 chr2 55516588 . G C 15550.4 PASS AC=2;AF=0.966;AN=2;DP=21528;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,504:504:99:15919,1510,0:0,0,262,242 chr2 55516723 . C T 15674.1 PASS AC=2;AF=0.966;AN=2;DP=18307;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,462:462:99:14821,1384,0:0,0,224,238 chr2 55516911 . AAGAGAGAGAG AAGAG,A,AAGAGAG,AAGAGAGAGAGAGAG,AAGAGAGAG 5542.8 PASS AC=2,0,0,0,0;AF=0.886,0.034,0.034,0.011,0.011;AN=2;DP=7833;set=Intersection GT:DP:GQ:SB 1/1:131:99:0,0,49,82 chr2 55517491 . G A 4122.87 PASS AC=1;AF=0.643;AN=2;DP=10442;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant33-variant35-variant36-variant37-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:154,145:299:99:3393,0,3626:88,66,79,66 chr2 55518742 . T C 998.45 PASS AC=2;AF=0.93;AN=2;DP=1302;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1097,99,0:0,0,22,11 chr2 55522422 . A G 2265.82 PASS AC=2;AF=0.977;AN=2;DP=2719;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,69:69:99:2324,207,0:0,0,34,35 chr2 55523308 . C CAA,CA,CAAA 503.29 PASS AC=0,2,0;AF=0.762,0.143,0.071;AN=2;DP=367;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 2/2:6:18:0,0,5,1 chr2 55523309 . C A 548.31 PASS AC=2;AF=0.965;AN=2;DP=390;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:270,18,0:0,0,5,1 chr2 55527108 . G A 1169.17 PASS AC=2;AF=0.86;AN=2;DP=3793;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,90:90:99:2699,269,0:0,0,37,53 chr2 55528257 . A C 1902.99 PASS AC=2;AF=0.966;AN=2;DP=2352;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1799,168,0:0,0,36,20 chr2 55559651 . CA C 82.4 PASS AC=1;AF=0.5;AN=2;DP=856;MQ=60;set=filterInvariant-filterInvariant2-filterInvariant3-variant6-variant7-variant10-variant12-variant15-variant21-variant22-variant24-variant26-variant27-variant29-variant32-variant35-variant36-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,12:42:99:151,0,562:22,8,8,4 chr2 55576634 . C T 1014.92 PASS AC=1;AF=0.618;AN=2;DP=3546;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,58:118:99:1450,0,1239:30,30,32,26 chr2 55582601 . T TTTGACACA 190.41 PASS AC=1;AF=0.618;AN=2;DP=427;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,5:13:99:219,0,417:7,1,5,0 chr2 55582635 . T C 306.71 PASS AC=1;AF=0.563;AN=2;DP=214;FractionInformativeReads=1;MQ=60;set=variant5-variant11-variant22-variant32-variant33-variant34-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,18:34:99:521,0,455:13,3,14,4 chr2 55582684 . A T 730.32 PASS AC=1;AF=0.609;AN=2;DP=1816;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,40:62:99:1006,0,561:14,8,25,15 chr2 55589434 . T A 494.67 PASS AC=1;AF=0.621;AN=2;DP=1221;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,12:27:99:337,0,394:10,5,9,3 chr2 55599655 . G A 286.99 PASS AC=1;AF=0.689;AN=2;DP=2289;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:31,35:66:99:900,0,698:15,16,15,20 chr2 55646761 . T C 1455.28 PASS AC=1;AF=0.884;AN=2;DP=3677;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,33:76:99:788,0,980:24,19,18,15 chr2 55749009 . A G 46.72 PASS AC=1;AF=0.5;AN=2;DP=5;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.231;QD=9.34;ReadPosRankSum=0.358;SOR=0.368;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:3,2:5:75:75,0,772:2,1,1,1 chr2 55749013 . A T 46.72 PASS AC=1;AF=0.5;AN=2;DP=5;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.231;QD=9.34;ReadPosRankSum=1.231;SOR=0.368;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:3,2:5:75:75,0,772:2,1,1,1 chr2 55749025 . G C 46.72 PASS AC=1;AF=0.5;AN=2;DP=5;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.358;QD=9.34;ReadPosRankSum=0.358;SOR=0.368;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:3,2:5:75:75,0,772:2,1,1,1 chr2 55749044 . G A 46.72 PASS AC=1;AF=0.5;AN=2;DP=5;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.358;QD=9.34;ReadPosRankSum=-1.231;SOR=0.368;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:3,2:5:75:75,0,772:2,1,1,1 chr2 55760940 . G T 1915.33 PASS AC=1;AF=0.869;AN=2;DP=2395;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,27:61:99:638,0,869:22,12,18,9 chr2 55762957 . C T 1482.21 PASS AC=1;AF=0.671;AN=2;DP=2994;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:42,43:85:99:1128,0,1018:24,18,20,23 chr2 55764754 . AATATGAATAC A 1088.6 PASS AC=1;AF=0.686;AN=2;DP=1008;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,9:18:99:351,0,905:5,4,4,5 chr2 55771050 . C G 789.51 PASS AC=1;AF=0.829;AN=2;DP=933;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,13:28:99:376,0,413:11,4,10,3 chr2 55771161 . A G 1772.9 PASS AC=1;AF=0.932;AN=2;DP=3054;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:47,41:88:99:955,0,1077:25,22,24,17 chr2 55776793 . G A 3085.55 PASS AC=1;AF=0.795;AN=2;DP=4030;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,60:108:99:1500,0,1278:34,14,37,23 chr2 55805440 . T C 1093.85 PASS AC=1;AF=0.977;AN=2;DP=1863;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:19,27:46:99:768,0,498:7,12,11,16 chr2 55808969 . C T 406.41 PASS AC=1;AF=0.932;AN=2;DP=600;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:12,5:17:99:166,0,357:3,9,2,3 chr2 55812073 . T G 1837.65 PASS AC=1;AF=0.686;AN=2;DP=1716;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:31,20:51:99:571,0,975:24,7,17,3 chr2 55844445 . T C 2881.7 PASS AC=1;AF=0.686;AN=2;DP=4117;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:65,71:136:99:2105,0,1741:25,40,30,41 chr2 55844616 . A AG 4697.75 PASS AC=2;AF=1;AN=2;DP=7394;FS=0;MQRankSum=0.655;ReadPosRankSum=-1.861;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,149:149:99:5443,448,0:0,0,79,70 chr2 55862440 . T C 3302.94 PASS AC=1;AF=0.932;AN=2;DP=4452;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:60,47:107:99:1162,0,1713:21,39,21,26 chr2 55862450 . ATT AT,A 925.38 PASS AC=1,0;AF=0.727,0.045;AN=2;DP=3779;set=Intersection GT:DP:GQ:SB 0/1:73:99:10,21,16,26 chr2 55862775 . C A 4495.58 PASS AC=1;AF=0.686;AN=2;DP=4632;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:82,82:164:99:1970,0,2006:40,42,41,41 chr2 55863360 . T TA 578.07 PASS AC=1;AF=0.694;AN=2;DP=1258;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:19,17:36:99:354,0,413:12,7,12,5 chr2 55871932 . AT A 48.98 DRAGENHardINDEL AC=1;AF=0.5;AN=2;DP=393;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:30,9:39:99:120,0,637:11,19,4,5 chr2 55873301 . T A 927.11 PASS AC=1;AF=0.686;AN=2;DP=664;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:10,8:18:99:210,0,302:7,3,6,2 chr2 55883317 . G T 1515.99 PASS AC=1;AF=0.736;AN=2;DP=1215;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:22,21:43:99:438,0,595:11,11,12,9 chr2 55889062 . G A 616.36 PASS AC=1;AF=0.932;AN=2;DP=831;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:8,10:18:99:303,0,186:5,3,8,2 chr2 55894247 . T C 3837.54 PASS AC=1;AF=0.7;AN=2;DP=3703;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:47,55:102:99:1337,0,1100:27,20,32,23 chr2 55898203 . A G 716.19 PASS AC=1;AF=0.721;AN=2;DP=714;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,11:19:99:300,0,203:6,2,8,3 chr2 55898290 . C G 1261.27 PASS AC=1;AF=0.7;AN=2;DP=1635;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:17,23:40:99:531,0,318:9,8,12,11 chr2 55898929 . A G 511.77 PASS AC=1;AF=0.93;AN=2;DP=405;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,9:13:99:355,0,269:4,0,7,2 chr2 55898930 . C T 511.77 PASS AC=1;AF=0.758;AN=2;DP=304;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,9:13:99:355,0,269:4,0,7,2 chr2 55899228 . A T 705.24 PASS AC=1;AF=0.932;AN=2;DP=1026;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:8,9:17:99:228,0,185:3,5,3,6 chr2 55900283 . A G 1536.74 PASS AC=1;AF=0.7;AN=2;DP=1614;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:10,24:34:99:607,0,229:4,6,10,14 chr2 55900459 . A G 403.89 PASS AC=2;AF=0.734;AN=2;DP=344;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant35-variant36-variant37-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:258,24,0:0,0,3,5 chr2 55912120 . T C 1935.19 PASS AC=1;AF=0.691;AN=2;DP=2401;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:34,59:93:99:1440,0,735:18,16,26,33 chr2 55914573 . C CA 109.97 PASS AC=1;AF=0.75;AN=2;DP=125;FS=0;set=variant-variant2-variant3-variant7-variant8-variant9-variant10-variant14-variant16-variant17-variant19-variant25-variant26-variant27-variant32-variant35-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:3,6:9:56:134,0,56:3,0,5,1 chr2 55914621 . T C 897.6 PASS AC=1;AF=0.691;AN=2;DP=660;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:14,15:29:99:418,0,363:10,4,11,4 chr2 55915155 . T A 196.77 PASS AC=1;AF=0.932;AN=2;DP=359;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:4,5:9:99:195,0,148:0,4,0,5 chr2 55921116 . C G 841.35 PASS AC=1;AF=0.691;AN=2;DP=1454;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:19,27:46:99:742,0,513:6,13,7,20 chr2 56094578 . CT C,CTT 44.18 PASS AC=0,1;AF=0.25,0.321;AN=2;DP=137;MQ=60;set=variant4-variant10-variant16-variant19-variant20-variant21-variant24-variant34-variant35-variant38-variant39-variant41-variant42-variant43 GT:DP:GQ:SB 0/2:6:34:1,1,0,4 chr2 56149475 . C G 1627.95 PASS AC=1;AF=0.607;AN=2;DP=2395;MQ=60;set=variant-variant5-variant8-variant11-variant12-variant14-variant16-variant20-variant25-variant26-variant27-variant32-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:83,97:180:99:2496,0,2001:43,40,50,47 chr2 56216052 . G A 3452.84 PASS AC=2;AF=0.869;AN=2;DP=4042;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,104:104:99:3199,310,0:0,0,57,47 chr2 56411157 . T C 432.81 PASS AC=1;AF=0.93;AN=2;DP=767;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,8:22:99:254,0,340:9,5,6,2 chr2 56411363 . G A 5865.67 PASS AC=1;AF=0.92;AN=2;DP=7659;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:99,88:187:99:1933,0,2462:57,42,46,42 chr2 56411817 . C T 3332.95 PASS AC=1;AF=0.881;AN=2;DP=5556;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,61:118:99:1402,0,1295:28,29,37,24 chr2 56603118 . C G 1312.43 PASS AC=2;AF=0.587;AN=2;DP=2941;MQ=60;set=variant-variant2-variant3-variant5-variant10-variant13-variant16-variant18-variant19-variant20-variant21-variant23-variant25-variant29-variant30-variant31-variant35-variant36-variant37-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,111:111:99:3543,332,0:0,0,42,69 chr2 56611543 . C CAAG 1884.61 PASS AC=1;AF=0.574;AN=2;DP=3114;set=variant-variant3-variant4-variant6-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant31-variant35-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:48,51:99:99:1968,0,2042:23,25,23,28 chr2 56611725 . C A 2220.82 PASS AC=1;AF=0.577;AN=2;DP=4001;MQ=60;set=variant-variant3-variant4-variant6-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant29-variant31-variant35-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:99,71:170:99:1802,0,2588:55,44,46,25 chr2 56612594 . C T 2272.57 PASS AC=1;AF=0.577;AN=2;DP=6675;MQ=60;set=variant-variant3-variant4-variant6-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant29-variant31-variant35-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:145,95:240:99:2368,0,4110:70,75,43,52 chr2 58135010 . C G 259.69 PASS AC=2;AF=0.736;AN=2;DP=745;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:700,48,0:0,0,5,11 chr2 58135011 . G A 259.69 PASS AC=2;AF=0.736;AN=2;DP=731;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:48:700,48,0:0,0,4,11 chr2 58135023 . T C 215.96 PASS AC=2;AF=0.611;AN=2;DP=463;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant21-variant22-variant24-variant25-variant27-variant32-variant33-variant35-variant37-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:501,39,0:0,0,2,11 chr2 58275666 . G A 770.53 PASS AC=2;AF=0.808;AN=2;DP=3637;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,85:85:99:2436,253,0:0,0,47,38 chr2 58316814 . A G 1066.7 PASS AC=2;AF=0.583;AN=2;DP=2533;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,73:73:99:2234,219,0:0,0,45,28 chr2 58362161 . G A 715.64 PASS AC=2;AF=0.603;AN=2;DP=852;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant32-variant33-variant35-variant37-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:53:675,53,0:0,0,16,2 chr2 58478843 . T TC 1016.1 PASS AC=1;AF=0.5;AN=2;DP=700;set=variant2-variant3-variant9-variant10-variant22-variant35-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,46:88:99:1241,0,1089:15,27,19,27 chr2 59230996 . A C 133.34 PASS AC=1;AF=0.636;AN=2;DP=439;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant6-variant8-variant9-variant11-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,6:14:99:144,0,231:6,2,4,2 chr2 59241436 . A G 1512.3 PASS AC=1;AF=0.671;AN=2;DP=4111;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,69:134:99:1734,0,1598:38,27,44,25 chr2 59241688 . A AGAT 421.29 PASS AC=1;AF=0.676;AN=2;DP=692;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,17:33:99:665,0,757:3,13,3,14 chr2 59246730 . CT CTT,C,CTTT 34.63 PASS AC=0,1,0;AF=0.13,0.391,0.022;AN=2;DP=566;set=filterInvariant4-variant5-variant6-variant7-variant8-variant12-variant13-variant14-variant17-variant19-filterInvariant23-variant25-variant26-variant28-variant29-variant31-variant33-filterInvariant34-variant35-variant36-variant37-variant38-filterInvariant43 GT:DP:GQ:SB 0/2:30:99:11,6,11,2 chr2 60614572 . G A 2027.77 PASS AC=1;AF=0.583;AN=2;DP=3809;MQ=60;set=variant2-variant4-variant5-variant11-variant12-variant13-variant15-variant16-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant31-variant33-variant34-variant35-variant37-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:87,67:154:99:1698,0,2277:44,43,29,38 chr2 60679226 . G A 1819.03 PASS AC=2;AF=0.712;AN=2;DP=6093;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,208:209:99:6662,581,0:1,0,123,85 chr2 60679942 . T C 874.26 PASS AC=1;AF=0.563;AN=2;DP=830;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant8-variant9-variant10-variant12-variant13-variant21-variant22-variant23-variant26-variant35-variant36-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:22,25:47:99:693,0,559:10,12,11,14 chr2 60687303 . GA G,GAA 182.53 PASS AC=1,0;AF=0.5,0.031;AN=2;DP=424;set=variant2-variant4-variant8-variant15-variant22-variant23-variant26-variant28-variant31-variant33-variant34-variant35-variant37-variant40-variant42-variant44 GT:DP:GQ:SB 0/1:16:83:1,4,1,10 chr2 60687959 . A G 5902.68 PASS AC=2;AF=0.73;AN=2;DP=7112;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,239:239:99:8079,715,0:0,0,97,142 chr2 60688968 . A G 227.62 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=1393;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:135,51:186:99:111,0,2517:100,35,0,51 chr2 60689748 . A G 319.82 PASS AC=2;AF=0.742;AN=2;DP=559;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:727,51,0:0,0,0,17 chr2 60997770 . T A 49.73 PASS AC=1;AF=0.648;AN=2;DP=313;MQ=60;set=variant-variant4-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant17-variant19-variant20-variant21-variant24-variant25-variant26-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,10:16:99:269,0,172:1,5,3,7 chr2 61007782 . A G 1353.97 PASS AC=1;AF=0.763;AN=2;DP=3820;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:72,47:119:99:1103,0,1894:47,25,30,17 chr2 61008036 . C T 1344.98 PASS AC=2;AF=1;AN=2;DP=1493;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1579,117,0:0,0,6,33 chr2 61009909 . C T 191.41 PASS AC=1;AF=0.632;AN=2;DP=1772;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,23:58:99:493,0,789:17,18,11,12 chr2 61014952 . A G 578.14 PASS AC=1;AF=0.69;AN=2;DP=289;MQ=60;set=variant4-variant5-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant28-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,8:15:99:291,0,229:0,7,1,7 chr2 61018788 . C T 71.25 PASS AC=1;AF=0.605;AN=2;DP=151;FractionInformativeReads=1;MQ=60;set=variant4-variant11-variant15-variant16-variant17-variant20-variant21-variant25-variant26-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:4,3:7:99:114,0,162:4,0,3,0 chr2 61021349 . A G 258.12 PASS AC=1;AF=0.618;AN=2;DP=645;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,11:26:99:401,0,390:4,11,0,11 chr2 61022377 . TTATTATC T 598.7 PASS AC=1;AF=0.5;AN=2;DP=363;MQ=60;set=variant4-variant14-variant26-variant30-variant35-variant36-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,14:40:99:508,0,1480:13,13,10,4 chr2 61022435 . A T 887.99 PASS AC=1;AF=0.5;AN=2;DP=558;FractionInformativeReads=1;MQ=60;set=variant4-variant14-variant26-variant30-variant35-variant36-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,27:56:99:682,0,667:13,16,15,12 chr2 61024661 . G GT,GTT 231.64 PASS AC=1,0;AF=0.273,0.295;AN=2;DP=1393;set=variant4-variant7-variant8-variant11-variant14-variant15-variant16-variant17-variant20-variant21-variant25-variant26-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant44 GT:DP:GQ:SB 0/1:66:99:33,8,18,7 chr2 61024667 . C T 885.91 PASS AC=1;AF=0.591;AN=2;DP=1481;set=variant4-variant7-variant8-variant11-variant14-variant15-variant16-variant17-variant20-variant21-variant25-variant26-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,32:77:99:880,0,1221:33,12,24,8 chr2 61024872 . T C 3418.16 PASS AC=1;AF=0.5;AN=2;DP=612;FractionInformativeReads=1;MQ=60;set=variant14-variant35 GT:AD:DP:GQ:PL:SB 0/1:150,142:292:99:3568,0,3561:74,76,69,73 chr2 61026177 . A G 4039.46 PASS AC=1;AF=0.5;AN=2;DP=1905;FractionInformativeReads=1;MQ=60;set=variant4-variant14-variant26-variant30-variant35-variant36-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:127,133:260:99:3268,0,3302:62,65,62,71 chr2 61026594 . A C 6395.01 PASS AC=1;AF=0.5;AN=2;DP=3224;MQ=60;set=variant4-variant14-variant26-variant30-variant35-variant36-variant37-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:149,203:352:99:5405,0,3743:84,65,103,100 chr2 61026739 . G GTTTGTTTTGTTTTGT,GTTTGT,GTTTGTTTTGT,GTTTTGTTTTGT,GTTTGTTTTGTTTTGTTTTGT 2112.88 PASS AC=0,0,0,0,1;AF=0.192,0.135,0.135,0.038,0.077;AN=2;DP=4996;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant14-variant18-variant19-variant24-variant26-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant37-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 0/5:107:99:12,32,18,45 chr2 61027921 . G T 3277.45 PASS AC=1;AF=0.5;AN=2;DP=1500;MQ=60;set=variant4-variant14-variant26-variant30-variant35-variant36-variant37-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:87,91:178:99:2633,0,2371:33,54,34,57 chr2 61028863 . C T 882.7 PASS AC=1;AF=0.5;AN=2;DP=382;MQ=60;set=variant4-variant14-variant26-variant30-variant35-variant36-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,34:64:99:895,0,837:21,9,23,11 chr2 61108996 . A T 3107.17 PASS AC=1;AF=0.583;AN=2;DP=421;FractionInformativeReads=1;MQ=60;set=variant11-variant14-variant17-variant22-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:29,35:64:99:935,0,717:14,15,20,15 chr2 61121492 . G A 1102.98 PASS AC=2;AF=0.966;AN=2;DP=1116;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:875,63,0:0,0,20,1 chr2 61128284 . T C 647.28 PASS AC=1;AF=0.742;AN=2;DP=483;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant22-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,7:15:99:209,0,259:1,7,2,5 chr2 61128285 . CTTT CT,CTTTT,C 1042.73 PASS AC=1,0,0;AF=0.3,0.125,0.225;AN=2;DP=363;set=variant4-variant7-variant8-variant9-variant10-variant12-variant15-variant22-variant23-variant25-variant26-variant27-variant29-variant32-variant34-variant35-variant36-variant40-variant41-variant43 GT:DP:GQ:SB 0/1:15:99:1,7,2,5 chr2 61175312 . T C 2472.33 PASS AC=1;AF=0.75;AN=2;DP=5057;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,67:124:99:1530,0,1405:31,26,36,31 chr2 61187478 . CAA CAAA,CA,C 149.62 PASS AC=1,0,0;AF=0.115,0.365,0.019;AN=2;DP=591;set=variant2-variant3-variant4-variant6-variant8-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant25-filterInvariant26-variant30-variant34-variant35-variant36-variant37-variant40-variant42-variant44 GT:DP:GQ:SB 0/1:25:99:9,4,8,4 chr2 61191995 . G C 88.71 PASS AC=2;AF=0.65;AN=2;DP=138;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant6-variant11-variant13-variant14-variant20-variant21-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant35-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:170,12,0:0,0,4,0 chr2 61235855 . C A 294.96 PASS AC=2;AF=0.667;AN=2;DP=295;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant6-variant8-variant9-variant10-variant11-variant13-variant16-variant17-variant18-variant22-variant24-variant27-variant30-variant32-variant33-variant35-variant36-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,19:19:56:716,56,0:0,0,16,3 chr2 61276263 . G A 10489.4 PASS AC=2;AF=1;AN=2;DP=14406;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,324:324:99:9977,970,0:0,0,140,184 chr2 61293199 . C T 715.5 PASS AC=2;AF=0.682;AN=2;DP=1519;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant6-variant8-variant9-variant10-variant11-variant13-variant16-variant17-variant18-variant22-variant24-variant27-variant28-variant30-variant32-variant33-variant35-variant36-variant40 GT:AD:DP:GQ:PL:SB 1/1:1,65:66:99:1942,186,0:1,0,27,38 chr2 61298684 . CA C,CAA 128.79 PASS AC=1,0;AF=0.463,0.037;AN=2;DP=784;set=variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant13-variant17-variant19-variant22-variant25-variant27-variant28-filterInvariant29-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant43-variant44 GT:DP:GQ:SB 0/1:32:99:15,3,10,4 chr2 61304002 . A G 537.6 PASS AC=2;AF=0.73;AN=2;DP=1148;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:657,54,0:0,0,15,3 chr2 61304271 . A G 1410.03 PASS AC=2;AF=0.682;AN=2;DP=1970;MQ=60;set=variant-variant2-variant3-variant6-variant8-variant9-variant10-variant11-variant13-variant16-variant17-variant18-variant22-variant27-variant28-variant30-variant32-variant33-variant35-variant36-variant40-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,113:113:99:3651,338,0:0,0,39,74 chr2 61308517 . A G 271.56 PASS AC=2;AF=0.73;AN=2;DP=825;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:65:716,65,0:0,0,16,6 chr2 61336523 . T C 398.25 PASS AC=1;AF=0.556;AN=2;DP=347;FractionInformativeReads=1;MQ=60;set=variant9-variant10-variant11-variant16-variant17-variant18-variant22-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:18,20:38:99:570,0,541:6,12,7,13 chr2 61349446 . G A 2279.35 PASS AC=2;AF=0.768;AN=2;DP=3403;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:2665,231,0:0,0,41,36 chr2 61349515 . C G 2304.49 PASS AC=1;AF=0.538;AN=2;DP=1809;FractionInformativeReads=1;set=variant9-variant10-variant11-variant16-variant17-variant18-variant22-variant34-variant35-variant36-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:74,77:151:99:2096,0,1936:50,24,44,33 chr2 61350137 . A G 4623.85 PASS AC=1;AF=0.548;AN=2;DP=8341;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant35-variant36-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:151,155:306:99:3799,0,3667:65,86,57,98 chr2 61351187 . T C 115.64 PASS AC=2;AF=0.706;AN=2;DP=499;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:45:667,45,0:0,0,8,4 chr2 61351188 . T C 115.64 PASS AC=2;AF=0.706;AN=2;DP=510;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:45:667,45,0:0,0,10,4 chr2 61351189 . T A 115.64 PASS AC=2;AF=0.706;AN=2;DP=519;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:667,45,0:0,0,11,4 chr2 61384906 . T C 260.58 PASS AC=1;AF=0.559;AN=2;DP=747;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,7:17:99:202,0,310:8,2,6,1 chr2 61385100 . G A 1337.41 PASS AC=1;AF=0.565;AN=2;DP=2663;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant35-variant36-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:36,48:84:99:1872,0,1877:15,21,24,24 chr2 61385105 . G C 1286.26 PASS AC=1;AF=0.565;AN=2;DP=2628;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant35-variant36-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:35,48:83:99:1868,0,1856:14,21,23,25 chr2 61385248 . A G 719.59 PASS AC=1;AF=0.559;AN=2;DP=2415;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,46:76:99:1125,0,701:17,13,23,23 chr2 61389737 . T G 707.84 PASS AC=1;AF=0.559;AN=2;DP=1486;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,20:41:99:535,0,569:6,15,6,14 chr2 61389799 . G A 187.66 PASS AC=1;AF=0.565;AN=2;DP=595;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant35-variant36-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:13,10:23:99:378,0,399:4,9,4,6 chr2 61404514 . G A 48.15 PASS AC=1;AF=0.583;AN=2;DP=363;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant16-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant32-variant35-variant36-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:4,9:13:74:264,0,74:3,1,5,4 chr2 61404905 . C G 742.97 PASS AC=1;AF=0.536;AN=2;DP=1627;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant27-variant33-variant34-variant35-variant36-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,27:58:99:640,0,946:19,12,14,13 chr2 61404931 . A T 538.78 PASS AC=1;AF=0.568;AN=2;DP=1404;MQ=60;set=variant2-variant4-variant9-variant10-variant14-variant16-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant29-variant32-variant35-variant36-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:27,41:68:99:1080,0,617:13,14,23,18 chr2 61405008 . C T 1373.71 PASS AC=1;AF=0.538;AN=2;DP=1250;MQ=60;set=variant2-variant3-variant9-variant11-variant16-variant17-variant18-variant20-variant21-variant22-variant35-variant36-variant38 GT:AD:DP:GQ:PL:SB 0/1:68,36:104:99:1375,0,2628:39,29,18,18 chr2 61405026 . G A 1427.76 PASS AC=1;AF=0.5;AN=2;DP=113;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=3.753;QD=12.64;ReadPosRankSum=-1.818;SOR=0.671;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:72,41:113:99:1456,0,2839:39,33,22,19 chr2 61405723 . G A 927.6 PASS AC=1;AF=0.536;AN=2;DP=860;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant9-variant11-variant16-variant17-variant18-variant20-variant21-variant22-variant35-variant36-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:38,32:70:99:739,0,984:22,16,17,15 chr2 61405795 . G T 1404.06 PASS AC=2;AF=0.73;AN=2;DP=2865;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,83:83:99:2601,248,0:0,0,40,43 chr2 61405865 . C G 524.68 PASS AC=1;AF=0.538;AN=2;DP=811;MQ=60;set=variant2-variant3-variant9-variant11-variant16-variant17-variant18-variant20-variant21-variant22-variant35-variant36-variant38 GT:AD:DP:GQ:PL:SB 0/1:44,26:70:99:650,0,1094:21,23,13,13 chr2 61412559 . C T 428 PASS AC=2;AF=0.766;AN=2;DP=340;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:293,24,0:0,0,7,1 chr2 61413037 . TATTA T 1037.43 PASS AC=1;AF=0.5;AN=2;DP=441;MQ=60;set=variant-variant3-variant5-variant6-variant8-variant10-variant13-variant22-variant28-variant30-variant35 GT:AD:DP:GQ:PL:SB 0/1:14,14:28:99:511,0,770:9,5,9,5 chr2 61413723 . A G 3806.65 PASS AC=2;AF=0.817;AN=2;DP=4981;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,140:140:99:4320,420,0:0,0,69,71 chr2 61414470 . C G 416.82 PASS AC=1;AF=0.545;AN=2;DP=725;MQ=60;set=variant2-variant3-variant11-variant16-variant17-variant18-variant20-variant21-variant22-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:34,36:70:99:1148,0,1000:13,21,11,25 chr2 61414639 . GCAAT G,GCAATCAAT 4038.64 PASS AC=2,0;AF=0.805,0.012;AN=2;DP=3710;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:90:99:0,0,47,43 chr2 61415492 . A G 783.78 PASS AC=1;AF=0.583;AN=2;DP=2142;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,34:64:99:862,0,824:21,9,23,11 chr2 61417617 . A G 1504.48 PASS AC=2;AF=0.722;AN=2;DP=3678;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,98:98:99:3081,293,0:0,0,47,51 chr2 61450454 . A G 478.29 PASS AC=1;AF=0.625;AN=2;DP=1482;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,31:44:99:807,0,363:2,11,10,21 chr2 61456610 . AC A 517.08 PASS AC=1;AF=0.583;AN=2;DP=101;FractionInformativeReads=1;set=variant2-variant9-variant17-variant21-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:14,8:22:99:257,0,1815:11,3,5,3 chr2 61456612 . AAAAAAAAAAAAC A 241 PASS AC=1;AF=0.625;AN=2;DP=82;FractionInformativeReads=1;set=variant9-variant17-variant21-variant35 GT:AD:DP:GQ:PL:SB 0/1:18,8:26:99:248,0,1900:13,5,5,3 chr2 61522123 . T C 1096.3 PASS AC=2;AF=0.989;AN=2;DP=2092;MQ=60;MQRankSum=0.3;ReadPosRankSum=1.004;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1269,126,0:0,0,25,17 chr2 61538602 . G GAAAAGAGAAAGAAAAAGAAAA,GAAAAGAGAAAGAAAAAGAAAAA 186.37 PASS AC=1,0;AF=0.875,0.013;AN=2;DP=265;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:6:99:3,1,1,1 chr2 61538613 . G GAAAA 151.54 PASS AC=1;AF=0.625;AN=2;DP=138;MQ=60;set=variant2-variant3-variant9-variant11-variant16-variant17-variant18-variant21-variant22-variant35-variant36-variant38 GT:AD:DP:GQ:PL:SB 0/1:6,4:10:99:234,0,235:4,2,3,1 chr2 61538615 . G GAAAAA 193.4 PASS AC=1;AF=0.625;AN=2;DP=147;MQ=60;set=variant2-variant3-variant9-variant11-variant16-variant17-variant18-variant21-variant22-variant35-variant36-variant38 GT:AD:DP:GQ:PL:SB 0/1:6,6:12:99:234,0,235:4,2,4,2 chr2 61552336 . A G 85.48 PASS AC=1;AF=0.6;AN=2;DP=25;FS=0;FractionInformativeReads=1;MQ=60;set=variant3-variant9-variant17-variant21-variant35 GT:AD:DP:GQ:PL:SB 0/1:5,2:7:69:69,0,124:2,3,2,0 chr2 61552484 . T A 572.13 PASS AC=1;AF=0.744;AN=2;DP=1010;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,15:30:99:341,0,335:9,6,7,8 chr2 61575308 . A G 5083.97 PASS AC=1;AF=0.977;AN=2;DP=6666;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:94,80:174:99:2239,0,2614:48,46,40,40 chr2 61576517 . G A 2632.37 PASS AC=2;AF=1;AN=2;DP=3511;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,80:80:99:2584,240,0:0,0,37,43 chr2 61577435 . T C 856.45 PASS AC=1;AF=0.538;AN=2;DP=1025;MQ=60;set=variant2-variant3-variant9-variant11-variant16-variant17-variant18-variant20-variant21-variant22-variant35-variant36-variant38 GT:AD:DP:GQ:PL:SB 0/1:49,39:88:99:789,0,1138:28,21,21,18 chr2 61605614 . T A 715.39 PASS AC=1;AF=0.622;AN=2;DP=1713;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,19:59:99:334,0,874:18,22,9,10 chr2 61607510 . G A 908.16 PASS AC=1;AF=0.542;AN=2;DP=936;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant9-variant11-variant16-variant17-variant18-variant20-variant21-variant22-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:27,41:68:99:1075,0,592:11,16,14,27 chr2 61622251 . C T 212.82 PASS AC=1;AF=0.609;AN=2;DP=548;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant9-variant10-variant14-variant15-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant29-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:12,9:21:99:244,0,327:5,7,6,3 chr2 61647901 . A G 994.45 PASS AC=1;AF=0.63;AN=2;DP=1874;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant12-variant13-variant14-variant15-variant18-variant19-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,38:65:99:1005,0,690:13,14,14,24 chr2 61648909 . AAC A,AACAC 55.9 PASS AC=1,0;AF=0.438,0.094;AN=2;DP=208;set=variant2-variant7-variant9-variant15-variant18-variant23-variant26-variant28-variant31-variant33-variant35-variant37-variant38-variant40-variant42-variant43 GT:DP:GQ:SB 0/1:9:99:4,1,2,2 chr2 61713209 . GGAAAATC G 456.11 PASS AC=1;AF=0.6;AN=2;DP=774;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,7:20:99:246,0,1953:1,12,0,7 chr2 61713218 . T A 467.75 PASS AC=1;AF=0.6;AN=2;DP=693;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,6:18:99:249,0,1920:1,11,0,6 chr2 61713220 . T G 412.58 PASS AC=1;AF=0.6;AN=2;DP=665;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,6:17:99:216,0,1923:0,11,0,6 chr2 61722519 . G GA 979.14 PASS AC=1;AF=0.73;AN=2;DP=2002;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,29:51:99:763,0,547:16,6,18,11 chr2 61729258 . A G 1752.22 PASS AC=1;AF=0.73;AN=2;DP=2833;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,36:63:99:1422,0,1698:15,12,21,15 chr2 61729268 . T C 1681 PASS AC=1;AF=0.73;AN=2;DP=2919;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,38:67:99:1490,0,1767:17,12,22,16 chr2 61749690 . C T 673.31 PASS AC=1;AF=0.73;AN=2;DP=1718;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,19:49:99:425,0,678:18,12,10,9 chr2 61749716 . C T 608.39 PASS AC=1;AF=0.73;AN=2;DP=2087;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-filterInvariant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,22:55:99:525,0,831:16,17,12,10 chr2 61761169 . G A 2578.68 PASS AC=2;AF=0.977;AN=2;DP=3132;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:2517,225,0:0,0,45,30 chr2 61764140 . C T 392.69 PASS AC=1;AF=0.743;AN=2;DP=2675;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,31:76:99:810,0,1197:19,26,13,18 chr2 61765074 . G A 820.59 PASS AC=1;AF=0.667;AN=2;DP=1335;FractionInformativeReads=1;set=variant2-variant4-variant6-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant29-variant32-variant33-variant35-variant36-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,23:63:99:599,0,1035:21,19,14,9 chr2 61765175 . GGCC GC,G 853.98 PASS AC=1,0;AF=0.62,0.02;AN=2;DP=695;MQ=60;set=variant2-variant4-variant6-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant32-variant33-variant35-variant38-variant39-variant41-variant42-variant44 GT:DP:GQ:SB 0/1:29:99:3,10,4,12 chr2 62052380 . A G 2629.88 PASS AC=1;AF=0.593;AN=2;DP=3437;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant17-variant18-variant20-variant23-variant25-variant26-variant27-variant28-variant31-variant33-variant34-variant35-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:63,96:159:99:2607,0,1609:35,28,53,43 chr2 62053290 . A G 1702.71 PASS AC=1;AF=0.593;AN=2;DP=2111;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant17-variant18-variant20-variant23-variant25-variant26-variant27-variant28-variant31-variant33-variant34-variant35-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,33:70:99:1014,0,1047:20,17,18,15 chr2 62053546 . CGCT C 2236.9 PASS AC=1;AF=0.5;AN=2;DP=2639;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant9-variant10-variant11-variant13-variant17-variant23-variant26-variant27-variant28-variant31-variant33-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:89,75:164:99:2869,0,4417:37,52,30,45 chr2 62053878 . G GA 105.18 PASS AC=2;AF=0.984;AN=2;DP=150;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:309,27,0:0,0,3,6 chr2 62063093 . TA T 721.45 PASS AC=2;AF=0.614;AN=2;DP=2245;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:5,44:49:28:845,28,0:3,2,29,15 chr2 62066417 . ATATAT A 171.57 PASS AC=1;AF=0.667;AN=2;DP=213;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant13-variant15-variant17-variant20-variant23-variant26-variant28-variant31-variant33-variant34-variant35-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,4:9:99:142,0,276:3,2,3,1 chr2 62066927 . A G 2581.82 PASS AC=2;AF=0.955;AN=2;DP=3671;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,87:87:99:2952,261,0:0,0,40,47 chr2 62073918 . C T 804.29 PASS AC=1;AF=0.667;AN=2;DP=3734;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,62:102:99:1565,0,989:23,17,38,24 chr2 62074097 . G A 534.02 PASS AC=1;AF=0.5;AN=2;DP=836;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant9-variant10-variant11-variant13-variant17-variant23-variant26-variant27-variant28-variant31-variant33-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:20,26:46:99:685,0,597:4,16,8,18 chr2 62074140 . A AAC 661.08 PASS AC=2;AF=0.955;AN=2;DP=861;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:741,51,0:0,0,1,16 chr2 62081012 . A C 4205.8 PASS AC=2;AF=0.955;AN=2;DP=9980;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,296:296:99:9225,887,0:0,0,175,121 chr2 62081217 . A G 3577.53 PASS AC=2;AF=0.955;AN=2;DP=4510;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,101:101:99:3184,302,0:0,0,29,72 chr2 62095994 . A G 599.79 PASS AC=2;AF=0.955;AN=2;DP=1001;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:765,69,0:0,0,8,15 chr2 62098993 . C T 470.9 PASS AC=1;AF=0.593;AN=2;DP=965;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant17-variant18-variant20-variant23-variant25-variant26-variant27-variant28-variant31-variant33-variant34-variant35-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,27:48:99:597,0,481:13,8,16,11 chr2 62099156 . T C 489.67 PASS AC=1;AF=0.593;AN=2;DP=1176;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant17-variant18-variant20-variant23-variant25-variant26-variant27-variant28-variant31-variant33-variant34-variant35-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,21:51:99:444,0,709:11,19,10,11 chr2 62100380 . G T 521.96 PASS AC=1;AF=0.5;AN=2;DP=610;FractionInformativeReads=1;MQ=60;set=variant3-variant15-variant22-variant24-variant27-variant28-variant29-variant30-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:38,23:61:99:611,0,1071:12,26,7,16 chr2 62104343 . C T 82.7 PASS AC=1;AF=0.676;AN=2;DP=373;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:99:107,0,114:1,2,0,3 chr2 62104660 . TA T,TAA 228.24 PASS AC=1,0;AF=0.554,0.018;AN=2;DP=1100;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant17-variant18-variant20-filterInvariant21-variant23-variant25-variant26-variant27-variant28-variant31-variant33-variant34-variant35-variant40-variant41-filterInvariant43-variant44 GT:DP:GQ:SB 0/1:40:99:3,11,8,18 chr2 62107376 . T TC 1468.54 PASS AC=2;AF=0.955;AN=2;DP=1632;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1309,102,0:0,0,25,9 chr2 62107632 . G A 185.17 PASS AC=1;AF=0.558;AN=2;DP=749;MQ=60;set=variant-variant3-variant4-variant5-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant19-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant35-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:24,22:46:99:648,0,690:7,17,4,18 chr2 62110551 . CAAAA C,CAA,CAAA,CA 191.92 PASS AC=0,0,1,0;AF=0.021,0.292,0.208,0.021;AN=2;DP=314;set=variant3-variant4-variant8-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant22-variant23-variant24-variant27-variant28-variant29-variant32-variant33-variant35-variant36-variant39-variant40-variant42 GT:DP:GQ:SB 0/3:11:0:2,0,9,0 chr2 62112221 . G GA 1070.81 PASS AC=1;AF=0.654;AN=2;DP=2468;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,21:51:99:450,0,976:13,17,6,15 chr2 62112222 . G A 1079.86 PASS AC=1;AF=0.667;AN=2;DP=2391;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,26:54:99:882,0,592:12,16,8,18 chr2 62112246 . C CT 357.68 PASS AC=1;AF=0.654;AN=2;DP=1687;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,9:22:99:180,0,254:2,11,3,6 chr2 62115776 . G A 1552.93 PASS AC=1;AF=0.5;AN=2;DP=1361;MQ=60;set=variant3-variant15-variant22-variant24-variant27-variant28-variant29-variant30-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:60,81:141:99:2097,0,1584:23,37,39,42 chr2 62196080 . CTTT C,CTT,CT,CTTTT 46.38 PASS AC=0,2,0,0;AF=0.111,0.333,0.278,0.056;AN=2;DP=52;FS=0;MQ=60;set=variant12-variant16-variant20-variant21-variant26-variant28-variant33-variant35-variant42 GT:DP:GQ:SB 2/2:4:12:0,0,2,2 chr2 62727445 . G A 1498.53 PASS AC=2;AF=0.711;AN=2;DP=4227;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,102:102:99:2778,305,0:0,0,53,49 chr2 62727902 . C T 1068.23 PASS AC=1;AF=0.567;AN=2;DP=858;MQ=60;set=variant2-variant10-variant11-variant14-variant17-variant18-variant19-variant22-variant23-variant28-variant30-variant35-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:40,32:72:99:964,0,1252:31,9,25,7 chr2 62727986 . C A 2317.15 PASS AC=1;AF=0.583;AN=2;DP=2100;MQ=60;set=variant2-variant10-variant11-variant14-variant17-variant18-variant19-variant23-variant28-variant30-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:110,87:197:99:2201,0,2623:66,44,52,35 chr2 62728046 . G A 3301.49 PASS AC=1;AF=0.583;AN=2;DP=3413;MQ=60;set=variant2-variant10-variant11-variant14-variant17-variant18-variant19-variant23-variant28-variant30-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:152,163:315:99:4302,0,3725:85,67,102,61 chr2 62728105 . A G 4033.44 PASS AC=1;AF=0.583;AN=2;DP=4599;MQ=60;set=variant2-variant10-variant11-variant14-variant17-variant18-variant19-variant23-variant28-variant30-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:185,193:378:99:7448,0,7106:107,78,113,80 chr2 62728112 . CA C 4016.25 PASS AC=1;AF=0.583;AN=2;DP=4788;MQ=60;set=variant2-variant10-variant11-variant14-variant17-variant18-variant19-variant23-variant28-variant30-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:198,206:404:99:7708,0,7334:110,88,118,88 chr2 62729297 . T C 278.12 PASS AC=1;AF=0.536;AN=2;DP=161;FractionInformativeReads=1;MQ=60;set=variant10-variant12-variant13-variant15-variant18-variant21-variant22-variant28-variant31-variant32-variant34-variant35-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:7,7:14:99:233,0,175:5,2,6,1 chr2 62729674 . T C 1975.41 PASS AC=1;AF=0.881;AN=2;DP=2867;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,43:68:99:1129,0,626:12,13,22,21 chr2 62729747 . G GA 2105.85 PASS AC=1;AF=0.881;AN=2;DP=3045;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,34:57:99:881,0,546:11,12,16,18 chr2 62733189 . C T 3485.4 PASS AC=1;AF=0.538;AN=2;DP=4343;MQ=60;set=variant10-variant12-variant13-variant15-variant18-variant21-variant22-variant28-variant31-variant32-variant34-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:194,198:392:99:4583,0,4449:88,106,89,109 chr2 62733253 . C T 2769.93 PASS AC=1;AF=0.542;AN=2;DP=4893;MQ=60;set=variant6-variant10-variant11-variant12-variant13-variant15-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:106,89:195:99:2308,0,2881:42,64,32,57 chr2 62738883 . C T 562.37 PASS AC=1;AF=0.756;AN=2;DP=2075;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,19:50:99:527,0,758:20,11,13,6 chr2 62738931 . G C 766.02 PASS AC=1;AF=0.756;AN=2;DP=3080;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,32:74:99:752,0,999:22,20,19,13 chr2 62739135 . A C 508.23 PASS AC=1;AF=0.881;AN=2;DP=570;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,6:10:99:215,0,106:1,3,0,6 chr2 63182611 . G GT 816.04 PASS AC=1;AF=0.567;AN=2;DP=748;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant10-variant11-variant15-variant28-variant29-variant30-variant35-variant37-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:40,20:60:99:364,0,905:33,7,18,2 chr2 63277843 . C G 95.44 PASS AC=1;AF=0.72;AN=2;DP=179;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant11-variant12-variant14-variant15-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant35-variant37-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,2:6:72:72,0,108:3,1,2,0 chr2 63380809 . G A 61.77 PASS AC=1;AF=0.914;AN=2;DP=96;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant7-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:1,2:3:37:81,0,37:0,1,0,2 chr2 63401973 . G A 887.4 PASS AC=1;AF=0.595;AN=2;DP=1235;MQ=60;set=variant2-variant3-variant7-variant10-variant12-variant14-variant19-variant20-variant23-variant25-variant27-variant30-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,24:58:99:682,0,926:13,21,6,18 chr2 63486429 . C T 793.21 PASS AC=1;AF=0.629;AN=2;DP=2606;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,41:84:99:970,0,1100:25,18,26,15 chr2 63540523 . A T 812.02 PASS AC=1;AF=0.725;AN=2;DP=928;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,21:39:99:690,0,442:6,12,4,17 chr2 63605772 . A G 528.08 PASS AC=1;AF=0.718;AN=2;DP=889;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,12:22:99:383,0,250:3,7,2,10 chr2 63609017 . A T 1094.1 PASS AC=1;AF=0.629;AN=2;DP=1156;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:24,11:35:99:225,0,676:17,7,8,3 chr2 63631830 . T C 661.89 PASS AC=1;AF=0.583;AN=2;DP=1214;MQ=60;set=variant-variant5-variant8-variant9-variant11-variant17-variant18-variant19-variant22-variant24-variant26-variant28-variant29-variant33-variant35-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:47,64:111:99:1571,0,1139:17,30,25,39 chr2 63631889 . A C 1101.87 PASS AC=1;AF=0.591;AN=2;DP=1030;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:18,33:51:99:946,0,417:5,13,9,24 chr2 63631921 . C T 645.99 PASS AC=1;AF=0.594;AN=2;DP=532;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,16:25:99:586,0,277:1,8,1,15 chr2 63664829 . A G 233.51 PASS AC=1;AF=0.579;AN=2;DP=249;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant8-variant9-variant11-variant17-variant18-variant19-variant22-variant24-variant26-variant28-variant29-variant33-variant35-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,12:23:99:444,0,378:6,5,10,2 chr2 63669625 . T C 6557.85 PASS AC=1;AF=0.731;AN=2;DP=7041;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:100,88:188:99:2389,0,2838:47,53,41,47 chr2 63720210 . A G 154.82 PASS AC=1;AF=0.73;AN=2;DP=320;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,9:14:99:356,0,165:0,5,0,9 chr2 63798333 . C T 1982.59 PASS AC=1;AF=0.718;AN=2;DP=2174;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,37:62:99:854,0,596:18,7,20,17 chr2 63816672 . C G 912.56 PASS AC=1;AF=0.718;AN=2;DP=780;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,9:24:99:222,0,550:1,14,2,7 chr2 63820546 . AT A 74.57 PASS AC=1;AF=0.579;AN=2;DP=380;MQ=60;set=variant-variant5-variant8-variant9-variant11-variant17-variant18-variant19-variant22-variant24-variant26-variant28-variant29-variant33-variant35-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,19:27:99:454,0,144:6,2,13,6 chr2 63822785 . T C 2099.61 PASS AC=1;AF=0.744;AN=2;DP=3070;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,31:88:99:694,0,1439:30,27,16,15 chr2 63824810 . T A 170.92 PASS AC=1;AF=0.5;AN=2;DP=53;FractionInformativeReads=1;MQ=60;set=variant11-variant28-variant35 GT:AD:DP:GQ:PL:SB 0/1:14,5:19:99:107,0,407:4,10,1,4 chr2 63826164 . C G 68.2 PASS AC=1;AF=0.579;AN=2;DP=251;MQ=60;set=variant-variant5-variant8-variant9-variant11-variant17-variant18-variant19-variant22-variant24-variant26-variant28-variant29-variant33-variant35-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,7:13:99:232,0,232:6,0,6,1 chr2 63826528 . T G 151.77 PASS AC=1;AF=0.743;AN=2;DP=308;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,2:8:66:66,0,250:0,6,0,2 chr2 63850098 . G C 548.53 PASS AC=1;AF=0.563;AN=2;DP=997;FractionInformativeReads=1;set=variant3-variant6-variant7-variant10-variant12-variant13-variant14-variant21-variant25-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,32:50:99:1000,0,408:6,12,8,24 chr2 64068278 . G C 750.55 PASS AC=1;AF=0.5;AN=2;DP=220;MQ=60;set=variant29-variant33-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:42,27:69:99:563,0,992:21,21,12,15 chr2 64068788 . G T 85.7 PASS AC=2;AF=0.808;AN=2;DP=460;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:803,63,0:0,0,16,5 chr2 64069732 . G A 906.41 PASS AC=2;AF=0.793;AN=2;DP=2985;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,74:74:99:2304,221,0:0,0,26,48 chr2 64083600 . G C 239.2 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=575;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:39,12:51:99:135,0,1017:3,36,11,1 chr2 64085114 . G A 1328.43 PASS AC=2;AF=0.78;AN=2;DP=4477;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,93:93:99:2833,278,0:0,0,48,45 chr2 64089748 . C A 450.24 PASS AC=2;AF=0.78;AN=2;DP=974;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:932,75,0:0,0,22,3 chr2 64118158 . TA TAA,TAAA,T 58.95 PASS AC=1,0,1;AF=0.524,0.024,0.071;AN=2;DP=274;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant11-variant13-variant14-variant15-variant20-variant21-variant25-variant27-variant28-variant29-variant34-variant35-variant38-variant39-variant42-variant43 GT:DP:GQ:SB 3/1:12:99:0,0,12,0 chr2 64126775 . C A 348.8 PASS AC=1;AF=0.587;AN=2;DP=996;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant11-variant12-variant13-variant14-variant15-variant20-variant21-variant25-variant27-variant28-variant30-variant33-variant34-variant35-variant36-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:18,17:35:99:417,0,525:6,12,8,9 chr2 64139901 . A T 377.99 PASS AC=2;AF=0.857;AN=2;DP=369;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:399,33,0:0,0,1,10 chr2 64140301 . A T 2372.06 PASS AC=2;AF=0.841;AN=2;DP=2328;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1207,108,0:0,0,24,12 chr2 64143884 . T C 142.42 PASS AC=1;AF=0.607;AN=2;DP=354;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant18-variant20-variant21-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:7,3:10:99:105,0,250:7,0,3,0 chr2 64331815 . CTT CT,CTTTT,C 209.92 PASS AC=1,0,0;AF=0.464,0.012,0.024;AN=2;DP=1612;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-filterInvariant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:42:99:16,8,12,6 chr2 64371109 . T TG 149.72 PASS AC=2;AF=1;AN=2;DP=568;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:299,24,0:0,0,7,1 chr2 64371569 . A G 935.43 PASS AC=1;AF=0.63;AN=2;DP=1950;MQ=60;set=variant-variant2-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant27-variant31-variant32-variant35-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:63,39:102:99:927,0,1704:30,33,21,18 chr2 64371615 . C G 1790.87 PASS AC=1;AF=0.805;AN=2;DP=2563;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,24:72:99:611,0,1124:26,22,10,14 chr2 64682364 . A C 829.52 PASS AC=2;AF=0.676;AN=2;DP=783;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:839,72,0:0,0,18,6 chr2 64687147 . GT GTT,G 86.95 PASS AC=0,1;AF=0.396,0.104;AN=2;DP=2012;set=filterInvariant-filterInvariant3-filterInvariant4-filterInvariant7-filterInvariant8-variant10-variant13-filterInvariant14-filterInvariant15-filterInvariant16-variant17-filterInvariant22-variant23-filterInvariant25-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant29-variant30-variant31-filterInvariant32-filterInvariant33-filterInvariant35-filterInvariant42 GT:DP:GQ:SB 0/2:81:77:36,31,7,7 chr2 64687665 . C A 1201.47 PASS AC=1;AF=0.563;AN=2;DP=1344;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant8-variant11-variant12-variant17-variant21-variant29-variant34-variant35-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,35:102:99:930,0,1813:39,28,23,12 chr2 64687777 . G T 2568.11 PASS AC=2;AF=0.75;AN=2;DP=6500;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,174:174:99:5232,521,0:0,0,92,82 chr2 64796479 . C T 324.79 PASS AC=1;AF=0.588;AN=2;DP=663;MQ=60;set=variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,9:17:99:313,0,261:1,7,1,8 chr2 64796847 . A G 1793.56 PASS AC=1;AF=0.591;AN=2;DP=3686;MQ=60;set=variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:71,43:114:99:1022,0,1845:28,43,15,28 chr2 64796932 . G A 456.78 PASS AC=1;AF=0.591;AN=2;DP=854;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:21,12:33:99:382,0,637:5,16,1,11 chr2 64799937 . TAA T 84.03 PASS AC=1;AF=0.603;AN=2;DP=394;set=variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,3:9:87:87,0,171:6,0,2,1 chr2 64819249 . TA T,TAAAA,TAAA,TAA 95.51 PASS AC=0,1,0,0;AF=0.071,0.286,0.2,0.014;AN=2;DP=1938;set=filterInvariant2-variant3-filterInvariant4-variant5-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:DP:GQ:SB 0/2:47:99:10,13,11,13 chr2 64819380 . G A 1891.05 PASS AC=1;AF=0.526;AN=2;DP=2990;MQ=60;set=variant5-variant6-variant7-variant10-variant11-variant12-variant15-variant17-variant20-variant22-variant25-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:76,54:130:99:1243,0,1874:44,32,33,21 chr2 64859377 . CTTT CT,CTT,C 2176.63 PASS AC=0,1,0;AF=0.227,0.489,0.011;AN=2;DP=8271;set=Intersection GT:DP:GQ:SB 0/2:160:99:46,57,25,32 chr2 64859679 . T C 2968.94 PASS AC=1;AF=0.833;AN=2;DP=4231;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:63,37:100:99:722,0,1600:30,33,19,18 chr2 64860017 . GA G 2933.35 PASS AC=1;AF=0.63;AN=2;DP=5227;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant9-variant11-variant15-variant16-variant18-variant21-variant22-variant27-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:112,113:225:99:2843,0,2786:57,55,58,55 chr2 64862055 . A G 550.92 PASS AC=1;AF=0.63;AN=2;DP=1389;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant9-variant11-variant15-variant16-variant18-variant21-variant22-variant27-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,32:60:99:885,0,658:16,12,20,12 chr2 64881017 . C G 1186.77 PASS AC=2;AF=1;AN=2;DP=1199;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:1156,78,0:0,0,10,16 chr2 64881018 . G C 1186.77 PASS AC=2;AF=1;AN=2;DP=1179;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:1156,78,0:0,0,10,16 chr2 65200518 . C G 294.51 PASS AC=1;AF=0.5;AN=2;DP=33;FractionInformativeReads=1;MQ=60;set=variant-variant35 GT:AD:DP:GQ:PL:SB 0/1:6,10:16:99:352,0,184:5,1,9,1 chr2 65215487 . C G 346.78 PASS AC=1;AF=0.567;AN=2;DP=217;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant7-variant11-variant12-variant16-variant18-variant22-variant23-variant24-variant27-variant31-variant35-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,3:12:59:59,0,256:7,2,2,1 chr2 65215789 . G A 583.11 PASS AC=1;AF=0.559;AN=2;DP=1241;MQ=60;set=variant-variant2-variant4-variant7-variant11-variant12-variant16-variant18-variant22-variant23-variant24-variant27-variant31-variant35-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,37:82:99:717,0,1146:19,26,17,20 chr2 65216487 . T C 345.37 PASS AC=1;AF=0.559;AN=2;DP=683;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant7-variant11-variant12-variant16-variant18-variant22-variant23-variant24-variant27-variant31-variant35-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,16:38:99:440,0,715:18,4,10,6 chr2 65216647 . C G 2521.91 PASS AC=1;AF=0.559;AN=2;DP=3019;MQ=60;set=variant-variant2-variant4-variant7-variant11-variant12-variant16-variant18-variant22-variant23-variant24-variant27-variant31-variant35-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:99,108:207:99:4177,0,5051:55,44,69,39 chr2 65216648 . G C 2521.91 PASS AC=1;AF=0.559;AN=2;DP=3032;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant7-variant11-variant12-variant16-variant18-variant22-variant23-variant24-variant27-variant31-variant35-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:97,108:205:99:4177,0,5051:54,43,69,39 chr2 65216903 . A G 2654.5 PASS AC=1;AF=0.5;AN=2;DP=189;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.938;QD=14.04;ReadPosRankSum=2.027;SOR=0.686;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:90,99:189:99:2683,0,2467:38,52,42,57 chr2 65217089 . G C 2337.24 PASS AC=1;AF=0.559;AN=2;DP=2726;MQ=60;set=variant-variant2-variant4-variant7-variant11-variant12-variant16-variant18-variant22-variant23-variant24-variant27-variant31-variant35-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:99,84:183:99:2129,0,2464:53,46,46,38 chr2 65245365 . G A 2324.74 PASS AC=1;AF=0.575;AN=2;DP=3257;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant12-variant14-variant19-variant25-variant27-variant28-variant30-variant31-variant32-variant35-variant36-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:99,91:190:99:2185,0,2617:48,51,48,43 chr2 65250452 . C CGTGTGTT 1917.39 PASS AC=1;AF=0.5;AN=2;DP=830;MQ=60;set=variant-variant3-variant12-variant14-variant30-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:64,75:139:99:2730,0,4133:16,48,18,57 chr2 65250453 . A G,ATGTGTGTTG 4286.49 PASS AC=1,0;AF=0.088,0.5;AN=2;DP=1817;MQ=60;set=variant14-variant19-variant20-variant21-variant22-variant25-variant27-variant28-variant31-variant32-variant33-variant35-variant36-variant39-variant40-variant42-variant43 GT:DP:GQ:SB 0/1:114:99:17,49,9,39 chr2 65283702 . G GC 778.93 PASS AC=2;AF=1;AN=2;DP=1532;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:1672,141,0:0,0,15,32 chr2 65283745 . C CG 261.39 PASS AC=2;AF=1;AN=2;DP=791;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:1182,96,0:0,0,12,20 chr2 65296798 . G A 1560.17 PASS AC=1;AF=0.536;AN=2;DP=2209;MQ=60;set=variant-variant3-variant7-variant12-variant14-variant15-variant21-variant22-variant30-variant33-variant35-variant36-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:80,77:157:99:1858,0,2113:42,38,43,34 chr2 65298839 . A G 1586.16 PASS AC=1;AF=0.526;AN=2;DP=3283;MQ=60;set=variant-variant2-variant3-variant7-variant12-variant13-variant14-variant15-variant17-variant21-variant22-variant23-variant28-variant30-variant33-variant35-variant36-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:104,76:180:99:1768,0,2650:45,59,38,38 chr2 65309878 . C G 757.83 PASS AC=1;AF=0.5;AN=2;DP=277;FractionInformativeReads=1;MQ=60;set=variant-variant12-variant14-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:34,35:69:99:811,0,966:12,22,14,21 chr2 65309988 . T C 32.42 PASS AC=1;AF=0.782;AN=2;DP=474;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,11:17:99:295,0,172:1,5,3,8 chr2 65310831 . A T 491.56 PASS AC=1;AF=0.768;AN=2;DP=1488;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,18:41:99:469,0,618:17,6,12,6 chr2 65311031 . A G 3122.39 PASS AC=1;AF=0.545;AN=2;DP=2110;MQ=60;set=variant-variant3-variant7-variant12-variant14-variant30-variant35-variant36-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:111,93:204:99:2311,0,2576:49,62,47,46 chr2 65311438 . G A 2318.32 PASS AC=1;AF=0.545;AN=2;DP=1802;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant7-variant12-variant14-variant30-variant35-variant36-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:93,71:164:99:1717,0,2577:41,52,33,38 chr2 65311555 . C T 2002.72 PASS AC=1;AF=0.78;AN=2;DP=4633;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,68:118:99:1808,0,1585:30,20,36,32 chr2 65311656 . TA TAA,TAAA,T 1713.95 PASS AC=1,0,0;AF=0.511,0.216,0.011;AN=2;DP=8450;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-filterInvariant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-filterInvariant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-filterInvariant43-variant44 GT:DP:GQ:SB 0/1:189:99:49,46,47,47 chr2 65312217 . C T 4777.8 PASS AC=1;AF=0.81;AN=2;DP=14498;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:231,152:383:99:3709,0,5781:119,112,71,81 chr2 65313215 . C CAG 664.41 PASS AC=1;AF=0.81;AN=2;DP=2261;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,32:59:99:1238,0,1116:14,13,19,13 chr2 65313758 . G C 5761.5 PASS AC=1;AF=0.55;AN=2;DP=3401;MQ=60;set=variant-variant3-variant7-variant12-variant14-variant30-variant35-variant36-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:138,188:326:99:5056,0,3491:70,68,82,106 chr2 65315880 . G C 434.73 PASS AC=1;AF=0.768;AN=2;DP=1237;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,14:33:99:406,0,569:5,14,4,10 chr2 65315903 . G A 355.62 PASS AC=1;AF=0.763;AN=2;DP=782;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,10:22:99:300,0,357:3,9,3,7 chr2 65325265 . A G 778.6 PASS AC=1;AF=0.55;AN=2;DP=608;MQ=60;set=variant-variant3-variant7-variant12-variant14-variant30-variant35-variant36-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:33,37:70:99:872,0,786:18,15,13,24 chr2 65341374 . T C 837.16 PASS AC=1;AF=0.545;AN=2;DP=635;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant7-variant12-variant14-variant30-variant35-variant36-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:25,29:54:99:842,0,644:8,17,8,21 chr2 65455301 . C T 402.18 PASS AC=1;AF=0.6;AN=2;DP=470;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant10-variant16-variant17-variant20-variant22-variant24-variant25-variant29-variant30-variant31-variant35-variant37-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,17:25:99:503,0,196:2,6,4,13 chr2 65473930 . AAAATTTTC A 1249.53 PASS AC=1;AF=0.75;AN=2;DP=2152;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,28:54:99:1098,0,2409:9,17,9,19 chr2 65478371 . T A 103.61 PASS AC=1;AF=0.765;AN=2;DP=532;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,7:15:99:213,0,258:1,7,1,6 chr2 65481008 . A C 2703.76 PASS AC=2;AF=0.864;AN=2;DP=4043;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,96:96:99:2743,286,0:0,0,41,55 chr2 65488538 . G A 3694.14 PASS AC=2;AF=0.864;AN=2;DP=3835;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,67:67:99:2002,201,0:0,0,29,38 chr2 65495570 . A C 2671.74 PASS AC=2;AF=0.864;AN=2;DP=2012;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1747,117,0:0,0,27,10 chr2 65495571 . T C 2709.15 PASS AC=2;AF=0.864;AN=2;DP=2039;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1747,117,0:0,0,28,10 chr2 65495573 . A AC 2700.03 PASS AC=2;AF=0.864;AN=2;DP=2086;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1747,117,0:0,0,29,10 chr2 65495887 . G A 5184.3 PASS AC=2;AF=0.898;AN=2;DP=8146;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,164:164:99:4755,489,0:0,0,74,90 chr2 65496075 . C T 2842.17 PASS AC=1;AF=0.571;AN=2;DP=898;FractionInformativeReads=1;set=variant-variant3-variant20-variant25-variant29-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:58,53:111:99:1475,0,1596:39,19,33,20 chr2 65496144 . A G 8818.26 PASS AC=2;AF=0.864;AN=2;DP=10210;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,222:222:99:6533,665,0:0,0,119,103 chr2 65497352 . A G 1190.71 PASS AC=2;AF=1;AN=2;DP=2417;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1505,153,0:0,0,23,28 chr2 65539087 . A G 344.17 PASS AC=1;AF=0.556;AN=2;DP=442;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant19-variant20-variant25-variant29-variant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:34,23:57:99:553,0,829:16,18,12,11 chr2 65539596 . G A 2308.24 PASS AC=1;AF=0.556;AN=2;DP=1233;MQ=60;set=variant-variant2-variant3-variant19-variant20-variant25-variant29-variant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:63,50:113:99:1405,0,1789:23,40,27,23 chr2 65539641 . C T 2207.77 PASS AC=2;AF=0.62;AN=2;DP=3366;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant12-variant14-variant15-variant18-variant19-variant20-variant25-variant26-variant27-variant29-variant31-variant34-variant35-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,121:122:99:4038,319,0:1,0,61,60 chr2 65540905 . C G 3396.1 PASS AC=1;AF=0.618;AN=2;DP=5136;MQ=60;set=variant2-variant6-variant7-variant8-variant9-variant12-variant14-variant15-variant18-variant26-variant27-variant34-variant35-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:158,168:326:99:4139,0,3953:70,88,72,96 chr2 65559027 . A G 3115.51 PASS AC=2;AF=0.662;AN=2;DP=4490;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,116:116:99:3723,348,0:0,0,61,55 chr2 65561392 . C T 1567.01 PASS AC=1;AF=0.524;AN=2;DP=2481;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant14-variant15-variant18-variant21-variant23-variant25-variant26-variant29-variant35-variant36-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:61,70:131:99:1592,0,1268:29,32,40,30 chr2 65561543 . T G 161.31 PASS AC=1;AF=0.5;AN=2;DP=249;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant19-variant20-variant25-variant29-variant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:18,8:26:99:198,0,589:4,14,4,4 chr2 65571277 . A AC 582.45 PASS AC=1;AF=0.524;AN=2;DP=687;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant14-variant15-variant18-variant21-variant23-variant25-variant26-variant29-variant35-variant36-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,21:30:99:861,0,754:8,1,18,3 chr2 65571280 . A AC 663.42 PASS AC=1;AF=0.524;AN=2;DP=783;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant14-variant15-variant18-variant21-variant23-variant25-variant26-variant29-variant35-variant36-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:10,22:32:99:958,0,863:9,1,19,3 chr2 65571284 . A C 715.3 PASS AC=1;AF=0.524;AN=2;DP=886;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant14-variant15-variant18-variant21-variant23-variant25-variant26-variant29-variant35-variant36-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,26:38:99:992,0,839:10,2,23,3 chr2 65593439 . A AAAC,AAACAACAACAAC,AAACAACAAC 257.51 PASS AC=1,1,0;AF=0.155,0.397,0.086;AN=2;DP=346;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant28-variant29-variant31-variant35-variant36-variant39-variant40-variant41-variant42-variant43 GT:DP:GQ:SB 1/2:14:99:0,0,9,5 chr2 65604911 . G C 377.73 PASS AC=1;AF=0.5;AN=2;DP=507;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant19-variant20-variant25-variant29-variant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:23,30:53:99:774,0,865:7,16,10,20 chr2 65604914 . A G 993.11 PASS AC=1;AF=0.762;AN=2;DP=2017;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,23:50:99:591,0,1088:9,18,7,16 chr2 66662875 . CTTTTT CTT,CT,CTTT,C,CTTTT 277.19 PASS AC=2,0,0,0,0;AF=0.162,0.059,0.294,0.029,0.059;AN=2;DP=1061;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant14-variant16-variant17-filterInvariant18-variant20-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-filterInvariant39-variant40-variant41-variant42-variant43 GT:DP:GQ:SB 1/1:28:15:4,2,14,8 chr2 66662907 . A G 46.38 PASS AC=1;AF=0.5;AN=2;DP=196;set=filterInvariant4-variant21-filterInvariant24-filterInvariant34-filterInvariant35 GT:AD:DP:GQ:PL:SB 0/1:28,10:38:77:77,0,756:11,17,10,0 chr2 66665146 . T C 1315.03 PASS AC=2;AF=0.695;AN=2;DP=5530;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,129:129:99:4044,387,0:0,0,49,80 chr2 66667186 . C T 191.7 PASS AC=2;AF=0.713;AN=2;DP=805;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:82:795,82,0:0,0,8,20 chr2 66667200 . A AACACACACACAC,AACACACAC,AAC,AACACACACACACAC,AACAC,AACACACACACACACAC,AACACACACAC,AACACACACACACACACAC 64.04 PASS AC=2,0,0,0,0,0,0,0;AF=0.243,0.029,0.086,0.257,0.014,0.129,0.014,0.014;AN=2;DP=516;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant29-variant30-variant31-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:13:38:0,0,3,10 chr2 66691348 . G A 1289.28 PASS AC=1;AF=0.5;AN=2;DP=101;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.077;QD=12.77;ReadPosRankSum=-2.483;SOR=0.641;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:50,51:101:99:1318,0,1361:17,33,18,33 chr2 66794834 . G A 1022.92 PASS AC=1;AF=0.625;AN=2;DP=3203;MQ=60;set=variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant17-variant19-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:76,58:134:99:1386,0,1971:45,31,35,23 chr2 66794923 . A AT 3959.97 PASS AC=2;AF=0.977;AN=2;DP=7234;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,162:162:99:4698,489,0:0,0,84,78 chr2 66798282 . G T 512.37 PASS AC=2;AF=0.977;AN=2;DP=901;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:477,42,0:0,0,11,3 chr2 66800974 . C A 2035.19 PASS AC=2;AF=0.977;AN=2;DP=2318;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:1909,177,0:0,0,18,41 chr2 67630980 . G A 3779.42 PASS AC=1;AF=0.825;AN=2;DP=5077;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:66,74:140:99:2043,0,1591:31,35,36,38 chr2 67631831 . G A 1559.38 PASS AC=1;AF=0.667;AN=2;DP=3052;FractionInformativeReads=1;set=variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,73:134:99:1957,0,1774:33,28,33,40 chr2 67632125 . C T 3945.89 PASS AC=1;AF=0.825;AN=2;DP=4353;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,56:109:99:1577,0,1314:25,28,30,26 chr2 67637196 . G A 4944.27 PASS AC=2;AF=0.977;AN=2;DP=8169;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,189:189:99:5649,566,0:0,0,96,93 chr2 68352515 . A C 2559.46 PASS AC=1;AF=0.647;AN=2;DP=8090;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant27-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:134,107:241:99:2767,0,3708:53,81,47,60 chr2 68357239 . G GATAT,GATATAT 573.31 PASS AC=2,0;AF=0.286,0.5;AN=2;DP=184;set=variant8-variant12-variant16-variant35-variant40-variant41-variant42 GT:DP:GQ:SB 1/1:16:6:1,0,1,14 chr2 68357241 . G T 583.21 PASS AC=2;AF=0.8;AN=2;DP=188;set=variant8-variant12-variant13-variant16-variant25-variant35-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,11:12:6:624,6,0:1,0,1,10 chr2 68357243 . G T 331.77 PASS AC=1;AF=0.75;AN=2;DP=155;FractionInformativeReads=1;set=variant8-variant12-variant13-variant16-variant25-variant35-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:0,8:8:5:459,0,5:0,0,0,8 chr2 68357245 . G T 286.77 PASS AC=2;AF=0.833;AN=2;DP=185;FractionInformativeReads=1;set=variant8-variant12-variant13-variant16-variant22-variant25-variant33-variant35-variant40-filterInvariant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:24:360,24,0:0,0,0,7 chr2 68357247 . G T 241.77 PASS AC=2;AF=0.857;AN=2;DP=201;FS=0;set=variant8-variant12-variant13-variant15-variant16-variant22-variant25-variant33-variant35-variant37-filterInvariant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:21:315,21,0:0,0,0,5 chr2 68358341 . T C 787.66 PASS AC=2;AF=0.661;AN=2;DP=2297;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant27-variant32-variant33-variant35-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:2396,230,0:0,0,52,25 chr2 68358653 . T C 211.57 PASS AC=2;AF=0.661;AN=2;DP=961;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant27-variant32-variant33-variant35-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:941,69,0:0,0,3,20 chr2 68385097 . A G 1729.64 PASS AC=2;AF=0.769;AN=2;DP=7780;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,203:203:99:6581,608,0:0,0,107,96 chr2 68388823 . A G 1604.94 PASS AC=2;AF=0.607;AN=2;DP=3932;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant27-variant33-variant35-variant37-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,124:124:99:3703,371,0:0,0,69,55 chr2 68389276 . G GA 282.62 PASS AC=2;AF=0.718;AN=2;DP=1790;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,55:57:99:1478,119,0:1,1,40,15 chr2 68389481 . CTT C 3293.3 PASS AC=2;AF=0.609;AN=2;DP=3737;MQ=60;set=variant-variant2-variant4-variant6-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant20-variant22-variant23-variant25-variant27-variant33-variant35-variant37-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,133:133:99:5954,401,0:0,0,51,82 chr2 68402012 . G T 920.58 PASS AC=2;AF=0.789;AN=2;DP=879;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:528,42,0:0,0,8,6 chr2 68402153 . TA T 3242.12 PASS AC=2;AF=0.782;AN=2;DP=3327;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:2952,238,0:0,0,39,40 chr2 68402786 . TTTGCAGTTTC T 8212.68 PASS AC=2;AF=0.782;AN=2;DP=6708;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,162:162:99:7178,489,0:0,0,99,63 chr2 68402830 . G C 11419.3 PASS AC=2;AF=0.782;AN=2;DP=8503;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,238:238:99:10874,743,0:0,0,142,96 chr2 68402835 . A G 11597.5 PASS AC=2;AF=0.782;AN=2;DP=8833;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,253:253:99:11020,761,0:0,0,146,107 chr2 68406141 . A AAAAAG,AAAAAAG,AAAAG,AAAG,AAAAAAAG 1622.28 PASS AC=1,1,0,0,0;AF=0.347,0.181,0.083,0.014,0.014;AN=2;DP=3494;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:DP:GQ:SB 1/2:59:99:5,0,16,38 chr2 68407926 . A G 7655.39 PASS AC=2;AF=0.607;AN=2;DP=7956;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant27-variant33-variant35-variant37-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,307:307:99:8817,919,0:0,0,158,149 chr2 68415767 . G A 3767.93 PASS AC=2;AF=0.661;AN=2;DP=3992;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant27-variant32-variant33-variant35-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,138:138:99:3881,413,0:0,0,61,77 chr2 68444171 . C CGCAG,CACGCAG,CACACGCAG 1877.6 PASS AC=1,1,0;AF=0.333,0.5,0.111;AN=2;DP=479;set=variant-variant2-variant4-variant9-variant10-variant22-variant27-variant13-variant35 GT:DP:GQ:SB 1/2:43:99:0,0,24,19 chr2 68479576 . G A 1375.2 PASS AC=2;AF=0.661;AN=2;DP=2055;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant27-variant32-variant33-variant35-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:2216,235,0:0,0,44,35 chr2 68479671 . A G 924.42 PASS AC=2;AF=0.782;AN=2;DP=2285;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:1953,203,0:0,0,29,39 chr2 68479717 . G GGGCGGAGGCGGGGGCGCGCGCGGGCCGGC 567.21 PASS AC=2;AF=0.789;AN=2;DP=1444;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:94:1369,94,0:0,0,10,18 chr2 68483396 . A T 834.7 PASS AC=2;AF=0.661;AN=2;DP=598;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant27-variant32-variant33-variant35-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:919,78,0:0,0,7,19 chr2 68511506 . GA G,GAA 1874.76 PASS AC=1,1;AF=0.634,0.159;AN=2;DP=2431;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/2:59:99:0,0,29,30 chr2 68511584 . A G 1003.44 PASS AC=1;AF=0.606;AN=2;DP=1899;MQ=60;set=variant-variant2-variant4-variant6-variant9-variant11-variant12-variant13-filterInvariant14-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,26:57:99:666,0,911:12,19,10,16 chr2 68543824 . A T 691.29 PASS AC=1;AF=0.559;AN=2;DP=824;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant10-variant12-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant32-variant33-variant34-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,24:40:99:677,0,482:12,4,18,6 chr2 68546304 . T C 283.38 PASS AC=1;AF=0.667;AN=2;DP=407;MQ=60;set=variant2-variant3-variant4-variant7-variant8-variant9-variant11-variant14-variant15-variant16-variant17-variant20-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,7:13:99:187,0,150:3,3,4,3 chr2 68546374 . T C 353.58 PASS AC=1;AF=0.667;AN=2;DP=706;MQ=60;set=variant2-variant3-variant4-variant7-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,13:19:91:307,0,91:3,3,7,6 chr2 68546449 . G A 336.55 PASS AC=1;AF=0.574;AN=2;DP=711;MQ=60;set=variant2-variant3-variant4-variant7-variant8-variant11-variant13-variant15-variant16-variant17-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant38-variant39-variant40-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,13:19:99:356,0,132:3,3,6,7 chr2 68592315 . A C 2163.06 PASS AC=1;AF=0.672;AN=2;DP=2360;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant9-variant10-variant11-variant12-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant31-variant32-variant33-variant34-variant35-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,40:95:99:893,0,1304:28,27,20,20 chr2 68592584 . T C 1364 PASS AC=2;AF=0.838;AN=2;DP=3247;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:2213,215,0:0,0,31,41 chr2 68592700 . A G 835.48 PASS AC=1;AF=0.646;AN=2;DP=734;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant9-variant10-variant12-variant16-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant31-variant32-variant33-variant34-variant35-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,21:37:99:466,0,449:5,11,10,11 chr2 68607947 . G T 3410.37 PASS AC=1;AF=0.676;AN=2;DP=1907;MQ=60;set=variant-variant2-variant4-variant6-variant10-variant21-variant22-variant23-variant25-variant26-variant31-variant32-variant33-variant34-variant35-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,47:115:99:1119,0,1724:34,34,24,23 chr2 68613710 . G A 5390.74 PASS AC=1;AF=0.58;AN=2;DP=3369;MQ=60;set=variant3-variant4-variant7-variant11-variant13-variant15-variant16-variant17-variant20-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:71,70:141:99:1677,0,2036:39,32,35,35 chr2 68615395 . C T 1120.77 PASS AC=1;AF=0.58;AN=2;DP=532;MQ=60;set=variant3-variant4-variant7-variant11-variant13-variant15-variant16-variant17-variant20-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,9:13:99:351,0,141:4,0,9,0 chr2 68615438 . A AG 1493.86 PASS AC=1;AF=0.676;AN=2;DP=669;MQ=60;set=variant-variant2-variant4-variant6-variant10-variant21-variant22-variant23-variant25-variant26-variant31-variant32-variant33-variant34-variant35-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,17:35:99:449,0,482:15,3,15,2 chr2 68615654 . T C 4257.05 PASS AC=1;AF=0.58;AN=2;DP=2706;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant7-variant11-variant13-variant15-variant16-variant17-variant20-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:57,49:106:99:1301,0,1472:23,34,20,29 chr2 68620151 . C T 280.31 PASS AC=1;AF=0.676;AN=2;DP=162;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant10-variant21-variant22-variant23-variant25-variant26-variant31-variant32-variant33-variant34-variant35-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,4:10:99:147,0,202:5,1,4,0 chr2 68620410 . T A 2751.47 PASS AC=1;AF=0.58;AN=2;DP=1932;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant7-variant11-variant13-variant15-variant16-variant17-variant20-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:37,43:80:99:1192,0,885:16,21,17,26 chr2 68620463 . G A 1561.12 PASS AC=1;AF=0.676;AN=2;DP=681;MQ=60;set=variant-variant2-variant4-variant6-variant10-variant21-variant22-variant23-variant25-variant26-variant31-variant32-variant33-variant34-variant35-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,20:38:99:538,0,510:5,13,6,14 chr2 68621338 . G T 2382.57 PASS AC=1;AF=0.621;AN=2;DP=1843;MQ=60;set=variant3-variant4-variant7-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:32,21:53:99:528,0,828:13,19,10,11 chr2 68621427 . G A 1475.99 PASS AC=1;AF=0.58;AN=2;DP=740;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant7-variant11-variant13-variant15-variant16-variant17-variant20-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,9:21:99:225,0,321:4,8,2,7 chr2 68622658 . C T 736.22 PASS AC=1;AF=0.672;AN=2;DP=634;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,15:19:99:575,0,114:4,0,15,0 chr2 68622914 . G A 4800.14 PASS AC=2;AF=0.838;AN=2;DP=7006;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,194:194:99:5855,581,0:0,0,80,114 chr2 68622952 . G C 4877.95 PASS AC=1;AF=0.667;AN=2;DP=4553;MQ=60;set=variant3-variant4-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:81,78:159:99:1864,0,1912:35,46,32,46 chr2 68623270 . C T 1951.85 PASS AC=1;AF=0.577;AN=2;DP=706;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant7-variant10-variant11-variant13-variant15-variant16-variant17-variant20-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:20,17:37:99:646,0,777:13,7,8,9 chr2 68623274 . T C 1951.77 PASS AC=1;AF=0.667;AN=2;DP=910;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:19,16:35:99:691,0,744:13,6,8,8 chr2 68623279 . TAA TA,T 429.45 PASS AC=1,1;AF=0.275,0.55;AN=2;DP=1189;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 2/1:35:99:0,0,20,15 chr2 68623302 . A G 1801.28 PASS AC=1;AF=0.667;AN=2;DP=1003;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:20,17:37:99:526,0,827:12,8,9,8 chr2 68623652 . T C 978.6 PASS AC=2;AF=0.838;AN=2;DP=1279;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:981,102,0:0,0,16,18 chr2 68623843 . GA G 799.17 PASS AC=1;AF=0.667;AN=2;DP=928;MQ=60;set=variant3-variant4-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,21:30:99:511,0,163:7,2,15,6 chr2 68623915 . T C 1865.69 PASS AC=1;AF=0.667;AN=2;DP=2062;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:26,37:63:99:943,0,614:14,12,21,16 chr2 68624260 . G A 8649.25 PASS AC=1;AF=0.667;AN=2;DP=7555;MQ=60;set=variant3-variant4-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:120,139:259:99:3322,0,2746:54,66,65,74 chr2 68691933 . G C 1008.98 PASS AC=1;AF=0.5;AN=2;DP=101;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.473;QD=9.99;ReadPosRankSum=-0.477;SOR=0.626;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:58,43:101:99:1037,0,1531:36,22,26,17 chr2 69043232 . A T 354.38 PASS AC=1;AF=0.5;AN=2;DP=30;FS=3.905;FractionInformativeReads=1;MQ=60;MQRankSum=1.172;QD=11.81;ReadPosRankSum=-2.762;SOR=1.863;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:17,13:30:99:383,0,420:11,6,11,2 chr2 69043539 . G C 566.89 PASS AC=1;AF=0.797;AN=2;DP=813;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,3:10:65:65,0,199:1,6,1,2 chr2 69046164 . C A 352.77 PASS AC=1;AF=0.5;AN=2;DP=357;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant10-variant18-variant21-variant22-variant25-variant28-variant29-variant33-variant35-variant36-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:16,18:34:99:493,0,542:14,2,13,5 chr2 69053115 . G T 1487.12 PASS AC=1;AF=0.5;AN=2;DP=699;FractionInformativeReads=1;MQ=60;set=variant4-variant7-variant11-variant14-variant23-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:55,49:104:99:1299,0,1267:33,22,30,19 chr2 69053557 . T C 679.13 PASS AC=1;AF=0.719;AN=2;DP=1725;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant29-variant30-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,17:39:99:499,0,567:11,11,11,6 chr2 69172923 . T C 387.69 PASS AC=1;AF=0.5;AN=2;DP=271;FractionInformativeReads=1;MQ=60;set=variant13-variant16-variant22-variant35-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:28,16:44:99:498,0,938:20,8,10,6 chr2 69173324 . G T 2972.22 PASS AC=1;AF=0.5;AN=2;DP=1745;MQ=60;set=variant13-variant16-variant22-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:177,192:369:99:4992,0,4344:71,106,67,125 chr2 69173570 . C T 818.32 PASS AC=1;AF=0.536;AN=2;DP=1093;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant13-variant15-variant16-variant20-variant22-variant29-variant32-variant34-variant35-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,32:72:99:720,0,916:17,23,12,20 chr2 69180161 . T A 1054 PASS AC=1;AF=0.821;AN=2;DP=1270;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,16:31:99:469,0,379:4,11,3,13 chr2 69201501 . G A 332.98 PASS AC=1;AF=0.744;AN=2;DP=1199;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,14:37:99:426,0,765:19,4,12,2 chr2 69201894 . C T 833.8 PASS AC=1;AF=0.691;AN=2;DP=1926;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,25:56:99:635,0,931:7,24,7,18 chr2 69297622 . C T 1848.69 PASS AC=2;AF=0.886;AN=2;DP=2765;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:1790,185,0:0,0,36,26 chr2 69298817 . T C 1158.56 PASS AC=2;AF=0.638;AN=2;DP=2369;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant24-variant25-variant29-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,66:66:99:2046,198,0:0,0,38,28 chr2 69317925 . G A 6041.88 PASS AC=1;AF=0.864;AN=2;DP=7209;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:111,79:190:99:1818,0,2691:54,57,37,42 chr2 69318129 . T G 1002.88 PASS AC=2;AF=0.909;AN=2;DP=905;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:881,63,0:0,0,2,19 chr2 69330284 . G A 251.97 PASS AC=2;AF=0.75;AN=2;DP=523;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:438,33,0:0,0,1,10 chr2 69351617 . G A 226.12 PASS AC=1;AF=0.5;AN=2;DP=229;FractionInformativeReads=1;MQ=60;set=variant8-variant14-variant18-variant22-variant26-variant28-variant31-variant35-variant36-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,9:14:99:304,0,151:5,0,8,1 chr2 69409029 . C A 3545.06 PASS AC=2;AF=0.7;AN=2;DP=4146;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,96:96:99:3118,288,0:0,0,35,61 chr2 69420591 . T TCTCA,TCACA,TCTCACA,TCACACA 614.72 PASS AC=1,1,0,0;AF=0.5,0.1,0.014,0.014;AN=2;DP=1592;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant43-variant44 GT:DP:GQ:SB 2/1:36:99:0,0,7,29 chr2 69420596 . T C 110.04 PASS AC=2;AF=0.706;AN=2;DP=1346;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant-variant39 GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1526,108,0:0,0,6,27 chr2 69552451 . G T 1985.61 PASS AC=2;AF=0.556;AN=2;DP=1400;MQ=60;set=variant2-variant3-variant21-variant24-variant34-variant35-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,138:138:99:4582,413,0:0,0,96,42 chr2 69552521 . C A 9954.42 PASS AC=2;AF=0.696;AN=2;DP=9246;MQ=60;set=variant2-variant3-variant4-variant7-variant10-variant11-variant12-variant16-variant19-variant21-variant23-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,331:333:99:10476,947,0:1,1,206,125 chr2 69553375 . GA G 996.2 PASS AC=2;AF=0.672;AN=2;DP=1567;set=variant2-variant3-variant4-variant7-variant10-variant11-variant12-variant13-variant16-variant19-variant21-variant23-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,59:61:99:1489,130,0:1,1,24,35 chr2 69565842 . TA T 305.67 PASS AC=2;AF=0.761;AN=2;DP=188;MQ=60;set=variant2-variant3-variant4-variant7-variant10-variant11-variant16-variant19-variant21-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:213,15,0:0,0,0,5 chr2 69565844 . A T 314.71 PASS AC=2;AF=0.75;AN=2;DP=174;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant7-variant10-variant11-variant16-variant19-variant21-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:213,15,0:0,0,0,5 chr2 69573029 . T C 2047.23 PASS AC=2;AF=0.696;AN=2;DP=1896;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant7-variant10-variant11-variant12-variant16-variant19-variant21-variant23-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:1767,177,0:0,0,31,28 chr2 69583873 . AT A 277.84 PASS AC=2;AF=0.725;AN=2;DP=241;set=variant2-variant3-variant7-variant8-variant10-variant12-variant16-variant19-variant21-variant24-variant27-variant29-variant31-variant32-variant35-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:27:397,27,0:0,0,1,7 chr2 69586293 . A C 1418.34 PASS AC=2;AF=0.696;AN=2;DP=1213;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant7-variant10-variant11-variant12-variant16-variant19-variant21-variant23-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:987,96,0:0,0,20,12 chr2 69586370 . A G 1301.89 PASS AC=2;AF=0.643;AN=2;DP=1152;MQ=60;set=variant2-variant3-variant7-variant10-variant11-variant12-variant16-variant19-variant21-variant23-variant24-variant27-variant29-variant32-variant34-variant35-variant37-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:1489,141,0:0,0,24,23 chr2 69597209 . A G 546.06 PASS AC=1;AF=0.5;AN=2;DP=53;FS=3.809;FractionInformativeReads=1;MQ=60;MQRankSum=1.992;QD=10.3;ReadPosRankSum=-1.045;SOR=1.23;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:29,24:53:99:574,0,743:13,16,8,16 chr2 69614161 . A G 2851.93 PASS AC=2;AF=0.696;AN=2;DP=3188;MQ=60;set=variant2-variant3-variant4-variant7-variant10-variant11-variant12-variant16-variant19-variant21-variant23-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,131:131:99:4352,393,0:0,0,77,54 chr2 69623136 . A G 6459.13 PASS AC=2;AF=0.696;AN=2;DP=6739;MQ=60;set=variant2-variant3-variant4-variant7-variant10-variant11-variant12-variant16-variant19-variant21-variant23-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,243:243:99:6915,724,0:0,0,126,117 chr2 69633382 . A T 170.22 PASS AC=2;AF=0.717;AN=2;DP=152;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant7-variant11-variant12-variant21-variant23-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:128,9,0:0,0,0,3 chr2 69642572 . T C 337.45 PASS AC=2;AF=0.704;AN=2;DP=302;set=variant2-variant3-variant4-variant7-variant10-variant11-variant12-variant16-variant19-variant21-variant23-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:527,45,0:0,0,3,12 chr2 69657349 . CTT CT,C 281.15 PASS AC=2,0;AF=0.655,0.017;AN=2;DP=425;MQ=60;set=variant2-variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant12-variant16-variant19-variant21-variant23-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:9:27:0,0,1,8 chr2 69659126 . A T 2617.5 PASS AC=2;AF=0.643;AN=2;DP=1782;set=variant2-variant3-variant7-variant10-variant11-variant12-variant16-variant19-variant21-variant23-variant24-variant27-variant29-variant32-variant34-variant35-variant37-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:1772,174,0:0,0,25,33 chr2 69688631 . CA CAA,C 1682.52 PASS AC=0,1;AF=0.128,0.372;AN=2;DP=15010;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-filterInvariant22-variant23-variant24-variant25-variant26-variant27-variant28-filterInvariant29-variant30-variant31-variant32-variant33-variant34-variant35-filterInvariant36-variant37-variant39-filterInvariant40-variant41-variant42-filterInvariant43-variant44 GT:DP:GQ:SB 0/2:310:99:106,99,54,51 chr2 69688727 . AT A,ATT 630.49 PASS AC=0,1;AF=0.489,0.011;AN=2;DP=11383;set=variant-variant2-filterInvariant3-variant4-filterInvariant5-filterInvariant6-filterInvariant7-variant8-filterInvariant9-variant10-filterInvariant11-filterInvariant12-filterInvariant13-filterInvariant14-filterInvariant15-variant16-variant17-filterInvariant18-variant19-filterInvariant20-filterInvariant21-variant22-variant23-filterInvariant24-variant25-filterInvariant26-filterInvariant27-filterInvariant28-variant29-filterInvariant30-filterInvariant31-filterInvariant32-variant33-filterInvariant34-variant35-filterInvariant36-variant37-filterInvariant38-filterInvariant39-filterInvariant40-variant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:DP:GQ:SB 0/2:209:99:49,76,38,46 chr2 69693006 . C T 4386.24 PASS AC=2;AF=0.625;AN=2;DP=4971;MQ=60;set=variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant19-variant20-variant21-variant23-variant24-variant27-variant29-variant32-variant34-variant35-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,186:186:99:5580,555,0:0,0,84,102 chr2 69741609 . C T 1199.06 PASS AC=1;AF=0.652;AN=2;DP=2947;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,40:90:99:938,0,1244:26,24,20,20 chr2 69741753 . CTGT C 1452.29 PASS AC=1;AF=0.652;AN=2;DP=3067;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,45:89:99:1633,0,1803:18,26,25,20 chr2 69741854 . T G 2356.42 PASS AC=2;AF=1;AN=2;DP=4093;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.643;ReadPosRankSum=0.711;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,95:95:99:2896,285,0:0,0,40,55 chr2 69747817 . G C 1028.19 PASS AC=1;AF=0.618;AN=2;DP=1800;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,24:58:99:697,0,952:22,12,18,6 chr2 69759415 . G A 394.46 PASS AC=1;AF=0.618;AN=2;DP=1070;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,17:36:99:448,0,441:5,14,4,13 chr2 69771484 . C T 1956.43 PASS AC=1;AF=0.625;AN=2;DP=3896;MQ=60;set=variant3-variant4-variant5-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,78:125:99:1930,0,1227:32,15,48,30 chr2 69784255 . C T 519.1 PASS AC=1;AF=0.593;AN=2;DP=621;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant8-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant33-variant34-variant35-variant36-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,9:27:99:292,0,627:2,16,0,9 chr2 69784278 . T C 425.29 PASS AC=1;AF=0.632;AN=2;DP=535;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant8-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,4:14:99:131,0,365:1,9,0,4 chr2 70014986 . T C 468.99 PASS AC=1;AF=0.536;AN=2;DP=453;MQ=60;set=variant-variant4-variant5-variant13-variant15-variant16-variant20-variant28-variant33-variant34-variant35-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:23,15:38:99:350,0,655:18,5,10,5 chr2 70015108 . A G 1575.26 PASS AC=1;AF=0.556;AN=2;DP=1196;MQ=60;set=variant-variant5-variant16-variant20-variant34-variant35-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:88,58:146:99:1407,0,2308:46,42,38,20 chr2 70031797 . C G 305.14 PASS AC=1;AF=0.633;AN=2;DP=1389;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,33:61:99:918,0,698:10,18,9,24 chr2 70033584 . C T 1905.61 PASS AC=1;AF=0.536;AN=2;DP=2433;MQ=60;set=variant-variant4-variant5-variant13-variant15-variant16-variant20-variant28-variant33-variant34-variant35-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:92,94:186:99:2244,0,2188:38,54,39,55 chr2 70033649 . G A 1045.93 PASS AC=1;AF=0.533;AN=2;DP=1239;set=variant-variant4-variant5-variant10-variant13-variant15-variant16-variant20-variant28-variant33-variant34-variant35-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:44,53:97:99:1506,0,1223:11,33,14,39 chr2 70039677 . A C 493.71 PASS AC=1;AF=0.633;AN=2;DP=1183;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,29:40:99:838,0,257:6,5,17,12 chr2 70053668 . A G 46.72 PASS AC=1;AF=0.696;AN=2;DP=141;FractionInformativeReads=1;set=variant-variant3-variant4-variant5-variant10-variant13-variant14-variant15-variant16-variant22-variant24-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,4:6:74:114,0,74:0,2,1,3 chr2 70057448 . T G 742.65 PASS AC=1;AF=0.629;AN=2;DP=1697;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,40:66:99:1029,0,525:12,14,23,17 chr2 70064927 . C A 568.94 PASS AC=1;AF=0.536;AN=2;DP=1012;MQ=60;set=variant-variant4-variant5-variant13-variant15-variant16-variant20-variant28-variant33-variant34-variant35-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:45,43:88:99:1051,0,1036:18,27,15,28 chr2 70066571 . C CTT 252.87 PASS AC=1;AF=0.536;AN=2;DP=479;MQ=60;set=variant-variant4-variant5-variant13-variant15-variant16-variant20-variant28-variant33-variant34-variant35-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:14,13:27:99:398,0,453:9,5,9,4 chr2 70068057 . G A 523.43 PASS AC=1;AF=0.536;AN=2;DP=349;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant13-variant15-variant16-variant20-variant28-variant33-variant34-variant35-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,16:29:99:390,0,396:11,2,9,7 chr2 70068258 . CT C 426.7 PASS AC=1;AF=0.633;AN=2;DP=824;MQ=60;set=variant-variant3-variant4-variant6-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,10:19:99:244,0,229:2,7,2,8 chr2 70076954 . A T 506.19 PASS AC=1;AF=0.645;AN=2;DP=808;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,4:14:99:135,0,247:4,6,1,3 chr2 70106832 . T C 2256.79 PASS AC=1;AF=0.629;AN=2;DP=4928;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:81,60:141:99:1399,0,2211:37,44,28,32 chr2 70107409 . A G 2707.23 PASS AC=1;AF=0.536;AN=2;DP=2738;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant13-variant15-variant16-variant20-variant28-variant33-variant34-variant35-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:64,90:154:99:2149,0,1486:32,32,42,48 chr2 70108256 . T A 888.56 PASS AC=1;AF=0.629;AN=2;DP=1889;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,34:67:99:885,0,848:18,15,17,17 chr2 70124269 . G GT 599.23 PASS AC=1;AF=0.613;AN=2;DP=1463;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,21:48:99:453,0,627:15,12,14,7 chr2 70124316 . T A 1316.12 PASS AC=1;AF=0.597;AN=2;DP=2698;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,42:84:99:906,0,1031:24,18,23,19 chr2 70131584 . G A 486.41 PASS AC=1;AF=0.538;AN=2;DP=470;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant13-variant15-variant16-variant20-variant28-variant33-variant35-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,16:29:99:505,0,487:1,12,1,15 chr2 70131954 . G GC 340.7 PASS AC=1;AF=0.5;AN=2;DP=70;FS=20.239;FractionInformativeReads=0.843;MQ=59.91;MQRankSum=0.472;QD=4.87;ReadPosRankSum=-1.097;SOR=3.241;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:39,20:59:99:378,0,896:17,22,2,18 chr2 70162534 . T G 1263.38 PASS AC=1;AF=0.6;AN=2;DP=2365;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:63,48:111:99:1153,0,1615:37,26,28,20 chr2 70164034 . T C 1222.1 PASS AC=1;AF=0.617;AN=2;DP=3227;set=variant-variant3-variant4-variant5-variant6-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,68:112:99:1693,0,995:29,15,38,30 chr2 70164097 . A AG 879.3 PASS AC=1;AF=0.5;AN=2;DP=1800;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant14-variant20-variant21-variant23-variant30-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:92,64:156:99:1665,0,2700:51,41,39,25 chr2 70164580 . C CAGGG 76.58 PASS AC=1;AF=0.621;AN=2;DP=478;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant22-variant24-variant25-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,8:16:99:311,0,423:0,8,1,7 chr2 70165966 . G A 186.96 PASS AC=1;AF=0.538;AN=2;DP=556;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant13-variant15-variant16-variant20-variant28-variant33-variant35-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:31,41:72:99:956,0,669:12,19,18,23 chr2 70167197 . C T 635.38 PASS AC=1;AF=0.6;AN=2;DP=1307;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant22-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,20:45:99:625,0,892:17,8,12,8 chr2 70167279 . AT A 893.23 PASS AC=1;AF=0.5;AN=2;DP=4870;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-filterInvariant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,26:81:99:295,0,946:29,26,15,11 chr2 70168995 . T C 2353.43 PASS AC=1;AF=0.5;AN=2;DP=2929;set=variant-variant4-variant5-variant13-variant15-variant16-variant20-variant28-variant33-variant35-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:115,99:214:99:2129,0,3083:57,58,54,45 chr2 70188676 . T C 1517.65 PASS AC=2;AF=0.676;AN=2;DP=5594;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,193:193:99:6062,578,0:0,0,89,104 chr2 70189331 . GACACACACACACAC GACACACACAC,GACACACACACAC,GACACAC,GACACACAC,G 299.81 PASS AC=1,0,0,0,1;AF=0.593,0.267,0.035,0.058,0.012;AN=2;DP=726;FS=0;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 5/1:14:99:0,0,5,9 chr2 70190288 . C T 169.11 PASS AC=1;AF=0.5;AN=2;DP=121;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant12-variant24-variant26-variant28-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,6:14:99:163,0,278:7,1,5,1 chr2 70315987 . C T 5045.68 PASS AC=1;AF=0.5;AN=2;DP=448;FS=0.518;FractionInformativeReads=1;MQ=60;MQRankSum=1.269;QD=11.26;ReadPosRankSum=0.97;SOR=0.734;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:232,216:448:99:5074,0,5754:113,119,103,113 chr2 70376944 . A C 50.98 PASS AC=2;AF=0.591;AN=2;DP=79;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant12-variant16-variant24-variant26-variant31-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:176,15,0:0,0,3,2 chr2 70376967 . TC T,TCC 31.8 PASS AC=0,2;AF=0.25,0.375;AN=2;DP=69;MQ=60;set=variant10-variant12-variant16-variant22-variant25-variant26-variant35-variant41 GT:DP:GQ:SB 2/2:5:14:0,0,2,3 chr2 70377653 . G A 1130.7 PASS AC=2;AF=0.545;AN=2;DP=1431;MQ=60;set=variant-variant3-variant5-variant12-variant20-variant24-variant26-variant28-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,127:127:99:3824,378,0:0,0,58,69 chr2 70418339 . T C 78.48 PASS AC=2;AF=0.621;AN=2;DP=306;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant9-variant10-variant11-variant12-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:35:460,35,0:0,0,0,11 chr2 70451402 . G C 958.67 PASS AC=2;AF=0.548;AN=2;DP=742;MQ=60;set=variant-variant3-variant10-variant12-variant16-variant17-variant18-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant34-variant35-variant37-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1297,108,0:0,0,30,6 chr2 70454794 . G C 166.64 PASS AC=2;AF=0.625;AN=2;DP=141;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant12-variant16-variant18-variant21-variant22-variant25-variant26-variant27-variant29-variant31-variant34-variant35-variant37-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:267,18,0:0,0,6,0 chr2 70455907 . A G 153.72 PASS AC=2;AF=0.64;AN=2;DP=280;FractionInformativeReads=1;MQ=60;set=variant3-variant8-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant34-variant35-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:211,18,0:0,0,4,2 chr2 70457784 . CA CAAA,CAA,CAAAA,C 193.21 PASS AC=2,0,0,0;AF=0.219,0.344,0.063,0.031;AN=2;DP=164;MQ=60;set=variant3-variant8-variant11-variant15-variant16-variant18-variant19-variant21-variant24-variant26-variant28-variant29-variant33-variant35-variant38-variant44 GT:DP:GQ:SB 1/1:6:21:0,0,5,1 chr2 70475933 . T G 305.87 PASS AC=2;AF=0.782;AN=2;DP=599;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:471,36,0:0,0,2,10 chr2 70485174 . A C 691.24 PASS AC=2;AF=0.545;AN=2;DP=294;FractionInformativeReads=1;MQ=60;set=variant3-variant12-variant16-variant18-variant20-variant24-variant26-variant28-variant35-variant37-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,23:23:68:893,68,0:0,0,13,10 chr2 70524427 . T C 148.32 PASS AC=1;AF=0.5;AN=2;DP=1380;FractionInformativeReads=1;set=variant-variant2-variant3-variant5-variant8-variant9-variant11-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant25-variant26-filterInvariant29-filterInvariant31-variant33-variant34-variant35-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:33,5:38:99:105,0,1443:23,10,5,0 chr2 70524433 . T G 181.26 PASS AC=1;AF=0.5;AN=2;DP=1437;FractionInformativeReads=1;set=variant-variant2-variant3-variant5-variant8-variant9-variant11-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant31-variant33-variant34-filterInvariant35-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:36,5:41:93:93,0,1623:26,10,5,0 chr2 70524437 . A G 184.27 PASS AC=1;AF=0.5;AN=2;DP=1525;FractionInformativeReads=1;set=variant-variant2-variant3-variant5-variant8-variant9-variant11-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant31-variant33-variant34-filterInvariant35-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:38,5:43:90:90,0,1665:27,11,5,0 chr2 70524444 . C G 178.25 PASS AC=1;AF=0.5;AN=2;DP=1671;FractionInformativeReads=1;set=variant-variant2-variant3-variant5-variant8-variant9-variant11-filterInvariant14-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant31-variant33-variant34-filterInvariant35-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:42,5:47:81:81,0,1791:31,11,5,0 chr2 70524451 . C T 154.21 PASS AC=1;AF=0.5;AN=2;DP=1911;FractionInformativeReads=1;set=variant-variant2-variant3-variant5-variant8-variant9-variant11-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant25-variant26-filterInvariant29-variant31-variant33-variant34-filterInvariant35-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:44,6:50:99:119,0,1829:33,11,5,1 chr2 70524452 . A G 115.23 PASS AC=1;AF=0.5;AN=2;DP=1935;FractionInformativeReads=1;set=variant-variant2-variant3-variant5-variant8-variant9-variant11-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant25-variant26-filterInvariant29-variant31-variant33-variant34-filterInvariant35-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:44,6:50:99:119,0,1829:33,11,5,1 chr2 70524477 . G C 370 PASS AC=1;AF=0.5;AN=2;DP=1657;set=variant2-filterInvariant3-variant9-variant14-variant15-variant18-variant19-variant20-variant22-filterInvariant23-variant25-variant31-variant33-variant34-variant35-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:56,10:66:99:251,0,2321:41,15,8,2 chr2 70524478 . G A 370 PASS AC=1;AF=0.5;AN=2;DP=2695;set=variant2-variant3-variant5-variant8-variant9-variant11-variant14-variant15-variant16-variant18-variant19-variant20-filterInvariant21-variant22-variant23-variant25-variant26-filterInvariant29-variant31-variant33-variant34-variant35-variant38-variant39-filterInvariant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:56,10:66:99:251,0,2321:41,15,8,2 chr2 70524508 . A ACAGC 405.64 PASS AC=1;AF=0.5;AN=2;DP=3622;set=variant2-variant3-variant5-variant8-variant9-variant11-variant14-variant15-filterInvariant16-variant18-variant19-variant20-filterInvariant21-variant22-variant23-variant25-variant26-variant29-filterInvariant31-variant33-variant34-variant35-variant38-filterInvariant39-filterInvariant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:99,16:115:99:368,0,4172:63,36,14,2 chr2 70524511 . ACTGT A 384.57 PASS AC=1;AF=0.5;AN=2;DP=3857;FractionInformativeReads=1;set=variant2-variant3-variant5-variant8-filterInvariant9-variant11-variant14-variant15-variant16-variant18-variant19-variant20-filterInvariant21-variant22-variant23-variant25-variant26-filterInvariant29-filterInvariant31-variant33-variant34-variant35-variant38-filterInvariant39-filterInvariant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:108,17:125:99:372,0,4423:68,40,15,2 chr2 70524577 . G A 1581.52 PASS AC=1;AF=0.5;AN=2;DP=3609;set=variant-variant3-variant12-variant16-variant17-variant18-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant34-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:16,174:190:99:4475,0,153:14,2,93,81 chr2 70528827 . G A 1847.22 PASS AC=2;AF=0.55;AN=2;DP=3641;MQ=60;set=variant-variant3-variant10-variant12-variant16-variant17-variant18-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant34-variant35-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,203:203:99:6023,606,0:0,0,116,87 chr2 70529242 . T C 350.88 PASS AC=2;AF=0.611;AN=2;DP=980;MQ=60;set=variant-variant3-variant8-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant34-variant35-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1054,99,0:0,0,14,19 chr2 70676098 . G A 3189.7 PASS AC=2;AF=0.559;AN=2;DP=1406;MQ=60;set=variant3-variant5-variant6-variant7-variant13-variant15-variant19-variant21-variant23-variant28-variant30-variant32-variant33-variant35-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,98:98:99:2979,293,0:0,0,50,48 chr2 70676318 . T TA 3060.63 PASS AC=2;AF=0.556;AN=2;DP=1222;MQ=60;set=variant3-variant5-variant6-variant7-variant10-variant13-variant15-variant19-variant21-variant23-variant28-variant30-variant32-variant33-variant35-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1132,120,0:0,0,20,20 chr2 70676769 . GA G 10663.5 PASS AC=2;AF=0.559;AN=2;DP=3752;MQ=60;set=variant3-variant5-variant6-variant7-variant13-variant15-variant19-variant21-variant23-variant28-variant30-variant32-variant33-variant35-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,189:189:99:5632,567,0:0,0,121,68 chr2 70677463 . G A 4705.27 PASS AC=2;AF=0.559;AN=2;DP=1950;MQ=60;set=variant3-variant5-variant6-variant7-variant13-variant15-variant19-variant21-variant23-variant28-variant30-variant32-variant33-variant35-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,111:111:99:3339,331,0:0,0,47,64 chr2 70677994 . G A 6005.18 PASS AC=2;AF=0.559;AN=2;DP=2412;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant6-variant7-variant13-variant15-variant19-variant21-variant23-variant28-variant30-variant32-variant33-variant35-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,170:170:99:4926,509,0:0,0,93,77 chr2 70678173 . C A 1801.13 PASS AC=2;AF=0.583;AN=2;DP=668;MQ=60;set=variant3-variant5-variant6-variant7-variant13-variant15-variant19-variant21-variant23-variant28-variant30-variant32-variant33-variant35-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1482,102,0:0,0,10,24 chr2 70678176 . G A 1765.47 PASS AC=2;AF=0.559;AN=2;DP=590;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant6-variant7-variant13-variant15-variant19-variant21-variant23-variant28-variant30-variant32-variant33-variant35-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,31:31:99:1458,99,0:0,0,9,22 chr2 70678198 . C A 203.87 PASS AC=1;AF=0.5;AN=2;DP=21;FS=4.506;FractionInformativeReads=1;MQ=60;MQRankSum=-0.709;QD=9.71;ReadPosRankSum=-0.112;SOR=0.16;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:14,7:21:99:232,0,442:3,11,3,4 chr2 70678265 . C T 72.4 PASS AC=2;AF=0.7;AN=2;DP=36;FS=0;MQ=60;set=variant15-variant19-variant23-variant32-variant35 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:14:100,14,0:0,0,1,4 chr2 70679067 . G A 3940.34 PASS AC=2;AF=0.559;AN=2;DP=1579;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant6-variant7-variant13-variant15-variant19-variant21-variant23-variant28-variant30-variant32-variant33-variant35-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,95:95:99:2848,285,0:0,0,34,61 chr2 70680211 . CT C 2826.76 PASS AC=2;AF=0.559;AN=2;DP=1275;MQ=60;set=variant3-variant5-variant6-variant7-variant13-variant15-variant19-variant21-variant23-variant28-variant30-variant32-variant33-variant35-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:3017,226,0:0,0,52,23 chr2 70683753 . T C 682.07 PASS AC=2;AF=0.579;AN=2;DP=358;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant6-variant7-variant13-variant15-variant16-variant19-variant21-variant23-variant28-variant30-variant32-variant33-variant35-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:482,36,0:0,0,1,11 chr2 70692557 . C T 675.03 PASS AC=2;AF=0.559;AN=2;DP=304;MQ=60;set=variant3-variant5-variant6-variant7-variant13-variant15-variant19-variant21-variant23-variant28-variant30-variant32-variant33-variant35-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:415,36,0:0,0,8,4 chr2 70905099 . T G 404.57 PASS AC=1;AF=0.817;AN=2;DP=1569;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,23:47:99:662,0,635:7,17,5,18 chr2 70906115 . C A 1711.56 PASS AC=1;AF=0.54;AN=2;DP=3380;MQ=60;set=variant2-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant17-variant19-variant21-variant22-variant25-variant27-variant30-variant32-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:71,53:124:99:1387,0,1763:31,40,23,30 chr2 70917812 . C T 2476.49 PASS AC=2;AF=0.854;AN=2;DP=4391;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,106:106:99:2641,315,0:0,0,66,40 chr2 70931400 . A C 90.68 PASS AC=1;AF=0.5;AN=2;DP=440;set=variant2-filterInvariant4-variant6-variant9-variant12-variant13-variant14-variant15-variant17-variant19-variant23-variant24-variant25-variant27-filterInvariant30-variant31-variant33-variant35-variant36-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,6:17:99:216,0,879:1,10,6,0 chr2 70931405 . A C 77.7 PASS AC=1;AF=0.5;AN=2;DP=410;set=variant2-variant4-variant6-variant9-variant12-variant13-variant14-variant15-variant17-variant19-variant23-variant24-variant31-variant33-variant35-variant36-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,6:22:99:201,0,1355:5,11,6,0 chr2 70931409 . T C 77.7 PASS AC=1;AF=0.5;AN=2;DP=432;set=variant2-variant4-variant6-variant9-variant12-variant13-variant14-variant15-variant17-variant19-variant23-variant24-variant31-variant33-variant35-variant36-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,6:24:99:192,0,1548:7,11,6,0 chr2 70931414 . T C 52.58 PASS AC=1;AF=0.5;AN=2;DP=481;set=variant2-variant4-variant6-variant9-variant12-variant13-variant14-variant15-variant17-variant19-variant23-variant24-variant31-variant33-variant35-variant36-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,6:33:99:166,0,1924:12,15,6,0 chr2 70931417 . A C 49.57 PASS AC=1;AF=0.5;AN=2;DP=494;set=variant2-variant4-variant6-variant9-variant12-variant13-variant14-variant15-variant17-variant19-variant23-variant24-variant31-variant33-variant35-variant36-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,6:35:99:163,0,1957:12,17,6,0 chr2 70933659 . T A 991.7 PASS AC=2;AF=0.63;AN=2;DP=1888;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant12-variant14-variant15-variant16-variant20-variant21-variant24-variant25-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,66:66:99:2138,196,0:0,0,18,48 chr2 70995129 . G A 1051.17 PASS AC=1;AF=0.645;AN=2;DP=5451;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:101,65:166:99:1463,0,2520:43,58,28,37 chr2 70995217 . A T 636.71 PASS AC=1;AF=0.645;AN=2;DP=4006;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:69,46:115:99:964,0,1611:33,36,20,26 chr2 71004368 . A G 228.53 PASS AC=1;AF=0.733;AN=2;DP=193;MQ=60;set=variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant12-variant13-variant14-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant29-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,2:6:65:65,0,164:4,0,2,0 chr2 71004413 . C CA,CAA 140.23 PASS AC=1,0;AF=0.5,0.04;AN=2;DP=394;set=variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-filterInvariant21-variant23-variant24-variant25-variant26-variant27-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-filterInvariant41-variant43 GT:DP:GQ:SB 0/1:12:90:5,2,4,1 chr2 71012604 . G A 869.59 PASS AC=1;AF=0.695;AN=2;DP=3743;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,50:85:99:1429,0,843:18,17,29,21 chr2 71012734 . C G 714.46 PASS AC=1;AF=0.684;AN=2;DP=2673;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,29:73:99:763,0,1065:19,25,7,22 chr2 71036189 . CA C 2181.24 PASS AC=1;AF=0.521;AN=2;DP=3382;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant14-variant15-variant19-variant21-variant22-variant27-variant28-variant29-variant30-variant31-variant35-variant36-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:76,68:144:99:2255,0,2635:37,39,38,30 chr2 71046535 . C T 1907.85 PASS AC=1;AF=0.5;AN=2;DP=168;FS=5.536;FractionInformativeReads=1;MQ=60;MQRankSum=-0.861;QD=11.36;ReadPosRankSum=1.959;SOR=0.574;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:84,84:168:99:1936,0,2285:48,36,40,44 chr2 71047410 . C G 699.43 PASS AC=1;AF=0.5;AN=2;DP=1069;MQ=60;set=variant-variant2-variant3-variant4-variant12-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant33-variant35-variant37-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:29,35:64:99:748,0,656:18,11,19,16 chr2 71057892 . A G 1367.84 PASS AC=2;AF=0.989;AN=2;DP=2317;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:1572,144,0:0,0,29,19 chr2 71058184 . C T 867.39 PASS AC=1;AF=0.595;AN=2;DP=1425;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant11-variant14-variant15-variant21-variant22-variant27-variant28-variant29-variant30-variant35-variant36-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:40,31:71:99:808,0,1088:21,19,15,16 chr2 71058226 . C T 808.25 PASS AC=1;AF=0.5;AN=2;DP=1411;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant12-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant33-variant35-variant37-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:33,43:76:99:1150,0,851:19,14,21,22 chr2 71060052 . C T 1023.21 PASS AC=1;AF=0.5;AN=2;DP=179;FractionInformativeReads=1;MQ=60;set=variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:48,47:95:99:1051,0,1159:27,21,29,18 chr2 71060936 . G C 2810.22 PASS AC=2;AF=0.591;AN=2;DP=4398;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant11-variant14-variant15-variant17-variant21-variant22-variant27-variant28-variant29-variant30-variant35-variant36-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,212:212:99:6591,635,0:0,0,112,100 chr2 71062833 . G GC 4573.48 PASS AC=2;AF=1;AN=2;DP=6997;FS=0;MQ=60;MQRankSum=1.234;ReadPosRankSum=0.693;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,159:160:99:5953,482,0:0,1,75,84 chr2 71063066 . A G 2160.64 PASS AC=1;AF=0.609;AN=2;DP=2194;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,26:65:99:597,0,911:15,24,8,18 chr2 71127607 . G A 137.44 PASS AC=1;AF=0.525;AN=2;DP=470;MQ=60;set=variant-variant4-variant6-variant8-variant10-variant17-variant23-variant24-variant25-variant26-variant28-variant30-variant32-variant35-variant36-variant37-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,12:23:99:290,0,309:8,3,8,4 chr2 71148045 . C T 782.27 PASS AC=1;AF=0.803;AN=2;DP=936;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,11:27:99:360,0,512:12,4,10,1 chr2 71159809 . C A 65.17 PASS AC=1;AF=0.5;AN=2;DP=74;FractionInformativeReads=1;MQ=60;set=variant3-variant18-variant22-variant29-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:5,9:14:99:267,0,132:2,3,8,1 chr2 71162930 . A G 622.64 PASS AC=1;AF=0.583;AN=2;DP=642;MQ=60;set=variant-variant4-variant6-variant7-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant24-variant25-variant26-variant28-variant32-variant35-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,23:33:99:599,0,234:7,3,15,8 chr2 71162996 . A G 1623.48 PASS AC=1;AF=0.743;AN=2;DP=1994;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,40:65:99:961,0,748:20,5,26,14 chr2 71163086 . T C 3781.72 PASS AC=1;AF=0.667;AN=2;DP=3866;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant24-variant25-variant26-variant28-variant32-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:89,87:176:99:1933,0,1980:50,39,45,42 chr2 71163225 . C T 1532.18 PASS AC=1;AF=0.667;AN=2;DP=1997;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant24-variant25-variant26-variant28-variant32-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,32:84:99:727,0,1369:17,35,10,22 chr2 71205976 . A G 201.94 PASS AC=1;AF=0.633;AN=2;DP=1349;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant11-variant12-variant13-variant14-variant16-variant19-variant20-variant23-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,26:52:99:514,0,599:9,17,10,16 chr2 71206058 . A C 439.59 PASS AC=1;AF=0.677;AN=2;DP=610;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant16-variant19-variant20-variant23-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,17:30:99:501,0,384:5,8,6,11 chr2 71208844 . A G 867.81 PASS AC=1;AF=0.688;AN=2;DP=1122;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant16-variant19-variant20-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,28:47:99:797,0,434:12,7,18,10 chr2 71297057 . C T 1576.3 PASS AC=1;AF=0.5;AN=2;DP=1418;FractionInformativeReads=1;MQ=60;set=variant-variant8-variant12-variant14-variant16-variant23-variant26-variant27-variant33-variant35-variant36-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,59:118:99:1668,0,1550:21,38,20,39 chr2 71297982 . C T 622.91 PASS AC=1;AF=0.65;AN=2;DP=4987;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant20-variant21-variant22-variant24-variant28-variant29-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:80,102:182:99:2412,0,1966:35,45,48,54 chr2 71300450 . T C 179.41 PASS AC=1;AF=0.5;AN=2;DP=17;FS=9.901;FractionInformativeReads=1;MQ=60;MQRankSum=-1.055;QD=10.55;ReadPosRankSum=3.065;SOR=3.611;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:11,6:17:99:208,0,619:6,5,6,0 chr2 71300454 . A C 35.46 PASS AC=1;AF=0.5;AN=2;DP=94;FractionInformativeReads=1;set=variant-variant15-variant25-variant26-variant27-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:12,9:21:99:290,0,653:6,6,9,0 chr2 71300461 . T C 77.17 PASS AC=1;AF=0.5;AN=2;DP=82;FractionInformativeReads=1;set=variant15-variant26-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:25,6:31:99:171,0,1384:16,9,6,0 chr2 71300463 . T C 68.67 PASS AC=1;AF=0.5;AN=2;DP=72;FractionInformativeReads=1;set=variant26-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:25,6:31:99:162,0,1534:17,8,6,0 chr2 71300467 . A C 37.53 PASS AC=1;AF=0.5;AN=2;DP=81;FractionInformativeReads=1;set=filterInvariant26-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:27,8:35:99:220,0,1257:16,11,8,0 chr2 71300473 . T C 52.43 PASS AC=1;AF=0.5;AN=2;DP=68;FractionInformativeReads=1;set=filterInvariant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:31,6:37:99:144,0,1864:17,14,6,0 chr2 71300474 . G C 37.38 PASS AC=1;AF=0.5;AN=2;DP=72;FractionInformativeReads=1;set=filterInvariant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:34,6:40:99:135,0,1939:18,16,6,0 chr2 71300477 . A C 109.2 PASS AC=1;AF=0.5;AN=2;DP=44;FS=11.716;FractionInformativeReads=1;MQ=60;MQRankSum=-0.701;QD=2.48;ReadPosRankSum=-1.317;SOR=3.521;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:38,6:44:99:137,0,1898:21,17,6,0 chr2 71300516 . T C 1293.59 PASS AC=1;AF=0.536;AN=2;DP=1242;MQ=60;set=variant2-variant4-variant8-variant9-variant10-variant12-variant13-variant22-variant28-variant34-variant35-variant36-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:55,47:102:99:1352,0,1374:30,25,32,15 chr2 71305359 . G A 582.99 PASS AC=1;AF=0.5;AN=2;DP=2267;MQ=60;set=variant-variant3-variant4-variant8-variant11-variant12-variant14-variant16-variant18-variant20-variant22-variant23-variant24-variant26-variant27-variant29-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,59:115:99:1350,0,1304:33,23,37,22 chr2 71305456 . C T 2898.53 PASS AC=2;AF=0.826;AN=2;DP=6168;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,174:174:99:5196,519,0:0,0,85,89 chr2 71351779 . T C 188.59 PASS AC=2;AF=0.583;AN=2;DP=148;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant6-variant9-variant10-variant12-variant13-variant22-variant28-variant35-variant36-variant39 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:507,42,0:0,0,2,12 chr2 71357417 . C A 1651.76 PASS AC=2;AF=0.769;AN=2;DP=7812;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,229:231:99:6977,662,0:2,0,87,142 chr2 71357634 . C T 2291.78 PASS AC=2;AF=0.769;AN=2;DP=6485;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,169:171:99:5049,461,0:1,1,96,73 chr2 71357710 . G C 3427.17 PASS AC=2;AF=0.614;AN=2;DP=5238;MQ=60;set=variant2-variant4-variant6-variant7-variant9-variant10-variant12-variant13-variant15-variant17-variant21-variant22-variant24-variant27-variant28-variant33-variant34-variant35-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,239:239:99:7430,717,0:0,0,129,110 chr2 71360144 . A C 1042.87 PASS AC=2;AF=0.614;AN=2;DP=1437;MQ=60;set=variant2-variant4-variant6-variant7-variant9-variant10-variant12-variant13-variant15-variant17-variant21-variant22-variant24-variant27-variant28-variant33-variant34-variant35-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1520,138,0:0,0,29,17 chr2 71360625 . G T 413.38 PASS AC=2;AF=0.614;AN=2;DP=1166;FractionInformativeReads=1;set=variant2-variant4-variant6-variant7-variant9-variant10-variant12-variant13-variant15-variant17-variant21-variant22-variant24-variant27-variant28-variant33-variant34-variant35-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:2002,173,0:0,0,22,36 chr2 71360723 . A G 805.17 PASS AC=2;AF=0.875;AN=2;DP=1592;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1698,120,0:0,0,16,24 chr2 71360735 . T TTCC 778.96 PASS AC=2;AF=0.875;AN=2;DP=1471;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1649,114,0:0,0,14,24 chr2 71360973 . A C 81.17 PASS AC=2;AF=0.632;AN=2;DP=306;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant7-variant9-variant10-variant12-variant13-variant15-variant17-variant21-variant22-variant27-variant28-variant33-variant35-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:547,51,0:0,0,10,7 chr2 71361332 . T G 1000.61 PASS AC=2;AF=0.614;AN=2;DP=2865;MQ=60;set=variant2-variant4-variant6-variant7-variant9-variant10-variant12-variant13-variant15-variant17-variant21-variant22-variant24-variant27-variant28-variant33-variant34-variant35-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,141:141:99:4087,422,0:0,0,58,83 chr2 71365509 . C T 49.73 PASS AC=2;AF=0.786;AN=2;DP=66;FS=0;FractionInformativeReads=1;MQ=60;set=variant4-variant7-variant9-variant10-variant12-variant13-variant15-variant17-variant21-variant22-variant24-variant28-variant35-variant38 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:90,6,0:0,0,2,0 chr2 71365676 . G A 907.14 PASS AC=2;AF=0.614;AN=2;DP=1470;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant6-variant7-variant9-variant10-variant12-variant13-variant15-variant17-variant21-variant22-variant24-variant27-variant28-variant33-variant34-variant35-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:1946,164,0:0,0,39,16 chr2 71375065 . A C 400.48 PASS AC=2;AF=0.614;AN=2;DP=580;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant6-variant7-variant9-variant10-variant12-variant13-variant15-variant17-variant21-variant22-variant24-variant27-variant28-variant33-variant34-variant35-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:659,66,0:0,0,11,11 chr2 71376999 . G A 1211.91 PASS AC=2;AF=0.614;AN=2;DP=2158;MQ=60;set=variant2-variant4-variant6-variant7-variant9-variant10-variant12-variant13-variant15-variant17-variant21-variant22-variant24-variant27-variant28-variant33-variant34-variant35-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,94:94:99:2857,282,0:0,0,52,42 chr2 71405776 . C T 405.21 PASS AC=2;AF=0.594;AN=2;DP=802;FractionInformativeReads=1;set=variant2-variant3-variant4-variant6-variant7-variant9-variant18-variant20-variant22-variant24-variant28-variant29-variant34-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,61:61:99:1863,183,0:0,0,34,27 chr2 71410890 . C T 2186.13 PASS AC=2;AF=0.611;AN=2;DP=3547;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant9-variant11-variant18-variant20-variant22-variant24-variant27-variant28-variant29-variant34-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,208:208:99:6425,621,0:0,0,135,73 chr2 71411329 . C G 1726.42 PASS AC=2;AF=0.588;AN=2;DP=2584;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant9-variant18-variant20-variant22-variant24-variant28-variant29-variant34-variant35-variant37-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,122:122:99:4214,366,0:0,0,49,73 chr2 71412951 . G GT 1356.33 PASS AC=2;AF=0.605;AN=2;DP=2339;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant9-variant11-variant18-variant20-variant22-variant24-variant27-variant28-variant29-variant34-variant35-variant37-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:1,117:118:99:3530,323,0:1,0,59,58 chr2 71413984 . A G 2643.39 PASS AC=2;AF=0.611;AN=2;DP=2255;MQ=60;set=variant2-variant4-variant6-variant22-variant28-variant34-variant35-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,230:230:99:7349,690,0:0,0,91,139 chr2 71414007 . A G 2345.04 PASS AC=2;AF=0.611;AN=2;DP=1928;MQ=60;set=variant2-variant4-variant6-variant22-variant28-variant34-variant35-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,205:205:99:6369,614,0:0,0,79,126 chr2 71414645 . A G 1723.44 PASS AC=2;AF=0.625;AN=2;DP=1431;MQ=60;set=variant2-variant4-variant6-variant22-variant28-variant34-variant35-variant41 GT:AD:DP:GQ:PL:SB 1/1:1,182:183:99:5368,510,0:0,1,85,97 chr2 71415479 . T C 1921.46 PASS AC=2;AF=0.898;AN=2;DP=3260;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,69:69:99:2222,207,0:0,0,36,33 chr2 71417065 . G T 3060.16 PASS AC=2;AF=0.898;AN=2;DP=4086;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,86:86:99:2681,258,0:0,0,40,46 chr2 71417134 . C T 308.69 PASS AC=2;AF=0.594;AN=2;DP=680;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant9-variant18-variant20-variant22-variant24-variant28-variant29-variant34-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1640,150,0:0,0,16,34 chr2 71503978 . T C 1219.84 PASS AC=2;AF=0.583;AN=2;DP=994;MQ=60;set=variant2-variant4-variant6-variant11-variant12-variant20-variant22-variant28-variant34-variant35-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,107:107:99:3483,321,0:0,0,45,62 chr2 71558782 . G GC 382.22 PASS AC=2;AF=1;AN=2;DP=993;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,23:23:72:781,72,0:0,0,22,1 chr2 71558911 . T G 2120.33 PASS AC=1;AF=0.5;AN=2;DP=181;FS=1.16;FractionInformativeReads=1;MQ=60;MQRankSum=1.704;QD=11.71;ReadPosRankSum=4.21;SOR=0.585;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:89,92:181:99:2149,0,2090:50,39,49,43 chr2 71558924 . G T 4055.11 PASS AC=2;AF=0.92;AN=2;DP=8117;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,193:193:99:5740,577,0:0,0,101,92 chr2 71559107 . T G 924.56 PASS AC=2;AF=0.71;AN=2;DP=1173;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant12-variant14-variant16-variant19-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1413,108,0:0,0,8,28 chr2 71607539 . G A 509.49 PASS AC=2;AF=0.717;AN=2;DP=398;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant12-variant14-variant16-variant19-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:834,63,0:0,0,11,10 chr2 71615571 . C T 706.36 PASS AC=2;AF=0.898;AN=2;DP=1366;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,28:28:83:1080,83,0:0,0,25,3 chr2 71620818 . C T 2340.56 PASS AC=2;AF=0.898;AN=2;DP=4238;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,99:99:99:3061,297,0:0,0,38,61 chr2 71627539 . C T 1744.56 PASS AC=2;AF=0.717;AN=2;DP=1334;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant12-variant14-variant16-variant19-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1299,123,0:0,0,27,14 chr2 71633275 . T C 4431.48 PASS AC=2;AF=0.726;AN=2;DP=4043;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant12-variant14-variant16-variant19-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,135:137:99:3829,360,0:1,1,75,60 chr2 71633389 . C T 2840.28 PASS AC=2;AF=0.742;AN=2;DP=2472;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant12-variant14-variant16-variant19-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,76:77:99:2284,185,0:0,1,28,48 chr2 71634588 . G A 5199.39 PASS AC=2;AF=0.898;AN=2;DP=6338;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,132:132:99:4455,394,0:0,0,46,86 chr2 71635931 . G T 2041.91 PASS AC=2;AF=0.898;AN=2;DP=3164;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,86:86:99:2901,258,0:0,0,23,63 chr2 71636036 . A G 149.59 PASS AC=2;AF=0.742;AN=2;DP=377;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant12-variant14-variant16-variant19-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:449,36,0:0,0,2,10 chr2 71645828 . G A 1883.94 PASS AC=2;AF=0.726;AN=2;DP=1831;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant12-variant14-variant16-variant19-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1238,132,0:0,0,18,26 chr2 71645890 . G C 675.3 PASS AC=2;AF=0.795;AN=2;DP=743;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,7:8:17:260,17,0:1,0,1,6 chr2 71645946 . G A 323.54 PASS AC=2;AF=0.769;AN=2;DP=179;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant12-variant16-variant21-variant22-variant23-variant26-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:135,9,0:0,0,0,3 chr2 71693805 . T C 290.31 PASS AC=2;AF=0.529;AN=2;DP=750;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant11-variant12-variant13-variant20-variant21-variant22-variant25-variant26-variant28-variant30-variant34-variant35-variant36-variant38-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1368,134,0:0,0,25,20 chr2 71693845 . G A 551.18 PASS AC=2;AF=0.529;AN=2;DP=982;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant11-variant12-variant13-variant20-variant21-variant22-variant25-variant26-variant28-variant30-variant34-variant35-variant36-variant38-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1588,148,0:0,0,28,22 chr2 71693943 . G A 1314.47 PASS AC=2;AF=0.529;AN=2;DP=1828;MQ=60;set=variant2-variant4-variant11-variant12-variant13-variant20-variant21-variant22-variant25-variant26-variant28-variant30-variant34-variant35-variant36-variant38-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,142:142:99:4467,425,0:0,0,86,56 chr2 71708825 . T TATCCATCC,TATCC,TATCCATCCATCC,TATCCATCCATCCATCC,TCC 160.48 PASS AC=0,2,0,0,0;AF=0.038,0.564,0.064,0.013,0.013;AN=2;DP=663;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 2/2:20:68:0,0,17,3 chr2 71747235 . A G 1168.21 PASS AC=2;AF=0.92;AN=2;DP=4365;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,105:105:99:3399,315,0:0,0,66,39 chr2 71747432 . G T 1152.6 PASS AC=2;AF=0.854;AN=2;DP=2682;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:2206,193,0:0,0,16,49 chr2 71747851 . T C 62.03 PASS AC=2;AF=0.92;AN=2;DP=1421;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1276,108,0:0,0,27,9 chr2 71747899 . G A 123.21 PASS AC=2;AF=0.689;AN=2;DP=2255;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2137,209,0:0,0,44,26 chr2 71755380 . A G 2858.37 PASS AC=2;AF=0.955;AN=2;DP=4289;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,102:102:99:3276,306,0:0,0,66,36 chr2 71762232 . C T 881.19 PASS AC=2;AF=0.779;AN=2;DP=4261;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,91:91:99:2556,271,0:0,0,46,45 chr2 71762310 . A G 1502.96 PASS AC=2;AF=0.826;AN=2;DP=2964;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,83:83:99:2980,249,0:0,0,50,33 chr2 71766487 . G A 2930.21 PASS AC=2;AF=0.793;AN=2;DP=4170;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,140:140:99:4495,418,0:0,0,44,96 chr2 71776345 . C T 953.03 PASS AC=2;AF=0.768;AN=2;DP=1720;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1953,135,0:0,0,26,16 chr2 71776346 . A G 953.03 PASS AC=2;AF=0.943;AN=2;DP=1924;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1953,135,0:0,0,27,18 chr2 71780215 . T C 1265.23 PASS AC=1;AF=0.802;AN=2;DP=6190;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:87,87:174:99:2154,0,2092:40,47,37,50 chr2 71791577 . G T 219.47 PASS AC=1;AF=0.538;AN=2;DP=133;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant9-variant21-variant22-variant25-variant29-variant32-variant34-variant35-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:4,5:9:99:122,0,106:1,3,1,4 chr2 71795152 . A T 566.22 PASS AC=1;AF=0.75;AN=2;DP=5941;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:125,75:200:99:1771,0,3079:58,67,36,39 chr2 71796865 . C G 152.99 PASS AC=1;AF=0.756;AN=2;DP=712;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,6:16:99:210,0,325:9,1,5,1 chr2 71797176 . A C 859.23 PASS AC=1;AF=0.629;AN=2;DP=1927;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant16-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:34,23:57:99:722,0,983:12,22,11,12 chr2 71817003 . A G 241.46 PASS AC=1;AF=0.789;AN=2;DP=794;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,12:24:99:374,0,400:2,10,2,10 chr2 71817571 . A T 701.66 PASS AC=1;AF=0.571;AN=2;DP=967;MQ=60;set=variant6-variant7-variant9-variant11-variant14-variant15-variant18-variant20-variant21-variant26-variant27-variant29-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,30:54:99:890,0,778:3,21,7,23 chr2 71828423 . A T 952.2 PASS AC=2;AF=0.977;AN=2;DP=1125;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:888,66,0:0,0,20,2 chr2 71829821 . G T 3490.52 PASS AC=2;AF=0.977;AN=2;DP=5773;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,152:152:99:4721,455,0:0,0,87,65 chr2 71847943 . C A 1206.75 PASS AC=2;AF=0.802;AN=2;DP=1508;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1145,105,0:0,0,13,22 chr2 71871039 . A G 2265.88 PASS AC=2;AF=0.895;AN=2;DP=3009;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2121,209,0:0,0,42,28 chr2 71871236 . A G 842.3 PASS AC=2;AF=0.895;AN=2;DP=1372;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1561,135,0:0,0,10,35 chr2 71891361 . C T 2311.26 PASS AC=2;AF=0.895;AN=2;DP=3742;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,98:98:99:3081,292,0:0,0,62,36 chr2 71901286 . C T 755.18 PASS AC=2;AF=0.86;AN=2;DP=1137;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:1064,96,0:0,0,24,8 chr2 71906171 . T C 1906.82 PASS AC=2;AF=0.919;AN=2;DP=3405;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:2318,204,0:0,0,49,19 chr2 71906278 . A C 1755.85 PASS AC=1;AF=0.615;AN=2;DP=2320;MQ=60;set=variant5-variant8-variant12-variant17-variant23-variant24-variant25-variant28-variant30-variant35-variant37-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:113,102:215:99:2278,0,2440:60,53,49,53 chr2 71907930 . G T 812.75 PASS AC=2;AF=0.881;AN=2;DP=746;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:541,42,0:0,0,12,2 chr2 71909822 . C T 854.38 PASS AC=1;AF=0.571;AN=2;DP=1095;MQ=60;set=variant4-variant5-variant8-variant11-variant23-variant24-variant25-variant27-variant28-variant30-variant35-variant37-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:38,50:88:99:1354,0,1102:9,29,15,35 chr2 72405641 . G GTA 1653.62 PASS AC=1;AF=0.58;AN=2;DP=1436;MQ=60;set=variant3-variant6-variant7-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant32-variant34-variant35-variant36-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:42,17:59:99:587,0,1718:19,23,8,9 chr2 72405665 . A G 340.6 PASS AC=1;AF=0.538;AN=2;DP=688;FractionInformativeReads=1;MQ=60;set=variant6-variant7-variant10-variant13-variant14-variant16-variant17-variant18-variant22-variant35-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:40,17:57:99:343,0,1043:17,23,8,9 chr2 72405827 . A T 1372.44 PASS AC=1;AF=0.58;AN=2;DP=976;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant7-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant32-variant34-variant35-variant36-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:18,17:35:99:657,0,1134:13,5,13,4 chr2 72405833 . A G 1443.66 PASS AC=1;AF=0.597;AN=2;DP=1272;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant6-variant7-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:19,18:37:99:695,0,1131:14,5,14,4 chr2 72406213 . T C 503.16 PASS AC=1;AF=0.5;AN=2;DP=229;FractionInformativeReads=1;MQ=60;set=variant7-variant16-variant17-variant18-variant22-variant35 GT:AD:DP:GQ:PL:SB 0/1:20,10:30:99:237,0,547:8,12,6,4 chr2 72606790 . T G 1906.62 PASS AC=1;AF=0.556;AN=2;DP=1158;MQ=60;set=variant7-variant10-variant13-variant14-variant22-variant28-variant35-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:72,58:130:99:1366,0,1744:43,29,35,23 chr2 72692272 . A AAG 5283.99 PASS AC=2;AF=0.989;AN=2;DP=5701;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,138:138:99:6205,415,0:0,0,81,57 chr2 72707874 . A G 701.76 PASS AC=1;AF=0.591;AN=2;DP=877;MQ=60;set=variant-variant3-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant18-variant21-variant22-variant24-variant28-variant31-variant34-variant35-variant36-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:19,18:37:99:537,0,546:5,14,4,14 chr2 72722464 . A C 275.15 PASS AC=2;AF=0.591;AN=2;DP=90;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant7-variant9-variant13-variant22-variant28-variant31-variant35-variant36-variant39-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:271,21,0:0,0,6,1 chr2 72742083 . GACAC GAC,G,GACACAC,GACACACAC 1455.95 PASS AC=1,1,0,0;AF=0.693,0.17,0.011,0.011;AN=2;DP=2385;set=Intersection GT:DP:GQ:SB 2/1:43:99:0,0,29,14 chr2 72958333 . T C 1241.15 PASS AC=2;AF=0.583;AN=2;DP=1611;FractionInformativeReads=1;MQ=60;set=variant-variant7-variant9-variant10-variant13-variant14-variant22-variant28-variant31-variant35-variant39-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,137:137:99:4075,410,0:0,0,67,70 chr2 73151153 . T TG 1574.87 PASS AC=1;AF=0.545;AN=2;DP=1306;MQ=60;set=variant-variant5-variant9-variant20-variant22-variant28-variant31-variant35-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:83,63:146:99:1912,0,2621:51,32,43,20 chr2 73151231 . C T 7557.27 PASS AC=2;AF=0.955;AN=2;DP=9336;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,225:225:99:6206,660,0:0,0,125,100 chr2 73161447 . A G 1196.96 PASS AC=1;AF=0.5;AN=2;DP=562;MQ=60;set=variant2-variant3-variant5-variant6-variant10-variant24-variant35 GT:AD:DP:GQ:PL:SB 0/1:55,58:113:99:1604,0,1469:17,38,18,40 chr2 73169494 . GT G 629.04 PASS AC=1;AF=0.538;AN=2;DP=976;MQ=60;set=variant-variant5-variant9-variant11-variant18-variant19-variant20-variant22-variant28-variant31-variant35-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:55,29:84:99:1052,0,2653:27,28,14,15 chr2 73169500 . G A 641.09 PASS AC=1;AF=0.536;AN=2;DP=1060;MQ=60;set=variant-variant5-variant9-variant11-variant18-variant19-variant20-variant22-variant28-variant31-variant35-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:54,29:83:99:1055,0,2615:26,28,14,15 chr2 73169582 . C G,A 572.16 PASS AC=1,0;AF=0.308,0.231;AN=2;DP=858;MQ=60;set=variant-variant5-variant9-variant11-variant18-variant19-variant20-variant22-variant28-variant31-variant35-variant39-variant42 GT:DP:GQ:SB 0/1:75:99:27,28,9,11 chr2 73195837 . TTTCC T 286.85 PASS AC=1;AF=0.647;AN=2;DP=968;MQ=60;set=variant-variant2-variant3-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,13:28:99:477,0,728:5,10,4,9 chr2 73280303 . G A 258.87 PASS AC=1;AF=0.537;AN=2;DP=766;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant12-variant13-variant14-variant15-variant17-variant19-variant21-variant22-variant23-variant25-variant28-variant29-variant31-variant32-variant33-variant34-filterInvariant35-variant37-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,7:34:61:61,0,679:18,9,5,2 chr2 73301602 . G T 541.89 PASS AC=1;AF=0.5;AN=2;DP=348;MQ=60;set=variant14-variant17-variant18-variant25-variant29-variant35 GT:AD:DP:GQ:PL:SB 0/1:38,31:69:99:642,0,1083:18,20,16,15 chr2 73339430 . T G 1975.91 PASS AC=2;AF=0.849;AN=2;DP=6444;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,187:187:99:5673,561,0:0,0,115,72 chr2 73339708 . G A 2255.88 PASS AC=2;AF=0.724;AN=2;DP=10900;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,310:310:99:9557,924,0:0,0,161,149 chr2 73454090 . C T 766.18 PASS AC=1;AF=0.5;AN=2;DP=308;FractionInformativeReads=1;MQ=60;set=variant9-variant14-variant16-variant18-variant25-variant35 GT:AD:DP:GQ:PL:SB 0/1:34,38:72:99:957,0,873:15,19,21,17 chr2 73492614 . A T 6207.98 PASS AC=1;AF=0.583;AN=2;DP=5660;MQ=60;set=variant-variant3-variant5-variant8-variant10-variant14-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant34-variant35-variant37-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:159,100:259:99:2440,0,4059:71,88,44,56 chr2 73613031 . TGGAGGAGGA TGGA,TGGAGGAGGAGGA,TGGAGGA,TGGAGGAGGAGGAGGA,T 601.68 PASS AC=1,0,0,0,0;AF=0.318,0.42,0.045,0.034,0.011;AN=2;DP=2483;set=Intersection GT:DP:GQ:SB 0/1:52:99:19,7,18,8 chr2 73613341 . G A 718.31 PASS AC=1;AF=0.568;AN=2;DP=1427;MQ=60;set=variant-variant2-variant6-variant7-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant31-variant35-variant36-variant37-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,36:65:99:899,0,761:9,20,10,26 chr2 73649928 . G A 849.68 PASS AC=1;AF=0.565;AN=2;DP=1410;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant7-variant10-variant13-variant14-variant15-variant16-variant19-variant20-variant22-variant23-variant24-variant25-variant31-variant34-variant35-variant36-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,29:62:99:662,0,902:24,9,17,12 chr2 73651967 . C T 1053.98 PASS AC=1;AF=0.563;AN=2;DP=2388;set=variant2-variant6-variant7-variant10-variant13-variant14-variant15-variant16-variant19-variant20-variant22-variant23-variant24-variant25-variant31-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,50:107:99:1160,0,1396:25,32,22,28 chr2 73675669 . T G 1353.97 PASS AC=1;AF=0.919;AN=2;DP=5417;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,70:138:99:1824,0,1808:37,31,39,31 chr2 73677833 . A G 3888.18 PASS AC=1;AF=0.565;AN=2;DP=7753;set=variant2-variant6-variant7-variant10-variant13-variant14-variant15-variant16-variant19-variant20-variant22-variant23-variant24-variant25-variant31-variant34-variant35-variant36-variant37-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:174,182:356:99:4533,0,4269:88,86,93,89 chr2 73677898 . G C 3933.08 PASS AC=1;AF=0.563;AN=2;DP=8111;set=variant2-variant6-variant7-variant10-variant13-variant14-variant15-variant16-variant19-variant20-variant22-variant23-variant24-variant25-variant31-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:159,197:356:99:5150,0,4042:79,80,104,93 chr2 73679280 . A G 1640.65 PASS AC=1;AF=0.563;AN=2;DP=3771;MQ=60;set=variant2-variant6-variant7-variant10-variant13-variant14-variant15-variant16-variant19-variant20-variant22-variant23-variant24-variant25-variant31-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:84,92:176:99:2392,0,2162:34,50,37,55 chr2 73679866 . T C 1260.66 PASS AC=1;AF=0.533;AN=2;DP=1617;MQ=60;set=variant2-variant7-variant13-variant14-variant16-variant19-variant20-variant23-variant24-variant25-variant31-variant35-variant36-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,65:106:99:1870,0,1076:20,21,29,36 chr2 73679990 . T A 1063.82 PASS AC=1;AF=0.563;AN=2;DP=2586;set=variant2-variant6-variant7-variant10-variant13-variant14-variant15-variant16-variant19-variant20-variant22-variant23-variant24-variant25-variant31-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,55:103:99:1416,0,1184:25,23,25,30 chr2 73680508 . G C 1400.65 PASS AC=1;AF=0.563;AN=2;DP=2219;FractionInformativeReads=1;set=variant2-variant6-variant7-variant10-variant13-variant14-variant15-variant16-variant19-variant20-variant22-variant23-variant24-variant25-variant31-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,47:93:99:1118,0,1241:23,23,21,26 chr2 73716810 . G A 1154.7 PASS AC=1;AF=0.563;AN=2;DP=879;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant6-variant17-variant21-variant25-variant32-variant35 GT:AD:DP:GQ:PL:SB 0/1:62,53:115:99:1190,0,1561:37,25,27,26 chr2 73717103 . G C 1108.21 PASS AC=1;AF=0.563;AN=2;DP=867;MQ=60;set=variant-variant5-variant6-variant17-variant21-variant25-variant32-variant35 GT:AD:DP:GQ:PL:SB 0/1:55,73:128:99:1857,0,1412:31,24,40,33 chr2 73717567 . G T 1104.89 PASS AC=1;AF=0.563;AN=2;DP=2034;MQ=60;set=variant2-variant6-variant7-variant10-variant13-variant14-variant15-variant16-variant19-variant20-variant22-variant23-variant24-variant25-variant31-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,37:86:99:937,0,1303:23,26,16,21 chr2 73717656 . A G 1131.43 PASS AC=1;AF=0.563;AN=2;DP=2410;MQ=60;set=variant2-variant6-variant7-variant10-variant13-variant14-variant15-variant16-variant19-variant20-variant22-variant23-variant24-variant25-variant31-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,47:91:99:1306,0,1280:23,21,30,17 chr2 73746923 . C T 684.32 PASS AC=1;AF=0.548;AN=2;DP=866;MQ=60;set=variant2-variant6-variant7-variant10-variant13-variant14-variant15-variant16-variant19-variant20-variant22-variant23-variant24-variant25-variant31-variant35-variant36-variant37-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,17:36:99:398,0,510:11,8,11,6 chr2 73761881 . G A 308.02 PASS AC=1;AF=0.563;AN=2;DP=738;MQ=60;set=variant2-variant6-variant7-variant10-variant13-variant14-variant15-variant16-variant19-variant20-variant22-variant23-variant24-variant25-variant31-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,19:34:99:545,0,448:12,3,15,4 chr2 73762236 . A G 333.28 PASS AC=1;AF=0.548;AN=2;DP=492;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant7-variant10-variant13-variant14-variant15-variant16-variant19-variant20-variant22-variant23-variant24-variant25-variant31-variant35-variant36-variant37-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,14:22:99:434,0,242:1,7,3,11 chr2 73829372 . C T 1433.23 PASS AC=1;AF=0.543;AN=2;DP=3463;set=variant2-variant6-variant7-variant10-variant14-variant15-variant16-variant19-variant20-variant22-variant23-variant24-variant25-variant31-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:72,76:148:99:1852,0,1681:40,32,43,33 chr2 73830581 . GA GAA,G 194.69 PASS AC=1,0;AF=0.478,0.043;AN=2;DP=705;set=variant2-filterInvariant5-variant6-filterInvariant7-filterInvariant8-variant10-variant13-variant14-variant15-variant16-variant19-variant20-variant22-variant23-variant24-variant25-variant31-variant35-variant36-variant37-variant39-variant43-variant44 GT:DP:GQ:SB 0/1:26:99:2,8,3,13 chr2 73837006 . T A 1840.36 PASS AC=1;AF=0.536;AN=2;DP=2271;MQ=60;set=variant2-variant7-variant14-variant16-variant19-variant20-variant23-variant24-variant25-variant31-variant35-variant36-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:93,74:167:99:1822,0,2405:32,61,27,47 chr2 73867862 . G C 144.18 PASS AC=1;AF=0.523;AN=2;DP=355;FractionInformativeReads=1;set=variant2-variant5-variant6-variant7-variant10-variant13-variant14-variant15-variant16-variant19-variant20-variant22-variant23-variant24-variant25-variant31-variant35-variant36-variant37-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,12:17:94:383,0,94:3,2,9,3 chr2 73867897 . A G 270.12 PASS AC=1;AF=0.919;AN=2;DP=1099;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,15:25:99:460,0,254:7,3,11,4 chr2 73868328 . A G 2765.46 PASS AC=1;AF=0.545;AN=2;DP=4756;set=variant2-variant5-variant6-variant7-variant10-variant13-variant14-variant15-variant16-variant19-variant20-variant22-variant23-variant24-variant25-variant31-variant35-variant36-variant37-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:109,114:223:99:2823,0,2745:57,52,68,46 chr2 73899955 . G T 3007.29 PASS AC=1;AF=0.93;AN=2;DP=13210;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:173,120:293:99:2958,0,4372:110,63,84,36 chr2 73900210 . A G 938.26 PASS AC=1;AF=0.919;AN=2;DP=3273;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,39:66:99:1267,0,870:3,24,6,33 chr2 73900900 . T C 200.61 PASS AC=1;AF=0.568;AN=2;DP=526;set=variant2-variant5-variant6-variant7-variant10-variant13-variant14-variant15-variant16-variant19-variant20-variant22-variant23-variant24-variant25-variant31-variant35-variant36-variant37-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,13:28:99:457,0,537:14,1,12,1 chr2 73900918 . CTT CT,C 42.93 PASS AC=1,0;AF=0.523,0.151;AN=2;DP=1727;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:41:99:21,5,11,4 chr2 73912256 . G A 70.04 PASS AC=1;AF=0.5;AN=2;DP=98;FractionInformativeReads=1;set=variant5-variant6-variant16-variant24-variant34-variant35-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,4:15:76:76,0,333:4,7,0,4 chr2 73994074 . G A 2540.04 PASS AC=1;AF=0.943;AN=2;DP=2506;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:25,43:68:99:1164,0,787:7,18,14,29 chr2 74035880 . A G 218.73 PASS AC=2;AF=0.989;AN=2;DP=461;FS=0;MQRankSum=-1.221;ReadPosRankSum=-0.322;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:247,30,0:0,0,5,5 chr2 74056564 . A G 705.86 PASS AC=2;AF=0.635;AN=2;DP=1255;MQ=60;set=variant-variant2-variant6-variant7-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant35-variant36-variant37-variant39-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1678,159,0:0,0,19,34 chr2 74087290 . T C 1005.22 PASS AC=2;AF=0.588;AN=2;DP=1437;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant7-variant12-variant13-variant16-variant19-variant21-variant24-variant25-variant27-variant30-variant31-variant32-variant35-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,82:82:99:2582,246,0:0,0,31,51 chr2 74090063 . TA T 3444.3 PASS AC=1;AF=0.587;AN=2;DP=5607;MQ=60;set=variant-variant2-variant6-variant7-variant10-variant13-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant27-variant30-variant31-variant35-variant36-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:125,114:239:99:2764,0,3004:66,59,64,50 chr2 74091327 . T C 808.6 PASS AC=2;AF=0.648;AN=2;DP=1557;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant7-variant10-variant12-variant13-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant35-variant36-variant37-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,64:64:99:2054,192,0:0,0,25,39 chr2 74091805 . C T 682.57 PASS AC=1;AF=0.587;AN=2;DP=1608;MQ=60;set=variant-variant2-variant6-variant7-variant10-variant13-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant27-variant30-variant31-variant35-variant36-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:34,38:72:99:998,0,841:16,18,24,14 chr2 74093652 . T C 1180.11 PASS AC=2;AF=0.58;AN=2;DP=2833;MQ=60;set=variant-variant2-variant6-variant7-variant12-variant13-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant35-variant36-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,145:145:99:4557,434,0:0,0,63,82 chr2 74093682 . T A 1210.94 PASS AC=2;AF=0.58;AN=2;DP=2445;MQ=60;set=variant-variant2-variant6-variant7-variant12-variant13-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant35-variant36-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,127:127:99:3896,380,0:0,0,56,71 chr2 74120181 . A G 976.83 PASS AC=2;AF=0.62;AN=2;DP=1403;MQ=60;set=variant3-variant6-variant7-variant8-variant10-variant12-variant13-variant15-variant16-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant35-variant36-variant37-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1192,120,0:0,0,15,25 chr2 74123827 . C T 131.98 PASS AC=2;AF=0.798;AN=2;DP=717;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:678,66,0:0,0,13,9 chr2 74124142 . C T 649.63 PASS AC=2;AF=0.791;AN=2;DP=3040;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,73:73:99:2341,219,0:0,0,36,37 chr2 74124171 . G A 507.99 PASS AC=2;AF=0.798;AN=2;DP=2694;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:2045,215,0:0,0,31,41 chr2 74124342 . A G 311.36 PASS AC=2;AF=0.791;AN=2;DP=1644;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1346,135,0:0,0,19,26 chr2 74124528 . T C 93.19 PASS AC=2;AF=0.868;AN=2;DP=354;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:283,27,0:0,0,3,6 chr2 74128361 . T G 2934.22 PASS AC=2;AF=0.656;AN=2;DP=2826;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant28-variant29-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,100:100:99:4523,307,0:0,0,72,28 chr2 74128369 . G A 3220.66 PASS AC=2;AF=0.656;AN=2;DP=3240;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant28-variant29-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,113:113:99:4955,346,0:0,0,81,32 chr2 74128391 . G C 1069.2 PASS AC=2;AF=0.814;AN=2;DP=5720;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,151:151:99:4911,453,0:0,0,99,52 chr2 74128433 . C T 1772.68 PASS AC=2;AF=0.814;AN=2;DP=8509;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,237:237:99:6805,708,0:0,0,132,105 chr2 74129664 . A G 4704.79 PASS AC=2;AF=0.662;AN=2;DP=7374;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,208:208:99:6730,623,0:0,0,108,100 chr2 74129712 . C G 5052.08 PASS AC=2;AF=0.662;AN=2;DP=7689;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,207:207:99:6596,619,0:0,0,106,101 chr2 74129895 . G A 4704.72 PASS AC=2;AF=0.662;AN=2;DP=5758;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,169:169:99:5205,507,0:0,0,70,99 chr2 74130024 . C A 1882.87 PASS AC=2;AF=0.672;AN=2;DP=2107;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,67:67:99:2057,199,0:0,0,28,39 chr2 74130240 . G A 2619.46 PASS AC=2;AF=0.672;AN=2;DP=2728;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,83:83:99:2493,249,0:0,0,42,41 chr2 74135380 . G A 3172.35 PASS AC=2;AF=0.672;AN=2;DP=3577;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,95:95:99:3059,284,0:0,0,56,39 chr2 74135797 . T C 1602.26 PASS AC=2;AF=0.692;AN=2;DP=2750;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2404,210,0:0,0,50,20 chr2 74135898 . A G 4935.28 PASS AC=2;AF=0.697;AN=2;DP=6365;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,174:174:99:5189,521,0:0,0,87,87 chr2 74140581 . A T 1163.01 PASS AC=2;AF=0.692;AN=2;DP=1986;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1793,150,0:0,0,41,9 chr2 74140789 . T C 3409.53 PASS AC=2;AF=0.692;AN=2;DP=5725;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,148:148:99:4564,443,0:0,0,66,82 chr2 74140888 . A C 953.72 PASS AC=2;AF=0.672;AN=2;DP=1416;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,45:46:99:1635,106,0:1,0,9,36 chr2 74142164 . GA G 242.62 PASS AC=2;AF=0.662;AN=2;DP=674;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:718,66,0:0,0,7,15 chr2 74146869 . G A 305.44 PASS AC=1;AF=0.744;AN=2;DP=1431;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,16:44:99:477,0,743:9,19,5,11 chr2 74153905 . C T 3881.89 PASS AC=2;AF=1;AN=2;DP=8005;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,217:217:99:6753,649,0:0,0,137,80 chr2 74166053 . G A 1169.98 PASS AC=1;AF=0.5;AN=2;DP=78;FS=0.884;FractionInformativeReads=1;MQ=60;MQRankSum=1.308;QD=15;ReadPosRankSum=0.115;SOR=0.821;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:36,42:78:99:1198,0,919:23,13,28,14 chr2 74174145 . A G 43.74 PASS AC=1;AF=0.763;AN=2;DP=437;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:99:115,0,113:1,3,1,3 chr2 74185876 . A T 1410.22 PASS AC=1;AF=0.708;AN=2;DP=5241;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:81,70:151:99:1527,0,1908:45,36,36,34 chr2 74229975 . G T 2360.22 PASS AC=1;AF=0.563;AN=2;DP=2392;MQ=60;set=variant4-variant8-variant12-variant16-variant17-variant22-variant24-variant25-variant26-variant28-variant34-variant35-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:91,78:169:99:1821,0,2156:54,37,46,32 chr2 74230310 . CGTGCGTGTGT C 1722.22 PASS AC=1;AF=0.563;AN=2;DP=1274;MQ=60;set=variant4-variant8-variant12-variant16-variant17-variant22-variant24-variant25-variant26-variant28-variant34-variant35-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:42,36:78:99:1373,0,4590:22,20,21,15 chr2 74328523 . G A 1894.18 PASS AC=1;AF=0.5;AN=2;DP=138;FS=3.098;FractionInformativeReads=1;MQ=60;MQRankSum=-0.977;QD=13.73;ReadPosRankSum=-2.27;SOR=0.797;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:57,81:138:99:1922,0,1353:30,27,37,44 chr2 74332825 . AAAGC A 1312.85 PASS AC=2;AF=0.977;AN=2;DP=2182;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:3070,211,0:0,0,37,33 chr2 74333220 . C CT 6402.99 PASS AC=2;AF=0.977;AN=2;DP=12538;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:10,280:290:99:7486,619,0:4,6,118,162 chr2 74334462 . G A 1112.29 PASS AC=2;AF=0.625;AN=2;DP=3140;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant11-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,111:111:99:3839,332,0:0,0,62,49 chr2 74361641 . T C 230.31 PASS AC=1;AF=0.645;AN=2;DP=289;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant36-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:3,6:9:49:235,0,49:2,1,6,0 chr2 74362090 . A G 623.04 PASS AC=2;AF=0.955;AN=2;DP=943;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:473,36,0:0,0,3,9 chr2 74372678 . A C 151.4 PASS AC=1;AF=0.548;AN=2;DP=341;MQ=60;set=variant2-variant3-variant4-variant6-variant10-variant11-variant12-variant17-variant20-variant21-variant23-variant25-variant26-variant29-variant32-variant33-variant34-variant35-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,9:15:99:264,0,145:3,3,2,7 chr2 74374884 . G A 358.84 PASS AC=1;AF=0.545;AN=2;DP=687;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant10-variant11-variant12-variant13-variant17-variant20-variant21-variant23-variant25-variant26-variant29-variant32-variant33-variant34-variant35-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,16:32:99:436,0,422:10,6,8,8 chr2 74375266 . CAGTCTCCCCA C 199.39 PASS AC=1;AF=0.55;AN=2;DP=270;MQ=60;set=variant2-variant3-variant4-variant6-variant10-variant11-variant12-variant17-variant20-variant21-variant23-variant25-variant26-variant29-variant32-variant33-variant34-variant35-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,6:13:99:213,0,841:3,4,2,4 chr2 74382561 . T G 3388.7 PASS AC=1;AF=0.5;AN=2;DP=310;FS=0.413;FractionInformativeReads=1;MQ=60;MQRankSum=5.331;QD=10.93;ReadPosRankSum=-1.637;SOR=0.649;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:167,143:310:99:3417,0,4224:86,81,72,71 chr2 74383911 . G A 103.6 PASS AC=1;AF=0.69;AN=2;DP=309;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant8-variant10-variant11-variant12-variant13-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant32-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,5:15:91:91,0,306:2,8,2,3 chr2 74400503 . GTTTT GTTTTT,GTTT,GTT,GTTTTTTT,GTTTTTT,G,GT 121.96 PASS AC=1,0,0,0,0,0,0;AF=0.167,0.095,0.024,0.024,0.095,0.095,0.024;AN=2;DP=571;set=variant2-variant3-filterInvariant7-variant9-variant13-variant16-variant17-variant18-variant19-filterInvariant21-filterInvariant22-filterInvariant23-variant25-variant26-filterInvariant31-variant35-variant37-variant40-variant41-variant43-variant44 GT:DP:GQ:SB 0/1:12:46:0,6,0,6 chr2 74406055 . G T 198.29 PASS AC=1;AF=0.543;AN=2;DP=678;MQ=60;set=variant2-variant3-variant4-variant6-variant10-variant11-variant12-variant13-variant17-variant20-variant21-variant23-variant25-variant26-variant29-variant32-variant33-variant34-variant35-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,10:29:99:247,0,530:9,10,3,7 chr2 74425938 . C T 2689.93 PASS AC=1;AF=0.5;AN=2;DP=157;FS=2.066;FractionInformativeReads=1;MQ=60;MQRankSum=-0.343;QD=17.13;ReadPosRankSum=-0.933;SOR=0.89;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:82,75:157:99:2718,0,4308:32,50,26,49 chr2 74425947 . G T 1234.17 PASS AC=1;AF=0.538;AN=2;DP=1579;MQ=60;set=variant2-variant4-variant5-variant7-variant15-variant16-variant18-variant19-variant20-variant24-variant30-variant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:75,68:143:99:2579,0,4110:28,47,23,45 chr2 74442407 . A G 2088.07 PASS AC=1;AF=0.542;AN=2;DP=2534;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant10-variant11-variant12-variant13-variant17-variant20-variant21-variant23-variant25-variant26-variant29-variant32-variant33-variant34-variant35-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,54:118:99:2012,0,3276:33,31,28,26 chr2 74442431 . T G 2207.15 PASS AC=1;AF=0.52;AN=2;DP=3047;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant10-variant11-variant12-variant13-variant17-variant20-variant21-variant23-variant24-variant25-variant26-variant29-variant32-variant33-variant34-variant35-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,60:128:99:2180,0,3314:33,35,30,30 chr2 74442550 . AT A,ATT 36.39 PASS AC=1,0;AF=0.357,0.143;AN=2;DP=598;set=filterInvariant2-filterInvariant3-filterInvariant5-variant6-filterInvariant15-variant21-variant25-variant31-filterInvariant32-filterInvariant33-variant35-filterInvariant42-filterInvariant43-variant44 GT:DP:GQ:SB 0/1:22:99:1,9,4,8 chr2 74443051 . T C 239.15 PASS AC=1;AF=0.5;AN=2;DP=119;FractionInformativeReads=1;MQ=60;set=variant13-variant26-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:25,15:40:99:422,0,631:15,10,8,7 chr2 74450058 . C T 2630.62 PASS AC=1;AF=0.5;AN=2;DP=711;MQ=60;set=variant15-variant19-variant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:93,72:165:99:1711,0,2071:43,50,30,42 chr2 74450125 . T C 1675.15 PASS AC=1;AF=0.556;AN=2;DP=1229;set=variant6-variant8-variant12-variant13-variant17-variant18-variant22-variant24-variant25-variant26-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,36:71:99:1019,0,1040:9,26,9,27 chr2 74450134 . CT C,CTT,CTTT 35.91 PASS AC=1,0,0;AF=0.375,0.083,0.042;AN=2;DP=689;MQ=60;set=filterInvariant5-variant9-filterInvariant11-filterInvariant19-variant20-variant24-filterInvariant27-filterInvariant28-filterInvariant35-variant39-filterInvariant41-filterInvariant42 GT:DP:GQ:SB 0/1:35:99:2,25,2,6 chr2 74453986 . A G 845.71 PASS AC=1;AF=0.5;AN=2;DP=342;FractionInformativeReads=1;MQ=60;set=variant13-variant26-variant35-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:34,48:82:99:1341,0,816:23,11,36,12 chr2 74454291 . A G 267.71 PASS AC=1;AF=0.5;AN=2;DP=329;MQ=60;set=variant13-variant26-variant35-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:47,30:77:99:771,0,1185:21,26,10,20 chr2 74460685 . C T 571 PASS AC=1;AF=0.5;AN=2;DP=196;MQ=60;set=variant26-variant35-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:28,28:56:99:804,0,823:6,22,6,22 chr2 74462641 . T G 61.77 PASS AC=1;AF=0.767;AN=2;DP=79;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant8-variant10-variant11-variant18-variant24-variant25-variant35-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,2:3:37:81,0,37:0,1,0,2 chr2 74466594 . G A 2080.68 PASS AC=1;AF=0.58;AN=2;DP=1769;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:47,38:85:99:918,0,1205:23,24,15,23 chr2 74477427 . G A 807.08 PASS AC=1;AF=0.5;AN=2;DP=187;FractionInformativeReads=1;MQ=60;set=variant26-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:43,42:85:99:1085,0,1073:27,16,29,13 chr2 74588605 . G A 1334.13 PASS AC=1;AF=0.5;AN=2;DP=855;FractionInformativeReads=1;MQ=60;set=variant6-variant8-variant12-variant15-variant19-variant24-variant35 GT:AD:DP:GQ:PL:SB 0/1:53,77:130:99:2009,0,1199:28,25,41,36 chr2 74601388 . A C 230.46 PASS AC=1;AF=0.5;AN=2;DP=1954;set=filterInvariant-filterInvariant11-filterInvariant12-filterInvariant13-filterInvariant14-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant20-filterInvariant21-filterInvariant25-filterInvariant27-variant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant33-filterInvariant35-variant38-filterInvariant39-filterInvariant40-variant42-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:60,23:83:99:347,0,2349:9,51,23,0 chr2 74649916 . TC T 98.53 PASS AC=1;AF=0.5;AN=2;DP=1590;set=filterInvariant-filterInvariant2-filterInvariant5-variant6-filterInvariant7-variant8-variant10-filterInvariant11-filterInvariant12-filterInvariant13-filterInvariant16-variant20-variant22-filterInvariant23-variant24-variant25-variant27-variant29-variant30-variant31-variant33-filterInvariant35-filterInvariant36-filterInvariant38-filterInvariant39-filterInvariant40-filterInvariant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,14:70:99:116,0,1323:33,23,10,4 chr2 74649921 . C A 773.95 PASS AC=1;AF=0.5;AN=2;DP=2512;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-filterInvariant17-variant18-variant19-variant20-variant21-variant22-filterInvariant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,50:76:99:1031,0,499:15,11,29,21 chr2 74718576 . A C 189.58 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=3046;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:146,45:191:86:86,0,7137:28,118,45,0 chr2 74718582 . T C 149.21 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=3246;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:134,55:189:99:554,0,2905:16,118,55,0 chr2 74720002 . C G 1754.44 PASS AC=2;AF=0.977;AN=2;DP=3163;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1831,168,0:0,0,28,28 chr2 74725144 . T C 7133.06 PASS AC=2;AF=0.907;AN=2;DP=9194;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,246:246:99:7384,735,0:0,0,130,116 chr2 75061873 . C G 6865 PASS AC=2;AF=0.841;AN=2;DP=7268;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,229:229:99:7114,685,0:0,0,79,150 chr2 75099477 . A T 1525.24 PASS AC=1;AF=0.525;AN=2;DP=1855;FractionInformativeReads=1;MQ=60;set=variant11-variant12-variant14-variant15-variant16-variant18-variant20-variant21-variant23-variant26-variant28-variant30-variant31-variant34-variant35-variant37-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,42:96:99:1064,0,1394:36,18,27,15 chr2 75101454 . T C 1939.5 PASS AC=1;AF=0.545;AN=2;DP=3479;set=variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant23-variant26-variant28-variant30-variant31-variant34-variant35-variant37-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:104,58:162:99:1213,0,2504:62,42,35,23 chr2 75105798 . A G 1862.74 PASS AC=2;AF=1;AN=2;DP=5195;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,138:138:99:4083,413,0:0,0,76,62 chr2 75107246 . C G 823.53 PASS AC=1;AF=0.5;AN=2;DP=229;FractionInformativeReads=1;MQ=60;set=variant23-variant30-variant35 GT:AD:DP:GQ:PL:SB 0/1:47,45:92:99:1355,0,1362:37,10,34,11 chr2 75113572 . G A 762.98 PASS AC=1;AF=0.659;AN=2;DP=5510;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,55:115:99:1324,0,1402:28,32,26,29 chr2 75113789 . C G 981.05 PASS AC=1;AF=0.655;AN=2;DP=6602;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:76,85:161:99:2042,0,1728:39,37,42,43 chr2 75113903 . A G 877.2 PASS AC=1;AF=0.528;AN=2;DP=1251;set=variant11-variant12-variant14-variant15-variant16-variant18-variant21-variant23-variant26-variant28-variant30-variant31-variant34-variant35-variant37-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,33:65:99:838,0,759:11,21,13,20 chr2 75116527 . G A 1300.07 PASS AC=1;AF=0.5;AN=2;DP=477;FractionInformativeReads=1;set=variant10-variant13-variant35-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:59,58:117:99:1580,0,1642:22,37,22,36 chr2 75118330 . T G 4410.86 PASS AC=1;AF=0.674;AN=2;DP=14783;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:170,164:334:99:3991,0,4146:74,96,77,87 chr2 75118884 . G GA 246.54 PASS AC=1;AF=0.684;AN=2;DP=1347;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant13-filterInvariant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-filterInvariant36-variant37-variant38-variant39-variant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:21,6:27:99:142,0,705:12,9,4,2 chr2 75118913 . TAATG T 451.45 PASS AC=1;AF=0.684;AN=2;DP=1326;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-filterInvariant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant34-variant35-filterInvariant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,5:27:99:144,0,1216:12,10,3,2 chr2 75119865 . C T 3856.07 PASS AC=1;AF=0.5;AN=2;DP=234;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.543;QD=16.48;ReadPosRankSum=1.764;SOR=0.693;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:131,103:234:99:3884,0,7585:56,75,44,59 chr2 75119869 . T G 3869.09 PASS AC=1;AF=0.5;AN=2;DP=232;FS=1.022;FractionInformativeReads=1;MQ=60;MQRankSum=2.695;QD=16.68;ReadPosRankSum=-1.849;SOR=0.77;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:129,103:232:99:3897,0,7555:55,74,42,61 chr2 75185667 . C G 1998.59 PASS AC=2;AF=0.849;AN=2;DP=3014;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:2536,228,0:0,0,41,35 chr2 75185856 . G T 1571.93 PASS AC=1;AF=0.618;AN=2;DP=6365;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:103,96:199:99:2266,0,2984:67,36,59,37 chr2 75187573 . G A 2690.39 PASS AC=2;AF=0.849;AN=2;DP=2738;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:1912,177,0:0,0,35,24 chr2 75187793 . A T 848.09 PASS AC=2;AF=0.845;AN=2;DP=1022;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:631,63,0:0,0,6,15 chr2 75187869 . T C 82.47 PASS AC=2;AF=0.768;AN=2;DP=192;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant6-variant7-variant9-variant10-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:243,18,0:0,0,0,6 chr2 75276290 . T C 165.43 PASS AC=1;AF=0.5;AN=2;DP=409;FractionInformativeReads=1;MQ=60;set=variant-variant9-variant10-variant13-variant17-variant26-variant32-variant33-variant35-variant36-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:19,20:39:99:476,0,522:13,6,12,8 chr2 75425623 . G A 221.67 PASS AC=1;AF=0.655;AN=2;DP=582;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant14-variant17-variant18-variant19-variant21-variant24-variant25-variant26-variant27-variant29-variant30-variant32-variant33-variant35-variant36-variant37-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,7:26:99:148,0,591:15,4,5,2 chr2 75425728 . A G 560.02 PASS AC=1;AF=0.652;AN=2;DP=2389;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,39:92:99:934,0,1314:32,21,24,15 chr2 75719537 . T TAA,TA,TTA,TTAA,TAAA 548.19 PASS AC=1,0,1,0,0;AF=0.261,0.193,0.205,0.011,0.011;AN=2;DP=4196;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-filterInvariant37-variant38-variant39-variant40-variant41-filterInvariant42-variant43-variant44 GT:DP:GQ:SB 1/3:54:99:2,2,21,29 chr2 75720664 . G A 1982.55 PASS AC=1;AF=0.575;AN=2;DP=2712;MQ=60;set=variant4-variant7-variant10-variant13-variant16-variant22-variant24-variant25-variant26-variant30-variant31-variant33-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:71,78:149:99:2058,0,1837:37,34,46,32 chr2 75744918 . T C 593.42 PASS AC=1;AF=0.645;AN=2;DP=2902;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,35:70:99:843,0,979:27,8,21,14 chr2 75745081 . T C 445.98 PASS AC=1;AF=0.574;AN=2;DP=2531;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant26-variant27-variant28-variant31-variant33-variant34-variant35-variant36-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:61,35:96:99:896,0,1759:33,28,19,16 chr2 75787767 . GC G 485.66 PASS AC=2;AF=1;AN=2;DP=997;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:654,60,0:0,0,13,7 chr2 75787917 . G C 781.91 PASS AC=1;AF=0.526;AN=2;DP=1180;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant11-variant12-variant13-variant16-variant17-variant18-variant19-variant21-variant24-variant28-variant33-variant34-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:37,36:73:99:721,0,821:16,21,16,20 chr2 75788500 . CTT C,CT 95.69 PASS AC=1,0;AF=0.314,0.357;AN=2;DP=769;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-filterInvariant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant38-variant39-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:11:72:2,2,1,6 chr2 75873733 . T C 560.53 PASS AC=2;AF=0.725;AN=2;DP=1146;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1692,123,0:0,0,38,3 chr2 75874390 . G C 1067.65 PASS AC=1;AF=0.538;AN=2;DP=3896;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant16-variant19-variant23-variant24-variant25-variant28-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:84,68:152:99:1559,0,2299:42,42,33,35 chr2 75879452 . G C 422.44 PASS AC=1;AF=0.54;AN=2;DP=933;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant11-variant12-variant13-variant15-variant16-variant19-variant24-variant25-variant28-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,22:34:99:579,0,237:5,7,9,13 chr2 75881828 . T C 1284.44 PASS AC=1;AF=0.6;AN=2;DP=3986;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant19-variant24-variant25-variant28-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:81,70:151:99:1655,0,2045:48,33,40,30 chr2 75882399 . G A 901.92 PASS AC=1;AF=0.54;AN=2;DP=1622;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant11-variant12-variant13-variant15-variant16-variant19-variant24-variant25-variant28-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:28,32:60:99:795,0,660:14,14,16,16 chr2 75882576 . T C 805.96 PASS AC=1;AF=0.6;AN=2;DP=1792;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant19-variant24-variant25-variant28-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:28,41:69:99:1330,0,671:16,12,27,14 chr2 75882855 . A G 2481.52 PASS AC=1;AF=0.54;AN=2;DP=5033;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant11-variant12-variant13-variant15-variant16-variant19-variant24-variant25-variant28-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:91,103:194:99:2486,0,2114:50,41,50,53 chr2 75883007 . G GAA,GA 1127.33 PASS AC=1,0;AF=0.483,0.117;AN=2;DP=3098;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant19-variant24-variant25-variant28-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:DP:GQ:SB 0/1:91:99:17,30,18,26 chr2 75883276 . C T 1915.39 PASS AC=1;AF=0.54;AN=2;DP=3549;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant11-variant12-variant13-variant15-variant16-variant19-variant24-variant25-variant28-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:90,80:170:99:1882,0,2304:52,38,42,38 chr2 75883390 . G T 2012.81 PASS AC=1;AF=0.6;AN=2;DP=4091;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant19-variant24-variant25-variant28-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:80,70:150:99:1667,0,2010:33,47,33,37 chr2 75883674 . AATTTTTGAGACCTTGCATGTCTCATGTT A 5799.15 PASS AC=1;AF=0.5;AN=2;DP=718;MQ=60;set=variant9-variant35 GT:AD:DP:GQ:PL:SB 0/1:212,153:365:99:5665,0,11566:118,94,85,68 chr2 75883878 . T C 6942.97 PASS AC=1;AF=0.586;AN=2;DP=13081;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant19-variant24-variant25-variant28-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:238,219:457:99:5733,0,5987:119,119,106,113 chr2 75884988 . CT C 759.16 PASS AC=1;AF=0.6;AN=2;DP=2024;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant19-variant24-variant25-variant28-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:31,38:69:99:862,0,639:7,24,7,31 chr2 75889728 . A ATT 49.42 PASS AC=1;AF=0.611;AN=2;DP=107;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant11-variant13-variant15-variant25-variant28-variant33-variant34-variant35-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:1,3:4:32:118,0,32:1,0,3,0 chr2 75890100 . G T 1882.06 PASS AC=1;AF=0.5;AN=2;DP=372;FractionInformativeReads=1;MQ=60;set=variant4-variant35 GT:AD:DP:GQ:PL:SB 0/1:107,86:193:99:2027,0,2612:58,49,49,37 chr2 75890408 . A G 671.21 PASS AC=1;AF=0.6;AN=2;DP=2231;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant19-variant24-variant25-variant28-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:29,40:69:99:1042,0,675:13,16,16,24 chr2 75890540 . T C 679.01 PASS AC=1;AF=0.6;AN=2;DP=1793;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant19-variant24-variant25-variant28-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:27,36:63:99:804,0,660:16,11,16,20 chr2 75892111 . T C 281.46 PASS AC=1;AF=0.54;AN=2;DP=800;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant11-variant12-variant13-variant15-variant16-variant19-variant24-variant25-variant28-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:10,12:22:99:399,0,299:2,8,3,9 chr2 75897939 . A C 71.28 PASS AC=2;AF=0.75;AN=2;DP=35;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant8-variant13-variant15-variant24-variant35-variant38-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:99,12,0:0,0,2,2 chr2 75900700 . C CA 140.32 PASS AC=1;AF=0.54;AN=2;DP=669;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant11-variant12-variant13-variant15-variant16-variant19-variant24-variant25-variant28-filterInvariant32-variant33-variant34-variant35-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:10,12:22:99:276,0,220:3,7,1,11 chr2 75906972 . G A 884.95 PASS AC=1;AF=0.54;AN=2;DP=1811;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant11-variant12-variant13-variant15-variant16-variant19-variant24-variant25-variant28-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:29,31:60:99:847,0,790:9,20,10,21 chr2 75915035 . C T 1533.76 PASS AC=1;AF=0.6;AN=2;DP=3715;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant19-variant24-variant25-variant28-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:53,52:105:99:1219,0,1250:24,29,24,28 chr2 75918986 . T TAA 40.38 PASS AC=1;AF=0.639;AN=2;DP=93;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant11-variant12-variant13-variant15-variant16-variant19-variant24-variant25-variant28-variant32-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:2,2:4:75:75,0,77:2,0,2,0 chr2 75919272 . AATATAT AAT,AATAT,A 979.76 PASS AC=2,0,0;AF=0.774,0.065,0.016;AN=2;DP=874;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant19-variant20-variant24-variant25-variant28-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:DP:GQ:SB 1/1:15:12:0,1,2,12 chr2 75919292 . T C 986.65 PASS AC=2;AF=0.86;AN=2;DP=474;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant11-variant12-variant13-variant15-variant16-variant19-variant24-variant25-variant28-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:630,42,0:0,0,2,12 chr2 75919294 . T C 986.54 PASS AC=2;AF=0.897;AN=2;DP=487;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant19-variant24-variant25-variant28-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:630,42,0:0,0,2,12 chr2 75919296 . T C 961.77 PASS AC=2;AF=0.9;AN=2;DP=468;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant19-variant24-variant25-variant28-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:630,42,0:0,0,2,12 chr2 75923413 . T C 2827.01 PASS AC=1;AF=0.622;AN=2;DP=3219;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,32:75:99:768,0,1082:24,19,14,18 chr2 75928300 . G T 1018.84 PASS AC=1;AF=0.6;AN=2;DP=1517;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant19-variant24-variant25-variant28-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:31,28:59:99:844,0,840:21,10,21,7 chr2 75929130 . C A 4449.34 PASS AC=1;AF=0.571;AN=2;DP=7247;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant19-variant24-variant25-variant28-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:145,101:246:99:2179,0,3434:74,71,51,50 chr2 75929238 . C A 1107.09 PASS AC=1;AF=0.6;AN=2;DP=2879;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant19-variant24-variant25-variant28-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:53,42:95:99:1140,0,1537:19,34,15,27 chr2 75933830 . T A 378.69 PASS AC=1;AF=0.6;AN=2;DP=998;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant19-variant24-variant25-variant28-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:20,14:34:99:396,0,595:6,14,4,10 chr2 76975666 . G GT 421.68 PASS AC=1;AF=0.577;AN=2;DP=356;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant12-variant13-variant22-variant32-variant33-variant35-variant36-variant41 GT:AD:DP:GQ:PL:SB 0/1:11,17:28:99:404,0,233:7,4,6,11 chr2 77744821 . CA CAA,C,CAAA 530.12 PASS AC=0,1,0;AF=0.238,0.429,0.024;AN=2;DP=2517;set=variant-filterInvariant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:54:99:10,16,14,14 chr2 77745255 . TAA TA,T,TAAA 641.91 PASS AC=1,0,0;AF=0.15,0.363,0.025;AN=2;DP=9981;set=filterInvariant-filterInvariant2-variant3-variant4-variant5-variant6-variant7-filterInvariant8-filterInvariant9-variant10-variant11-variant12-variant13-variant14-variant15-filterInvariant16-variant17-variant18-variant19-variant21-variant22-filterInvariant23-variant25-variant26-variant27-variant28-variant29-filterInvariant30-variant31-variant32-variant34-filterInvariant35-filterInvariant36-variant37-variant38-variant39-filterInvariant41-variant42-filterInvariant43-filterInvariant44 GT:DP:GQ:SB 0/1:203:99:83,86,17,17 chr2 79252761 . A G 351.31 PASS AC=1;AF=0.528;AN=2;DP=525;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant8-variant11-variant12-variant16-variant18-variant22-variant23-variant24-variant26-variant28-variant30-variant34-variant35-variant36-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,8:32:99:217,0,567:13,11,6,2 chr2 79252950 . A G 144.28 PASS AC=2;AF=0.786;AN=2;DP=1329;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1408,114,0:0,0,22,16 chr2 79253029 . T G 1399.93 PASS AC=1;AF=0.528;AN=2;DP=996;MQ=60;set=variant3-variant5-variant8-variant11-variant12-variant16-variant18-variant22-variant23-variant24-variant26-variant28-variant30-variant34-variant35-variant36-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,36:58:99:1101,0,561:15,7,30,6 chr2 79253150 . A G 3607.6 PASS AC=1;AF=0.528;AN=2;DP=4326;MQ=60;set=variant3-variant5-variant8-variant11-variant12-variant16-variant18-variant22-variant23-variant24-variant26-variant28-variant30-variant34-variant35-variant36-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:110,140:250:99:3602,0,2655:65,45,79,61 chr2 79253375 . C T 1730.96 PASS AC=1;AF=0.528;AN=2;DP=1635;set=variant3-variant5-variant8-variant11-variant12-variant16-variant18-variant22-variant23-variant24-variant26-variant28-variant30-variant34-variant35-variant36-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,46:82:99:1306,0,955:8,28,12,34 chr2 79253818 . C G 908.29 PASS AC=1;AF=0.528;AN=2;DP=1019;FractionInformativeReads=1;set=variant3-variant5-variant8-variant11-variant12-variant16-variant18-variant22-variant23-variant24-variant26-variant28-variant30-variant34-variant35-variant36-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,33:69:99:937,0,930:21,15,21,12 chr2 79253987 . ATAGGGGAAAGT A 328.44 PASS AC=1;AF=0.587;AN=2;DP=2593;set=variant-variant3-variant5-variant8-variant9-variant11-variant12-variant14-variant16-variant17-variant18-filterInvariant22-variant23-variant24-variant26-variant28-variant30-variant31-variant34-variant35-variant36-filterInvariant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:110,30:140:99:854,0,4519:53,57,8,22 chr2 79254000 . CATGCA C 339.63 PASS AC=1;AF=0.587;AN=2;DP=2426;set=variant-variant3-variant5-variant8-variant9-variant11-variant12-variant14-variant16-variant17-variant18-filterInvariant22-variant23-variant24-variant26-variant28-variant30-variant31-variant34-variant35-variant36-filterInvariant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:106,27:133:99:863,0,4382:50,56,5,22 chr2 79254029 . C CA 41.43 PASS AC=1;AF=0.587;AN=2;DP=2220;set=filterInvariant-variant3-variant5-variant8-variant9-variant11-variant12-variant14-variant16-variant17-variant18-variant22-variant23-variant24-variant26-filterInvariant28-filterInvariant30-variant31-variant34-variant35-variant36-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:90,23:113:99:625,0,3255:40,50,10,13 chr2 79254065 . C T 228.81 PASS AC=1;AF=0.587;AN=2;DP=2687;set=variant-variant3-variant5-variant8-variant9-variant11-variant12-variant14-variant16-variant17-variant18-variant22-variant23-variant24-variant26-filterInvariant28-variant30-variant31-variant34-variant35-variant36-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:88,40:128:99:855,0,2629:42,46,27,13 chr2 79254101 . T G 524.62 PASS AC=1;AF=0.587;AN=2;DP=3754;set=variant-variant3-variant5-variant8-variant9-variant11-variant12-variant14-variant16-variant17-variant18-variant22-variant23-variant24-variant26-variant28-variant30-variant31-variant34-variant35-variant36-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:87,69:156:99:1531,0,2328:41,46,42,27 chr2 79254261 . T C 270.18 PASS AC=2;AF=0.786;AN=2;DP=4728;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,98:98:99:2943,294,0:0,0,36,62 chr2 79255325 . G C 1210.51 PASS AC=1;AF=0.609;AN=2;DP=3078;MQ=60;set=variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant25-variant27-variant30-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:75,41:116:99:962,0,1894:42,33,22,19 chr2 79255426 . G C 963.91 PASS AC=2;AF=0.786;AN=2;DP=4495;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,135:135:99:4316,405,0:0,0,67,68 chr2 79255588 . T C 935.59 PASS AC=1;AF=0.587;AN=2;DP=2304;MQ=60;set=variant-variant3-variant5-variant8-variant9-variant11-variant12-variant14-variant16-variant17-variant18-variant22-variant23-variant24-variant26-variant28-variant30-variant31-variant34-variant35-variant36-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,42:99:99:1037,0,1375:23,34,14,28 chr2 79255629 . G T 619.67 PASS AC=2;AF=0.786;AN=2;DP=2472;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,61:61:99:2089,182,0:0,0,15,46 chr2 79312414 . G A 3141.16 PASS AC=2;AF=0.789;AN=2;DP=3641;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,80:80:99:2603,240,0:0,0,37,43 chr2 79313815 . G T 3395.65 PASS AC=2;AF=0.788;AN=2;DP=4983;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,106:106:99:3349,318,0:0,0,59,47 chr2 79314081 . T C 847.32 PASS AC=1;AF=0.58;AN=2;DP=1584;set=variant-variant2-variant3-variant4-variant6-variant8-variant10-variant11-variant13-variant14-variant17-variant21-variant23-variant24-variant25-variant26-variant29-variant31-variant33-variant35-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:25,44:69:99:1198,0,701:5,20,14,30 chr2 79314094 . G T 1098.52 PASS AC=2;AF=0.788;AN=2;DP=2002;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:1958,185,0:0,0,17,45 chr2 79314876 . C A 1572.08 PASS AC=2;AF=0.795;AN=2;DP=2321;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,52:52:99:1723,156,0:0,0,18,34 chr2 79347487 . G A 266.39 PASS AC=2;AF=1;AN=2;DP=1031;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1158,117,0:0,0,21,18 chr2 79347603 . T C 92.13 PASS AC=1;AF=0.596;AN=2;DP=1057;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,23:52:99:433,0,868:11,18,12,11 chr2 79347745 . T G 234.38 PASS AC=1;AF=0.697;AN=2;DP=896;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,17:26:99:473,0,189:3,6,9,8 chr2 79348129 . GAA G,GA 1813.01 PASS AC=0,2;AF=0.068,0.92;AN=2;DP=4834;set=Intersection GT:DP:GQ:SB 2/2:79:59:2,5,24,48 chr2 79348196 . G T 581.9 PASS AC=1;AF=0.538;AN=2;DP=557;MQ=60;set=variant2-variant5-variant9-variant10-variant13-variant18-variant24-variant34-variant35-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:20,16:36:99:514,0,566:5,15,2,14 chr2 79350186 . G A 1572.11 PASS AC=1;AF=0.593;AN=2;DP=3656;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:66,74:140:99:1791,0,1752:29,37,34,40 chr2 79350347 . A G 3490.96 PASS AC=2;AF=1;AN=2;DP=5169;FS=0;MQ=60;MQRankSum=1.347;ReadPosRankSum=1.629;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,122:122:99:3864,366,0:0,0,69,53 chr2 79350505 . C T 758.98 PASS AC=1;AF=0.593;AN=2;DP=1703;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,38:85:99:883,0,1315:15,32,13,25 chr2 79385758 . A C 499.78 PASS AC=1;AF=0.5;AN=2;DP=4136;set=variant-variant3-variant5-variant8-variant9-variant11-variant12-variant14-variant16-variant17-variant18-variant22-variant23-variant24-variant26-variant28-variant30-variant31-variant34-variant35-variant36-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:143,53:196:99:835,0,3757:80,63,24,29 chr2 79385786 . T C 696.28 PASS AC=1;AF=0.5;AN=2;DP=4088;FractionInformativeReads=1;set=variant-variant3-variant5-variant8-variant9-variant11-variant12-variant14-variant16-variant17-variant18-variant22-variant23-variant24-variant26-variant28-variant30-variant31-variant34-variant35-variant36-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:158,46:204:99:1442,0,7018:82,76,20,26 chr2 79385787 . G A 696.28 PASS AC=1;AF=0.5;AN=2;DP=4067;FractionInformativeReads=1;set=variant-variant3-variant5-variant8-variant9-variant11-variant12-variant14-variant16-variant17-variant18-variant22-variant23-variant24-variant26-variant28-variant30-variant31-variant34-variant35-variant36-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:158,46:204:99:1442,0,7018:82,76,20,26 chr2 79385823 . T G 204.8 PASS AC=1;AF=0.5;AN=2;DP=3006;set=filterInvariant3-filterInvariant5-variant8-filterInvariant9-filterInvariant11-filterInvariant12-filterInvariant14-variant16-filterInvariant17-filterInvariant18-variant22-variant24-filterInvariant26-variant28-filterInvariant30-variant31-variant34-filterInvariant35-filterInvariant36-variant37-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:125,27:152:99:309,0,3319:64,61,10,17 chr2 79412540 . G GA 129.18 PASS AC=1;AF=0.605;AN=2;DP=395;MQ=60;set=variant-variant2-variant8-variant9-variant11-variant15-variant16-variant18-variant25-variant27-variant28-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:10,9:19:99:200,0,228:4,6,1,8 chr2 79422965 . C G 1453.13 PASS AC=1;AF=0.661;AN=2;DP=2073;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant18-variant19-variant20-variant24-variant25-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,34:63:99:737,0,743:15,14,16,18 chr2 79539988 . G C 893.85 PASS AC=1;AF=0.529;AN=2;DP=980;MQ=60;set=variant5-variant8-variant15-variant18-variant22-variant23-variant24-variant25-variant27-variant29-variant32-variant34-variant35-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:29,33:62:99:814,0,717:11,18,11,22 chr2 79600914 . C T 238.54 PASS AC=1;AF=0.843;AN=2;DP=330;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant35-variant36-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,4:5:17:124,0,17:1,0,2,2 chr2 79600948 . A C 63.56 PASS AC=2;AF=0.846;AN=2;DP=476;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:409,36,0:0,0,7,5 chr2 79601000 . G C 75.16 PASS AC=2;AF=0.825;AN=2;DP=732;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:387,42,0:0,0,7,7 chr2 79601273 . A T 51.23 PASS AC=2;AF=0.829;AN=2;DP=807;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:681,66,0:0,0,12,10 chr2 79914570 . C CT,CTT 369.89 PASS AC=2,0;AF=0.646,0.037;AN=2;DP=2049;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:47:27:4,1,33,9 chr2 80529041 . CA C 192.72 PASS AC=1;AF=0.5;AN=2;DP=143;MQ=60;set=variant6-variant7-variant10-variant30-variant35 GT:AD:DP:GQ:PL:SB 0/1:15,13:28:99:253,0,300:7,8,7,6 chr2 80801346 . T C 3038.46 PASS AC=1;AF=0.625;AN=2;DP=3393;MQ=60;set=variant-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:54,63:117:99:1406,0,1413:34,20,31,32 chr2 80801524 . T C 604.48 PASS AC=1;AF=0.5;AN=2;DP=653;FractionInformativeReads=1;MQ=60;set=variant4-variant7-variant12-variant16-variant17-variant24-variant25-variant27-variant28-variant35-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:26,33:59:99:846,0,630:10,16,11,22 chr2 80809027 . C G 203.53 PASS AC=1;AF=0.611;AN=2;DP=568;MQ=60;set=variant5-variant6-variant7-variant8-variant9-variant10-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:13,9:22:99:287,0,485:2,11,1,8 chr2 80831481 . G A 876.51 PASS AC=1;AF=0.586;AN=2;DP=1368;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:30,22:52:99:539,0,857:10,20,8,14 chr2 80831591 . G C 127.43 PASS AC=1;AF=0.7;AN=2;DP=348;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant16-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:6,5:11:99:130,0,195:1,5,1,4 chr2 80846147 . C CT 67.41 PASS AC=1;AF=0.6;AN=2;DP=918;set=filterInvariant4-variant5-variant6-variant7-variant8-variant9-variant10-filterInvariant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-filterInvariant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:5,13:18:40:267,0,40:3,2,8,5 chr2 80875611 . C A 6044.82 PASS AC=1;AF=0.589;AN=2;DP=12380;MQ=60;set=variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:302,189:491:99:4211,0,8022:132,170,87,102 chr2 80875726 . C CT 1575.98 PASS AC=1;AF=0.589;AN=2;DP=3962;MQ=60;set=variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:86,50:136:99:1166,0,2291:24,62,13,37 chr2 83083845 . C T 804.7 PASS AC=1;AF=0.534;AN=2;DP=1163;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant35-variant37-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,22:52:99:596,0,979:25,5,17,5 chr2 84650707 . A G 6583.48 PASS AC=2;AF=0.907;AN=2;DP=9380;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,217:217:99:6360,650,0:0,0,105,112 chr2 84676163 . C A 920.05 PASS AC=2;AF=0.907;AN=2;DP=1936;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1213,120,0:0,0,16,24 chr2 84676886 . TAAAAAAA TAAAA,TAAA,TAAAAA,TAAAAAA,TA,TAA,T 235.32 PASS AC=0,2,0,0,0,0,0;AF=0.292,0.361,0.042,0.028,0.014,0.042,0.014;AN=2;DP=853;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant17-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 2/2:11:32:0,0,4,7 chr2 84686610 . A G 1169.68 PASS AC=1;AF=0.5;AN=2;DP=799;MQ=60;set=variant5-variant10-variant11-variant12-variant15-variant18-variant19-variant21-variant22-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:37,40:77:99:1056,0,1092:15,22,13,27 chr2 84755996 . A AT,ATT,ATTT 1688.6 PASS AC=2,0,0;AF=0.709,0.163,0.047;AN=2;DP=2582;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:66:99:0,0,46,20 chr2 84756049 . G A 3190.51 PASS AC=2;AF=0.919;AN=2;DP=4512;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,110:110:99:3266,325,0:0,0,65,45 chr2 84756341 . T G 310.27 PASS AC=2;AF=0.94;AN=2;DP=400;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:304,24,0:0,0,1,7 chr2 84771480 . G A 1821.59 PASS AC=2;AF=0.919;AN=2;DP=2807;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,64:64:99:1899,191,0:0,0,35,29 chr2 84771567 . C T 1220.31 PASS AC=2;AF=0.907;AN=2;DP=1815;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1354,138,0:0,0,19,27 chr2 84775673 . A T 211.45 PASS AC=1;AF=0.583;AN=2;DP=250;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant13-variant15-variant19-variant20-variant21-variant23-variant24-variant25-variant28-variant31-variant32-variant33-variant34-variant35-variant37-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,5:8:99:181,0,109:0,3,0,5 chr2 84800605 . C A 2659.02 PASS AC=2;AF=0.919;AN=2;DP=2446;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:1618,170,0:0,0,28,29 chr2 84806553 . G A 724.62 PASS AC=2;AF=0.93;AN=2;DP=538;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:477,33,0:0,0,11,0 chr2 84822715 . C T 950.41 PASS AC=2;AF=0.919;AN=2;DP=1291;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:83:996,83,0:0,0,23,5 chr2 84831767 . G A 233.51 PASS AC=2;AF=0.921;AN=2;DP=194;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:214,18,0:0,0,1,5 chr2 84834063 . T C 3698.27 PASS AC=2;AF=0.93;AN=2;DP=5262;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,118:118:99:3620,353,0:0,0,74,44 chr2 84834237 . T C 2248.83 PASS AC=2;AF=0.895;AN=2;DP=2793;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,63:63:99:2172,189,0:0,0,15,48 chr2 84897361 . T A 369.76 PASS AC=2;AF=0.872;AN=2;DP=275;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:226,18,0:0,0,5,1 chr2 84897517 . A G 1905 PASS AC=2;AF=0.93;AN=2;DP=2575;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,66:66:99:1875,198,0:0,0,36,30 chr2 84899360 . G A 1090.12 PASS AC=2;AF=0.86;AN=2;DP=1510;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,31:31:92:1004,92,0:0,0,21,10 chr2 85108252 . G GC 1448.48 PASS AC=2;AF=1;AN=2;DP=1595;FS=0;MQ=60;MQRankSum=1.238;ReadPosRankSum=1.65;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1866,150,0:0,0,16,34 chr2 85280043 . G C 243.95 PASS AC=2;AF=0.542;AN=2;DP=134;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant9-variant22-variant24-variant25-variant30-variant35-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:210,18,0:0,0,5,1 chr2 85360828 . GGGC G 926.79 PASS AC=1;AF=0.667;AN=2;DP=1559;MQ=60;set=variant-variant4-variant6-variant8-variant9-variant11-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:33,33:66:99:1278,0,1262:24,9,21,12 chr2 85510965 . A G 125.14 PASS AC=1;AF=0.764;AN=2;DP=717;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,8:19:99:181,0,283:3,8,3,5 chr2 85510978 . C T 91.36 PASS AC=1;AF=0.538;AN=2;DP=218;MQ=60;set=variant2-variant5-variant13-variant16-variant25-variant27-variant30-variant31-variant35-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,5:13:99:145,0,281:1,7,1,4 chr2 85532205 . C G 320.14 PASS AC=2;AF=0.779;AN=2;DP=1834;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1263,120,0:0,0,24,16 chr2 85537312 . G A 2167.39 PASS AC=2;AF=0.703;AN=2;DP=8491;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,279:279:99:8318,832,0:0,0,154,125 chr2 85545490 . T C 1175.19 PASS AC=1;AF=0.625;AN=2;DP=3079;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant10-variant13-variant14-variant17-variant18-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:72,58:130:99:1366,0,1970:26,46,26,32 chr2 85545949 . CCT C 1400.27 PASS AC=1;AF=0.529;AN=2;DP=1197;MQ=60;set=variant3-variant6-variant8-variant11-variant12-variant13-variant15-variant19-variant21-variant22-variant29-variant32-variant35-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:37,35:72:99:1349,0,1630:17,20,16,19 chr2 85546052 . A G 257.37 PASS AC=2;AF=0.716;AN=2;DP=928;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1230,113,0:0,0,14,24 chr2 85546192 . C T 192.67 PASS AC=2;AF=0.743;AN=2;DP=843;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:736,75,0:0,0,12,13 chr2 85546615 . C T 199.36 PASS AC=2;AF=0.731;AN=2;DP=759;FractionInformativeReads=1;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:703,66,0:0,0,14,8 chr2 85546932 . A C 444.94 PASS AC=2;AF=0.731;AN=2;DP=2314;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1146,99,0:0,0,19,14 chr2 85547376 . C G 258.19 PASS AC=2;AF=0.75;AN=2;DP=911;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:671,63,0:0,0,12,9 chr2 85547429 . G T 325.48 PASS AC=2;AF=0.75;AN=2;DP=870;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:703,60,0:0,0,11,9 chr2 85547963 . C T 314.9 PASS AC=2;AF=0.744;AN=2;DP=1973;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1639,159,0:0,0,25,28 chr2 85548068 . TA T 358.05 PASS AC=2;AF=0.731;AN=2;DP=1210;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:1101,96,0:0,0,14,18 chr2 85548639 . A G 2749.58 PASS AC=2;AF=0.738;AN=2;DP=6110;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,159:159:99:5006,476,0:0,0,99,60 chr2 85549527 . T C 795.81 PASS AC=2;AF=0.716;AN=2;DP=2068;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:1758,173,0:0,0,28,30 chr2 85549547 . C T 702.63 PASS AC=2;AF=0.716;AN=2;DP=1920;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,52:52:99:1495,153,0:0,0,26,26 chr2 85549868 . A G 997.74 PASS AC=2;AF=0.738;AN=2;DP=3295;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,85:85:99:3215,255,0:0,0,37,48 chr2 85549874 . A G 648.77 PASS AC=1;AF=0.625;AN=2;DP=2185;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant10-variant13-variant14-variant17-variant18-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:37,44:81:99:1073,0,870:16,21,20,24 chr2 85551696 . T G 56.56 PASS AC=2;AF=0.716;AN=2;DP=709;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:758,66,0:0,0,16,6 chr2 85551779 . G A 456.03 PASS AC=2;AF=0.716;AN=2;DP=1519;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1637,153,0:0,0,33,18 chr2 85552186 . C A 831.48 PASS AC=2;AF=0.744;AN=2;DP=2603;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:2523,237,0:0,0,38,41 chr2 85552261 . A G 742.84 PASS AC=1;AF=0.5;AN=2;DP=484;MQ=60;set=variant3-variant6-variant8-variant11-variant19-variant21-variant32-variant35-variant37-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:29,20:49:99:623,0,762:13,16,4,16 chr2 85553784 . C T 3077.57 PASS AC=2;AF=0.731;AN=2;DP=8130;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,251:251:99:7691,753,0:0,0,130,121 chr2 85554080 . G A 3068.47 PASS AC=2;AF=0.722;AN=2;DP=10489;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:2,313:315:99:10136,895,0:1,1,197,116 chr2 85555262 . T G 2114.62 PASS AC=2;AF=0.763;AN=2;DP=8467;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,243:243:99:7706,728,0:0,0,137,106 chr2 85555277 . G A 2464.08 PASS AC=2;AF=0.756;AN=2;DP=9184;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,263:263:99:7520,783,0:0,0,142,121 chr2 85555478 . C T 1603.56 PASS AC=2;AF=0.744;AN=2;DP=4872;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,144:144:99:4737,430,0:0,0,59,85 chr2 85569294 . T C 5167.04 PASS AC=1;AF=0.55;AN=2;DP=7382;MQ=60;set=variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant19-variant21-variant22-variant30-variant32-variant35-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:163,216:379:99:5204,0,3706:88,75,118,98 chr2 85570146 . G A 202.48 PASS AC=1;AF=0.5;AN=2;DP=267;FractionInformativeReads=1;set=variant3-variant11-variant12-variant13-variant17-variant18-variant22-variant23-filterInvariant24-variant25-variant27-variant32-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:15,6:21:99:207,0,1191:14,1,6,0 chr2 85570152 . A G 241.46 PASS AC=1;AF=0.5;AN=2;DP=256;FractionInformativeReads=1;set=variant3-variant11-variant13-variant17-variant18-variant22-variant23-filterInvariant25-variant27-variant32-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:17,7:24:99:243,0,1343:15,2,7,0 chr2 85570157 . C T 238.45 PASS AC=1;AF=0.5;AN=2;DP=261;FractionInformativeReads=1;set=variant3-variant11-variant13-variant17-variant18-variant23-variant25-variant27-variant32-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:17,7:24:99:276,0,1340:15,2,7,0 chr2 85570159 . T G 238.45 PASS AC=1;AF=0.5;AN=2;DP=271;FractionInformativeReads=1;set=variant3-variant11-variant13-variant17-variant18-variant23-variant25-variant27-variant32-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:17,8:25:99:276,0,1340:15,2,8,0 chr2 85570186 . G A 66.86 PASS AC=1;AF=0.5;AN=2;DP=1303;FractionInformativeReads=1;set=variant2-variant3-variant4-variant5-variant6-filterInvariant7-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-filterInvariant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:27,19:46:99:496,0,902:22,5,12,7 chr2 85570942 . G C 609.64 PASS AC=1;AF=0.667;AN=2;DP=2569;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,60:86:99:1982,0,693:5,21,13,47 chr2 85571513 . C T 1499.69 PASS AC=1;AF=0.5;AN=2;DP=283;MQ=60;set=variant18-variant34-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:31,40:71:99:1228,0,905:9,22,10,30 chr2 85571710 . A G 1275.37 PASS AC=2;AF=0.849;AN=2;DP=4406;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,139:139:99:4647,417,0:0,0,99,40 chr2 85573033 . G A 2141.17 PASS AC=2;AF=0.788;AN=2;DP=7891;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,179:181:99:5105,491,0:1,1,86,93 chr2 85573049 . G A 1515.49 PASS AC=1;AF=0.617;AN=2;DP=5495;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant10-variant13-variant14-variant17-variant18-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:87,87:174:99:2003,0,2025:41,46,40,47 chr2 85573403 . C A 75 PASS AC=2;AF=0.788;AN=2;DP=398;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:321,27,0:0,0,3,6 chr2 85576451 . GTC G 568.61 PASS AC=1;AF=0.575;AN=2;DP=489;MQ=60;set=variant3-variant4-variant6-variant7-variant9-variant11-variant12-variant13-variant15-variant19-variant21-variant22-variant30-variant32-variant35-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,18:33:99:711,0,583:13,2,12,6 chr2 85622059 . T C 2793 PASS AC=1;AF=0.797;AN=2;DP=4680;MQ=60;set=variant-variant2-variant3-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:77,73:150:99:1745,0,1831:34,43,32,41 chr2 85641187 . C T 965.33 PASS AC=1;AF=0.533;AN=2;DP=965;MQ=60;set=variant6-variant9-variant11-variant12-variant13-variant19-variant21-variant22-variant30-variant32-variant35-variant36-variant37-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,35:63:99:792,0,612:14,14,15,20 chr2 85656616 . T C 1054.63 PASS AC=1;AF=0.583;AN=2;DP=1409;MQ=60;set=variant6-variant9-variant12-variant13-variant19-variant21-variant22-variant23-variant30-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,41:97:99:861,0,1442:30,26,19,22 chr2 85658257 . C G 200.48 PASS AC=1;AF=0.673;AN=2;DP=787;MQ=60;set=variant2-variant3-variant4-variant6-filterInvariant7-variant9-variant12-variant13-variant14-variant15-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant30-variant32-variant35-variant36-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,8:23:99:208,0,367:9,6,5,3 chr2 85658279 . G GGGAACCCACCTGGGA 519.55 PASS AC=1;AF=0.5;AN=2;DP=404;MQ=60;set=variant6-variant9-variant12-variant13-variant19-variant21-variant22-variant30-variant32-variant35-variant36-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,11:24:99:506,0,811:8,5,7,4 chr2 85660126 . A G 1589.81 PASS AC=1;AF=0.703;AN=2;DP=1992;MQ=60;set=variant-variant2-variant3-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,29:68:99:659,0,961:25,14,17,12 chr2 85662017 . G A 1897.14 PASS AC=1;AF=0.703;AN=2;DP=2038;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,27:72:99:517,0,1024:20,25,12,15 chr2 85662636 . C T 499.05 PASS AC=1;AF=0.5;AN=2;DP=1132;MQ=60;set=variant2-variant4-variant6-variant7-variant12-variant19-variant21-variant27-variant32-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:56,58:114:99:1601,0,1448:24,32,25,33 chr2 85662650 . A G 2562.35 PASS AC=1;AF=0.75;AN=2;DP=3121;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,56:104:99:1568,0,1228:23,25,23,33 chr2 85766282 . C G 1730.47 PASS AC=1;AF=0.5;AN=2;DP=486;FractionInformativeReads=1;MQ=60;set=variant16-variant28-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:64,59:123:99:1646,0,1789:48,16,43,16 chr2 85769246 . G A 6428.72 PASS AC=2;AF=1;AN=2;DP=8187;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,220:220:99:6760,659,0:0,0,110,110 chr2 85769711 . C G 1396.12 PASS AC=1;AF=0.629;AN=2;DP=1792;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant33-variant35-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,32:77:99:789,0,1048:23,22,16,16 chr2 85776490 . C CTTTA 322.35 PASS AC=1;AF=0.638;AN=2;DP=522;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant33-variant35-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,6:21:99:200,0,789:6,9,3,3 chr2 85776832 . C T 753.11 PASS AC=1;AF=0.5;AN=2;DP=345;FractionInformativeReads=1;MQ=60;set=variant16-variant23-variant28-variant35-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,25:46:99:578,0,531:11,10,15,10 chr2 85777572 . A C 447.11 PASS AC=1;AF=0.5;AN=2;DP=182;FractionInformativeReads=1;MQ=60;set=variant16-variant23-variant28-variant35-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,9:33:99:241,0,715:16,8,7,2 chr2 85777598 . T C 962.78 PASS AC=1;AF=0.5;AN=2;DP=55;FS=6.798;FractionInformativeReads=0.982;MQ=60;MQRankSum=0.205;QD=17.51;ReadPosRankSum=0.41;SOR=0.167;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:17,37:54:99:991,0,485:14,3,23,14 chr2 85780536 . C T 1243.64 PASS AC=1;AF=0.591;AN=2;DP=1723;MQ=60;set=variant-variant3-variant10-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant28-variant33-variant35-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,23:88:99:553,0,1669:31,34,12,11 chr2 85781318 . T G 1817.45 PASS AC=2;AF=1;AN=2;DP=4199;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,99:99:99:2958,296,0:0,0,48,51 chr2 85782587 . C A 1281.06 PASS AC=1;AF=0.5;AN=2;DP=680;FractionInformativeReads=1;MQ=60;set=variant16-variant23-variant28-variant35-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,44:98:99:1087,0,1346:30,24,26,18 chr2 85788212 . G GCTCAATGAGGTTGC 263.84 PASS AC=1;AF=0.5;AN=2;DP=74;FS=0;MQ=60;set=variant21-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:9,5:14:99:222,0,1277:1,8,0,5 chr2 85788402 . AC A 595.26 PASS AC=2;AF=0.735;AN=2;DP=657;MQ=60;set=variant2-variant3-filterInvariant4-variant5-variant6-variant7-variant8-variant9-variant11-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:3,24:27:4:545,4,0:2,1,15,9 chr2 85804540 . A G 994.18 PASS AC=2;AF=1;AN=2;DP=1490;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1199,114,0:0,0,21,17 chr2 85833906 . CT C,CTT 102.32 PASS AC=1,0;AF=0.45,0.05;AN=2;DP=10567;set=filterInvariant-filterInvariant2-variant3-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant13-filterInvariant14-filterInvariant15-variant16-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant27-variant28-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant38-filterInvariant39-filterInvariant40-filterInvariant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:DP:GQ:SB 0/1:191:99:55,92,13,31 chr2 85834194 . G A 243.73 PASS AC=1;AF=0.5;AN=2;DP=297;MQ=60;set=variant2-variant8-variant9-variant17-variant19-variant21-variant25-variant35-variant36-variant38 GT:AD:DP:GQ:PL:SB 0/1:14,9:23:99:174,0,384:10,4,5,4 chr2 85848747 . CT C 679.49 PASS AC=1;AF=0.732;AN=2;DP=1578;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-filterInvariant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,21:32:99:444,0,159:2,9,8,13 chr2 85863308 . C T 134.38 PASS AC=1;AF=0.5;AN=2;DP=21;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.634;QD=6.4;ReadPosRankSum=0.56;SOR=0.368;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:14,7:21:99:163,0,434:3,11,2,5 chr2 85890771 . T G 3719.85 PASS AC=2;AF=0.943;AN=2;DP=5064;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,116:116:99:3848,347,0:0,0,69,47 chr2 85893616 . CTGTG CTG,CTGTGTG,C 341.26 PASS AC=1,0,0;AF=0.446,0.203,0.041;AN=2;DP=1086;set=variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-filterInvariant19-variant20-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:18:98:11,2,4,1 chr2 85893741 . G A 4955.47 PASS AC=2;AF=0.657;AN=2;DP=6524;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,183:185:99:5381,503,0:1,1,98,85 chr2 85894308 . G T 505.25 PASS AC=1;AF=0.7;AN=2;DP=1977;MQ=60;set=variant-variant2-variant4-variant8-variant9-variant11-variant12-variant14-variant15-variant17-variant19-variant20-variant21-variant24-variant25-variant27-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:51,46:97:99:950,0,1280:21,30,20,26 chr2 85895338 . T G 1205.1 PASS AC=1;AF=0.654;AN=2;DP=2345;MQ=60;set=variant-variant2-variant4-variant8-variant9-variant11-variant12-variant14-variant15-variant17-variant19-variant20-variant21-variant24-variant25-variant27-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:43,61:104:99:1414,0,1016:19,24,29,32 chr2 85921353 . G T 75.19 PASS AC=1;AF=0.596;AN=2;DP=698;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant9-variant12-variant13-variant14-variant17-variant19-variant20-variant21-variant24-variant25-variant27-variant29-variant32-variant33-variant34-variant35-filterInvariant36-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,8:30:99:213,0,582:14,8,7,1 chr2 85921389 . G C 959.17 PASS AC=1;AF=0.625;AN=2;DP=1264;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant9-variant12-variant13-variant14-variant17-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,17:56:99:353,0,1050:24,15,11,6 chr2 85921992 . T C 1938.38 PASS AC=1;AF=0.718;AN=2;DP=3428;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,50:85:99:1255,0,869:21,14,26,24 chr2 85924729 . C T 943.03 PASS AC=1;AF=0.617;AN=2;DP=3701;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:77,66:143:99:1643,0,2152:40,37,37,29 chr2 85924899 . T A 1335.32 PASS AC=1;AF=0.617;AN=2;DP=2957;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,51:111:99:1303,0,1508:24,36,22,29 chr2 85924989 . C T 1038.23 PASS AC=1;AF=0.617;AN=2;DP=1996;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,36:76:99:891,0,974:16,24,17,19 chr2 85925084 . G A 394.11 PASS AC=1;AF=0.621;AN=2;DP=470;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant12-variant14-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,11:21:99:341,0,299:1,9,3,8 chr2 85925529 . A G 323.88 PASS AC=1;AF=0.617;AN=2;DP=2231;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,42:82:99:1035,0,1163:27,13,23,19 chr2 85925667 . G A 529.07 PASS AC=1;AF=0.617;AN=2;DP=3223;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,66:125:99:2546,0,2509:27,32,32,34 chr2 85925680 . T G 500.84 PASS AC=1;AF=0.617;AN=2;DP=3025;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,67:122:99:2589,0,2352:23,32,34,33 chr2 85925756 . C G 677.46 PASS AC=1;AF=0.617;AN=2;DP=2311;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,53:100:99:1385,0,1222:19,28,26,27 chr2 85925848 . C G 1121.16 PASS AC=1;AF=0.617;AN=2;DP=2254;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,42:84:99:1130,0,1283:26,16,21,21 chr2 85926077 . T TGCG 538.38 PASS AC=1;AF=0.617;AN=2;DP=1262;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,34:50:99:1379,0,570:4,12,11,23 chr2 85926089 . A G 379.66 PASS AC=1;AF=0.5;AN=2;DP=46;FS=1.407;FractionInformativeReads=1;MQ=60;MQRankSum=1.64;QD=8.25;ReadPosRankSum=-0.258;SOR=1.098;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:31,15:46:99:408,0,840:9,22,3,12 chr2 85981761 . T C 3407.31 PASS AC=1;AF=0.7;AN=2;DP=3549;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,53:117:99:1504,0,1721:38,26,31,22 chr2 86071393 . G C 322.27 PASS AC=1;AF=0.583;AN=2;DP=550;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant11-variant12-variant13-variant14-variant15-variant20-variant21-variant22-variant23-variant25-variant27-variant29-variant32-variant34-variant35-variant36-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:5,11:16:99:309,0,126:3,2,8,3 chr2 86075582 . C T 685.41 PASS AC=1;AF=0.524;AN=2;DP=1482;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant11-variant12-variant14-variant15-variant21-variant22-variant23-variant25-variant27-variant29-variant32-variant35-variant36-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:34,55:89:99:1388,0,920:11,23,22,33 chr2 86078478 . C T 540.28 PASS AC=1;AF=0.5;AN=2;DP=820;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant12-variant14-variant15-variant21-variant22-variant27-variant32-variant35-variant36-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:25,25:50:99:597,0,742:15,10,13,12 chr2 86088311 . T C 842.89 PASS AC=1;AF=0.5;AN=2;DP=964;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant12-variant14-variant15-variant21-variant22-variant27-variant32-variant35-variant36-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:30,25:55:99:614,0,780:19,11,17,8 chr2 86094686 . C T 1224.82 PASS AC=1;AF=0.5;AN=2;DP=1426;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant12-variant14-variant15-variant21-variant22-variant27-variant32-variant35-variant36-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:44,47:91:99:1265,0,1266:30,14,30,17 chr2 86248309 . T C 824.71 PASS AC=2;AF=0.788;AN=2;DP=3041;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,91:91:99:2932,273,0:0,0,43,48 chr2 86253581 . T C 2392.18 PASS AC=2;AF=0.788;AN=2;DP=8986;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,279:279:99:7734,833,0:0,0,135,144 chr2 86254268 . G A 649.64 PASS AC=2;AF=0.697;AN=2;DP=2549;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:2671,236,0:0,0,34,45 chr2 86258784 . T G 634.94 PASS AC=2;AF=0.697;AN=2;DP=2479;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:2377,212,0:0,0,22,49 chr2 86259443 . C T 710.99 PASS AC=2;AF=0.737;AN=2;DP=4647;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,103:103:99:2905,307,0:0,0,48,55 chr2 86272191 . G A 103.64 PASS AC=2;AF=0.697;AN=2;DP=558;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:602,42,0:0,0,14,0 chr2 86275985 . A G 1583.6 PASS AC=2;AF=0.697;AN=2;DP=3604;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,126:126:99:4039,378,0:0,0,80,46 chr2 86279837 . G C 265.91 PASS AC=1;AF=0.5;AN=2;DP=73;FractionInformativeReads=1;MQ=60;set=variant4-variant14-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:8,12:20:99:382,0,222:5,3,9,3 chr2 86292656 . C T 1225.83 PASS AC=2;AF=0.872;AN=2;DP=4099;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,109:109:99:3275,327,0:0,0,50,59 chr2 86302103 . A G 516.52 PASS AC=2;AF=0.895;AN=2;DP=1647;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:1680,171,0:0,0,37,20 chr2 86304932 . GCGCACACACACACACACA GCACACACACACACA,GCA,GCACACA,GCACACACA,GCACA,GCACACACACACA,G 479.58 PASS AC=0,0,2,0,0,0,0;AF=0.033,0.25,0.483,0.067,0.033,0.033,0.017;AN=2;DP=312;set=variant-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant39-variant41-variant43 GT:DP:GQ:SB 3/3:8:25:0,0,7,1 chr2 86305123 . T C 922.23 PASS AC=2;AF=0.965;AN=2;DP=2829;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,74:74:99:2420,222,0:0,0,48,26 chr2 86310110 . C T 496.99 PASS AC=2;AF=0.837;AN=2;DP=2446;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:2072,195,0:0,0,44,21 chr2 86315741 . C T 458.88 PASS AC=2;AF=0.837;AN=2;DP=1721;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:1498,163,0:0,0,32,23 chr2 86317037 . G C 974.38 PASS AC=2;AF=0.884;AN=2;DP=3841;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,90:90:99:2767,270,0:0,0,45,45 chr2 86332809 . G A 588.15 PASS AC=2;AF=0.837;AN=2;DP=4656;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,117:117:99:3861,351,0:0,0,78,39 chr2 86334199 . G A 626.29 PASS AC=2;AF=0.849;AN=2;DP=2089;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1358,123,0:0,0,28,13 chr2 86343476 . C A 274.3 PASS AC=2;AF=0.837;AN=2;DP=685;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:686,57,0:0,0,14,5 chr2 86343494 . G A 356.85 PASS AC=2;AF=0.849;AN=2;DP=915;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:699,57,0:0,0,15,4 chr2 86344367 . T C 398.09 PASS AC=2;AF=0.965;AN=2;DP=1151;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:877,81,0:0,0,9,18 chr2 86346308 . G A 408.76 PASS AC=2;AF=0.93;AN=2;DP=1021;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:828,66,0:0,0,3,19 chr2 86352010 . G T 489.51 PASS AC=2;AF=0.895;AN=2;DP=1237;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:844,69,0:0,0,16,7 chr2 86352785 . G A 1441.57 PASS AC=2;AF=0.837;AN=2;DP=2521;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:1789,179,0:0,0,33,27 chr2 86352825 . C T 1750.48 PASS AC=2;AF=0.837;AN=2;DP=3323;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,74:74:99:2240,221,0:0,0,42,32 chr2 86357960 . AT A,ATT 125.84 PASS AC=1,0;AF=0.441,0.088;AN=2;DP=335;MQ=60;set=variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant17-variant21-variant22-variant28-variant34-variant35-variant36-variant40-variant41 GT:DP:GQ:SB 0/1:6:7:0,1,1,4 chr2 86359405 . G T 1497.29 PASS AC=2;AF=0.837;AN=2;DP=5091;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,152:152:99:4341,453,0:0,0,92,60 chr2 86359745 . GTTTT GTT,GT,GTTT,G 255.36 PASS AC=1,0,0,0;AF=0.25,0.092,0.289,0.026;AN=2;DP=1230;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-filterInvariant25-variant26-variant27-variant28-variant30-variant31-variant32-variant35-variant36-variant38-filterInvariant39-filterInvariant40-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:12:35:2,2,1,7 chr2 86362204 . C T 615.79 PASS AC=2;AF=0.849;AN=2;DP=1866;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1797,147,0:0,0,11,38 chr2 86363074 . A G 2005.87 PASS AC=2;AF=0.837;AN=2;DP=6233;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,160:160:99:5023,480,0:0,0,88,72 chr2 86363855 . G C 274.38 PASS AC=2;AF=0.942;AN=2;DP=851;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:794,57,0:0,0,2,17 chr2 86364706 . TG T 1767.65 PASS AC=2;AF=0.965;AN=2;DP=4271;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,105:105:99:3727,316,0:0,0,58,47 chr2 86365607 . T C 1263.95 PASS AC=2;AF=0.694;AN=2;DP=3478;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant35-variant37-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,132:132:99:3860,395,0:0,0,68,64 chr2 86365713 . G A 1085.27 PASS AC=2;AF=0.826;AN=2;DP=3949;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,107:107:99:3593,321,0:0,0,59,48 chr2 86365799 . C CA 280.64 PASS AC=1;AF=0.512;AN=2;DP=4968;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,98:113:23:2056,0,23:7,8,49,49 chr2 86365884 . G A 1750.1 PASS AC=2;AF=0.826;AN=2;DP=5236;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,118:118:99:3917,354,0:0,0,56,62 chr2 86367350 . CAAA CA,CAA,C 2350.58 PASS AC=1,0,0;AF=0.337,0.244,0.058;AN=2;DP=7722;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-filterInvariant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:DP:GQ:SB 0/1:136:99:35,47,31,23 chr2 86367741 . C G 5086.53 PASS AC=2;AF=0.895;AN=2;DP=16070;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,398:399:99:12305,1172,0:1,0,171,227 chr2 86368042 . A C,AAAC,AAAAC,AAC 511.6 PASS AC=0,2,0,0;AF=0.36,0.56,0.02,0.06;AN=2;DP=211;FS=0;set=variant11-variant5-variant13-variant7-variant14-variant15-variant16-variant20-variant25-variant26-variant8-variant29-variant31-variant34-variant35-variant36-variant38-variant22-variant9-variant39-variant40-variant4-variant42-variant43-variant44 GT:DP:GQ:SB 2/2:8:24:0,0,6,2 chr2 86369180 . AG A 1582.07 PASS AC=2;AF=0.895;AN=2;DP=4744;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,105:105:99:3339,316,0:0,0,49,56 chr2 86371012 . T C 2389.48 PASS AC=2;AF=0.694;AN=2;DP=5344;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant35-variant37-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,200:201:99:6324,560,0:1,0,135,65 chr2 86371883 . T C 967.36 PASS AC=2;AF=0.694;AN=2;DP=2795;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant35-variant37-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,98:99:99:2881,255,0:0,1,39,59 chr2 86385668 . T C 409.57 PASS AC=2;AF=0.694;AN=2;DP=565;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant35-variant37-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:30:443,30,0:0,0,9,0 chr2 86385682 . TC T 522.46 PASS AC=2;AF=0.694;AN=2;DP=755;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant35-variant37-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:482,33,0:0,0,11,0 chr2 86385886 . A G 1061.49 PASS AC=2;AF=0.977;AN=2;DP=3581;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,99:99:99:2975,297,0:0,0,42,57 chr2 86398074 . A G 348.94 PASS AC=2;AF=0.694;AN=2;DP=1199;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant35-variant37-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,41:42:99:1383,99,0:1,0,12,29 chr2 86398291 . G A 123.37 PASS AC=2;AF=0.732;AN=2;DP=223;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant30-variant32-variant33-variant35-variant37-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:324,27,0:0,0,7,2 chr2 86406438 . A G 1428.52 PASS AC=2;AF=0.694;AN=2;DP=2491;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant35-variant37-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,86:86:99:3064,257,0:0,0,71,15 chr2 86406889 . G A 400.08 PASS AC=2;AF=0.694;AN=2;DP=1179;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant35-variant37-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1289,126,0:0,0,14,28 chr2 86408385 . A G 905.59 PASS AC=2;AF=0.694;AN=2;DP=2364;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant35-variant37-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,73:73:99:2328,219,0:0,0,45,28 chr2 86419932 . C G 453.78 PASS AC=2;AF=0.694;AN=2;DP=1266;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant35-variant37-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1323,111,0:0,0,28,9 chr2 86420255 . G A 168.97 PASS AC=2;AF=0.7;AN=2;DP=426;FractionInformativeReads=1;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant32-variant33-variant35-variant37-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:531,42,0:0,0,3,11 chr2 86422073 . G C 1613.39 PASS AC=2;AF=0.694;AN=2;DP=4262;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant35-variant37-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,130:131:99:3890,381,0:1,0,74,56 chr2 86422416 . T C 2001.89 PASS AC=2;AF=0.706;AN=2;DP=5503;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,131:131:99:6004,415,0:0,0,74,57 chr2 86422421 . T G 2182.72 PASS AC=2;AF=0.694;AN=2;DP=5027;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant35-variant37-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,139:139:99:6061,418,0:0,0,80,59 chr2 86422660 . C T 1522.71 PASS AC=2;AF=0.694;AN=2;DP=4211;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant35-variant37-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,152:152:99:4485,452,0:0,0,77,75 chr2 86422793 . G C 2035.22 PASS AC=2;AF=0.706;AN=2;DP=3191;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,121:121:99:5285,367,0:0,0,56,65 chr2 86422796 . A AGCT 2068.17 PASS AC=2;AF=0.706;AN=2;DP=3112;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,117:117:99:5228,361,0:0,0,54,63 chr2 86422816 . T G 976.12 PASS AC=2;AF=0.706;AN=2;DP=2719;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,98:98:99:3072,293,0:0,0,44,54 chr2 86422945 . G A 73.78 PASS AC=2;AF=0.707;AN=2;DP=439;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant35-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:900,72,0:0,0,3,21 chr2 86433240 . C T 631.29 PASS AC=2;AF=0.7;AN=2;DP=1101;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant32-variant33-variant35-variant37-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1646,123,0:0,0,38,3 chr2 86437551 . T G 340.07 PASS AC=2;AF=0.953;AN=2;DP=1205;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1424,126,0:0,0,24,18 chr2 86437898 . C T 2257.66 PASS AC=2;AF=0.953;AN=2;DP=5077;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,103:103:99:3686,309,0:0,0,70,33 chr2 86438146 . A G 1415.67 PASS AC=2;AF=0.732;AN=2;DP=5188;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,137:137:99:4112,410,0:0,0,62,75 chr2 86440963 . G A 1555.11 PASS AC=2;AF=0.953;AN=2;DP=3693;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,90:90:99:3271,269,0:0,0,21,69 chr2 86479035 . A G 307.79 PASS AC=1;AF=0.69;AN=2;DP=483;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant13-variant14-variant17-variant19-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,5:12:99:132,0,238:6,1,4,1 chr2 86479287 . G T 856.54 PASS AC=1;AF=0.69;AN=2;DP=1892;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant13-variant14-variant17-variant19-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,26:52:99:724,0,730:8,18,8,18 chr2 86481835 . C T 410.16 PASS AC=1;AF=0.655;AN=2;DP=1013;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant17-variant19-variant21-variant23-variant24-variant26-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,16:37:99:380,0,540:14,7,12,4 chr2 86491245 . C T 493.8 PASS AC=1;AF=0.661;AN=2;DP=1970;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant13-variant14-variant17-variant19-variant21-variant23-variant24-variant26-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,36:71:99:831,0,967:11,24,14,22 chr2 86509267 . G A 838.79 PASS AC=1;AF=0.655;AN=2;DP=2302;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant13-variant14-variant17-variant19-variant21-variant23-variant24-variant26-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,39:84:99:894,0,1137:22,23,21,18 chr2 86509388 . T G 590.8 PASS AC=1;AF=0.677;AN=2;DP=1948;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant17-variant19-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,25:61:99:633,0,913:15,21,8,17 chr2 86678378 . C T 417.81 PASS AC=1;AF=0.5;AN=2;DP=27;FS=1.792;FractionInformativeReads=1;MQ=60;MQRankSum=1.391;QD=15.47;ReadPosRankSum=1.732;SOR=1.449;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:12,15:27:99:446,0,315:4,8,3,12 chr2 86683642 . A G 280.08 PASS AC=1;AF=0.756;AN=2;DP=1521;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,17:40:99:361,0,557:11,12,8,9 chr2 86683901 . G C 712.62 PASS AC=1;AF=0.5;AN=2;DP=691;MQ=60;set=variant-variant7-variant8-variant9-variant11-variant16-variant23-variant26-variant28-variant35-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:22,19:41:99:509,0,665:18,4,14,5 chr2 86691250 . G A 1304.11 PASS AC=1;AF=0.756;AN=2;DP=4256;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:69,42:111:99:906,0,1644:29,40,19,23 chr2 86693826 . T C 2128.67 PASS AC=1;AF=0.5;AN=2;DP=2491;MQ=60;set=variant-variant7-variant8-variant9-variant11-variant16-variant23-variant26-variant28-variant35-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:100,81:181:99:1854,0,2369:49,51,39,42 chr2 86707504 . T C 437.79 PASS AC=1;AF=0.768;AN=2;DP=3368;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,36:82:99:823,0,1074:20,26,17,19 chr2 86712731 . G C 225.37 PASS AC=1;AF=0.536;AN=2;DP=303;FractionInformativeReads=1;MQ=60;set=variant-variant7-variant8-variant9-variant11-variant16-variant23-variant26-variant28-variant35-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:13,3:16:87:87,0,376:10,3,3,0 chr2 86712820 . A T 1110.28 PASS AC=1;AF=0.536;AN=2;DP=1237;MQ=60;set=variant-variant7-variant8-variant9-variant11-variant16-variant23-variant26-variant28-variant35-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:51,45:96:99:1155,0,1275:31,20,31,14 chr2 86717002 . CTG C 558.95 PASS AC=1;AF=0.5;AN=2;DP=409;MQ=60;set=variant-variant7-variant8-variant9-variant11-variant16-variant23-variant26-variant28-variant35-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:12,13:25:99:469,0,439:3,9,2,11 chr2 86733287 . C T 208.69 PASS AC=1;AF=0.536;AN=2;DP=610;FractionInformativeReads=1;MQ=60;set=variant-variant7-variant8-variant9-variant11-variant16-variant23-variant26-variant28-variant35-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:21,19:40:99:495,0,608:6,15,5,14 chr2 86756209 . C G 658.38 PASS AC=1;AF=0.756;AN=2;DP=2039;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,19:52:99:487,0,948:25,8,13,6 chr2 86756381 . T G 2301.12 PASS AC=1;AF=0.536;AN=2;DP=2638;MQ=60;set=variant-variant7-variant8-variant9-variant11-variant16-variant23-variant26-variant28-variant35-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:111,118:229:99:2840,0,2743:59,52,58,60 chr2 86790525 . AG A 2022.17 PASS AC=1;AF=0.538;AN=2;DP=2054;MQ=60;set=variant-variant7-variant8-variant9-variant16-variant23-variant26-variant28-variant35-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:91,80:171:99:2481,0,2882:37,54,39,41 chr2 86790716 . C A 254.95 PASS AC=1;AF=0.538;AN=2;DP=383;MQ=60;set=variant-variant7-variant8-variant9-variant16-variant23-variant26-variant28-variant35-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:12,14:26:99:493,0,299:5,7,3,11 chr2 86839316 . G A 932.84 PASS AC=1;AF=0.5;AN=2;DP=90;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.533;QD=10.36;ReadPosRankSum=-1.826;SOR=0.712;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:47,43:90:99:961,0,1195:26,21,24,19 chr2 86850022 . T C 808.4 PASS AC=1;AF=0.764;AN=2;DP=4875;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:73,74:147:99:1691,0,1879:35,38,34,40 chr2 86947783 . C T 4365.68 PASS AC=2;AF=0.793;AN=2;DP=6719;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,205:206:99:6028,604,0:0,1,127,78 chr2 86978895 . G T 196.77 PASS AC=1;AF=0.771;AN=2;DP=232;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,2:5:67:67,0,118:3,0,2,0 chr2 86979093 . G A 1488.09 PASS AC=1;AF=0.75;AN=2;DP=2422;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,42:71:99:908,0,671:13,16,20,22 chr2 86992337 . T TAA 3273.38 PASS AC=1;AF=0.744;AN=2;DP=2772;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,29:54:99:1142,0,1025:9,16,12,17 chr2 86998659 . CTT CT,CTTT,C 758.29 PASS AC=1,0,0;AF=0.488,0.024,0.012;AN=2;DP=2027;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:46:99:15,6,17,8 chr2 87002229 . C T 1665.54 PASS AC=1;AF=0.744;AN=2;DP=3339;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,63:109:99:1608,0,1027:24,22,29,34 chr2 87002706 . G A 529.46 PASS AC=1;AF=0.75;AN=2;DP=1151;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,19:41:99:442,0,547:12,10,8,11 chr2 87003028 . C T 1890.7 PASS AC=1;AF=0.744;AN=2;DP=2549;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,24:71:99:691,0,1307:27,20,18,6 chr2 87003197 . C G 13854.3 PASS AC=1;AF=0.744;AN=2;DP=15131;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:180,176:356:99:4024,0,4738:108,72,96,80 chr2 87015633 . T TGA 1265.36 PASS AC=1;AF=0.81;AN=2;DP=2230;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,25:69:99:897,0,1750:29,15,18,7 chr2 87018452 . A G 1124.19 PASS AC=1;AF=0.756;AN=2;DP=2503;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,37:69:99:1024,0,838:14,18,17,20 chr2 87048702 . T G 526.1 PASS AC=1;AF=0.932;AN=2;DP=1550;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:17,20:37:99:592,0,446:12,5,15,5 chr2 87060318 . CT C,CTT 48.76 PASS AC=1,0;AF=0.386,0.136;AN=2;DP=767;set=variant-filterInvariant4-filterInvariant5-filterInvariant9-variant10-filterInvariant11-variant14-filterInvariant17-variant19-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant28-filterInvariant29-variant30-filterInvariant32-variant34-variant35-variant36-variant39-filterInvariant40-variant43 GT:DP:GQ:SB 0/1:39:99:7,12,4,16 chr2 87069379 . G A 567.37 PASS AC=1;AF=0.716;AN=2;DP=898;FractionInformativeReads=1;set=variant-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant26-variant27-variant28-filterInvariant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,9:21:99:228,0,359:2,10,2,7 chr2 87069431 . C T 481.22 PASS AC=1;AF=0.716;AN=2;DP=978;set=filterInvariant-filterInvariant4-variant5-variant6-variant7-filterInvariant8-variant10-variant11-filterInvariant12-filterInvariant14-filterInvariant15-variant16-variant17-filterInvariant18-variant19-variant21-filterInvariant22-variant23-filterInvariant25-variant26-variant27-variant28-filterInvariant29-variant30-variant31-variant32-filterInvariant33-filterInvariant35-variant36-variant37-variant38-variant39-filterInvariant40-variant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:14,12:26:99:268,0,332:8,6,6,6 chr2 87073743 . A G 140.45 PASS AC=1;AF=0.716;AN=2;DP=1246;set=variant-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,14:44:99:353,0,753:18,12,11,3 chr2 87085598 . T C 135.83 PASS AC=1;AF=0.675;AN=2;DP=659;set=variant-filterInvariant7-variant8-variant11-variant12-variant15-variant16-variant17-variant19-variant23-variant25-variant28-filterInvariant29-filterInvariant30-variant31-filterInvariant35-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,6:54:59:59,0,1330:17,31,0,6 chr2 87092750 . CA C,CAA,CAAA 40.62 PASS AC=0,0,2;AF=0.1,0.3,0.4;AN=2;DP=27;set=variant3-variant7-variant21-variant27-variant35 GT:DP:GQ:SB 3/3:3:9:0,0,1,2 chr2 87169316 . T G 323.36 PASS AC=1;AF=0.571;AN=2;DP=829;FractionInformativeReads=1;set=variant-filterInvariant5-variant7-variant8-variant10-filterInvariant12-variant13-variant14-variant15-filterInvariant16-variant17-variant18-variant19-variant23-variant27-variant29-variant35-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:29,24:53:99:465,0,797:21,8,13,11 chr2 87169417 . C T 561.24 PASS AC=1;AF=0.5;AN=2;DP=811;FractionInformativeReads=1;set=variant9-variant14-variant19-variant20-variant24-variant30-variant34-variant35-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:36,70:106:99:1663,0,612:15,21,36,34 chr2 87205161 . A C 77.64 PASS AC=1;AF=0.583;AN=2;DP=41;FractionInformativeReads=1;set=variant7-variant13-variant31-variant35-variant36-variant42 GT:AD:DP:GQ:PL:SB 0/1:4,5:9:72:118,0,72:2,2,1,4 chr2 87276811 . T C 153.73 DRAGENHardSNP AC=1;AF=0.556;AN=2;DP=759;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:22,17:39:99:344,0,437:10,12,9,8 chr2 87303060 . C G 1356.13 PASS AC=1;AF=0.556;AN=2;DP=4094;set=variant-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant25-variant27-variant28-variant29-variant31-variant35-variant37-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:83,86:169:99:1913,0,2043:47,36,44,42 chr2 87345696 . A C 88.9 PASS AC=1;AF=0.522;AN=2;DP=482;FractionInformativeReads=1;set=variant-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant27-variant28-variant29-variant30-variant31-variant35-variant37-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,21:33:99:472,0,240:5,7,9,12 chr2 87355912 . C T 40.02 PASS AC=1;AF=0.5;AN=2;DP=2086;set=filterInvariant-filterInvariant7-variant9-filterInvariant11-filterInvariant13-filterInvariant15-filterInvariant18-variant19-variant22-variant27-variant28-variant30-filterInvariant31-variant32-variant33-filterInvariant34-variant35-filterInvariant37-filterInvariant39-variant40-filterInvariant41-filterInvariant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:60,25:85:99:410,0,1366:29,31,16,9 chr2 87356024 . C A 57.33 PASS AC=1;AF=0.5;AN=2;DP=1995;FractionInformativeReads=1;set=filterInvariant-variant2-filterInvariant3-filterInvariant5-filterInvariant6-variant7-filterInvariant8-variant9-filterInvariant10-variant11-variant13-variant14-filterInvariant15-variant16-variant18-variant19-variant22-variant23-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-filterInvariant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,33:60:99:696,0,655:9,18,14,19 chr2 87371260 . T C 455.82 PASS AC=1;AF=0.545;AN=2;DP=1510;set=variant-variant2-variant5-variant6-variant7-variant8-variant10-filterInvariant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,20:46:99:426,0,587:11,15,8,12 chr2 87371339 . C T 153.94 PASS AC=1;AF=0.58;AN=2;DP=253;FS=0;FractionInformativeReads=1;set=variant-variant2-filterInvariant5-variant7-variant8-variant13-variant14-filterInvariant15-variant17-filterInvariant18-filterInvariant19-variant21-variant25-filterInvariant27-variant28-variant29-variant30-variant31-variant33-variant35-variant37-filterInvariant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,3:12:66:66,0,272:0,9,0,3 chr2 87376944 . G A 358.27 PASS AC=1;AF=0.569;AN=2;DP=1558;set=variant-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant25-variant27-variant28-variant29-variant30-variant31-variant35-variant37-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,23:45:99:519,0,521:11,11,13,10 chr2 87616737 . T C 57.73 DRAGENHardSNP AC=1;AF=0.767;AN=2;DP=473;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:5,3:8:61:61,0,123:0,5,0,3 chr2 88272798 . C T 208.58 PASS AC=1;AF=0.5;AN=2;DP=2069;set=variant-variant5-variant7-variant8-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant23-variant25-variant27-variant29-variant35-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:94,62:156:99:1184,0,2035:48,46,35,27 chr2 88289368 . G A 423.77 PASS AC=2;AF=0.932;AN=2;DP=771;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:680,78,0:0,0,12,14 chr2 88328163 . CT C,CTT,CTTT,CTTTT,CTTTTT 159.35 PASS AC=0,1,0,0,0;AF=0.032,0.194,0.274,0.032,0.016;AN=2;DP=1510;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant16-variant17-variant20-variant21-variant23-variant24-variant25-variant26-variant27-filterInvariant28-variant29-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant43 GT:DP:GQ:SB 0/2:31:74:4,7,6,14 chr2 88328208 . G A 109.41 PASS AC=2;AF=0.756;AN=2;DP=589;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:445,33,0:0,0,0,11 chr2 88367176 . C G 136.72 PASS AC=1;AF=0.5;AN=2;DP=123;FractionInformativeReads=1;MQ=60;set=variant2-variant8-variant9-variant13-variant17-variant21-variant22-variant27-variant30-variant33-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,6:10:99:159,0,145:3,1,4,2 chr2 88383970 . G A 1067.58 PASS AC=1;AF=0.5;AN=2;DP=682;FractionInformativeReads=1;MQ=60;set=variant13-variant19-variant21-variant22-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:66,57:123:99:1522,0,1701:25,41,23,34 chr2 88387403 . C A 649.18 PASS AC=1;AF=0.71;AN=2;DP=2389;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant34-variant35-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,45:97:99:1038,0,1296:30,22,30,15 chr2 88396080 . A C 1123.95 PASS AC=1;AF=0.667;AN=2;DP=2992;MQ=60;set=variant-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant24-variant25-variant29-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,58:111:99:1523,0,1223:24,29,31,27 chr2 88396120 . G A 1620.26 PASS AC=1;AF=0.667;AN=2;DP=2978;MQ=60;set=variant-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant24-variant25-variant29-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,63:111:99:2448,0,1996:22,26,31,32 chr2 88396123 . C G 1617.25 PASS AC=1;AF=0.667;AN=2;DP=2990;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant24-variant25-variant29-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,60:112:99:2411,0,2084:24,28,30,30 chr2 88396174 . T C 1281.55 PASS AC=1;AF=0.667;AN=2;DP=2909;MQ=60;set=variant-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant24-variant25-variant29-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,66:123:99:1657,0,1332:31,26,32,34 chr2 88408172 . A G 265.56 PASS AC=2;AF=0.756;AN=2;DP=1158;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1265,117,0:0,0,11,28 chr2 88409719 . A AGAGT,AGTGT,AGAGTGTGTGT,AGAGTGTGTGTGT,AGAGTGTGT,AGT,AGTGTGT,AGAGTGTGTGTGTGT 887.92 PASS AC=1,0,1,0,0,0,0,0;AF=0.131,0.214,0.298,0.095,0.071,0.012,0.024,0.012;AN=2;DP=1293;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/3:26:99:1,0,18,7 chr2 88410102 . C G 560.39 PASS AC=2;AF=0.756;AN=2;DP=2456;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,80:80:99:2417,240,0:0,0,35,45 chr2 88410168 . A G 726.61 PASS AC=2;AF=0.756;AN=2;DP=1905;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:1600,144,0:0,0,20,28 chr2 88410731 . A G 2004.28 PASS AC=2;AF=0.756;AN=2;DP=4981;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,134:135:99:4265,394,0:0,1,79,55 chr2 88411305 . C T 630.09 PASS AC=2;AF=0.652;AN=2;DP=1621;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant34-variant35-variant36-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1607,147,0:0,0,26,23 chr2 88411793 . C A 1098.72 PASS AC=2;AF=0.756;AN=2;DP=2625;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:2249,195,0:0,0,31,34 chr2 88423374 . T C 998.06 PASS AC=2;AF=1;AN=2;DP=1575;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1277,123,0:0,0,21,20 chr2 88423621 . C T 1188.92 PASS AC=2;AF=0.989;AN=2;DP=2123;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,52:52:99:1663,156,0:0,0,26,26 chr2 88469770 . G C 807.73 PASS AC=2;AF=0.854;AN=2;DP=2589;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:2203,228,0:0,0,35,41 chr2 88469863 . G C 2362.3 PASS AC=2;AF=0.849;AN=2;DP=4174;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,109:110:99:3884,285,0:1,0,40,69 chr2 88469891 . G T 492.82 PASS AC=1;AF=0.542;AN=2;DP=889;MQ=60;set=variant5-variant10-variant13-variant15-variant21-variant23-variant26-variant31-variant35-variant36-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:66,30:96:99:655,0,1658:29,37,9,21 chr2 88469933 . TCGCGCCCCGCGCCC T,TCGCGCCCCGCGCCCCGCGCCCCGCGCCCCGCGCCC,TCGCGCCCCGCGCCCCGCGCCC,TCGCGCCC 738.45 PASS AC=1,0,0,0;AF=0.571,0.012,0.214,0.024;AN=2;DP=3109;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:44:99:2,5,16,21 chr2 88471894 . G T 437.53 PASS AC=1;AF=0.583;AN=2;DP=756;FractionInformativeReads=1;MQ=60;set=variant5-variant9-variant10-variant13-variant15-variant21-variant23-variant26-variant31-variant32-variant34-variant35-variant36-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,15:35:99:448,0,502:9,11,4,11 chr2 88472141 . G A 399.71 PASS AC=1;AF=0.588;AN=2;DP=451;FractionInformativeReads=1;MQ=60;set=variant5-variant9-variant10-variant13-variant15-variant21-variant23-variant26-variant31-variant32-variant34-variant35-variant36-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,14:22:99:345,0,174:5,3,8,6 chr2 88472249 . G C 447.71 PASS AC=1;AF=0.625;AN=2;DP=1206;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant25-variant27-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:21,16:37:99:395,0,611:14,7,9,7 chr2 88472280 . C T 1217.1 PASS AC=2;AF=0.943;AN=2;DP=1918;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1351,131,0:0,0,23,21 chr2 88472791 . G A 1459.83 PASS AC=2;AF=0.943;AN=2;DP=2222;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:1817,171,0:0,0,32,25 chr2 88472925 . A G 752.09 PASS AC=1;AF=0.583;AN=2;DP=1456;MQ=60;set=variant5-variant9-variant10-variant13-variant15-variant21-variant23-variant26-variant31-variant32-variant34-variant35-variant36-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,31:96:99:726,0,1453:32,33,15,16 chr2 88474370 . A G 3157.66 PASS AC=2;AF=0.943;AN=2;DP=4675;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,126:126:99:3883,378,0:0,0,58,68 chr2 88485392 . G C 4455.81 PASS AC=2;AF=0.943;AN=2;DP=4697;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,118:118:99:3951,354,0:0,0,47,71 chr2 88485968 . A AC 1166.76 PASS AC=2;AF=0.807;AN=2;DP=2364;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1854,171,0:0,0,27,29 chr2 88748390 . A T 2826.13 PASS AC=2;AF=0.636;AN=2;DP=3748;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,126:126:99:3739,378,0:0,0,52,74 chr2 88751751 . A AG 893.91 PASS AC=2;AF=1;AN=2;DP=1353;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1536,126,0:0,0,10,32 chr2 88824015 . A T 192.5 PASS AC=2;AF=0.667;AN=2;DP=154;FractionInformativeReads=1;MQ=60;set=variant5-variant7-variant9-variant12-variant14-variant17-variant18-variant19-variant23-variant24-variant26-variant27-variant28-variant30-variant31-variant33-variant35-variant37-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:229,18,0:0,0,5,1 chr2 88824104 . A G 109.71 PASS AC=2;AF=0.583;AN=2;DP=390;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant10-variant14-variant18-variant19-variant23-variant26-variant27-variant31-variant33-variant34-variant35-variant37-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:872,87,0:0,0,16,13 chr2 88825315 . GT GTT,G 186.93 PASS AC=1,0;AF=0.35,0.2;AN=2;DP=1601;MQ=60;set=variant-filterInvariant3-variant4-variant5-variant6-variant8-variant9-variant10-filterInvariant11-variant13-variant14-variant17-variant18-variant19-filterInvariant23-variant24-variant26-variant27-variant29-variant31-variant33-variant34-variant35-variant37-variant38-variant40-filterInvariant41-filterInvariant42-variant43-filterInvariant44 GT:DP:GQ:SB 0/1:33:99:4,8,6,15 chr2 88825334 . CAAG C 365.44 PASS AC=2;AF=0.553;AN=2;DP=649;MQ=60;set=variant-variant4-variant5-variant10-variant13-variant14-variant18-variant19-variant23-variant26-variant27-variant31-variant33-variant34-variant35-variant37-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:900,60,0:0,0,2,18 chr2 88826184 . AT A 272.17 PASS AC=2;AF=0.553;AN=2;DP=477;MQ=60;set=variant-variant4-variant5-variant10-variant13-variant14-variant18-variant19-variant23-variant26-variant27-variant31-variant33-variant34-variant35-variant37-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:458,48,0:0,0,2,14 chr2 88826219 . G A 121.65 PASS AC=2;AF=0.6;AN=2;DP=272;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant9-variant10-variant13-variant14-variant17-variant18-variant19-variant23-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant37-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:420,36,0:0,0,2,10 chr2 88870632 . A T 649.19 PASS AC=2;AF=0.756;AN=2;DP=904;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:53:534,53,0:0,0,5,13 chr2 88874891 . C A 3492.08 PASS AC=2;AF=0.75;AN=2;DP=5412;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,122:122:99:3583,365,0:0,0,58,64 chr2 88875981 . TA T 36.59 PASS AC=1;AF=0.5;AN=2;DP=81;FractionInformativeReads=1;MQ=60;set=variant4-variant24-variant31-variant35-filterInvariant41 GT:AD:DP:GQ:PL:SB 0/1:5,12:17:90:269,0,90:5,0,7,5 chr2 88882942 . T A 1247.28 PASS AC=2;AF=0.583;AN=2;DP=2208;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant10-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,64:64:99:2106,192,0:0,0,46,18 chr2 88895123 . T C 3091.6 PASS AC=2;AF=0.756;AN=2;DP=4515;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,118:118:99:3330,354,0:0,0,55,63 chr2 88895351 . T C 2065.26 PASS AC=2;AF=0.75;AN=2;DP=2779;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,74:74:99:2280,222,0:0,0,42,32 chr2 89050126 . T G 912.3 PASS AC=2;AF=0.589;AN=2;DP=1802;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant10-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,54:55:99:1826,119,0:1,0,32,22 chr2 89082373 . G A 72.78 PASS AC=1;AF=0.5;AN=2;DP=330;FractionInformativeReads=1;set=filterInvariant28-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:98,17:115:99:458,0,6738:49,49,14,3 chr2 89082379 . G A 498.66 PASS AC=1;AF=0.5;AN=2;DP=352;FractionInformativeReads=1;set=variant28-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:101,22:123:99:656,0,7321:51,50,17,5 chr2 89082381 . C T 644.95 PASS AC=1;AF=0.5;AN=2;DP=359;FractionInformativeReads=1;set=variant28-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:103,23:126:99:1025,0,7581:52,51,18,5 chr2 89082388 . G T 766.22 PASS AC=1;AF=0.5;AN=2;DP=386;FractionInformativeReads=1;set=variant28-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:105,33:138:99:1103,0,7833:52,53,22,11 chr2 89082399 . G A 1227.81 PASS AC=1;AF=0.5;AN=2;DP=399;FractionInformativeReads=1;set=variant28-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:106,38:144:99:1274,0,7967:52,54,24,14 chr2 89082404 . T C 1245.83 PASS AC=1;AF=0.5;AN=2;DP=412;FractionInformativeReads=1;set=variant28-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:104,41:145:99:1435,0,7936:49,55,25,16 chr2 89082422 . A G 1274.04 PASS AC=1;AF=0.5;AN=2;DP=421;FractionInformativeReads=1;set=variant28-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:105,48:153:99:1524,0,7890:48,57,28,20 chr2 89082471 . T C 220.23 PASS AC=1;AF=0.5;AN=2;DP=4845;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-filterInvariant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-filterInvariant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:76,54:130:99:1958,0,5049:32,44,26,28 chr2 89082495 . T G,A 256.23 PASS AC=0,1;AF=0.444,0.056;AN=2;DP=3623;set=variant-variant2-variant4-variant5-variant6-filterInvariant7-filterInvariant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-filterInvariant19-variant20-variant21-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-filterInvariant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:110:99:22,38,22,28 chr2 89082503 . C T 271.26 PASS AC=1;AF=0.5;AN=2;DP=3937;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-filterInvariant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,48:102:99:1895,0,4331:20,34,21,27 chr2 89082520 . G A 295.34 PASS AC=1;AF=0.5;AN=2;DP=2367;FractionInformativeReads=1;set=variant-variant3-variant4-variant5-variant7-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-filterInvariant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:45,37:82:99:1457,0,3479:17,28,14,23 chr2 89082536 . T G 154.47 PASS AC=1;AF=0.5;AN=2;DP=1672;set=variant-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:31,20:51:99:746,0,1890:9,22,6,14 chr2 89082549 . G C 163.5 PASS AC=1;AF=0.5;AN=2;DP=1299;FractionInformativeReads=1;set=variant-filterInvariant3-variant4-variant5-variant7-variant9-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-filterInvariant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:25,12:37:99:510,0,1388:8,17,3,9 chr2 89082552 . C T 118.5 PASS AC=1;AF=0.5;AN=2;DP=1223;FractionInformativeReads=1;set=variant-filterInvariant3-variant4-variant5-variant7-variant9-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-filterInvariant27-variant28-variant29-filterInvariant31-variant32-variant34-variant35-variant36-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:24,11:35:99:387,0,1331:7,17,2,9 chr2 89082554 . C T 121.51 PASS AC=1;AF=0.5;AN=2;DP=1163;FractionInformativeReads=1;set=variant-filterInvariant3-variant4-variant5-variant7-variant9-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-filterInvariant34-variant35-variant36-variant39-filterInvariant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:23,8:31:99:390,0,1264:7,16,1,7 chr2 89082565 . C G 52.58 PASS AC=1;AF=0.5;AN=2;DP=764;FractionInformativeReads=1;set=variant-filterInvariant3-filterInvariant4-variant7-variant9-variant11-variant13-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-filterInvariant31-variant34-variant35-variant36-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:19,7:26:99:237,0,920:6,13,0,7 chr2 89084327 . G C 1472.47 PASS AC=2;AF=0.784;AN=2;DP=1612;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1411,120,0:0,0,18,22 chr2 89100619 . C T 136.89 PASS AC=1;AF=0.5;AN=2;DP=4656;set=filterInvariant-variant2-filterInvariant3-variant4-variant5-variant6-variant7-variant8-filterInvariant9-variant10-filterInvariant11-variant12-filterInvariant13-filterInvariant14-variant15-filterInvariant16-variant17-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-filterInvariant39-filterInvariant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:91,20:111:99:252,0,2499:53,38,20,0 chr2 89100657 . G A 547.36 PASS AC=1;AF=0.5;AN=2;DP=6848;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:106,48:154:99:1014,0,2638:55,51,33,15 chr2 89100697 . C G 1539.39 PASS AC=1;AF=0.5;AN=2;DP=7393;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:104,73:177:99:2752,0,4113:47,57,42,31 chr2 89100701 . A G 1539.39 PASS AC=1;AF=0.5;AN=2;DP=7409;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:102,74:176:99:2819,0,4085:46,56,42,32 chr2 89100725 . G A 1701.57 PASS AC=1;AF=0.5;AN=2;DP=7008;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:86,79:165:99:2950,0,3346:35,51,41,38 chr2 89100759 . A C 1610.33 PASS AC=1;AF=0.5;AN=2;DP=5631;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:69,69:138:99:2637,0,2590:22,47,27,42 chr2 89100764 . A G 1545.53 PASS AC=1;AF=0.5;AN=2;DP=5229;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:61,68:129:99:2652,0,2459:19,42,26,42 chr2 89100799 . GA G 355.9 PASS AC=1;AF=0.5;AN=2;DP=75;FS=4.442;FractionInformativeReads=0.893;MQ=56.82;MQRankSum=4.611;QD=4.75;ReadPosRankSum=0.118;SOR=0.276;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:48,19:67:99:393,0,1771:10,38,6,13 chr2 89100805 . A G 735.26 PASS AC=1;AF=0.5;AN=2;DP=2839;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:28,39:67:99:1473,0,1041:6,22,10,29 chr2 89100806 . A G 148.21 PASS AC=1;AF=0.5;AN=2;DP=2024;set=variant-variant2-variant3-filterInvariant4-variant5-variant6-variant7-variant8-variant9-filterInvariant10-filterInvariant11-variant12-variant14-variant15-variant16-filterInvariant17-filterInvariant18-variant19-variant23-filterInvariant25-variant26-variant28-filterInvariant29-filterInvariant30-filterInvariant32-variant33-variant34-variant35-variant38-variant39-filterInvariant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:52,15:67:99:309,0,1810:12,40,4,11 chr2 89100808 . C A 735.26 PASS AC=1;AF=0.5;AN=2;DP=2673;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:26,38:64:99:1473,0,1041:6,20,10,28 chr2 89100816 . A G 544.42 PASS AC=1;AF=0.5;AN=2;DP=2302;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:22,30:52:99:1274,0,869:3,19,7,23 chr2 89100865 . T C 103.93 PASS AC=1;AF=0.5;AN=2;DP=725;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,9:13:99:290,0,124:0,4,1,8 chr2 89103755 . C A 1504.99 PASS AC=1;AF=0.5;AN=2;DP=1562;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:22,13:35:99:522,0,906:12,10,6,7 chr2 89103761 . C G 1697.62 PASS AC=1;AF=0.5;AN=2;DP=1694;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:22,15:37:99:561,0,945:13,9,7,8 chr2 89103765 . A C 869.7 PASS AC=1;AF=0.5;AN=2;DP=1811;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:22,15:37:99:564,0,903:13,9,7,8 chr2 89103806 . AT A 278.08 PASS AC=1;AF=0.5;AN=2;DP=1832;set=variant2-filterInvariant4-variant5-variant6-variant7-variant8-variant9-variant10-filterInvariant11-filterInvariant15-filterInvariant16-filterInvariant19-variant21-filterInvariant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-filterInvariant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,10:54:99:177,0,1293:23,21,4,6 chr2 89103862 . T C 811.44 PASS AC=1;AF=0.5;AN=2;DP=2599;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:36,17:53:99:370,0,961:17,19,6,11 chr2 89103894 . C T 408.29 PASS AC=1;AF=0.5;AN=2;DP=2179;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,12:43:99:411,0,1186:15,16,4,8 chr2 89103904 . C T 637.52 PASS AC=1;AF=0.557;AN=2;DP=1961;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:30,9:39:99:330,0,1185:13,17,3,6 chr2 89104251 . G GTT 287.42 PASS AC=1;AF=0.5;AN=2;DP=892;set=variant-filterInvariant3-filterInvariant4-variant9-variant10-filterInvariant12-variant17-variant23-variant25-filterInvariant27-variant29-variant31-filterInvariant32-variant34-filterInvariant35-variant37-filterInvariant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,6:62:83:83,0,2333:35,21,6,0 chr2 89104252 . A T 451.93 PASS AC=1;AF=0.5;AN=2;DP=423;set=variant-variant17-variant23-variant29-variant31-variant34-variant35-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,6:56:99:182,0,2117:29,21,6,0 chr2 89104259 . A C 910.14 PASS AC=1;AF=0.5;AN=2;DP=2465;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,16:70:99:477,0,2150:30,24,14,2 chr2 89104266 . G A 1021.56 PASS AC=1;AF=0.5;AN=2;DP=2793;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,11:75:99:180,0,2637:40,24,8,3 chr2 89104333 . C T 1050.5 PASS AC=1;AF=0.5;AN=2;DP=4724;set=variant2-variant4-variant5-variant6-filterInvariant7-variant8-variant9-filterInvariant10-filterInvariant11-variant15-variant16-variant17-variant19-filterInvariant20-variant21-filterInvariant23-variant25-variant26-variant27-filterInvariant28-filterInvariant29-filterInvariant30-variant31-variant32-variant33-variant34-variant35-filterInvariant36-variant37-variant38-variant39-filterInvariant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:82,56:138:99:1071,0,2776:42,40,30,26 chr2 89104334 . T G,A 2489.17 PASS AC=1,0;AF=0.5,0.023;AN=2;DP=5893;set=Intersection GT:DP:GQ:SB 0/1:135:99:24,26,46,39 chr2 89104362 . C T 1042.42 PASS AC=1;AF=0.5;AN=2;DP=4380;set=variant2-variant4-variant5-variant6-filterInvariant7-variant8-variant9-filterInvariant10-filterInvariant11-variant15-variant16-variant17-variant19-filterInvariant20-variant21-variant25-variant26-variant27-variant28-filterInvariant29-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-filterInvariant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:77,62:139:99:1179,0,2458:35,42,30,32 chr2 89104364 . A G 2873.31 PASS AC=1;AF=0.5;AN=2;DP=5824;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:42,97:139:99:3312,0,830:16,26,48,49 chr2 89104405 . C A 286.12 PASS AC=1;AF=0.5;AN=2;DP=704;set=variant8-filterInvariant17-filterInvariant20-variant27-filterInvariant35-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:91,18:109:99:142,0,2460:33,58,7,11 chr2 89104978 . C G,T 499.26 PASS AC=1,0;AF=0.375,0.125;AN=2;DP=4603;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-filterInvariant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant20-variant22-variant23-variant24-variant25-variant26-filterInvariant27-filterInvariant28-variant29-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-filterInvariant34-filterInvariant35-variant36-filterInvariant37-filterInvariant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:103:99:35,57,5,6 chr2 89105008 . T C 895.02 PASS AC=1;AF=0.5;AN=2;DP=4304;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:60,25:85:99:850,0,1620:20,40,11,14 chr2 89105019 . A C 901.79 PASS AC=1;AF=0.5;AN=2;DP=3857;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:47,24:71:99:867,0,1292:16,31,10,14 chr2 89105045 . C T 437.45 PASS AC=1;AF=0.5;AN=2;DP=1063;set=variant2-variant4-variant5-variant8-variant9-variant15-variant17-variant27-variant28-filterInvariant29-filterInvariant30-variant31-variant32-variant34-variant35-filterInvariant37-variant38-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:38,9:47:99:204,0,1203:11,27,4,5 chr2 89157129 . G A 97485.2 PASS AC=2;AF=0.966;AN=2;DP=129362;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:173,2719:2892:99:83802,3294,0:83,90,1621,1098 chr2 89157196 . C CGTTTGAG,CGTTTGAT,CGTTTG,CGTTTGATCTCCA,CATTTGAT,CGTTTGATCT,CGTTTGACCTCCACCTTGGTA,CGTTTGATCTCCACCTTGGTACCAGGGCCGAAAGTGAATGGAGTACTATAATATTGCTGACAGTAATAAACTGCCACATCTT 19807 PASS AC=0,0,0,1,0,0,0,0;AF=0.036,0.107,0.143,0.107,0.036,0.036,0.036,0.036;AN=2;DP=20138;set=variant4-variant7-filterInvariant8-filterInvariant10-variant13-filterInvariant16-variant22-variant26-filterInvariant28-variant32-filterInvariant35-filterInvariant36-filterInvariant38-variant43 GT:DP:GQ:SB 0/4:1104:99:734,262,11,97 chr2 89160889 . G T 5611.65 PASS AC=2;AF=0.659;AN=2;DP=2942;MQ=60;set=variant4-variant5-variant8-variant9-variant11-variant12-variant13-variant14-variant18-variant19-variant20-variant21-variant23-variant26-variant28-variant31-variant33-variant34-variant35-variant36-variant38-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,125:125:99:3776,374,0:0,0,63,62 chr2 89161322 . C G 5726.86 PASS AC=2;AF=0.646;AN=2;DP=4428;MQ=60;set=variant4-variant5-variant8-variant9-variant11-variant12-variant13-variant14-variant18-variant19-variant20-variant21-variant23-variant26-variant27-variant28-variant31-variant33-variant34-variant35-variant36-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,168:170:99:5001,460,0:1,1,95,73 chr2 89161547 . A G 776.22 PASS AC=2;AF=0.615;AN=2;DP=1523;MQ=60;set=variant2-variant4-variant8-variant9-variant11-variant12-variant13-variant14-variant18-variant19-variant20-variant21-variant23-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:2045,165,0:0,0,9,46 chr2 89185449 . G C 84395.1 PASS AC=2;AF=0.92;AN=2;DP=108047;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:176,1995:2171:99:61390,1359,0:97,79,1079,916 chr2 89185477 . C G 150662 PASS AC=1;AF=0.784;AN=2;DP=137390;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:198,2619:2817:99:110046,0,901:103,95,1433,1186 chr2 89185492 . C T 160266 PASS AC=1;AF=0.83;AN=2;DP=153774;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:209,2936:3145:99:117589,0,347:107,102,1590,1346 chr2 89185519 . G C 128388 PASS AC=2;AF=0.966;AN=2;DP=173121;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:196,3357:3553:99:98284,4506,0:96,100,1764,1593 chr2 89185552 . C T 121320 PASS AC=2;AF=0.966;AN=2;DP=173346;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:194,3377:3571:99:97182,4499,0:101,93,1672,1705 chr2 89185668 . CTCCCACAGTG CATCCCACAGTG,CATTCCCACAGTG,CATTCACTTTCCCACAGTG,CAGTCCCACAGTG,C,CATTTACTTTCCCACAGTG,CATTCACTTCCCACAGTG,CCTTCCCACAGTG 4447.73 PASS AC=0,1,0,0,0,0,0,0;AF=0.056,0.278,0.056,0.019,0.019,0.019,0.037,0.019;AN=2;DP=47262;set=variant2-variant3-filterInvariant4-filterInvariant6-filterInvariant8-filterInvariant9-variant10-filterInvariant12-variant13-filterInvariant14-variant17-filterInvariant18-filterInvariant19-filterInvariant20-variant21-variant23-filterInvariant24-filterInvariant25-variant27-variant28-filterInvariant29-filterInvariant34-filterInvariant35-filterInvariant36-variant38-filterInvariant39-variant41 GT:DP:GQ:SB 0/2:1185:99:768,250,9,158 chr2 89185674 . CAG C 4933.8 PASS AC=1;AF=0.5;AN=2;DP=1896;MQ=60;set=variant8-filterInvariant18-filterInvariant20-variant21-variant28-variant35 GT:AD:DP:GQ:PL:SB 0/1:186,49:235:99:1143,0,10236:91,95,0,49 chr2 89185677 . TGC T 4284.74 PASS AC=1;AF=0.5;AN=2;DP=1809;MQ=60;set=variant8-filterInvariant18-filterInvariant20-filterInvariant21-variant28-variant35 GT:AD:DP:GQ:PL:SB 0/1:181,47:228:99:1207,0,9763:88,93,0,47 chr2 89185683 . A G 3189.18 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=1411;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:181,45:226:99:1211,0,9581:89,92,0,45 chr2 89277798 . C G 141.62 PASS AC=1;AF=0.75;AN=2;DP=50;FractionInformativeReads=1;set=variant4-filterInvariant13-filterInvariant23-filterInvariant33-filterInvariant35-filterInvariant41 GT:AD:DP:GQ:PL:SB 0/1:5,5:10:99:99,0,134:5,0,3,2 chr2 89278103 . T C 2006.9 PASS AC=1;AF=0.591;AN=2;DP=2325;FractionInformativeReads=1;set=variant-variant4-variant6-variant7-variant9-variant10-variant12-variant13-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant30-variant31-variant33-variant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:77,47:124:99:1151,0,1773:37,40,25,22 chr2 89278489 . A C 2597.25 PASS AC=1;AF=0.571;AN=2;DP=3101;set=variant-variant4-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant30-variant31-variant33-variant34-variant35-variant37-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:70,39:109:99:955,0,1803:39,31,21,18 chr2 89339720 . G A 974.2 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=1719;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:116,61:177:99:1082,0,2734:81,35,39,22 chr2 89340106 . T TG 588.03 PASS AC=1;AF=0.5;AN=2;DP=424;set=variant4-variant7-variant14-variant16-variant27-variant30-variant33-variant34-variant35-filterInvariant42 GT:AD:DP:GQ:PL:SB 0/1:15,13:28:99:460,0,983:3,12,2,11 chr2 89340108 . A G 597.07 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=369;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:15,11:26:99:460,0,983:3,12,0,11 chr2 89340110 . C T 519.8 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=293;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:15,9:24:99:417,0,989:3,12,0,9 chr2 89340116 . T A 109.62 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=153;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:8,7:15:99:264,0,660:1,7,0,7 chr2 89340118 . A T 79.68 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=129;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:7,6:13:99:270,0,538:1,6,0,6 chr2 89459133 . C G 397.57 PASS AC=1;AF=0.5;AN=2;DP=157;FractionInformativeReads=1;set=variant4-variant12-variant16-variant31-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:11,12:23:99:360,0,426:11,0,10,2 chr2 89512819 . G C 100.14 PASS AC=1;AF=0.5;AN=2;DP=214;set=filterInvariant10-filterInvariant14-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:50,13:63:99:302,0,1384:34,16,13,0 chr2 89999076 . T C 470.82 PASS AC=2;AF=0.955;AN=2;DP=1611;set=variant-filterInvariant2-variant3-filterInvariant4-variant5-variant6-variant7-filterInvariant8-variant9-filterInvariant10-variant11-variant12-variant13-filterInvariant14-variant15-variant16-filterInvariant17-filterInvariant18-variant19-variant20-filterInvariant21-filterInvariant22-filterInvariant23-variant24-variant25-variant26-variant27-variant28-filterInvariant29-variant30-variant31-filterInvariant32-variant33-variant34-variant35-filterInvariant36-filterInvariant37-variant38-variant39-filterInvariant40-variant41-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:939,81,0:0,0,4,23 chr2 90008208 . T G 2296.05 PASS AC=1;AF=0.769;AN=2;DP=5131;set=variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:79,72:151:99:1903,0,1855:29,50,21,51 chr2 90008231 . C A 1369.26 PASS AC=1;AF=0.5;AN=2;DP=739;set=variant4-variant12-variant13-variant31-variant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,56:117:99:1244,0,1680:14,47,20,36 chr2 90008287 . A C 319.66 PASS AC=1;AF=0.729;AN=2;DP=1279;set=variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-filterInvariant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,15:37:99:472,0,670:3,19,1,14 chr2 90108416 . G A 921.29 PASS AC=2;AF=0.932;AN=2;DP=3946;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,101:101:99:2933,303,0:0,0,58,43 chr2 90121675 . T C 1146.02 PASS AC=1;AF=0.898;AN=2;DP=2780;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:40,25:65:99:748,0,1284:29,11,18,7 chr2 90138961 . C G 53.7 PASS AC=1;AF=0.5;AN=2;DP=118;FractionInformativeReads=1;set=variant2-variant4-variant5-variant8-variant9-variant14-variant19-variant21-variant23-variant35 GT:AD:DP:GQ:PL:SB 0/1:9,4:13:78:78,0,267:6,3,3,1 chr2 90139116 . G A 267.18 PASS AC=1;AF=0.5;AN=2;DP=2784;set=variant-variant2-filterInvariant3-variant6-filterInvariant9-variant10-filterInvariant11-variant12-filterInvariant13-variant14-variant18-filterInvariant19-filterInvariant20-filterInvariant22-variant23-filterInvariant26-filterInvariant27-variant28-variant29-filterInvariant30-filterInvariant32-filterInvariant35-filterInvariant36-variant37-filterInvariant39-filterInvariant40-filterInvariant41-filterInvariant42-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:100,17:117:97:97,0,2675:61,39,7,10 chr2 90154131 . C T 867.39 DRAGENHardSNP AC=1;AF=0.55;AN=2;DP=684;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:46,21:67:99:327,0,967:25,21,11,10 chr2 90154203 . G T 726.78 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=504;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:38,14:52:99:205,0,858:15,23,7,7 chr2 90154255 . G A 421.49 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=169;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:7,16:23:99:320,0,129:2,5,7,9 chr2 90193417 . A G 964.32 DRAGENHardSNP AC=1;AF=0.55;AN=2;DP=516;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:12,16:28:99:630,0,621:8,4,9,7 chr2 90193429 . T C 961.77 DRAGENHardSNP AC=1;AF=0.55;AN=2;DP=561;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:15,20:35:99:726,0,639:9,6,10,10 chr2 90211808 . T G 699.18 PASS AC=1;AF=0.5;AN=2;DP=801;FractionInformativeReads=1;set=variant4-variant7-variant14-variant16-variant27-variant30-variant34-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:57,27:84:99:882,0,2853:28,29,22,5 chr2 90211809 . C T 699.18 PASS AC=1;AF=0.5;AN=2;DP=808;FractionInformativeReads=1;set=variant4-variant7-variant14-variant16-variant27-variant30-variant34-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:58,26:84:99:882,0,2853:29,29,21,5 chr2 90211923 . A G 2001.83 PASS AC=1;AF=0.5;AN=2;DP=947;set=variant4-variant12-variant13-variant31-variant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:69,69:138:99:1670,0,1876:34,35,33,36 chr2 90212050 . G A 689.37 PASS AC=2;AF=0.66;AN=2;DP=1669;set=variant-variant4-variant6-variant7-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant22-variant24-variant25-variant27-variant30-variant31-variant33-variant34-variant35-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1995,159,0:0,0,24,29 chr2 90229260 . T C 3043.48 PASS AC=1;AF=0.55;AN=2;DP=1730;MQ=60;set=variant4-variant7-variant14-variant16-variant27-variant30-variant33-variant34-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:69,105:174:99:2619,0,1765:31,38,52,53 chr2 90259848 . T G 2225.56 PASS AC=1;AF=0.55;AN=2;DP=1799;set=variant4-variant7-variant14-variant16-variant27-variant30-variant33-variant34-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:101,98:199:99:2590,0,2548:60,41,61,37 chr2 90259965 . T C 4590.74 PASS AC=1;AF=0.5;AN=2;DP=2589;set=variant4-variant7-variant14-variant16-variant27-variant30-variant34-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:135,136:271:99:3540,0,3579:67,68,77,59 chr2 90260191 . T C 4461 PASS AC=1;AF=0.55;AN=2;DP=2850;set=variant4-variant7-variant14-variant16-variant27-variant30-variant33-variant34-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:144,164:308:99:4372,0,3665:68,76,65,99 chr2 90458538 . T C 1200.33 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=12807;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:186,115:301:99:2336,0,4279:127,59,83,32 chr2 90458594 . T C 4017.35 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=28619;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:352,319:671:99:6324,0,7035:196,156,186,133 chr2 90458745 . T C 1030.78 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=7326;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:67,76:143:99:1839,0,1542:15,52,15,61 chr2 91678903 . A G 691.11 PASS AC=1;AF=0.5;AN=2;DP=10717;set=filterInvariant-filterInvariant2-filterInvariant3-variant4-variant6-variant7-variant8-filterInvariant9-variant10-variant11-filterInvariant12-filterInvariant13-variant14-filterInvariant15-variant16-filterInvariant17-filterInvariant18-variant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant26-variant27-filterInvariant28-filterInvariant29-variant30-filterInvariant31-filterInvariant32-variant33-variant34-variant35-filterInvariant36-filterInvariant37-variant38-filterInvariant39-filterInvariant40-filterInvariant41-variant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:241,71:312:99:1315,0,5750:165,76,37,34 chr2 91679044 . A G 4264.55 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=30008;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:371,343:714:99:6511,0,7406:161,210,159,184 chr2 91710132 . C T 70.68 PASS AC=1;AF=0.95;AN=2;DP=80;FS=0;FractionInformativeReads=1;set=variant3-variant5-variant10-variant12-variant19-variant20-variant21-variant22-variant25-variant28-variant31-variant32-variant35-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,2:4:37:69,0,37:1,1,1,1 chr2 91714722 . C G 70.05 PASS AC=1;AF=0.536;AN=2;DP=132;FS=0;FractionInformativeReads=1;set=variant3-filterInvariant10-filterInvariant13-filterInvariant17-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant27-variant33-filterInvariant35-filterInvariant39-filterInvariant41-filterInvariant42-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:2,4:6:31:81,0,31:1,1,2,2 chr2 91766609 . G A 542.72 PASS AC=1;AF=0.5;AN=2;DP=3894;set=filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant12-filterInvariant13-variant16-filterInvariant28-filterInvariant29-filterInvariant31-filterInvariant35-filterInvariant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:272,46:318:99:286,0,6902:129,143,20,26 chr2 91766685 . G T 1005.02 PASS AC=1;AF=0.5;AN=2;DP=7478;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-filterInvariant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:142,35:177:99:959,0,5784:56,86,12,23 chr2 91766686 . A G 1005.02 PASS AC=1;AF=0.5;AN=2;DP=7372;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-filterInvariant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:142,34:176:99:959,0,5784:56,86,11,23 chr2 91766729 . C CAG 2478.6 PASS AC=1;AF=0.5;AN=2;DP=4330;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:23,70:93:99:2862,0,754:10,13,27,43 chr2 91767199 . A C 296.47 PASS AC=1;AF=0.5;AN=2;DP=1317;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,15:36:99:465,0,750:18,3,12,3 chr2 91767507 . T A 906.27 PASS AC=1;AF=0.5;AN=2;DP=7675;set=variant-filterInvariant3-variant6-filterInvariant7-variant8-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant13-filterInvariant14-filterInvariant15-filterInvariant16-variant17-filterInvariant18-variant19-variant21-variant22-variant23-variant25-filterInvariant26-filterInvariant27-variant28-variant29-filterInvariant30-filterInvariant31-filterInvariant33-variant34-variant35-filterInvariant36-filterInvariant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:209,41:250:99:538,0,5555:87,122,14,27 chr2 91809227 . A G 612.8 PASS AC=1;AF=0.5;AN=2;DP=8401;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:154,77:231:99:1561,0,3923:92,62,42,35 chr2 91809324 . C T 1120.08 PASS AC=1;AF=0.5;AN=2;DP=11677;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:197,100:297:99:1924,0,4708:95,102,46,54 chr2 91809385 . C G 827.56 PASS AC=1;AF=0.5;AN=2;DP=9198;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:141,83:224:99:2602,0,5403:58,83,37,46 chr2 91809404 . G C 723.9 PASS AC=1;AF=0.5;AN=2;DP=7729;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:114,63:177:99:2313,0,4603:45,69,22,41 chr2 91809456 . T G 74.82 PASS AC=1;AF=0.5;AN=2;DP=3669;set=filterInvariant-variant2-filterInvariant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-filterInvariant19-variant20-filterInvariant21-variant22-variant23-variant25-variant26-filterInvariant27-variant28-variant29-filterInvariant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,19:79:99:561,0,2392:22,38,5,14 chr2 91809468 . C CTAA 190.02 PASS AC=1;AF=0.5;AN=2;DP=3248;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:50,17:67:99:557,0,2209:17,33,3,14 chr2 91809470 . G A 199.23 PASS AC=1;AF=0.5;AN=2;DP=3125;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:48,17:65:99:563,0,2123:17,31,3,14 chr2 91809472 . G GTGACTAACAA 277.27 PASS AC=1;AF=0.5;AN=2;DP=3017;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:46,17:63:99:569,0,2014:17,29,3,14 chr2 91893801 . A C 162.68 PASS AC=1;AF=0.534;AN=2;DP=310;set=filterInvariant-filterInvariant4-filterInvariant7-filterInvariant8-filterInvariant10-filterInvariant11-filterInvariant13-filterInvariant15-variant16-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant27-filterInvariant29-filterInvariant31-filterInvariant32-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant38-filterInvariant39-filterInvariant42-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:5,6:11:99:143,0,114:4,1,5,1 chr2 91924782 . C A 147.31 PASS AC=1;AF=0.512;AN=2;DP=685;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,7:12:99:266,0,177:4,1,7,0 chr2 91924804 . T C 170.86 PASS AC=1;AF=0.5;AN=2;DP=1065;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:7,16:23:99:629,0,172:5,2,16,0 chr2 91924967 . C T 372.47 PASS AC=1;AF=0.5;AN=2;DP=3490;set=variant-filterInvariant2-variant5-variant6-variant9-variant12-filterInvariant13-filterInvariant14-variant16-variant17-variant19-filterInvariant20-filterInvariant26-variant30-variant31-variant32-variant33-variant34-variant35-filterInvariant37-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:165,29:194:99:678,0,7346:98,67,20,9 chr2 91924972 . G A 354.47 PASS AC=1;AF=0.5;AN=2;DP=6310;set=variant-filterInvariant2-filterInvariant3-filterInvariant4-variant5-variant6-variant8-variant9-filterInvariant10-variant11-variant12-variant13-filterInvariant14-variant16-variant17-filterInvariant18-variant19-filterInvariant20-filterInvariant22-variant23-filterInvariant24-filterInvariant26-filterInvariant27-filterInvariant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-filterInvariant36-filterInvariant37-variant39-variant40-filterInvariant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:170,29:199:99:669,0,7416:98,72,20,9 chr2 91925022 . C A 1690.56 PASS AC=1;AF=0.5;AN=2;DP=10048;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:128,140:268:99:3367,0,3245:80,48,72,68 chr2 91925139 . C G 737.32 PASS AC=1;AF=0.5;AN=2;DP=10046;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:146,97:243:99:2205,0,3657:57,89,34,63 chr2 91925151 . C T 2717.45 PASS AC=1;AF=0.5;AN=2;DP=9169;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:77,140:217:99:3646,0,1807:30,47,46,94 chr2 91925267 . T C 150.24 PASS AC=1;AF=0.5;AN=2;DP=490;FractionInformativeReads=1;set=variant-variant3-variant5-variant8-variant9-variant10-variant11-variant16-variant17-variant19-variant21-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,6:15:99:150,0,301:1,8,0,6 chr2 91926926 . C T 101.87 PASS AC=1;AF=0.5;AN=2;DP=562;FractionInformativeReads=1;set=variant3-variant4-variant6-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,6:20:99:129,0,396:11,3,4,2 chr2 91927088 . G A 337.99 PASS AC=1;AF=0.5;AN=2;DP=4763;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:91,70:161:99:1558,0,2327:51,40,42,28 chr2 91927130 . C G 676.27 PASS AC=1;AF=0.5;AN=2;DP=6507;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:123,85:208:99:3178,0,5145:70,53,44,41 chr2 91927131 . C G 676.27 PASS AC=1;AF=0.5;AN=2;DP=6507;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:124,85:209:99:3178,0,5145:69,55,44,41 chr2 91927133 . GT G 667.24 PASS AC=1;AF=0.5;AN=2;DP=6573;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:128,83:211:99:3184,0,5100:70,58,43,40 chr2 91927214 . T C 349.26 PASS AC=1;AF=0.5;AN=2;DP=7559;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-filterInvariant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-filterInvariant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:163,67:230:99:1355,0,4380:82,81,25,42 chr2 91927230 . C T 472.03 PASS AC=1;AF=0.5;AN=2;DP=7250;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:163,50:213:99:1595,0,6696:87,76,16,34 chr2 91927231 . A G 472.03 PASS AC=1;AF=0.5;AN=2;DP=7206;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:163,50:213:99:1595,0,6696:88,75,16,34 chr2 91927530 . G A 168.37 PASS AC=1;AF=0.5;AN=2;DP=1269;set=variant4-variant5-filterInvariant7-variant8-filterInvariant9-variant10-variant11-variant12-variant13-filterInvariant16-variant17-filterInvariant20-filterInvariant21-variant26-variant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant34-variant35-filterInvariant36-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:44,10:54:99:142,0,1257:15,29,5,5 chr2 91933207 . T C 44.51 PASS AC=1;AF=0.5;AN=2;DP=6764;set=filterInvariant-filterInvariant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-filterInvariant14-filterInvariant15-variant16-variant17-variant18-variant19-variant20-variant22-filterInvariant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-filterInvariant32-filterInvariant33-variant34-filterInvariant35-variant36-variant37-variant39-filterInvariant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:146,23:169:99:192,0,3959:53,93,5,18 chr2 91935981 . C T 117.79 PASS AC=1;AF=0.5;AN=2;DP=3416;set=variant-filterInvariant3-variant4-variant5-variant8-filterInvariant9-filterInvariant11-filterInvariant12-variant13-filterInvariant15-variant16-filterInvariant17-filterInvariant19-filterInvariant20-filterInvariant23-variant24-variant26-filterInvariant27-variant28-variant29-filterInvariant30-variant31-variant32-variant33-variant34-filterInvariant35-variant36-filterInvariant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:83,11:94:99:157,0,2450:58,25,10,1 chr2 91936030 . A G 94.13 PASS AC=1;AF=0.5;AN=2;DP=6505;set=filterInvariant-filterInvariant2-variant3-variant4-variant5-filterInvariant6-variant8-filterInvariant10-filterInvariant11-variant12-variant13-filterInvariant16-filterInvariant17-filterInvariant18-variant19-variant20-filterInvariant21-variant22-variant23-filterInvariant24-variant26-filterInvariant27-variant29-filterInvariant30-filterInvariant31-variant32-filterInvariant33-variant34-variant35-variant36-variant37-variant40-variant41-filterInvariant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:127,27:154:99:599,0,3354:76,51,27,0 chr2 91936054 . T C 629.64 PASS AC=1;AF=0.5;AN=2;DP=10104;set=variant-filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant8-filterInvariant9-variant10-filterInvariant11-filterInvariant12-filterInvariant13-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-variant23-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant27-variant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant32-variant33-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant39-filterInvariant40-filterInvariant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:186,48:234:99:1132,0,4887:110,76,47,1 chr2 91936121 . A G 1923.88 PASS AC=1;AF=0.5;AN=2;DP=18647;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:238,196:434:99:4588,0,5837:125,113,123,73 chr2 91936138 . G A 3734.32 PASS AC=1;AF=0.5;AN=2;DP=19839;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:259,225:484:99:8468,0,10060:133,126,127,98 chr2 91936147 . G A 3792.82 PASS AC=1;AF=0.5;AN=2;DP=20368;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:258,236:494:99:8705,0,9951:131,127,129,107 chr2 91937490 . T C 57.01 PASS AC=1;AF=0.5;AN=2;DP=1477;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-filterInvariant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,17:48:99:338,0,873:22,9,10,7 chr2 91937662 . A G 757.2 PASS AC=1;AF=0.5;AN=2;DP=5106;set=variant-variant2-variant3-variant4-variant5-variant6-filterInvariant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:114,62:176:99:1109,0,2618:55,59,31,31 chr2 91937699 . C T 790.65 PASS AC=1;AF=0.5;AN=2;DP=4742;set=variant-variant2-variant3-variant4-variant5-variant6-filterInvariant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:98,52:150:99:1074,0,2484:39,59,20,32 chr2 91937761 . C T 483.13 PASS AC=1;AF=0.5;AN=2;DP=2361;set=variant-filterInvariant2-variant3-variant4-variant5-variant6-filterInvariant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-filterInvariant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,22:70:99:491,0,1286:16,32,6,16 chr2 91937775 . G A 395.34 PASS AC=1;AF=0.5;AN=2;DP=1891;set=variant-filterInvariant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,16:54:99:423,0,1093:11,27,4,12 chr2 91940297 . C T 225.41 PASS AC=1;AF=0.5;AN=2;DP=13062;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant4-variant5-filterInvariant8-filterInvariant9-filterInvariant10-variant11-variant12-filterInvariant13-filterInvariant15-filterInvariant16-filterInvariant17-variant18-filterInvariant19-filterInvariant20-filterInvariant22-filterInvariant23-variant24-variant26-filterInvariant27-variant28-filterInvariant29-filterInvariant30-filterInvariant31-variant32-variant33-variant34-filterInvariant35-variant36-filterInvariant37-variant39-variant40-filterInvariant41-variant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:398,41:439:99:478,0,19732:199,199,33,8 chr2 91940306 . G A 336.2 PASS AC=1;AF=0.5;AN=2;DP=13486;set=filterInvariant-variant2-filterInvariant3-filterInvariant4-variant5-filterInvariant8-variant9-variant10-variant11-variant12-filterInvariant13-filterInvariant15-variant16-variant17-variant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-variant23-variant24-variant26-variant27-variant28-filterInvariant29-variant30-variant31-variant32-filterInvariant33-variant34-filterInvariant35-variant36-filterInvariant37-filterInvariant39-variant40-variant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:379,44:423:99:651,0,19319:192,187,37,7 chr2 91940522 . C T,A 1246.62 PASS AC=1,0;AF=0.45,0.05;AN=2;DP=1794;set=variant4-variant7-variant14-variant16-variant23-variant27-variant30-variant35-variant38-variant42 GT:DP:GQ:SB 0/1:183:99:55,72,19,37 chr2 91943835 . T C 64.29 PASS AC=1;AF=0.5;AN=2;DP=4468;set=filterInvariant2-variant3-variant4-variant5-filterInvariant6-variant8-filterInvariant9-filterInvariant10-variant11-variant12-filterInvariant13-filterInvariant14-variant16-filterInvariant17-variant18-variant19-variant20-variant22-variant23-filterInvariant24-filterInvariant25-variant26-filterInvariant28-filterInvariant29-variant31-variant32-variant33-variant34-variant35-variant36-filterInvariant37-filterInvariant39-variant40-variant41-variant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:111,25:136:99:397,0,2712:62,49,7,18 chr2 91944151 . C T 78.82 PASS AC=1;AF=0.5;AN=2;DP=3365;set=variant-variant3-variant4-filterInvariant5-variant7-filterInvariant8-filterInvariant9-variant10-variant11-variant13-filterInvariant15-variant16-variant17-filterInvariant18-variant19-variant23-variant25-filterInvariant26-filterInvariant27-variant28-variant29-variant30-variant32-variant34-filterInvariant35-filterInvariant36-variant37-variant39-filterInvariant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:87,9:96:99:157,0,5135:25,62,5,4 chr2 91944161 . G A 103.55 PASS AC=1;AF=0.5;AN=2;DP=3159;FractionInformativeReads=1;set=variant-variant3-variant4-filterInvariant5-variant7-filterInvariant8-filterInvariant9-variant10-variant11-variant13-filterInvariant15-variant16-variant17-filterInvariant18-variant19-variant23-filterInvariant25-variant26-filterInvariant27-variant28-variant29-variant30-variant32-variant34-filterInvariant35-filterInvariant36-variant37-variant39-filterInvariant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:77,11:88:99:181,0,4866:24,53,6,5 chr2 91955313 . G A 2265.41 PASS AC=1;AF=0.5;AN=2;DP=15384;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:226,172:398:99:3963,0,5719:101,125,69,103 chr2 91955404 . T C 852.14 PASS AC=1;AF=0.5;AN=2;DP=6036;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-filterInvariant9-variant10-variant11-variant12-variant13-filterInvariant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:119,45:164:99:1267,0,3444:38,81,7,38 chr2 91960776 . AG A 307.04 PASS AC=1;AF=0.5;AN=2;DP=376;set=variant4-variant10-variant12-variant13-variant15-variant30-variant31-variant34-variant35-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,11:32:99:219,0,503:12,9,6,5 chr2 91962876 . G A 523.33 PASS AC=1;AF=0.5;AN=2;DP=2181;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-filterInvariant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-filterInvariant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,18:44:99:704,0,1090:12,14,6,12 chr2 91962879 . A T 490.42 PASS AC=1;AF=0.5;AN=2;DP=2158;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-filterInvariant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-filterInvariant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,17:41:99:704,0,1090:11,13,7,10 chr2 91962942 . G A 362.96 PASS AC=1;AF=0.5;AN=2;DP=911;set=variant-variant2-variant4-variant5-variant8-variant9-variant11-variant12-variant13-filterInvariant18-variant19-variant20-variant22-variant23-variant25-variant27-variant29-variant30-variant31-filterInvariant33-variant35-variant36-variant37-filterInvariant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:21,5:26:92:92,0,505:9,12,2,3 chr2 91962954 . C A 338.31 PASS AC=1;AF=0.5;AN=2;DP=863;set=variant-variant2-variant4-variant5-variant8-variant9-variant11-filterInvariant12-variant13-filterInvariant18-variant19-variant20-variant22-variant23-variant25-variant27-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:19,6:25:99:100,0,447:8,11,2,4 chr2 92031664 . T C 61.45 PASS AC=1;AF=0.583;AN=2;DP=73;FractionInformativeReads=1;set=variant4-variant13-variant31-variant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,9:16:99:235,0,226:5,2,5,4 chr2 92031762 . G T 220.98 PASS AC=1;AF=0.571;AN=2;DP=163;FractionInformativeReads=1;set=variant4-variant12-variant13-variant31-variant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,14:25:99:353,0,291:4,7,7,7 chr2 92031844 . C T 97.58 PASS AC=1;AF=0.5;AN=2;DP=75;FractionInformativeReads=1;set=variant2-variant5-filterInvariant35 GT:AD:DP:GQ:PL:SB 0/1:34,4:38:66:66,0,1454:15,19,3,1 chr2 92031850 . C T 73.53 PASS AC=1;AF=0.5;AN=2;DP=74;FractionInformativeReads=1;set=variant2-variant5-filterInvariant35 GT:AD:DP:GQ:PL:SB 0/1:27,4:31:84:84,0,1213:8,19,3,1 chr2 92031870 . C T 76.56 PASS AC=1;AF=0.5;AN=2;DP=69;FractionInformativeReads=1;set=variant2-filterInvariant5-variant35 GT:AD:DP:GQ:PL:SB 0/1:24,4:28:93:93,0,1087:1,23,3,1 chr2 92075572 . T C 96.87 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=1235;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:89,9:98:99:107,0,3741:45,44,5,4 chr2 92075583 . C T 42.3 PASS AC=1;AF=0.5;AN=2;DP=857;FractionInformativeReads=1;set=filterInvariant10-filterInvariant17-filterInvariant22-filterInvariant25-variant35-filterInvariant37-filterInvariant38-filterInvariant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:86,12:98:99:245,0,3576:40,46,6,6 chr2 92075584 . G A 141.84 PASS AC=1;AF=0.5;AN=2;DP=1227;FractionInformativeReads=1;set=filterInvariant-filterInvariant11-filterInvariant15-filterInvariant17-filterInvariant21-filterInvariant22-variant24-filterInvariant25-filterInvariant30-filterInvariant35-filterInvariant36-filterInvariant42-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:89,9:98:99:107,0,3890:41,48,5,4 chr2 92075596 . C T 78.88 PASS AC=1;AF=0.5;AN=2;DP=837;FractionInformativeReads=1;set=filterInvariant10-variant17-filterInvariant22-filterInvariant25-variant35-filterInvariant37-filterInvariant38-filterInvariant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:85,12:97:99:245,0,3576:39,46,6,6 chr2 92075603 . C G 177.94 PASS AC=1;AF=0.5;AN=2;DP=1472;FractionInformativeReads=1;set=variant-filterInvariant4-filterInvariant9-variant11-filterInvariant15-filterInvariant17-variant21-filterInvariant22-variant24-filterInvariant25-filterInvariant30-filterInvariant35-filterInvariant36-filterInvariant38-filterInvariant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:82,10:92:99:164,0,3697:36,46,5,5 chr2 92075610 . G T 594.56 PASS AC=1;AF=0.5;AN=2;DP=1820;set=variant3-filterInvariant4-variant9-variant12-variant13-filterInvariant15-variant16-filterInvariant18-variant20-filterInvariant21-filterInvariant22-filterInvariant24-filterInvariant25-variant26-filterInvariant27-variant29-variant32-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:66,22:88:99:725,0,2826:28,38,11,11 chr2 92075615 . A G 551.33 PASS AC=1;AF=0.5;AN=2;DP=3785;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:66,22:88:99:725,0,2847:27,39,11,11 chr2 92075618 . T C 551.33 PASS AC=1;AF=0.5;AN=2;DP=3699;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:61,22:83:99:737,0,2679:24,37,11,11 chr2 92075628 . A G 238.15 PASS AC=1;AF=0.5;AN=2;DP=1590;FractionInformativeReads=1;set=variant-filterInvariant3-filterInvariant4-filterInvariant9-variant11-filterInvariant15-variant17-variant21-filterInvariant22-variant24-filterInvariant25-filterInvariant27-filterInvariant30-filterInvariant31-variant35-variant36-filterInvariant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:68,10:78:99:209,0,3047:27,41,5,5 chr2 92075709 . A G 247.64 PASS AC=1;AF=0.5;AN=2;DP=617;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,4:10:81:81,0,203:1,5,0,4 chr2 92129194 . C T 210.75 PASS AC=1;AF=0.5;AN=2;DP=1102;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-filterInvariant8-variant9-variant10-filterInvariant11-variant13-filterInvariant14-variant15-variant16-filterInvariant18-variant19-variant20-filterInvariant21-variant22-variant23-variant24-variant25-variant27-filterInvariant30-variant31-variant32-filterInvariant33-variant34-variant35-variant37-variant38-variant39-filterInvariant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,9:20:99:186,0,335:2,9,2,7 chr2 92129281 . G A 61.44 PASS AC=1;AF=0.5;AN=2;DP=33;FractionInformativeReads=1;set=variant14-variant35 GT:AD:DP:GQ:PL:SB 0/1:9,3:12:60:60,0,270:4,5,0,3 chr2 92129749 . T C 2867.22 PASS AC=2;AF=0.648;AN=2;DP=2536;FractionInformativeReads=1;set=variant-variant4-variant7-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,110:112:99:3156,286,0:1,1,46,64 chr2 95464577 . T C 212.71 PASS AC=1;AF=0.55;AN=2;DP=116;FractionInformativeReads=1;set=variant4-variant12-variant13-variant14-variant31-variant34-variant35-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,6:10:69:153,0,69:2,2,4,2 chr2 95481396 . C T 1051.13 PASS AC=1;AF=0.556;AN=2;DP=1157;set=variant4-variant12-variant13-variant14-variant31-variant34-variant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:86,52:138:99:929,0,2168:44,42,21,31 chr2 95488700 . A C 310.46 PASS AC=1;AF=0.556;AN=2;DP=289;FractionInformativeReads=1;set=variant4-variant12-variant13-variant14-variant31-variant34-variant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,9:27:99:277,0,423:11,7,7,2 chr2 95513809 . C T 37.08 PASS AC=1;AF=0.5;AN=2;DP=2083;set=filterInvariant-variant2-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant7-variant8-filterInvariant11-variant12-variant13-filterInvariant14-filterInvariant16-filterInvariant21-filterInvariant22-variant23-filterInvariant25-variant29-variant31-variant33-filterInvariant34-variant35-variant36-variant37-variant39-filterInvariant40-variant41-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:67,10:77:99:215,0,2781:34,33,8,2 chr2 95513817 . G T 31.1 PASS AC=1;AF=0.5;AN=2;DP=3081;set=filterInvariant-filterInvariant2-variant3-filterInvariant4-variant5-variant7-variant8-filterInvariant10-variant11-variant12-variant13-filterInvariant14-variant15-variant16-variant17-filterInvariant18-filterInvariant19-filterInvariant20-variant21-filterInvariant22-variant23-filterInvariant24-variant25-filterInvariant27-variant29-variant30-variant31-filterInvariant32-variant33-filterInvariant34-variant35-variant36-variant37-variant38-variant39-filterInvariant40-variant41-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:69,12:81:99:296,0,2791:33,36,9,3 chr2 95513852 . C T 88.77 PASS AC=1;AF=0.5;AN=2;DP=2951;set=filterInvariant-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant7-variant8-filterInvariant11-variant12-variant13-filterInvariant15-variant16-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-variant23-filterInvariant24-variant25-filterInvariant27-variant29-variant30-filterInvariant31-filterInvariant32-variant33-filterInvariant34-variant35-variant36-variant37-variant38-variant39-filterInvariant40-variant41-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:62,11:73:99:290,0,1592:27,35,8,3 chr2 95513877 . A G 82.09 PASS AC=1;AF=0.5;AN=2;DP=3077;set=filterInvariant-variant2-variant3-filterInvariant4-variant5-filterInvariant6-variant7-variant8-variant10-filterInvariant11-variant12-variant13-filterInvariant15-variant16-variant17-filterInvariant18-variant19-filterInvariant20-variant21-filterInvariant22-variant23-filterInvariant24-variant25-filterInvariant26-filterInvariant27-variant29-variant30-variant31-variant32-variant33-filterInvariant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:56,14:70:99:461,0,2297:20,36,8,6 chr2 95513880 . C T 82.09 PASS AC=1;AF=0.5;AN=2;DP=3052;FractionInformativeReads=1;set=filterInvariant-variant2-variant3-variant4-variant5-filterInvariant6-variant7-variant8-variant10-filterInvariant11-variant12-variant13-filterInvariant15-variant16-variant17-filterInvariant18-variant19-filterInvariant20-variant21-filterInvariant22-variant23-filterInvariant24-variant25-filterInvariant26-filterInvariant27-variant29-variant30-variant31-variant32-variant33-filterInvariant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:55,14:69:99:464,0,2264:20,35,7,7 chr2 95513889 . T A 118.84 PASS AC=1;AF=0.5;AN=2;DP=2317;set=filterInvariant-variant2-variant3-variant5-variant7-variant8-filterInvariant11-filterInvariant12-variant13-variant16-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-variant23-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant27-variant29-variant30-filterInvariant31-variant33-variant35-variant36-variant37-filterInvariant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:55,13:68:99:359,0,2270:21,34,6,7 chr2 95513893 . A G 118.84 PASS AC=1;AF=0.5;AN=2;DP=2817;FractionInformativeReads=1;set=filterInvariant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-filterInvariant11-variant12-variant13-filterInvariant15-variant16-variant17-filterInvariant18-variant19-variant20-variant21-variant22-variant23-filterInvariant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-filterInvariant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:49,15:64:99:479,0,2037:19,30,7,8 chr2 95513964 . T C 30.36 PASS AC=1;AF=0.5;AN=2;DP=444;set=filterInvariant2-variant3-filterInvariant4-variant8-variant16-filterInvariant19-filterInvariant22-filterInvariant23-variant27-variant29-variant30-filterInvariant31-variant35-variant36-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:15,6:21:99:163,0,446:3,12,0,6 chr2 95513989 . C T 36.63 PASS AC=1;AF=0.5;AN=2;DP=341;FractionInformativeReads=1;set=variant2-variant3-variant4-variant8-variant11-variant16-variant19-filterInvariant21-variant22-variant23-variant26-variant27-variant29-variant30-variant35-variant36-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,6:15:99:178,0,262:2,7,0,6 chr2 95522747 . C G 1372.03 PASS AC=1;AF=0.66;AN=2;DP=2346;FractionInformativeReads=1;set=variant-variant4-variant7-variant12-variant13-variant14-variant16-variant18-variant19-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,34:91:99:806,0,1470:32,25,21,13 chr2 95537179 . TAC T 4385.88 PASS AC=1;AF=0.556;AN=2;DP=1470;set=variant4-variant12-variant13-variant14-variant31-variant34-variant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:92,92:184:99:3517,0,3466:53,39,57,35 chr2 95537245 . C G 5011.33 PASS AC=1;AF=0.64;AN=2;DP=5555;MQ=60;set=variant-variant4-variant7-variant12-variant13-variant14-variant16-variant18-variant19-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:125,113:238:99:2867,0,3134:65,60,62,51 chr2 95537572 . C T 1221.36 PASS AC=1;AF=0.583;AN=2;DP=3882;MQ=60;set=variant-variant4-variant7-variant12-variant13-variant14-variant16-variant18-variant19-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant34-variant35-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:100,68:168:99:1755,0,2886:55,45,38,30 chr2 95537622 . A G 4356.82 PASS AC=1;AF=0.66;AN=2;DP=4811;set=variant-variant4-variant7-variant12-variant13-variant14-variant16-variant18-variant19-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:127,105:232:99:2601,0,3149:68,59,57,48 chr2 95537871 . GC GCC,GCCC,G 278.28 PASS AC=0,1,0;AF=0.37,0.148,0.093;AN=2;DP=999;MQ=60;set=variant-variant4-variant7-variant9-variant12-variant13-variant14-variant15-variant16-variant18-variant22-variant23-filterInvariant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant41-variant43-variant44 GT:DP:GQ:SB 0/2:24:99:3,13,2,6 chr2 95691596 . C T 6112.74 PASS AC=1;AF=0.5;AN=2;DP=2689;MQ=60;set=variant4-variant12-variant31-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:317,277:594:99:6205,0,7706:169,148,144,133 chr2 95719703 . C A 267.83 PASS AC=1;AF=0.5;AN=2;DP=118;MQ=60;set=variant4-variant12-variant31-variant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,16:19:45:440,0,45:1,2,6,10 chr2 95766553 . TA T 349.71 PASS AC=1;AF=0.5;AN=2;DP=44;FS=1.236;FractionInformativeReads=0.886;MQ=60;MQRankSum=0.576;QD=7.95;ReadPosRankSum=1.559;SOR=0.644;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:20,19:39:99:387,0,390:9,11,10,9 chr2 95771980 . G A 1146.22 PASS AC=1;AF=0.5;AN=2;DP=91;FS=0.802;FractionInformativeReads=1;MQ=60;MQRankSum=0.068;QD=12.6;ReadPosRankSum=-0.756;SOR=0.857;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:40,51:91:99:1174,0,933:22,18,30,21 chr2 95775761 . G A 1173.02 PASS AC=1;AF=0.5;AN=2;DP=498;MQ=60;set=variant4-variant12-variant13-variant31-variant35-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,29:79:99:670,0,1235:28,22,17,12 chr2 95787501 . G A 1284.82 PASS AC=1;AF=0.5;AN=2;DP=95;FS=2.889;FractionInformativeReads=0.989;MQ=60;MQRankSum=-1.868;QD=13.52;ReadPosRankSum=1.822;SOR=1.119;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:47,47:94:99:1313,0,1141:29,18,33,14 chr2 95787810 . T G 911.64 PASS AC=2;AF=1;AN=2;DP=1155;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:1120,84,0:0,0,6,22 chr2 95816017 . TA TAA,T,TAAA 149.45 PASS AC=1,0,0;AF=0.545,0.023,0.045;AN=2;DP=411;set=variant2-variant3-variant5-variant6-variant11-variant12-variant13-variant14-filterInvariant16-variant17-variant20-variant21-variant24-variant27-variant28-variant32-variant35-variant36-variant38-variant42-filterInvariant43-variant44 GT:DP:GQ:SB 0/1:8:28:0,3,0,5 chr2 95830737 . C CA 2069.45 PASS AC=1;AF=0.885;AN=2;DP=2398;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,31:64:99:792,0,859:20,13,22,9 chr2 95846158 . T C 288.47 PASS AC=1;AF=0.885;AN=2;DP=403;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,7:15:99:186,0,295:0,8,1,6 chr2 95847040 . TGCG T 3818.12 PASS AC=2;AF=0.989;AN=2;DP=5863;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,130:130:99:5796,392,0:0,0,68,62 chr2 95848018 . T C 458.45 PASS AC=1;AF=0.885;AN=2;DP=959;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,9:28:99:199,0,526:7,12,4,5 chr2 95848354 . G A 1783.06 PASS AC=1;AF=0.885;AN=2;DP=2045;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,27:62:99:695,0,917:18,17,16,11 chr2 95849653 . T C 548.1 PASS AC=1;AF=0.885;AN=2;DP=766;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,9:14:82:249,0,82:2,3,7,2 chr2 95944902 . A AC 806.43 PASS AC=2;AF=1;AN=2;DP=1442;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1371,110,0:0,0,17,22 chr2 95945561 . T C 1055.4 PASS AC=1;AF=0.5;AN=2;DP=69;FS=0.958;FractionInformativeReads=1;MQ=60;MQRankSum=-0.719;QD=15.3;ReadPosRankSum=-0.301;SOR=0.499;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:27,42:69:99:1084,0,1092:17,10,24,18 chr2 95945568 . G A 1280.23 PASS AC=1;AF=0.875;AN=2;DP=2620;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,31:72:99:791,0,1629:23,18,21,10 chr2 95945830 . G T 1563.51 PASS AC=1;AF=0.875;AN=2;DP=2480;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,30:61:99:673,0,808:11,20,15,15 chr2 95947085 . A G 5268.92 PASS AC=1;AF=0.885;AN=2;DP=7995;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:109,141:250:99:3561,0,2420:44,65,60,81 chr2 95952177 . C G 1978.49 PASS AC=2;AF=0.966;AN=2;DP=2944;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:2159,195,0:0,0,29,36 chr2 95963242 . C G 1130.95 PASS AC=1;AF=0.872;AN=2;DP=2414;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,46:100:99:1050,0,802:42,12,38,8 chr2 96012907 . C G 4012.71 PASS AC=1;AF=0.859;AN=2;DP=7832;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:134,89:223:99:1881,0,3245:56,78,39,50 chr2 96048862 . C T 41.28 PASS AC=1;AF=0.683;AN=2;DP=597;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant10-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant24-variant25-variant26-variant28-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,9:16:99:328,0,173:5,2,8,1 chr2 96049917 . TACAC TAC,TACACACAC,TACACAC,TACACACACAC,TACACACACACACAC,TACACACACACAC,T 411.61 PASS AC=0,0,1,1,0,0,0;AF=0.05,0.1,0.275,0.125,0.063,0.075,0.013;AN=2;DP=1366;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-filterInvariant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 3/4:34:99:2,0,16,16 chr2 96076409 . C T 183.53 PASS AC=2;AF=0.989;AN=2;DP=699;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,22:22:65:694,65,0:0,0,12,10 chr2 96517570 . C T 187.42 PASS AC=1;AF=0.5;AN=2;DP=2996;set=variant-variant2-variant3-variant4-filterInvariant5-variant7-filterInvariant9-variant11-variant13-variant14-filterInvariant17-variant18-filterInvariant19-variant20-filterInvariant22-filterInvariant25-filterInvariant27-filterInvariant28-variant35-filterInvariant36-filterInvariant37-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:117,20:137:99:489,0,2923:59,58,11,9 chr2 96517641 . C T 1110.84 PASS AC=1;AF=0.5;AN=2;DP=3146;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-filterInvariant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,43:81:99:1099,0,1673:11,27,16,27 chr2 96517642 . A G 398.93 PASS AC=1;AF=0.5;AN=2;DP=3143;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:21,60:81:99:2404,0,1023:5,16,22,38 chr2 96517785 . A T 143.12 PASS AC=1;AF=0.5;AN=2;DP=1335;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,21:36:99:602,0,479:12,3,14,7 chr2 96517824 . C T 1756.23 PASS AC=1;AF=0.5;AN=2;DP=2883;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:26,34:60:99:1103,0,707:19,7,23,11 chr2 96517825 . T C 250.13 PASS AC=1;AF=0.5;AN=2;DP=1434;set=variant-filterInvariant5-variant8-variant9-filterInvariant10-variant11-filterInvariant13-filterInvariant16-filterInvariant17-variant20-variant26-variant32-variant33-filterInvariant34-variant35-variant37-filterInvariant39-filterInvariant40-variant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,16:61:99:283,0,1615:33,12,10,6 chr2 96517885 . G A 1893.62 PASS AC=1;AF=0.5;AN=2;DP=5733;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:60,73:133:99:2596,0,1564:33,27,36,37 chr2 96517893 . T C 995.89 PASS AC=1;AF=0.5;AN=2;DP=5682;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-filterInvariant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:93,50:143:99:1708,0,3175:45,48,25,25 chr2 96517905 . A T 1043.23 PASS AC=1;AF=0.5;AN=2;DP=5520;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-filterInvariant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:96,48:144:99:844,0,2686:43,53,24,24 chr2 96517957 . ATT A 859.2 PASS AC=1;AF=0.5;AN=2;DP=3797;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-filterInvariant12-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-filterInvariant24-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-filterInvariant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:71,36:107:99:724,0,2416:27,44,14,22 chr2 96517960 . T A 2495.45 PASS AC=1;AF=0.5;AN=2;DP=4421;set=variant-filterInvariant2-variant3-variant4-variant5-variant6-variant7-variant8-filterInvariant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-filterInvariant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:72,35:107:99:798,0,2341:26,46,15,20 chr2 96517961 . T A,TAAA 2412.03 PASS AC=1,0;AF=0.468,0.048;AN=2;DP=2995;set=variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:111:99:12,24,31,44 chr2 96518022 . G A 259.94 PASS AC=1;AF=0.585;AN=2;DP=1099;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-filterInvariant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,10:30:99:303,0,662:4,16,2,8 chr2 96518047 . G C 68.16 PASS AC=1;AF=0.5;AN=2;DP=54;FractionInformativeReads=1;set=variant16-variant19-variant32-variant35 GT:AD:DP:GQ:PL:SB 0/1:11,3:14:59:59,0,317:3,8,2,1 chr2 96519386 . C G 85.48 PASS AC=1;AF=0.5;AN=2;DP=23;FS=0;FractionInformativeReads=1;set=variant-variant11-variant35 GT:AD:DP:GQ:PL:SB 0/1:5,4:9:99:144,0,186:5,0,4,0 chr2 96521138 . T C 3992.6 PASS AC=1;AF=0.5;AN=2;DP=9226;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-filterInvariant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-filterInvariant26-variant27-variant28-variant29-variant30-filterInvariant31-filterInvariant32-filterInvariant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:106,83:189:99:2130,0,2672:61,45,59,24 chr2 96521220 . G A 971.32 PASS AC=1;AF=0.5;AN=2;DP=19581;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:238,171:409:99:3300,0,6141:134,104,106,65 chr2 96521244 . GTTTT G 1994.87 PASS AC=1;AF=0.5;AN=2;DP=17999;set=variant-filterInvariant2-variant3-variant4-filterInvariant6-variant8-variant9-variant10-filterInvariant11-variant12-variant13-filterInvariant14-filterInvariant15-variant16-variant17-filterInvariant18-variant19-variant20-variant22-variant23-variant24-filterInvariant27-variant28-variant29-filterInvariant30-filterInvariant31-filterInvariant32-variant33-variant34-variant35-variant36-variant40-filterInvariant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:370,91:461:99:2604,0,16129:200,170,49,42 chr2 96521297 . T C 8779.58 PASS AC=1;AF=0.5;AN=2;DP=20274;set=variant-filterInvariant2-filterInvariant3-variant4-filterInvariant5-variant6-variant7-variant8-filterInvariant9-variant10-variant11-filterInvariant12-filterInvariant13-filterInvariant14-variant15-filterInvariant16-filterInvariant17-filterInvariant18-variant19-variant20-variant21-variant22-variant23-filterInvariant24-variant25-variant26-variant27-variant28-variant29-filterInvariant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:110,291:401:99:8311,0,2276:52,58,139,152 chr2 96521324 . A G 10694.2 PASS AC=1;AF=0.5;AN=2;DP=17852;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:115,258:373:99:8354,0,2285:55,60,121,137 chr2 96521334 . T C 1965.1 PASS AC=1;AF=0.5;AN=2;DP=15910;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-filterInvariant14-variant15-variant16-filterInvariant18-variant19-filterInvariant20-variant21-variant22-variant23-filterInvariant24-variant25-variant26-filterInvariant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-filterInvariant40-variant41-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:252,103:355:99:1928,0,9786:124,128,55,48 chr2 96521336 . T C 10288.7 PASS AC=1;AF=0.5;AN=2;DP=17180;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:119,239:358:99:8480,0,4091:62,57,118,121 chr2 96521337 . G A 388.05 PASS AC=1;AF=0.5;AN=2;DP=3295;set=filterInvariant-filterInvariant16-filterInvariant19-filterInvariant22-filterInvariant33-filterInvariant34-filterInvariant35-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:296,60:356:99:581,0,11766:149,147,31,29 chr2 96521406 . C T 4495.78 PASS AC=1;AF=0.5;AN=2;DP=14488;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:130,219:349:99:5566,0,3139:64,66,126,93 chr2 96521438 . A G 4788.23 PASS AC=1;AF=0.5;AN=2;DP=14884;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:143,224:367:99:8506,0,5437:75,68,134,90 chr2 96521455 . A G 5263.9 PASS AC=1;AF=0.5;AN=2;DP=16664;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:147,267:414:99:10307,0,5463:80,67,143,124 chr2 96521477 . A AG 3187.63 PASS AC=1;AF=0.5;AN=2;DP=19223;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:181,292:473:99:11420,0,7160:104,77,150,142 chr2 96521479 . A AAT,AT 4351.96 PASS AC=0,1;AF=0.057,0.443;AN=2;DP=19680;set=Intersection GT:DP:GQ:SB 0/2:482:99:103,78,155,146 chr2 96521482 . ATGAG AAG,A 4540.29 PASS AC=1,0;AF=0.477,0.023;AN=2;DP=20603;set=Intersection GT:DP:GQ:SB 0/1:494:99:107,82,155,150 chr2 96521486 . G A 3753.22 PASS AC=1;AF=0.5;AN=2;DP=20360;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:187,310:497:99:12433,0,7166:104,83,160,150 chr2 96521512 . A C 8609.47 PASS AC=1;AF=0.5;AN=2;DP=23974;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:228,343:571:99:7996,0,5809:137,91,149,194 chr2 96521548 . G A 10644.3 PASS AC=1;AF=0.5;AN=2;DP=24943;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:307,257:564:99:9600,0,12057:166,141,109,148 chr2 96521556 . T C 10201.5 PASS AC=1;AF=0.5;AN=2;DP=24673;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:310,242:552:99:9321,0,12171:167,143,102,140 chr2 96521563 . G A 5279.32 PASS AC=1;AF=0.5;AN=2;DP=24321;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:340,190:530:99:7058,0,13647:183,157,77,113 chr2 96521607 . G C 5230.99 PASS AC=1;AF=0.5;AN=2;DP=23105;set=variant-variant2-filterInvariant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:387,111:498:99:3446,0,15953:201,186,44,67 chr2 96521608 . G A 5230.99 PASS AC=1;AF=0.5;AN=2;DP=22920;set=variant-variant2-variant3-filterInvariant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:384,108:492:99:3449,0,15911:199,185,42,66 chr2 96521609 . T C 5230.99 PASS AC=1;AF=0.5;AN=2;DP=22870;set=variant-variant2-filterInvariant3-filterInvariant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:385,108:493:99:3449,0,15911:200,185,41,67 chr2 96523006 . A C 40.7 PASS AC=2;AF=0.767;AN=2;DP=763;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,23:23:72:1060,72,0:0,0,15,8 chr2 96523009 . A C 40.7 PASS AC=2;AF=0.767;AN=2;DP=777;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:1060,72,0:0,0,15,9 chr2 96523047 . A G 73.02 PASS AC=2;AF=0.75;AN=2;DP=1227;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:948,105,0:0,0,20,15 chr2 96523096 . T C 97.42 PASS AC=2;AF=0.698;AN=2;DP=1601;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:992,105,0:0,0,15,20 chr2 96523194 . A C 113.05 PASS AC=1;AF=0.778;AN=2;DP=84;FractionInformativeReads=1;set=variant3-variant4-variant5-variant14-variant24-variant25-variant26-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:6,2:8:66:66,0,146:2,4,0,2 chr2 96592970 . G GAT 138.96 PASS AC=1;AF=0.5;AN=2;DP=1096;set=filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-variant12-variant14-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant29-variant30-filterInvariant32-filterInvariant35-filterInvariant39 GT:AD:DP:GQ:PL:SB 0/1:89,8:97:99:110,0,4004:49,40,8,0 chr2 96592974 . GTT G 90.64 PASS AC=1;AF=0.5;AN=2;DP=1713;FractionInformativeReads=1;set=filterInvariant2-filterInvariant3-filterInvariant5-variant6-filterInvariant7-filterInvariant8-filterInvariant10-variant12-variant14-filterInvariant20-variant21-filterInvariant22-filterInvariant23-filterInvariant25-variant29-variant30-variant32-filterInvariant35-filterInvariant37-filterInvariant39 GT:AD:DP:GQ:PL:SB 0/1:92,10:102:99:212,0,4813:50,42,10,0 chr2 96592982 . T C 205.03 PASS AC=1;AF=0.5;AN=2;DP=3139;FractionInformativeReads=1;set=variant-filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-filterInvariant15-filterInvariant16-variant18-filterInvariant19-filterInvariant20-variant21-variant22-filterInvariant23-variant24-variant25-filterInvariant26-filterInvariant28-variant29-variant30-variant32-filterInvariant34-variant35-filterInvariant36-filterInvariant37-variant39-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:93,15:108:99:464,0,4874:51,42,10,5 chr2 96593000 . A G 549.98 PASS AC=1;AF=0.5;AN=2;DP=4366;FractionInformativeReads=1;set=variant-variant2-variant3-filterInvariant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-filterInvariant15-variant16-filterInvariant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-filterInvariant38-variant39-filterInvariant40-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:100,24:124:99:746,0,5498:54,46,12,12 chr2 96593016 . C A 601.02 PASS AC=1;AF=0.5;AN=2;DP=4516;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-filterInvariant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-filterInvariant38-variant39-filterInvariant40-variant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:98,27:125:99:833,0,5498:53,45,12,15 chr2 96593025 . C T 601.05 PASS AC=1;AF=0.5;AN=2;DP=4498;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-filterInvariant38-variant39-filterInvariant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:96,27:123:99:842,0,5369:52,44,12,15 chr2 96593048 . G GA 625.13 PASS AC=1;AF=0.5;AN=2;DP=4227;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:89,26:115:99:812,0,5128:42,47,11,15 chr2 96593057 . TAATC T 619.06 PASS AC=1;AF=0.5;AN=2;DP=4200;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:92,23:115:99:689,0,5273:42,50,9,14 chr2 96593108 . T G 506.09 PASS AC=1;AF=0.5;AN=2;DP=3082;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-filterInvariant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-filterInvariant39-variant40-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:64,21:85:99:680,0,2977:25,39,7,14 chr2 96593118 . T A 295.35 PASS AC=1;AF=0.5;AN=2;DP=2774;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-filterInvariant13-variant14-filterInvariant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-filterInvariant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-filterInvariant39-filterInvariant40-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:58,19:77:99:614,0,2822:24,34,6,13 chr2 96594697 . G C 154.85 PASS AC=1;AF=0.5;AN=2;DP=1833;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:17,13:30:99:243,0,532:14,3,8,5 chr2 96594723 . A G 213.54 PASS AC=1;AF=0.5;AN=2;DP=2131;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-filterInvariant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,9:30:99:251,0,699:18,3,6,3 chr2 96594735 . C T 130.8 PASS AC=1;AF=0.5;AN=2;DP=2247;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-filterInvariant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,7:32:99:180,0,1272:19,6,5,2 chr2 96594742 . C T 115.79 PASS AC=1;AF=0.5;AN=2;DP=2377;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-filterInvariant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,5:39:99:135,0,1528:25,9,3,2 chr2 96594759 . G A 104.11 PASS AC=1;AF=0.5;AN=2;DP=2690;set=variant-filterInvariant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-filterInvariant12-variant13-variant14-variant15-filterInvariant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-filterInvariant35-variant36-filterInvariant37-variant38-variant39-variant40-variant41-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,5:54:59:59,0,2309:34,15,3,2 chr2 96594906 . G GA 223.45 PASS AC=1;AF=0.5;AN=2;DP=2692;set=variant-variant2-variant3-filterInvariant4-variant5-variant6-variant8-variant10-variant11-variant12-filterInvariant13-variant15-filterInvariant19-variant20-filterInvariant21-variant22-filterInvariant23-filterInvariant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-filterInvariant35-filterInvariant36-variant37-filterInvariant38-filterInvariant39-variant40-filterInvariant41-filterInvariant42 GT:AD:DP:GQ:PL:SB 0/1:67,9:76:99:176,0,2753:29,38,5,4 chr2 96594915 . TAATC T 223.25 PASS AC=1;AF=0.5;AN=2;DP=2676;FractionInformativeReads=1;set=variant-variant2-variant3-filterInvariant4-variant5-variant6-filterInvariant7-variant8-variant10-variant11-variant12-filterInvariant13-variant15-filterInvariant17-filterInvariant19-variant20-filterInvariant21-variant22-filterInvariant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-filterInvariant35-filterInvariant36-variant37-filterInvariant38-filterInvariant39-variant40-filterInvariant41-filterInvariant42 GT:AD:DP:GQ:PL:SB 0/1:64,9:73:99:182,0,2705:27,37,5,4 chr2 96594924 . T C 241.31 PASS AC=1;AF=0.5;AN=2;DP=2544;set=variant-variant2-variant3-filterInvariant4-variant5-variant6-filterInvariant7-variant8-variant10-variant11-variant12-filterInvariant13-variant15-filterInvariant16-filterInvariant17-variant19-variant20-filterInvariant21-variant22-filterInvariant23-variant24-variant25-variant26-filterInvariant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-filterInvariant38-filterInvariant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:60,10:70:99:221,0,2608:25,35,6,4 chr2 96594966 . T G 310.9 PASS AC=1;AF=0.5;AN=2;DP=2222;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-filterInvariant18-filterInvariant19-variant20-variant21-variant22-variant23-variant24-filterInvariant25-variant26-variant27-variant28-variant29-filterInvariant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-filterInvariant38-variant39-variant40-variant41-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,12:47:99:199,0,921:15,20,5,7 chr2 96595032 . A T 244.3 PASS AC=1;AF=0.5;AN=2;DP=1652;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant10-variant11-filterInvariant12-filterInvariant13-filterInvariant14-filterInvariant15-variant16-filterInvariant17-filterInvariant18-filterInvariant19-variant20-filterInvariant21-filterInvariant22-filterInvariant23-variant24-filterInvariant25-filterInvariant26-filterInvariant27-variant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant38-filterInvariant39-filterInvariant40-variant41-filterInvariant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,21:35:99:634,0,303:4,10,8,13 chr2 96595037 . TAATC T 247.52 PASS AC=1;AF=0.5;AN=2;DP=759;set=variant2-variant3-variant5-variant7-variant9-variant10-variant12-filterInvariant16-variant17-variant22-variant23-variant26-filterInvariant29-variant30-filterInvariant31-filterInvariant34-variant35-variant36-variant37-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:27,6:33:99:171,0,1075:9,18,3,3 chr2 96601240 . G A 969.49 PASS AC=1;AF=0.5;AN=2;DP=2675;FractionInformativeReads=1;set=filterInvariant-variant2-variant3-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-variant10-variant11-filterInvariant12-filterInvariant13-filterInvariant14-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant19-variant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-variant25-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant29-variant30-variant31-filterInvariant32-filterInvariant33-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant38-filterInvariant39-filterInvariant40-variant41-variant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:28,21:49:99:411,0,598:14,14,14,7 chr2 96601296 . A ATGATTAAT 2297.79 PASS AC=1;AF=0.5;AN=2;DP=4730;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:45,51:96:99:2006,0,1846:24,21,28,23 chr2 96601345 . T C,G 968.37 PASS AC=1,0;AF=0.477,0.045;AN=2;DP=4777;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant13-filterInvariant14-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-variant25-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant38-filterInvariant39-filterInvariant40-filterInvariant41-variant42-filterInvariant43-filterInvariant44 GT:DP:GQ:SB 0/1:75:99:22,20,16,17 chr2 96601364 . C T 556.89 PASS AC=1;AF=0.5;AN=2;DP=4212;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant13-filterInvariant14-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant37-variant38-filterInvariant39-filterInvariant40-filterInvariant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:47,37:84:99:761,0,975:25,22,13,24 chr2 96601547 . A T 31.89 PASS AC=1;AF=0.5;AN=2;DP=140;FractionInformativeReads=1;set=variant3-variant6-variant11-variant12-variant20-variant21-variant23-variant24-variant26-variant31-variant35-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,2:10:60:60,0,475:0,8,1,1 chr2 96604516 . C T,A 4590.81 PASS AC=1,0;AF=0.5,0.011;AN=2;DP=9502;set=Intersection GT:DP:GQ:SB 0/1:179:99:36,18,87,38 chr2 96604591 . A G 7666.28 PASS AC=1;AF=0.5;AN=2;DP=19381;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:113,275:388:99:7805,0,1997:60,53,132,143 chr2 96604606 . C A 1311.8 PASS AC=1;AF=0.5;AN=2;DP=9708;set=variant2-variant3-variant5-variant7-variant9-variant11-variant12-variant14-filterInvariant19-variant22-filterInvariant23-filterInvariant24-filterInvariant26-variant27-variant30-filterInvariant31-variant35-variant36-filterInvariant38-filterInvariant39-variant41-variant42-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:294,83:377:99:1118,0,9372:132,162,37,46 chr2 96604632 . A T 6850.98 PASS AC=1;AF=0.5;AN=2;DP=16994;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:101,226:327:99:6414,0,1904:42,59,89,137 chr2 96604675 . T C 497.03 PASS AC=1;AF=0.5;AN=2;DP=4948;set=variant2-variant3-variant5-variant7-variant9-variant11-filterInvariant12-variant14-filterInvariant19-variant22-variant24-filterInvariant26-filterInvariant27-filterInvariant30-filterInvariant31-variant35-variant36-filterInvariant38-filterInvariant39-variant41-variant42-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:169,40:209:99:606,0,5943:58,111,13,27 chr2 96604679 . C T 3878.31 PASS AC=1;AF=0.5;AN=2;DP=9345;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:74,108:182:99:3559,0,1688:26,48,34,74 chr2 96604680 . A G 72.19 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=386;FS=0;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:162,22:184:99:100,0,6085:52,110,7,15 chr2 96604730 . T C 714.98 PASS AC=1;AF=0.5;AN=2;DP=2410;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:23,21:44:99:646,0,729:3,20,0,21 chr2 96604747 . C T 153.91 PASS AC=1;AF=0.5;AN=2;DP=476;set=variant4-filterInvariant5-variant6-variant9-variant12-variant15-variant21-variant26-variant28-variant29-filterInvariant31-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:21,5:26:99:104,0,938:1,20,0,5 chr2 96610329 . G C 261.73 PASS AC=1;AF=0.5;AN=2;DP=3626;set=variant-variant2-filterInvariant3-variant4-variant5-variant6-variant7-variant8-filterInvariant9-variant10-variant11-variant12-filterInvariant13-variant14-variant15-filterInvariant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-filterInvariant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,18:86:99:216,0,1872:37,31,11,7 chr2 96610395 . C CA 873.71 PASS AC=1;AF=0.5;AN=2;DP=5264;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:85,28:113:99:917,0,3476:40,45,15,13 chr2 96610399 . C A 879.76 PASS AC=1;AF=0.5;AN=2;DP=5267;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:87,28:115:99:914,0,3498:41,46,15,13 chr2 96610410 . T A 885.77 PASS AC=1;AF=0.5;AN=2;DP=5253;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:87,28:115:99:911,0,3590:40,47,15,13 chr2 96610413 . C T 888.79 PASS AC=1;AF=0.5;AN=2;DP=5235;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:87,28:115:99:914,0,3569:39,48,15,13 chr2 96610420 . G T 903.83 PASS AC=1;AF=0.5;AN=2;DP=5227;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:82,28:110:99:929,0,3359:38,44,15,13 chr2 96610455 . C A 182.19 PASS AC=1;AF=0.5;AN=2;DP=2142;set=filterInvariant2-variant5-filterInvariant6-variant7-variant8-filterInvariant9-filterInvariant12-filterInvariant18-filterInvariant20-filterInvariant21-filterInvariant23-filterInvariant27-variant29-filterInvariant31-filterInvariant33-filterInvariant35-variant36-variant37-filterInvariant40-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:80,17:97:99:144,0,2314:34,46,8,9 chr2 96610787 . C CA 1405.28 PASS AC=1;AF=0.5;AN=2;DP=2312;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:33,21:54:99:1034,0,1679:25,8,21,0 chr2 96610806 . AGAAAG A,AAAAG 243.13 PASS AC=1,0;AF=0.476,0.024;AN=2;DP=2706;set=filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant8-filterInvariant10-variant15-filterInvariant17-filterInvariant18-filterInvariant20-filterInvariant21-filterInvariant24-filterInvariant26-filterInvariant28-filterInvariant29-filterInvariant33-variant35-filterInvariant36-variant37-variant39-filterInvariant43-filterInvariant44 GT:DP:GQ:SB 0/1:114:99:63,26,19,6 chr2 96610836 . T C 6020.84 PASS AC=1;AF=0.5;AN=2;DP=10747;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:66,161:227:99:5571,0,2326:42,24,116,45 chr2 96610899 . T C 13827.2 PASS AC=1;AF=0.5;AN=2;DP=20014;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:94,331:425:99:13415,0,2698:51,43,193,138 chr2 96610921 . T G 14826.9 PASS AC=1;AF=0.5;AN=2;DP=21280;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:93,368:461:99:14228,0,2535:48,45,198,170 chr2 96610952 . T C 9921.75 PASS AC=1;AF=0.5;AN=2;DP=19242;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:81,333:414:99:8080,0,1128:35,46,164,169 chr2 96611018 . G A 5017.04 PASS AC=1;AF=0.5;AN=2;DP=8528;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:33,142:175:99:4696,0,691:7,26,36,106 chr2 96611069 . T G 144.34 PASS AC=1;AF=0.5;AN=2;DP=197;set=variant23-filterInvariant34-filterInvariant35 GT:AD:DP:GQ:PL:SB 0/1:60,9:69:99:106,0,2292:5,55,1,8 chr2 96611078 . T G 2043.99 PASS AC=1;AF=0.5;AN=2;DP=2927;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:15,46:61:99:1893,0,449:1,14,4,42 chr2 96611088 . G A 1792.3 PASS AC=1;AF=0.5;AN=2;DP=2478;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:11,41:52:99:1665,0,338:0,11,3,38 chr2 96614212 . A G 46.96 PASS AC=1;AF=0.676;AN=2;DP=132;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant7-variant8-variant9-variant11-variant16-variant20-variant22-variant23-variant29-variant33-variant34-variant35-variant36-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,2:3:37:81,0,37:1,0,2,0 chr2 96614383 . A G 468.55 PASS AC=1;AF=0.5;AN=2;DP=2681;set=variant2-filterInvariant3-variant4-variant5-filterInvariant6-variant8-filterInvariant9-filterInvariant10-variant12-variant13-filterInvariant15-filterInvariant17-filterInvariant18-variant20-variant21-filterInvariant22-filterInvariant24-filterInvariant25-filterInvariant28-variant29-variant31-filterInvariant32-filterInvariant35-filterInvariant36-variant38-variant39-filterInvariant40-filterInvariant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:78,11:89:99:153,0,1757:41,37,6,5 chr2 96614407 . G A 496.39 PASS AC=1;AF=0.5;AN=2;DP=2672;set=variant2-filterInvariant3-variant4-variant5-filterInvariant6-filterInvariant7-variant8-filterInvariant9-filterInvariant10-variant12-variant13-variant15-filterInvariant18-variant20-variant21-filterInvariant22-filterInvariant24-filterInvariant25-filterInvariant27-filterInvariant28-variant29-variant31-filterInvariant32-filterInvariant35-filterInvariant36-filterInvariant37-variant38-variant39-filterInvariant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:77,10:87:99:99,0,1820:39,38,5,5 chr2 96614424 . G T 528.2 PASS AC=1;AF=0.5;AN=2;DP=2637;set=variant2-variant3-variant4-variant5-variant6-filterInvariant7-variant8-filterInvariant9-filterInvariant10-variant12-variant13-variant15-filterInvariant17-filterInvariant18-variant20-variant21-filterInvariant22-variant24-variant25-filterInvariant27-variant28-variant29-variant31-filterInvariant32-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant37-variant38-variant39-filterInvariant40-filterInvariant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:64,10:74:99:153,0,1658:29,35,5,5 chr2 96614434 . A AC 250.04 PASS AC=1;AF=0.5;AN=2;DP=3018;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-filterInvariant16-variant17-variant18-filterInvariant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-filterInvariant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,11:69:99:282,0,2390:24,34,6,5 chr2 96614438 . C A 259.1 PASS AC=1;AF=0.5;AN=2;DP=2990;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-filterInvariant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-filterInvariant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,11:70:99:279,0,2412:24,35,6,5 chr2 96616348 . C G 871.33 PASS AC=1;AF=0.5;AN=2;DP=2197;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:19,30:49:99:1286,0,1019:12,7,26,4 chr2 96616353 . GT G 223.14 PASS AC=1;AF=0.5;AN=2;DP=2394;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,20:56:99:638,0,1773:27,9,17,3 chr2 96616354 . T C 433.13 PASS AC=1;AF=0.5;AN=2;DP=2396;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,15:56:99:461,0,1901:30,11,14,1 chr2 96616355 . T C 232.18 PASS AC=1;AF=0.5;AN=2;DP=2455;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,20:56:99:638,0,1773:27,9,17,3 chr2 96616378 . C T 1420.08 PASS AC=1;AF=0.5;AN=2;DP=3987;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:26,65:91:99:2182,0,1151:17,9,48,17 chr2 96616442 . C A 2224.37 PASS AC=1;AF=0.5;AN=2;DP=6541;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:37,113:150:99:4571,0,1193:21,16,55,58 chr2 96616448 . G T 2224.37 PASS AC=1;AF=0.5;AN=2;DP=6535;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:40,112:152:99:4541,0,1261:22,18,54,58 chr2 96616485 . C G 1892.5 PASS AC=1;AF=0.5;AN=2;DP=6060;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:46,98:144:99:3820,0,1571:23,23,41,57 chr2 96616501 . C CAA 1836.5 PASS AC=1;AF=0.5;AN=2;DP=5439;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:47,91:138:99:3648,0,1694:24,23,32,59 chr2 96616505 . AGC A 1671.82 PASS AC=1;AF=0.5;AN=2;DP=5086;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:47,81:128:99:3390,0,1740:24,23,25,56 chr2 96616532 . T G 1021.08 PASS AC=1;AF=0.5;AN=2;DP=3677;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:42,59:101:99:2426,0,1620:20,22,13,46 chr2 96616571 . C A 208.25 PASS AC=1;AF=0.5;AN=2;DP=1713;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:36,16:52:99:560,0,1495:14,22,1,15 chr2 96616576 . T C 178.4 PASS AC=1;AF=0.5;AN=2;DP=1554;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:36,16:52:99:563,0,1463:14,22,1,15 chr2 96616580 . A G 181.41 PASS AC=1;AF=0.5;AN=2;DP=1422;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-filterInvariant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,12:45:99:489,0,1344:13,20,1,11 chr2 96616597 . A G 85.54 PASS AC=1;AF=0.5;AN=2;DP=1064;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,8:36:99:249,0,1194:10,18,1,7 chr2 96616599 . G A 85.54 PASS AC=1;AF=0.5;AN=2;DP=1050;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-filterInvariant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,8:36:99:336,0,1146:10,18,1,7 chr2 96616607 . G T 85.54 PASS AC=1;AF=0.5;AN=2;DP=841;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-filterInvariant12-variant15-variant16-variant17-variant18-filterInvariant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,9:35:99:300,0,1065:9,17,1,8 chr2 96616622 . C T 106.61 PASS AC=1;AF=0.5;AN=2;DP=573;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,6:26:99:192,0,822:6,14,1,5 chr2 96616654 . C A 124.68 PASS AC=1;AF=0.5;AN=2;DP=385;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,3:11:99:102,0,315:2,6,1,2 chr2 96616667 . A C 127.69 PASS AC=1;AF=0.5;AN=2;DP=351;FractionInformativeReads=1;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,3:10:99:105,0,285:2,5,1,2 chr2 96616951 . A G 289.63 PASS AC=1;AF=0.5;AN=2;DP=343;FractionInformativeReads=1;set=variant2-variant3-variant5-variant6-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,3:14:93:93,0,453:10,1,3,0 chr2 96616957 . A G 115.65 PASS AC=1;AF=0.5;AN=2;DP=383;FractionInformativeReads=1;set=variant-variant2-variant3-variant5-variant6-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,4:15:99:132,0,492:10,1,4,0 chr2 96616967 . G C 115.65 PASS AC=1;AF=0.5;AN=2;DP=432;FractionInformativeReads=1;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,6:18:99:213,0,528:11,1,6,0 chr2 96616976 . A G 154.63 PASS AC=1;AF=0.5;AN=2;DP=505;FractionInformativeReads=1;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,7:22:99:246,0,651:13,2,7,0 chr2 96616979 . G C 154.63 PASS AC=1;AF=0.5;AN=2;DP=535;FractionInformativeReads=1;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,7:23:99:240,0,732:14,2,7,0 chr2 96616997 . T G 184.36 PASS AC=1;AF=0.5;AN=2;DP=819;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,11:35:99:329,0,911:19,5,9,2 chr2 96617023 . C A 772.3 PASS AC=1;AF=0.5;AN=2;DP=1905;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:37,19:56:99:700,0,1628:30,7,14,5 chr2 96617025 . C A 769.29 PASS AC=1;AF=0.5;AN=2;DP=2072;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:41,20:61:99:694,0,1683:32,9,14,6 chr2 96617039 . A C 710.6 PASS AC=1;AF=0.5;AN=2;DP=1541;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant14-variant17-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant34-variant35-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,23:70:99:624,0,1744:33,14,16,7 chr2 96617069 . A G 1943.37 PASS AC=1;AF=0.5;AN=2;DP=4560;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,39:92:99:1516,0,2065:34,19,24,15 chr2 96617090 . A G 2301.37 PASS AC=1;AF=0.5;AN=2;DP=5770;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:58,51:109:99:1985,0,2363:33,25,34,17 chr2 96617106 . A C 2451.26 PASS AC=1;AF=0.5;AN=2;DP=6278;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:73,52:125:99:2048,0,2903:40,33,32,20 chr2 96617111 . G A 2445.24 PASS AC=1;AF=0.5;AN=2;DP=6470;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:75,51:126:99:1955,0,3035:40,35,32,19 chr2 96617113 . G A 2484.22 PASS AC=1;AF=0.5;AN=2;DP=6524;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:76,51:127:99:1940,0,3245:41,35,31,20 chr2 96617125 . T C 2505.14 PASS AC=1;AF=0.5;AN=2;DP=6851;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:83,53:136:99:1976,0,3326:43,40,30,23 chr2 96617132 . T C 2571.07 PASS AC=1;AF=0.5;AN=2;DP=6999;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:79,57:136:99:2217,0,3223:40,39,30,27 chr2 96617155 . A G 2383.85 PASS AC=1;AF=0.5;AN=2;DP=7215;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:90,56:146:99:2002,0,3398:43,47,27,29 chr2 96617194 . A G 1819.3 PASS AC=1;AF=0.5;AN=2;DP=6574;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:94,51:145:99:1840,0,3808:44,50,21,30 chr2 96617209 . G T 1631.36 PASS AC=1;AF=0.5;AN=2;DP=5894;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:93,43:136:99:1544,0,3794:42,51,17,26 chr2 96617228 . T A 256.11 PASS AC=1;AF=0.5;AN=2;DP=5083;set=filterInvariant-variant2-variant3-variant4-variant5-filterInvariant6-variant7-variant8-variant9-variant10-variant11-filterInvariant12-filterInvariant13-filterInvariant14-variant15-filterInvariant16-filterInvariant17-filterInvariant18-variant19-variant20-variant21-variant22-variant23-variant24-filterInvariant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:87,30:117:99:696,0,3689:38,49,6,24 chr2 96617231 . G A 1156.27 PASS AC=1;AF=0.5;AN=2;DP=4895;set=variant-variant2-filterInvariant3-variant4-variant5-variant6-filterInvariant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-filterInvariant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:85,29:114:99:998,0,3563:38,47,5,24 chr2 96617256 . A G 991.36 PASS AC=1;AF=0.5;AN=2;DP=4015;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-filterInvariant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-filterInvariant26-variant27-variant28-filterInvariant29-variant30-filterInvariant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:71,19:90:99:584,0,2924:29,42,0,19 chr2 96617262 . A G 894.66 PASS AC=1;AF=0.5;AN=2;DP=3727;FractionInformativeReads=1;set=variant-variant2-filterInvariant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-filterInvariant26-variant27-variant28-filterInvariant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,17:82:99:509,0,2804:27,38,0,17 chr2 96617304 . A T 442.43 PASS AC=1;AF=0.5;AN=2;DP=1687;set=variant-variant2-variant3-variant5-filterInvariant6-variant7-variant8-variant9-variant10-filterInvariant12-variant13-filterInvariant14-variant15-variant16-filterInvariant18-filterInvariant19-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-filterInvariant35-variant37-variant38-filterInvariant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,5:42:61:61,0,1417:11,26,0,5 chr2 96619641 . A C 322.58 PASS AC=1;AF=0.5;AN=2;DP=1088;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,5:16:99:174,0,805:11,0,5,0 chr2 96619642 . A T 322.58 PASS AC=1;AF=0.5;AN=2;DP=1115;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,5:17:99:174,0,805:12,0,5,0 chr2 96619688 . T G 1326.56 PASS AC=1;AF=0.5;AN=2;DP=4300;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:41,49:90:99:1189,0,1202:35,6,40,9 chr2 96619734 . C T 2545.12 PASS AC=1;AF=0.5;AN=2;DP=9351;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:100,128:228:99:3107,0,2340:63,37,82,46 chr2 96619773 . A C 332.65 PASS AC=1;AF=0.5;AN=2;DP=4053;set=filterInvariant2-variant3-variant9-variant12-filterInvariant14-variant22-filterInvariant23-variant27-variant30-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:278,43:321:99:306,0,9514:152,126,31,12 chr2 96619774 . G A 3994.44 PASS AC=1;AF=0.5;AN=2;DP=13083;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:154,171:325:99:5113,0,3425:88,66,98,73 chr2 96619799 . A C 4041.73 PASS AC=1;AF=0.5;AN=2;DP=14181;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:166,185:351:99:5371,0,3737:88,78,98,87 chr2 96619831 . T C 2442.43 PASS AC=1;AF=0.5;AN=2;DP=13007;set=variant-variant2-variant3-variant4-filterInvariant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-filterInvariant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:150,172:322:99:6638,0,5789:71,79,72,100 chr2 96619832 . A G,T 2151.94 PASS AC=1,0;AF=0.419,0.081;AN=2;DP=12510;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:316:99:70,79,67,100 chr2 96619837 . C G 4169.79 PASS AC=1;AF=0.5;AN=2;DP=12243;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:145,156:301:99:6259,0,5803:65,80,61,95 chr2 96619838 . A C 4088.82 PASS AC=1;AF=0.5;AN=2;DP=12153;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:145,155:300:99:6228,0,5722:64,81,61,94 chr2 96619853 . T C 1451.23 PASS AC=1;AF=0.5;AN=2;DP=10256;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-filterInvariant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-filterInvariant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:203,63:266:99:1539,0,5916:87,116,22,41 chr2 96619873 . C A 907.77 PASS AC=1;AF=0.5;AN=2;DP=8150;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-filterInvariant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-filterInvariant34-variant35-variant36-variant37-variant38-filterInvariant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:170,37:207:99:915,0,7023:64,106,12,25 chr2 96619896 . A G 472.99 PASS AC=1;AF=0.5;AN=2;DP=692;set=variant9-variant12-variant30-variant35-filterInvariant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:116,26:142:99:324,0,3637:41,75,4,22 chr2 96626292 . C T 452.58 PASS AC=2;AF=0.955;AN=2;DP=1013;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:826,81,0:0,0,9,18 chr2 96681081 . C T 38 PASS AC=1;AF=0.692;AN=2;DP=146;FractionInformativeReads=1;set=variant8-filterInvariant9-filterInvariant20-filterInvariant22-filterInvariant23-filterInvariant29-filterInvariant33-filterInvariant34-filterInvariant35-variant36-filterInvariant37-filterInvariant40-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:5,3:8:73:73,0,108:3,2,1,2 chr2 96684876 . A G 607.65 PASS AC=2;AF=0.955;AN=2;DP=2819;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,95:95:99:2733,285,0:0,0,50,45 chr2 96685021 . A G 607.56 PASS AC=1;AF=0.688;AN=2;DP=342;FractionInformativeReads=1;set=variant6-variant7-variant8-variant9-variant16-variant20-variant22-variant23-variant29-variant33-variant34-variant35-variant36-variant37-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,19:29:99:599,0,272:3,7,7,12 chr2 96687426 . CT C 286.61 PASS AC=2;AF=0.779;AN=2;DP=1647;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1894,129,0:0,0,14,27 chr2 96687428 . GC G 286.64 PASS AC=2;AF=0.779;AN=2;DP=1593;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1895,130,0:0,0,15,28 chr2 96778665 . T TA,TAA 653.12 PASS AC=1,0;AF=0.6,0.025;AN=2;DP=1756;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:46:99:18,7,13,8 chr2 96780122 . G T 2650.69 PASS AC=1;AF=0.588;AN=2;DP=1623;MQ=60;set=variant6-variant7-variant8-variant9-variant12-variant16-variant20-variant23-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,49:105:99:1197,0,1514:26,30,21,28 chr2 96780716 . T G 7471.45 PASS AC=1;AF=0.825;AN=2;DP=13670;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:196,206:402:99:5300,0,4508:105,91,117,89 chr2 96780986 . C CTCCTCCTCT 8025.12 PASS AC=1;AF=0.825;AN=2;DP=10009;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:138,138:276:99:5423,0,7495:76,62,70,68 chr2 96781986 . G C 1639.51 PASS AC=1;AF=0.825;AN=2;DP=1830;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,24:45:99:696,0,579:7,14,7,17 chr2 96789787 . T C 6227.09 PASS AC=1;AF=0.609;AN=2;DP=4511;MQ=60;set=variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant16-variant19-variant20-variant22-variant23-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:147,134:281:99:3143,0,3308:63,84,67,67 chr2 96795608 . T G 2682.82 PASS AC=1;AF=0.609;AN=2;DP=2079;MQ=60;set=variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant16-variant19-variant20-variant22-variant23-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,63:107:99:1569,0,983:21,23,31,32 chr2 96795714 . G A 2665.32 PASS AC=1;AF=0.609;AN=2;DP=2391;set=variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant16-variant19-variant20-variant22-variant23-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,52:96:99:1351,0,1002:23,21,25,27 chr2 96795857 . T C 2568.51 PASS AC=1;AF=0.817;AN=2;DP=4096;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,50:94:99:1167,0,1048:21,23,24,26 chr2 96795944 . A G 1226.38 PASS AC=1;AF=0.604;AN=2;DP=1197;MQ=60;set=variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant16-variant19-variant20-variant22-variant23-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,20:45:99:490,0,671:8,17,9,11 chr2 96798510 . G A 2126.32 PASS AC=1;AF=0.609;AN=2;DP=1638;FractionInformativeReads=1;MQ=60;set=variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant16-variant19-variant20-variant22-variant23-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,45:89:99:1149,0,1025:18,26,18,27 chr2 96809331 . T C 1006.59 PASS AC=1;AF=0.694;AN=2;DP=3715;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,48:108:99:1273,0,1470:28,32,21,27 chr2 96851119 . C A 1811.1 PASS AC=1;AF=0.78;AN=2;DP=9437;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:121,103:224:99:2402,0,3146:66,55,59,44 chr2 96917588 . T G 685.24 PASS AC=1;AF=0.697;AN=2;DP=2882;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,56:89:99:1580,0,830:17,16,20,36 chr2 96931846 . T C 2654.87 PASS AC=1;AF=0.588;AN=2;DP=1995;MQ=60;set=variant6-variant7-variant8-variant9-variant12-variant16-variant20-variant22-variant23-variant29-variant31-variant33-variant34-variant35-variant36-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:66,66:132:99:1728,0,1622:33,33,34,32 chr2 96944553 . G A 3509.84 PASS AC=1;AF=0.639;AN=2;DP=4087;MQ=60;set=variant4-variant6-variant7-variant8-variant9-variant12-variant16-variant20-variant22-variant23-variant29-variant31-variant33-variant34-variant35-variant36-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:128,131:259:99:3144,0,3080:71,57,58,73 chr2 96956315 . T G 2070.12 PASS AC=2;AF=0.989;AN=2;DP=3297;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,64:64:99:2099,191,0:0,0,27,37 chr2 96963684 . A G 559.01 PASS AC=1;AF=0.618;AN=2;DP=303;MQ=60;set=variant6-variant7-variant8-variant9-variant12-variant16-variant20-variant22-variant23-variant29-variant31-variant33-variant34-variant35-variant36-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,10:13:56:289,0,56:1,2,3,7 chr2 96991492 . A G 583.6 PASS AC=1;AF=0.744;AN=2;DP=5147;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:79,65:144:99:1745,0,1853:45,34,40,25 chr2 97032981 . T A 1226.25 PASS AC=1;AF=0.5;AN=2;DP=84;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.145;QD=14.6;ReadPosRankSum=-0.871;SOR=0.686;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:35,49:84:99:1254,0,890:23,12,32,17 chr2 97166204 . A G 2401.78 PASS AC=1;AF=0.73;AN=2;DP=7872;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:116,106:222:99:2724,0,2875:45,71,51,55 chr2 97203137 . A C 1308.78 PASS AC=1;AF=0.73;AN=2;DP=3476;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:70,33:103:99:765,0,1840:36,34,22,11 chr2 97203224 . T C 3968.43 PASS AC=2;AF=0.953;AN=2;DP=3899;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,108:108:99:3322,324,0:0,0,53,55 chr2 97284917 . G A 781.77 PASS AC=1;AF=0.611;AN=2;DP=1815;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant21-variant22-variant25-variant26-variant27-variant28-variant32-variant33-variant35-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,37:71:99:959,0,881:22,12,24,13 chr2 97315570 . C T 589.98 PASS AC=1;AF=0.607;AN=2;DP=640;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant21-variant22-variant25-variant26-variant27-variant28-variant32-variant33-variant34-variant35-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,12:23:99:354,0,366:2,9,2,10 chr2 97319534 . G C 76.7 PASS AC=1;AF=0.607;AN=2;DP=315;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant21-variant22-variant25-variant26-variant27-variant28-variant32-variant33-variant34-variant35-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,5:9:99:145,0,145:0,4,1,4 chr2 97369546 . CTTTTT CTTTT,CTTT,CTTTTTT,CTTTTTTTT,CTTTTTTT,C,CTT 43.85 PASS AC=1,0,0,0,0,0,0;AF=0.222,0.083,0.139,0.028,0.028,0.028,0.028;AN=2;DP=572;set=filterInvariant3-variant4-variant6-variant7-filterInvariant9-filterInvariant11-variant12-filterInvariant17-variant20-filterInvariant21-variant25-variant27-variant31-variant34-variant35-variant37-variant40-variant43 GT:DP:GQ:SB 0/1:19:59:4,9,0,6 chr2 97526963 . C T 2221.79 PASS AC=1;AF=0.5;AN=2;DP=223;FS=3.008;FractionInformativeReads=1;MQ=60;MQRankSum=-2.284;QD=9.96;ReadPosRankSum=-0.308;SOR=0.517;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:123,100:223:99:2250,0,3103:70,53,52,48 chr2 97532132 . C T 2781.41 PASS AC=1;AF=0.5;AN=2;DP=235;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.733;QD=11.84;ReadPosRankSum=3.85;SOR=0.663;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:113,122:235:99:2810,0,2665:62,51,66,56 chr2 97563745 . T C 546.81 PASS AC=1;AF=0.538;AN=2;DP=1588;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant9-variant10-variant13-variant16-variant17-variant18-variant21-variant23-variant24-variant25-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:34,43:77:99:1140,0,892:16,18,29,14 chr2 97587049 . T C 1880.1 PASS AC=2;AF=0.818;AN=2;DP=2904;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:2399,225,0:0,0,28,47 chr2 97595109 . T C 631.58 PASS AC=2;AF=0.852;AN=2;DP=1987;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1186,117,0:0,0,15,24 chr2 97613616 . T C 799.72 PASS AC=2;AF=0.864;AN=2;DP=1772;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:1463,140,0:0,0,27,20 chr2 97613748 . C A 567.65 PASS AC=2;AF=0.852;AN=2;DP=1052;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-filterInvariant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:686,57,0:0,0,5,14 chr2 97617140 . T C 6736.53 PASS AC=2;AF=0.864;AN=2;DP=10243;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,238:238:99:7232,711,0:0,0,137,101 chr2 97617227 . A G 5472.07 PASS AC=2;AF=0.864;AN=2;DP=8303;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,188:188:99:5994,564,0:0,0,96,92 chr2 97633013 . A G 154.82 PASS AC=2;AF=0.95;AN=2;DP=238;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:328,30,0:0,0,7,3 chr2 97637516 . T C 763.98 PASS AC=2;AF=0.92;AN=2;DP=1575;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1462,138,0:0,0,30,16 chr2 97637905 . T C 7470.91 PASS AC=2;AF=0.92;AN=2;DP=9469;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,272:272:99:8362,813,0:0,0,134,138 chr2 97638038 . A G 3403.48 PASS AC=2;AF=0.92;AN=2;DP=3721;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,105:105:99:3499,315,0:0,0,40,65 chr2 97643576 . T C 3354.48 PASS AC=2;AF=0.795;AN=2;DP=6004;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,168:168:99:5093,503,0:0,0,74,94 chr2 97693966 . A G 1990.46 PASS AC=2;AF=0.788;AN=2;DP=3278;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,92:94:99:2474,206,0:1,1,46,46 chr2 97747894 . T C 340.68 PASS AC=2;AF=0.932;AN=2;DP=1841;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1421,129,0:0,0,13,30 chr2 97747978 . C T 472.79 PASS AC=2;AF=0.75;AN=2;DP=873;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:499,39,0:0,0,5,8 chr2 97751782 . T C 61.77 PASS AC=2;AF=0.859;AN=2;DP=381;FractionInformativeReads=1;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant31-variant33-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:42:617,42,0:0,0,3,10 chr2 97751783 . G A 61.77 PASS AC=2;AF=0.859;AN=2;DP=376;FractionInformativeReads=1;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant31-variant33-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:42:617,42,0:0,0,3,9 chr2 97751786 . G A 61.77 PASS AC=2;AF=0.859;AN=2;DP=364;FractionInformativeReads=1;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant31-variant33-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:582,39,0:0,0,4,9 chr2 97757509 . C T 2851.35 PASS AC=2;AF=0.795;AN=2;DP=5613;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,153:153:99:4679,459,0:0,0,57,96 chr2 97784295 . C A 1010.22 PASS AC=2;AF=0.788;AN=2;DP=1001;FS=0;FractionInformativeReads=1;set=variant-variant2-variant3-filterInvariant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:987,84,0:0,0,0,28 chr2 97808394 . C G 46.1 PASS AC=1;AF=0.5;AN=2;DP=3024;set=filterInvariant-variant2-variant3-filterInvariant4-variant5-variant6-variant7-variant8-filterInvariant9-variant10-variant11-variant12-variant13-variant14-filterInvariant16-variant17-variant18-filterInvariant19-variant20-variant21-filterInvariant22-filterInvariant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-filterInvariant33-variant34-variant35-variant36-variant37-filterInvariant38-variant39-variant40-variant41-variant42-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:44,25:69:99:425,0,1217:27,17,10,15 chr2 97814956 . G A 4544.24 PASS AC=2;AF=0.857;AN=2;DP=5095;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-filterInvariant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,117:117:99:3288,350,0:0,0,60,57 chr2 97817393 . A T 682.83 PASS AC=1;AF=0.5;AN=2;DP=1592;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:22,14:36:99:389,0,876:20,2,13,1 chr2 97817394 . T G 682.83 PASS AC=1;AF=0.5;AN=2;DP=1645;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:22,14:36:99:484,0,875:20,2,13,1 chr2 97817420 . G A 2314.15 PASS AC=1;AF=0.5;AN=2;DP=3471;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:26,48:74:99:1937,0,941:22,4,38,10 chr2 97817429 . A C 2560.07 PASS AC=1;AF=0.5;AN=2;DP=3917;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:27,55:82:99:2270,0,959:22,5,41,14 chr2 97817449 . C T 2841.67 PASS AC=1;AF=0.5;AN=2;DP=4603;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:35,63:98:99:2559,0,1319:24,11,43,20 chr2 97817450 . C G 2841.67 PASS AC=1;AF=0.5;AN=2;DP=4627;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:36,63:99:99:2559,0,1319:24,12,43,20 chr2 97817469 . T A 2883.63 PASS AC=1;AF=0.5;AN=2;DP=4996;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:39,80:119:99:2877,0,1328:25,14,43,37 chr2 97817511 . T C 1701.54 PASS AC=1;AF=0.5;AN=2;DP=5447;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:44,81:125:99:1792,0,925:26,18,40,41 chr2 97817545 . A T 420.28 PASS AC=1;AF=0.5;AN=2;DP=4798;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-filterInvariant13-variant14-variant15-filterInvariant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,59:110:99:1189,0,1725:23,28,26,33 chr2 97817563 . C CA 1122.57 PASS AC=1;AF=0.5;AN=2;DP=3477;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:35,46:81:99:1780,0,1267:15,20,13,33 chr2 97817564 . C CT,T 3001.82 PASS AC=1,1;AF=0.5,0.5;AN=2;DP=3275;FS=0;set=Intersection GT:DP:GQ:SB 2/1:79:99:0,0,26,53 chr2 97817572 . A C 135.09 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=74;FS=1.293;FractionInformativeReads=1;MQ=38.19;MQRankSum=-2.883;QD=1.83;ReadPosRankSum=-0.511;SOR=1.061;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:61,13:74:99:163,0,2444:20,41,3,10 chr2 97817578 . T C 493.2 PASS AC=1;AF=0.5;AN=2;DP=3041;set=variant-variant2-filterInvariant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-filterInvariant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-filterInvariant22-variant23-filterInvariant24-filterInvariant25-filterInvariant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:43,30:73:99:1206,0,1548:18,25,3,27 chr2 97817799 . G A 142.59 PASS AC=1;AF=0.5;AN=2;DP=53;FractionInformativeReads=1;set=variant3-filterInvariant15-variant35 GT:AD:DP:GQ:PL:SB 0/1:9,4:13:99:141,0,536:0,9,2,2 chr2 97817801 . C G 142.59 PASS AC=1;AF=0.5;AN=2;DP=134;FractionInformativeReads=1;set=variant3-variant12-filterInvariant15-variant19-variant20-variant27-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:8,4:12:99:141,0,536:0,8,2,2 chr2 97817811 . T C 145.59 PASS AC=1;AF=0.5;AN=2;DP=155;FractionInformativeReads=1;set=variant3-variant12-variant15-filterInvariant16-variant19-variant20-variant27-variant30-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:6,4:10:99:150,0,367:0,6,2,2 chr2 97817817 . T C 148.6 PASS AC=1;AF=0.5;AN=2;DP=147;FractionInformativeReads=1;set=variant3-variant12-variant15-filterInvariant16-variant19-variant20-variant27-variant30-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:5,4:9:99:153,0,300:0,5,2,2 chr2 97817821 . C T 31.66 PASS AC=1;AF=0.5;AN=2;DP=150;FractionInformativeReads=1;set=variant2-variant3-variant12-variant15-filterInvariant16-variant19-variant20-variant27-variant30-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:5,4:9:99:153,0,300:0,5,2,2 chr2 97818146 . G A 304.52 PASS AC=1;AF=0.5;AN=2;DP=921;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-filterInvariant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-filterInvariant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,8:27:99:321,0,750:13,6,4,4 chr2 97818161 . C A 328.45 PASS AC=1;AF=0.5;AN=2;DP=1203;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-filterInvariant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,14:36:99:516,0,966:14,8,7,7 chr2 97818169 . C T 325.44 PASS AC=1;AF=0.5;AN=2;DP=1385;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-filterInvariant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,16:39:99:681,0,996:15,8,8,8 chr2 97818188 . T C 319.42 PASS AC=1;AF=0.5;AN=2;DP=1776;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:30,23:53:99:863,0,1554:20,10,10,13 chr2 97818192 . A G 322.43 PASS AC=1;AF=0.5;AN=2;DP=1865;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:34,23:57:99:860,0,1600:21,13,10,13 chr2 97818197 . G T 319.43 PASS AC=1;AF=0.5;AN=2;DP=1950;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:35,23:58:99:860,0,1559:20,15,10,13 chr2 97818236 . A C 263.04 PASS AC=1;AF=0.5;AN=2;DP=2600;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:56,25:81:99:855,0,2633:30,26,11,14 chr2 97818260 . GGC G 217.22 PASS AC=1;AF=0.5;AN=2;DP=2920;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:63,24:87:99:812,0,3003:34,29,10,14 chr2 97818264 . G GTT 208.22 PASS AC=1;AF=0.5;AN=2;DP=2925;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-filterInvariant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:63,24:87:99:812,0,2995:35,28,10,14 chr2 97818283 . G C 34.35 PASS AC=1;AF=0.5;AN=2;DP=3023;set=filterInvariant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-filterInvariant12-variant13-variant14-variant15-variant16-variant17-variant18-filterInvariant19-filterInvariant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-filterInvariant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:71,20:91:99:707,0,3155:39,32,9,11 chr2 97818348 . A G 1424.36 PASS AC=2;AF=0.803;AN=2;DP=2272;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:1859,195,0:0,0,28,37 chr2 97823971 . T C 684.08 PASS AC=2;AF=0.788;AN=2;DP=1521;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:909,75,0:0,0,8,17 chr2 97827737 . C T 448.77 PASS AC=1;AF=0.5;AN=2;DP=528;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-filterInvariant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,2:5:97:97,0,106:2,1,2,0 chr2 97827757 . A G 571.7 PASS AC=1;AF=0.5;AN=2;DP=734;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,8:14:99:217,0,182:5,1,5,3 chr2 97827787 . G A 985.39 PASS AC=1;AF=0.5;AN=2;DP=1045;FractionInformativeReads=1;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,11:18:99:441,0,261:5,2,5,6 chr2 97827800 . A G 1028.85 PASS AC=1;AF=0.5;AN=2;DP=1066;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,11:19:99:438,0,283:5,3,5,6 chr2 97827818 . C CT 252.21 PASS AC=1;AF=0.566;AN=2;DP=968;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-filterInvariant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,15:20:99:447,0,165:2,3,8,7 chr2 97827830 . T A 210.29 PASS AC=1;AF=0.5;AN=2;DP=520;set=variant2-variant3-variant5-variant7-variant9-filterInvariant15-variant17-variant23-variant24-variant26-variant28-filterInvariant29-filterInvariant30-variant31-variant35-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,5:20:99:165,0,615:8,7,2,3 chr2 97827839 . G A 768.59 PASS AC=1;AF=0.5;AN=2;DP=1005;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,11:20:99:313,0,179:4,5,5,6 chr2 97827912 . G C 240.29 PASS AC=1;AF=0.5;AN=2;DP=127;FractionInformativeReads=1;set=variant2-variant3-variant6-variant7-variant17-variant19-variant22-variant26-variant28-variant29-variant30-variant31-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:3,2:5:61:61,0,85:0,3,0,2 chr2 97828929 . A G 431.68 PASS AC=1;AF=0.733;AN=2;DP=672;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,18:21:72:589,0,72:3,0,15,3 chr2 97828982 . C T 587.92 PASS AC=1;AF=0.534;AN=2;DP=1200;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-filterInvariant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,40:46:99:996,0,102:6,0,19,21 chr2 97829003 . CAAAAATAA C 809.79 PASS AC=1;AF=0.5;AN=2;DP=1461;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:9,35:44:99:1397,0,273:7,2,12,23 chr2 97829022 . G A 50.96 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=45;FS=1.67;FractionInformativeReads=1;MQ=35.4;MQRankSum=-0.642;QD=1.13;ReadPosRankSum=-0.11;SOR=1.302;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:38,7:45:79:79,0,1318:17,21,2,5 chr2 97829029 . G A 722.49 PASS AC=1;AF=0.5;AN=2;DP=1596;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:15,32:47:99:1270,0,566:11,4,8,24 chr2 97829030 . T G 722.49 PASS AC=1;AF=0.5;AN=2;DP=1604;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:16,32:48:99:1270,0,566:12,4,8,24 chr2 97829119 . ATG A 325.28 PASS AC=1;AF=0.5;AN=2;DP=853;set=variant-variant2-variant4-variant5-variant6-variant8-variant12-variant13-filterInvariant14-filterInvariant15-variant16-variant20-variant22-filterInvariant23-variant25-variant28-variant31-variant32-variant34-variant35-variant37-filterInvariant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,6:34:99:125,0,1106:13,15,0,6 chr2 97829144 . T G 90.7 PASS AC=1;AF=0.5;AN=2;DP=331;set=variant-filterInvariant8-variant11-variant14-variant15-filterInvariant22-variant25-filterInvariant26-variant32-variant34-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:19,4:23:97:97,0,498:8,11,0,4 chr2 97830053 . A G 75.77 PASS AC=1;AF=0.5;AN=2;DP=1896;set=filterInvariant-variant2-filterInvariant3-variant4-variant5-filterInvariant6-variant7-variant8-filterInvariant9-variant11-filterInvariant12-variant13-variant15-filterInvariant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-filterInvariant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-filterInvariant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,10:47:99:106,0,1170:29,8,5,5 chr2 97830104 . G A 195.03 PASS AC=1;AF=0.5;AN=2;DP=3172;set=filterInvariant2-variant5-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant11-filterInvariant13-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-variant22-filterInvariant23-variant24-filterInvariant25-filterInvariant26-filterInvariant28-variant29-variant30-variant31-variant32-variant33-filterInvariant34-filterInvariant35-filterInvariant36-variant37-variant38-filterInvariant39-variant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:97,11:108:99:111,0,2323:55,42,5,6 chr2 97833159 . T A 105.87 PASS AC=1;AF=0.5;AN=2;DP=723;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-filterInvariant6-variant7-variant8-variant9-variant10-filterInvariant11-variant12-filterInvariant13-filterInvariant14-variant15-filterInvariant16-variant17-filterInvariant18-variant19-variant20-filterInvariant21-variant22-filterInvariant23-variant24-variant25-variant26-filterInvariant27-variant28-variant29-filterInvariant30-filterInvariant31-variant32-variant33-variant34-variant35-filterInvariant36-variant37-variant38-variant39-variant40-variant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:8,7:15:99:213,0,447:8,0,6,1 chr2 97833193 . G A 423.98 PASS AC=1;AF=0.5;AN=2;DP=1938;set=filterInvariant-filterInvariant2-variant3-variant4-filterInvariant5-filterInvariant6-variant7-filterInvariant8-variant9-filterInvariant10-filterInvariant11-variant12-filterInvariant13-filterInvariant14-variant15-filterInvariant16-variant17-filterInvariant18-variant19-filterInvariant20-filterInvariant21-variant22-filterInvariant23-filterInvariant24-filterInvariant25-variant26-filterInvariant27-variant28-variant29-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-variant34-filterInvariant35-filterInvariant36-variant37-filterInvariant38-variant39-variant40-variant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:16,25:41:99:641,0,346:13,3,17,8 chr2 97833215 . T C 1435.66 PASS AC=1;AF=0.5;AN=2;DP=3179;set=filterInvariant-filterInvariant2-variant3-variant4-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant8-variant9-filterInvariant10-filterInvariant11-variant12-filterInvariant13-filterInvariant14-variant15-filterInvariant16-filterInvariant17-filterInvariant18-variant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-variant26-filterInvariant27-variant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-variant34-variant35-filterInvariant36-filterInvariant37-filterInvariant38-filterInvariant39-variant40-variant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:26,43:69:99:1722,0,999:17,9,25,18 chr2 97833217 . C T 1435.66 PASS AC=1;AF=0.5;AN=2;DP=3306;set=filterInvariant-filterInvariant2-variant3-variant4-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant8-variant9-filterInvariant10-filterInvariant11-variant12-filterInvariant13-filterInvariant14-variant15-filterInvariant16-filterInvariant17-filterInvariant18-variant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-variant26-filterInvariant27-variant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-filterInvariant34-variant35-filterInvariant36-filterInvariant37-filterInvariant38-filterInvariant39-variant40-variant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:26,44:70:99:1722,0,999:17,9,26,18 chr2 97833342 . G A 546.62 PASS AC=1;AF=0.5;AN=2;DP=3997;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant13-filterInvariant14-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant18-variant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant38-filterInvariant39-filterInvariant40-filterInvariant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:63,36:99:99:639,0,1424:32,31,14,22 chr2 97833361 . A G,C 84.78 PASS AC=1,0;AF=0.488,0.012;AN=2;DP=2981;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-variant7-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant13-filterInvariant14-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-variant23-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant29-filterInvariant30-filterInvariant31-variant32-filterInvariant33-filterInvariant34-filterInvariant35-filterInvariant37-filterInvariant38-filterInvariant39-filterInvariant40-filterInvariant41-filterInvariant43-filterInvariant44 GT:DP:GQ:SB 0/1:79:99:30,34,4,11 chr2 97833466 . C T 88.35 PASS AC=1;AF=0.5;AN=2;DP=1233;FractionInformativeReads=1;set=variant-variant2-variant3-variant5-variant6-filterInvariant7-variant8-filterInvariant11-variant12-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-filterInvariant25-variant26-variant27-variant28-variant29-filterInvariant30-variant31-variant32-filterInvariant33-variant34-variant35-filterInvariant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,7:33:99:167,0,690:6,20,6,1 chr2 97833546 . G A 68.93 PASS AC=1;AF=0.5;AN=2;DP=131;FractionInformativeReads=1;set=variant3-variant5-variant9-variant26-variant27-variant35-variant36-variant39 GT:AD:DP:GQ:PL:SB 0/1:4,3:7:73:73,0,173:2,2,2,1 chr2 97833553 . C T 218.8 PASS AC=1;AF=0.511;AN=2;DP=722;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:1,7:8:9:265,0,9:0,1,4,3 chr2 97833567 . A G 214.68 PASS AC=1;AF=0.512;AN=2;DP=674;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,7:8:41:291,0,41:0,1,4,3 chr2 97833569 . C T 214.68 PASS AC=1;AF=0.523;AN=2;DP=694;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:1,7:8:41:291,0,41:0,1,4,3 chr2 97833583 . C T 223.72 PASS AC=1;AF=0.523;AN=2;DP=668;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:1,7:8:9:194,0,9:0,1,2,5 chr2 97847606 . A G 653.01 PASS AC=2;AF=0.795;AN=2;DP=905;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-filterInvariant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-filterInvariant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:693,63,0:0,0,13,8 chr2 97849219 . T C 816.64 PASS AC=2;AF=0.788;AN=2;DP=1572;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1322,132,0:0,0,19,25 chr2 97851069 . A G 2389.73 PASS AC=2;AF=0.7;AN=2;DP=3896;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:5,111:116:99:2975,135,0:3,2,63,48 chr2 97860487 . T C 2506.47 PASS AC=1;AF=0.5;AN=2;DP=7120;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,112:165:99:2801,0,1011:29,24,62,50 chr2 97862260 . T A 3299.91 PASS AC=2;AF=0.932;AN=2;DP=3896;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,95:95:99:3000,282,0:0,0,59,36 chr2 97862396 . G A 2047.84 PASS AC=1;AF=0.5;AN=2;DP=6302;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,100:147:99:2629,0,1094:19,28,44,56 chr2 97864288 . T C 2756.12 PASS AC=2;AF=0.788;AN=2;DP=4295;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,106:106:99:3306,317,0:0,0,45,61 chr2 97864333 . C A 2716.77 PASS AC=2;AF=0.788;AN=2;DP=3195;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:3523,238,0:0,0,27,52 chr2 97864334 . C T 2716.77 PASS AC=2;AF=0.788;AN=2;DP=3168;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:3523,238,0:0,0,27,52 chr2 97864374 . G T 1382.59 PASS AC=2;AF=0.788;AN=2;DP=2117;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1652,158,0:0,0,16,37 chr2 97866088 . C A 1343.84 PASS AC=1;AF=0.5;AN=2;DP=163;FS=0.617;FractionInformativeReads=1;MQ=59.99;MQRankSum=0.851;QD=8.24;ReadPosRankSum=-2.653;SOR=0.769;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:106,57:163:99:1372,0,2856:63,43,35,22 chr2 97866299 . C A 404.51 PASS AC=1;AF=0.5;AN=2;DP=1385;FractionInformativeReads=1;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,6:34:99:165,0,1033:3,25,1,5 chr2 97867870 . G C 2367.85 PASS AC=2;AF=0.78;AN=2;DP=3470;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:2061,186,0:0,0,40,22 chr2 97870051 . G A 308.41 PASS AC=1;AF=0.5;AN=2;DP=1690;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,23:35:99:639,0,322:2,10,7,16 chr2 97873515 . C T 843.92 PASS AC=2;AF=0.788;AN=2;DP=1385;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:723,75,0:0,0,13,12 chr2 97873630 . A T 851.47 PASS AC=2;AF=0.795;AN=2;DP=1245;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:863,90,0:0,0,15,15 chr2 97877292 . C A 2242.22 PASS AC=2;AF=0.932;AN=2;DP=2890;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:1889,165,0:0,0,31,24 chr2 97877399 . T C 5181.84 PASS AC=2;AF=0.932;AN=2;DP=6451;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,123:123:99:3623,368,0:0,0,72,51 chr2 97877440 . T C 1817.69 PASS AC=2;AF=0.526;AN=2;DP=6791;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,150:152:99:4186,405,0:1,1,73,77 chr2 97909718 . C T 109.49 PASS AC=1;AF=0.5;AN=2;DP=1058;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant5-filterInvariant6-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant14-variant15-filterInvariant16-filterInvariant17-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-variant35-filterInvariant36-filterInvariant37-filterInvariant38-filterInvariant39-filterInvariant40-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:17,4:21:99:201,0,720:8,9,3,1 chr2 97909719 . A G 106.48 PASS AC=1;AF=0.5;AN=2;DP=1065;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant5-filterInvariant6-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant14-variant15-filterInvariant16-filterInvariant17-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant26-variant27-filterInvariant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-variant35-filterInvariant36-filterInvariant37-filterInvariant38-filterInvariant39-filterInvariant40-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:17,4:21:99:201,0,720:8,9,3,1 chr2 97909726 . C T 106.48 PASS AC=1;AF=0.5;AN=2;DP=1132;FractionInformativeReads=1;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant5-filterInvariant6-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant14-variant15-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant26-variant27-filterInvariant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant38-filterInvariant39-filterInvariant40-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:17,7:24:99:243,0,717:8,9,6,1 chr2 97909727 . A G 106.48 PASS AC=1;AF=0.5;AN=2;DP=1146;FractionInformativeReads=1;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant5-filterInvariant6-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant14-variant15-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant26-variant27-filterInvariant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant38-filterInvariant39-filterInvariant40-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:17,7:24:99:243,0,717:8,9,6,1 chr2 97909739 . G A 180 PASS AC=1;AF=0.5;AN=2;DP=799;set=filterInvariant3-filterInvariant5-filterInvariant6-filterInvariant8-filterInvariant10-filterInvariant11-variant15-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant25-filterInvariant26-variant27-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant38-filterInvariant40-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:15,6:21:99:120,0,382:7,8,5,1 chr2 97909778 . T C 263.78 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=481;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:10,5:15:87:87,0,223:7,3,3,2 chr2 97909803 . CTT C 202.48 PASS AC=1;AF=0.511;AN=2;DP=1145;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:4,13:17:99:534,0,139:2,2,9,4 chr2 97909820 . T C 211.53 PASS AC=1;AF=0.5;AN=2;DP=1165;FractionInformativeReads=1;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-variant13-filterInvariant14-filterInvariant15-filterInvariant16-variant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-variant34-variant35-filterInvariant36-filterInvariant37-variant38-filterInvariant39-filterInvariant40-filterInvariant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:4,13:17:99:534,0,178:2,2,9,4 chr2 97909822 . C A 211.53 PASS AC=1;AF=0.5;AN=2;DP=1164;FractionInformativeReads=1;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-variant13-filterInvariant14-filterInvariant15-filterInvariant16-variant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-variant34-variant35-filterInvariant36-filterInvariant37-variant38-filterInvariant39-filterInvariant40-filterInvariant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:4,13:17:99:534,0,178:2,2,9,4 chr2 97909823 . C T 211.53 PASS AC=1;AF=0.5;AN=2;DP=1164;FractionInformativeReads=1;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-variant13-filterInvariant14-filterInvariant15-filterInvariant16-variant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-variant34-variant35-filterInvariant36-filterInvariant37-variant38-filterInvariant39-filterInvariant40-filterInvariant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:4,13:17:99:534,0,178:2,2,9,4 chr2 97909839 . C T 569.36 PASS AC=1;AF=0.512;AN=2;DP=1121;set=filterInvariant2-filterInvariant3-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-variant13-filterInvariant14-filterInvariant15-filterInvariant16-variant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant26-variant27-filterInvariant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-variant34-variant35-filterInvariant36-filterInvariant37-variant38-filterInvariant39-filterInvariant40-filterInvariant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:4,13:17:48:271,0,48:2,2,9,4 chr2 97909853 . G A 212.34 PASS AC=1;AF=0.511;AN=2;DP=943;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-variant13-filterInvariant14-filterInvariant15-filterInvariant16-variant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant26-variant27-filterInvariant28-filterInvariant29-filterInvariant30-filterInvariant31-variant32-filterInvariant33-variant34-variant35-filterInvariant36-filterInvariant37-variant38-filterInvariant39-filterInvariant40-filterInvariant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:3,12:15:99:475,0,119:1,2,8,4 chr2 97909857 . G A 212.34 PASS AC=1;AF=0.511;AN=2;DP=872;FractionInformativeReads=1;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-variant13-filterInvariant14-filterInvariant15-filterInvariant16-variant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant26-variant27-filterInvariant28-filterInvariant29-filterInvariant30-filterInvariant31-variant32-filterInvariant33-variant34-variant35-filterInvariant36-filterInvariant37-variant38-filterInvariant39-filterInvariant40-filterInvariant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:3,11:14:99:453,0,122:1,2,7,4 chr2 97909862 . A G 154.63 PASS AC=1;AF=0.512;AN=2;DP=749;FractionInformativeReads=1;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant8-variant9-filterInvariant10-filterInvariant11-filterInvariant12-variant13-filterInvariant14-filterInvariant15-filterInvariant16-variant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant26-variant27-filterInvariant28-filterInvariant29-filterInvariant30-filterInvariant31-variant32-filterInvariant33-variant34-variant35-variant36-filterInvariant37-variant38-filterInvariant39-filterInvariant40-filterInvariant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:2,9:11:99:369,0,128:0,2,6,3 chr2 98128135 . G A 2671.77 DRAGENHardSNP AC=1;AF=0.807;AN=2;DP=5507;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:87,117:204:99:4890,0,3282:57,30,90,27 chr2 98128139 . C T 221.81 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=2808;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:183,42:225:99:1169,0,7708:128,55,26,16 chr2 98128143 . T C 3200.56 DRAGENHardSNP AC=1;AF=0.807;AN=2;DP=6729;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:100,144:244:99:5924,0,3590:62,38,97,47 chr2 98128150 . G A 1734.46 DRAGENHardSNP AC=1;AF=0.568;AN=2;DP=8022;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:160,126:286:99:4160,0,6106:89,71,84,42 chr2 98128172 . C A 6271.77 DRAGENHardSNP AC=1;AF=0.807;AN=2;DP=11877;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:120,237:357:99:9868,0,4514:64,56,128,109 chr2 98128194 . G C 6766.77 DRAGENHardSNP AC=1;AF=0.807;AN=2;DP=13568;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:138,271:409:99:10963,0,4979:69,69,135,136 chr2 98128195 . G A 6766.77 DRAGENHardSNP AC=1;AF=0.807;AN=2;DP=13560;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:138,271:409:99:10963,0,4979:69,69,135,136 chr2 98128196 . T C 6766.77 DRAGENHardSNP AC=1;AF=0.807;AN=2;DP=13552;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:138,271:409:99:10963,0,4979:69,69,135,136 chr2 98128228 . G A 518.69 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=6082;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:316,66:382:99:459,0,6966:148,168,33,33 chr2 98128256 . C T 5956.77 DRAGENHardSNP AC=1;AF=0.807;AN=2;DP=11393;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:81,242:323:99:9748,0,2580:29,52,108,134 chr2 98128258 . G C 5911.77 DRAGENHardSNP AC=1;AF=0.807;AN=2;DP=11097;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:78,237:315:99:9748,0,2580:26,52,103,134 chr2 98128300 . A G 834.32 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=4463;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:98,23:121:99:290,0,2659:22,76,6,17 chr2 98128313 . G A 510.55 PASS AC=1;AF=0.557;AN=2;DP=2487;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant13-filterInvariant14-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant37-variant38-filterInvariant39-filterInvariant40-variant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:27,44:71:99:1058,0,543:8,19,8,36 chr2 98128515 . C T 124.68 DRAGENHardSNP AC=1;AF=0.536;AN=2;DP=581;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:10,5:15:99:180,0,418:6,4,3,2 chr2 98128520 . G A 124.68 DRAGENHardSNP AC=1;AF=0.536;AN=2;DP=591;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:10,5:15:99:180,0,418:6,4,3,2 chr2 98128531 . C A 43.71 DRAGENHardSNP AC=1;AF=0.539;AN=2;DP=537;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:10,5:15:79:79,0,212:6,4,3,2 chr2 98128574 . C T 40.72 DRAGENHardSNP AC=1;AF=0.539;AN=2;DP=556;FS=0;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:12,5:17:73:73,0,231:6,6,3,2 chr2 98128630 . G T 98.18 PASS AC=1;AF=0.536;AN=2;DP=89;set=filterInvariant5-filterInvariant6-filterInvariant8-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant25-filterInvariant29-filterInvariant30-filterInvariant32-filterInvariant35-filterInvariant36-filterInvariant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:5,3:8:99:111,0,212:1,4,1,2 chr2 98129682 . T C 121.68 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=1353;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:30,21:51:99:791,0,1221:15,15,12,9 chr2 98129683 . G A 121.68 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=1358;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:30,21:51:99:791,0,1221:15,15,12,9 chr2 98129690 . T C 166.67 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=1434;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:30,21:51:99:791,0,1221:15,15,12,9 chr2 98129691 . G A 166.67 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=1436;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:30,21:51:99:791,0,1221:15,15,12,9 chr2 98129707 . G T 334.63 DRAGENHardSNP AC=1;AF=0.511;AN=2;DP=1607;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:29,22:51:99:836,0,1156:14,15,12,10 chr2 98129716 . A G 370.59 DRAGENHardSNP AC=1;AF=0.511;AN=2;DP=1647;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:28,22:50:99:839,0,1134:13,15,12,10 chr2 98129717 . C T 370.59 DRAGENHardSNP AC=1;AF=0.511;AN=2;DP=1649;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:28,22:50:99:839,0,1134:13,15,12,10 chr2 98129731 . C T 451.56 DRAGENHardSNP AC=1;AF=0.511;AN=2;DP=1717;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:29,21:50:99:794,0,1179:13,16,11,10 chr2 98129733 . A C 451.56 DRAGENHardSNP AC=1;AF=0.511;AN=2;DP=1723;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:29,21:50:99:794,0,1179:13,16,11,10 chr2 98129734 . T C 451.56 DRAGENHardSNP AC=1;AF=0.511;AN=2;DP=1730;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:29,21:50:99:794,0,1179:13,16,11,10 chr2 98129744 . C T 451.56 DRAGENHardSNP AC=1;AF=0.511;AN=2;DP=1782;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:29,21:50:99:794,0,1179:13,16,11,10 chr2 98129817 . T C 31.68 DRAGENHardSNP AC=1;AF=0.514;AN=2;DP=810;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:13,6:19:91:91,0,328:1,12,3,3 chr2 98164020 . C T 771.01 PASS AC=1;AF=0.743;AN=2;DP=701;FractionInformativeReads=1;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,3:20:90:90,0,731:9,8,2,1 chr2 98164021 . T C 771.01 PASS AC=1;AF=0.743;AN=2;DP=700;FractionInformativeReads=1;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,4:21:90:90,0,731:9,8,2,2 chr2 98164084 . T A 395.14 PASS AC=1;AF=0.743;AN=2;DP=1081;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-filterInvariant31-variant33-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,10:20:99:285,0,276:5,5,6,4 chr2 98164184 . C G 1055.85 PASS AC=1;AF=0.736;AN=2;DP=2030;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,26:43:99:648,0,392:9,8,16,10 chr2 98169583 . G T 239.21 PASS AC=1;AF=0.75;AN=2;DP=795;FractionInformativeReads=1;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,11:24:99:261,0,351:7,6,6,5 chr2 98169742 . A C 942.28 PASS AC=1;AF=0.736;AN=2;DP=1157;FractionInformativeReads=1;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,12:27:99:335,0,404:9,6,7,5 chr2 98173368 . C T 1740.66 PASS AC=1;AF=0.743;AN=2;DP=1317;FractionInformativeReads=1;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,14:24:99:558,0,441:6,4,9,5 chr2 98173369 . A G 1740.66 PASS AC=1;AF=0.743;AN=2;DP=1329;FractionInformativeReads=1;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,14:24:99:558,0,441:6,4,9,5 chr2 98177124 . T G 1948.72 PASS AC=1;AF=0.736;AN=2;DP=2718;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,21:71:99:419,0,1188:27,23,11,10 chr2 98192743 . A AAC 212.4 PASS AC=1;AF=0.861;AN=2;DP=83;FractionInformativeReads=1;set=variant-variant3-variant4-variant11-variant12-variant14-variant17-variant20-variant21-variant22-variant26-variant28-variant33-variant35-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,5:7:99:246,0,120:1,1,4,1 chr2 98192749 . T C 221.37 PASS AC=1;AF=0.868;AN=2;DP=114;FractionInformativeReads=1;set=variant-variant3-variant4-variant8-variant11-filterInvariant12-filterInvariant14-variant17-variant20-variant21-variant22-variant26-variant28-variant33-variant35-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,5:7:99:204,0,123:1,1,4,1 chr2 98196849 . G A 1276.77 PASS AC=1;AF=0.736;AN=2;DP=1080;FractionInformativeReads=1;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,19:26:99:766,0,461:6,1,13,6 chr2 98196859 . T G 1338.26 PASS AC=1;AF=0.736;AN=2;DP=1279;FractionInformativeReads=1;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,23:32:99:897,0,521:8,1,16,7 chr2 98205924 . C G 737.08 PASS AC=1;AF=0.743;AN=2;DP=784;FractionInformativeReads=1;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,12:28:99:374,0,573:15,1,12,0 chr2 98206188 . C G 3652.09 PASS AC=1;AF=0.743;AN=2;DP=5000;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,54:112:99:1410,0,1626:19,39,18,36 chr2 98264857 . C T 1439.99 PASS AC=1;AF=0.736;AN=2;DP=1480;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,34:61:99:795,0,511:12,15,17,17 chr2 98272734 . A G 2417.07 PASS AC=1;AF=0.825;AN=2;DP=3101;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,53:104:99:1486,0,1181:30,21,31,22 chr2 98273290 . C T 3745.97 PASS AC=1;AF=0.736;AN=2;DP=4601;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,75:143:99:1975,0,1758:41,27,44,31 chr2 98273661 . A G 738.33 PASS AC=1;AF=0.813;AN=2;DP=1193;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,18:37:99:461,0,658:6,13,8,10 chr2 98274527 . G C 4909.86 PASS AC=1;AF=0.813;AN=2;DP=8370;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:137,127:264:99:3033,0,3307:75,62,72,55 chr2 98276014 . CCCTCACCTGCCCTGACCAGAA C 1436.95 PASS AC=1;AF=0.736;AN=2;DP=2826;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,32:58:99:1236,0,1529:5,21,4,28 chr2 98317685 . G A 1963.29 PASS AC=1;AF=0.722;AN=2;DP=3654;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,56:117:99:1305,0,1464:25,36,25,31 chr2 98317771 . C A 739.7 PASS AC=1;AF=0.825;AN=2;DP=1868;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,30:52:99:852,0,628:5,17,11,19 chr2 98330218 . A G 147.77 PASS AC=1;AF=0.855;AN=2;DP=626;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,9:13:98:267,0,98:1,3,6,3 chr2 98340364 . A C 1174.51 PASS AC=2;AF=0.878;AN=2;DP=2248;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:2234,213,0:0,0,44,27 chr2 98372980 . A G 3977.38 PASS AC=2;AF=0.581;AN=2;DP=11718;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant10-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant33-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,345:346:99:10158,999,0:1,0,165,180 chr2 98373006 . C T 12461.7 PASS AC=2;AF=0.792;AN=2;DP=12774;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,321:321:99:9573,962,0:0,0,145,176 chr2 98376989 . TA T 224.27 PASS AC=2;AF=0.863;AN=2;DP=494;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:619,57,0:0,0,14,5 chr2 98392302 . G A 1325.2 PASS AC=1;AF=0.56;AN=2;DP=2308;MQ=60;set=variant3-variant4-variant5-variant10-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant33-variant35-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,33:75:99:970,0,1157:28,14,23,10 chr2 98418812 . CA C 330.69 PASS AC=2;AF=0.632;AN=2;DP=746;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:643,54,0:0,0,14,4 chr2 98435246 . T C 731.27 PASS AC=1;AF=0.5;AN=2;DP=372;FractionInformativeReads=1;MQ=60;set=variant2-variant19-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:62,53:115:99:1187,0,1684:22,40,20,33 chr2 98443694 . C T 2056.24 PASS AC=2;AF=0.583;AN=2;DP=5772;set=variant2-variant3-variant4-variant5-variant7-variant10-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant33-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,181:181:99:5623,540,0:0,0,119,62 chr2 98449796 . C T 523.11 PASS AC=2;AF=1;AN=2;DP=750;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.542;ReadPosRankSum=0.385;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:362,39,0:0,0,7,6 chr2 98451036 . TA T 78.79 PASS AC=2;AF=0.679;AN=2;DP=112;MQ=60;set=variant3-variant14-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant33-variant35-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:105,12,0:0,0,3,1 chr2 98460441 . TAG T 217.55 PASS AC=2;AF=0.685;AN=2;DP=234;MQ=60;set=variant4-variant5-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant29-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:489,33,0:0,0,9,2 chr2 98460742 . G A 193.94 PASS AC=2;AF=0.648;AN=2;DP=346;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant7-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant30-variant33-variant35-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:358,27,0:0,0,2,7 chr2 98475979 . C T 225.93 PASS AC=2;AF=0.645;AN=2;DP=418;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant28-variant29-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:467,33,0:0,0,0,11 chr2 98525107 . T C 2335.59 PASS AC=2;AF=0.866;AN=2;DP=3185;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,80:80:99:2445,240,0:0,0,36,44 chr2 98544058 . T C 134.92 PASS AC=2;AF=0.667;AN=2;DP=366;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant10-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:372,30,0:0,0,1,9 chr2 98611833 . T C 501.44 PASS AC=2;AF=0.875;AN=2;DP=602;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:495,42,0:0,0,11,3 chr2 98611994 . G T 1341.73 PASS AC=2;AF=0.866;AN=2;DP=3016;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,96:97:99:2662,279,0:0,1,50,46 chr2 98612266 . A G 3462.48 PASS AC=2;AF=0.866;AN=2;DP=5309;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,141:141:99:4067,422,0:0,0,79,62 chr2 98797744 . C T 1148.55 PASS AC=1;AF=0.767;AN=2;DP=1653;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,24:40:99:689,0,487:3,13,5,19 chr2 98804314 . G A 855.91 PASS AC=1;AF=0.872;AN=2;DP=963;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,16:25:99:475,0,224:6,3,12,4 chr2 98811075 . A G 1340.37 PASS AC=1;AF=0.86;AN=2;DP=1716;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,24:40:99:624,0,431:5,11,9,15 chr2 98833445 . A ACCC,ACCCC,ACCCCC,ACC 205.58 PASS AC=1,0,0,0;AF=0.273,0.303,0.061,0.076;AN=2;DP=704;MQ=60;set=variant-variant2-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:19:99:0,10,1,8 chr2 98833449 . G GC,C 930.54 PASS AC=0,1;AF=0.125,0.65;AN=2;DP=339;MQ=60;set=variant19-variant22-variant25-variant26-variant27-variant30-variant32-variant33-variant2-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant3-variant41-variant5-variant44 GT:DP:GQ:SB 0/2:20:99:0,10,1,9 chr2 98844575 . A G 243.51 PASS AC=1;AF=0.707;AN=2;DP=1050;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,9:25:99:316,0,473:13,3,9,0 chr2 98844674 . C G 1379.61 PASS AC=1;AF=0.702;AN=2;DP=5520;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,53:112:99:1410,0,1542:34,25,33,20 chr2 98853173 . G A 1736.35 PASS AC=1;AF=0.671;AN=2;DP=3704;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,32:72:99:812,0,1219:14,26,12,20 chr2 98862097 . A G 852.69 PASS AC=1;AF=0.802;AN=2;DP=2080;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,25:43:99:783,0,442:7,11,6,19 chr2 98872662 . C CT,CTT 545.65 PASS AC=1,0;AF=0.698,0.035;AN=2;DP=1751;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:51:99:4,17,8,22 chr2 98887116 . G C 978.99 PASS AC=1;AF=0.55;AN=2;DP=2069;MQ=60;set=variant-variant2-variant4-variant6-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:39,35:74:99:875,0,1056:26,13,24,11 chr2 98928494 . G A 2477.28 PASS AC=2;AF=0.966;AN=2;DP=3758;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,93:93:99:2878,277,0:0,0,55,38 chr2 98928929 . A G 1443.33 PASS AC=1;AF=0.603;AN=2;DP=4342;MQ=60;set=variant-variant2-variant4-variant6-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant22-variant24-variant25-variant26-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:99,89:188:99:2224,0,2339:47,52,44,45 chr2 98929209 . A T 3706.83 PASS AC=1;AF=0.603;AN=2;DP=7985;MQ=60;set=variant-variant2-variant4-variant6-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant22-variant24-variant25-variant26-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:171,133:304:99:3238,0,4363:98,73,80,53 chr2 98948224 . C A 1062.69 PASS AC=1;AF=0.569;AN=2;DP=2999;MQ=60;set=variant-variant2-variant4-variant6-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant22-variant24-variant25-variant26-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:71,69:140:99:1537,0,1864:24,47,29,40 chr2 98950659 . T C 163.47 PASS AC=1;AF=0.571;AN=2;DP=594;MQ=60;set=variant-variant2-variant4-variant6-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant20-variant22-variant24-variant25-variant26-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,15:24:99:488,0,293:3,6,7,8 chr2 98950730 . TC T 51.37 PASS AC=1;AF=0.5;AN=2;DP=20;FS=0;FractionInformativeReads=1;MQ=60;set=variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:5,4:9:89:89,0,124:3,2,2,2 chr2 98986510 . T C 1896.78 PASS AC=1;AF=0.531;AN=2;DP=3071;MQ=60;set=variant2-variant4-variant9-variant14-variant15-variant16-variant17-variant20-variant22-variant25-variant26-variant28-variant31-variant35-variant36-variant40 GT:AD:DP:GQ:PL:SB 0/1:84,111:195:99:2685,0,1991:40,44,57,54 chr2 98993635 . A G 46.75 PASS AC=1;AF=0.682;AN=2;DP=323;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,10:18:99:231,0,224:6,2,6,4 chr2 98994414 . T C 1043.23 PASS AC=1;AF=0.714;AN=2;DP=3117;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,45:95:99:1296,0,1294:34,16,31,14 chr2 99136266 . T C 524.06 PASS AC=1;AF=0.64;AN=2;DP=596;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant9-variant11-variant14-variant15-variant16-variant17-variant20-variant22-variant24-variant25-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:14,19:33:99:505,0,376:9,5,14,5 chr2 99149946 . G A 1217.07 PASS AC=1;AF=0.6;AN=2;DP=3508;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant9-variant11-variant14-variant15-variant16-variant17-variant20-variant22-variant24-variant25-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:80,86:166:99:2035,0,1795:31,49,37,49 chr2 99154229 . C T 1228.51 PASS AC=1;AF=0.62;AN=2;DP=2267;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant9-variant11-variant14-variant15-variant16-variant17-variant20-variant22-variant24-variant25-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:44,55:99:99:1459,0,1184:31,13,36,19 chr2 99160508 . GCA G 223.78 PASS AC=1;AF=0.659;AN=2;DP=663;MQ=60;set=variant2-variant3-variant4-variant5-variant9-variant11-variant14-variant15-variant16-variant17-variant20-variant22-variant24-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:15,9:24:99:263,0,539:4,11,0,9 chr2 99160510 . A G 357.82 PASS AC=1;AF=0.5;AN=2;DP=32;FS=0;FractionInformativeReads=0.969;MQ=60;MQRankSum=0.615;QD=11.18;ReadPosRankSum=0.417;SOR=0.481;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:17,14:31:99:386,0,524:4,13,4,10 chr2 99163261 . T A 579.8 PASS AC=1;AF=0.62;AN=2;DP=1614;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant9-variant11-variant14-variant15-variant16-variant17-variant20-variant22-variant24-variant25-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:40,36:76:99:925,0,1059:16,24,12,24 chr2 99168953 . T C 234.68 PASS AC=2;AF=0.976;AN=2;DP=266;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:349,24,0:0,0,8,0 chr2 99172243 . C T 981.68 PASS AC=1;AF=0.5;AN=2;DP=326;FractionInformativeReads=1;MQ=60;set=variant11-variant12-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:53,32:85:99:802,0,2108:21,32,12,20 chr2 99172244 . A G 171.9 PASS AC=1;AF=0.62;AN=2;DP=2067;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant9-variant11-variant14-variant15-variant16-variant17-variant20-variant22-variant24-variant25-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:32,53:85:99:1338,0,1186:12,20,21,32 chr2 99181315 . AT A 2163.71 PASS AC=1;AF=0.62;AN=2;DP=3681;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant9-variant11-variant14-variant15-variant16-variant17-variant20-variant22-variant24-variant25-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:102,60:162:99:1936,0,3618:46,56,18,42 chr2 99193496 . C T 268.73 PASS AC=1;AF=0.62;AN=2;DP=2010;set=variant-variant2-variant3-variant4-variant5-variant9-variant11-variant14-variant15-variant16-variant17-variant20-variant22-variant24-variant25-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:59,44:103:99:941,0,1360:28,31,19,25 chr2 99204428 . C T 4153.96 PASS AC=1;AF=0.6;AN=2;DP=5938;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant9-variant11-variant14-variant15-variant16-variant17-variant20-variant22-variant24-variant25-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:108,137:245:99:3841,0,2959:42,66,58,79 chr2 99205962 . T C 4898.5 PASS AC=1;AF=0.6;AN=2;DP=7848;set=variant-variant2-variant3-variant4-variant5-variant9-variant11-variant14-variant15-variant16-variant17-variant20-variant22-variant24-variant25-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:159,160:319:99:3839,0,3885:83,76,82,78 chr2 99216531 . A G 721.65 PASS AC=1;AF=0.6;AN=2;DP=1341;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant9-variant11-variant14-variant15-variant16-variant17-variant20-variant22-variant24-variant25-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:27,31:58:99:872,0,752:14,13,21,10 chr2 99216593 . T A 832.8 PASS AC=1;AF=0.6;AN=2;DP=1504;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant9-variant11-variant14-variant15-variant16-variant17-variant20-variant22-variant24-variant25-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:33,39:72:99:1061,0,834:15,18,24,15 chr2 99219071 . T C 80.46 PASS AC=1;AF=0.595;AN=2;DP=208;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant9-variant11-variant14-variant15-variant16-variant20-variant22-variant24-variant25-variant28-variant29-variant31-variant33-variant35-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:7,3:10:99:105,0,284:6,1,3,0 chr2 99219206 . T A 284.5 PASS AC=1;AF=0.6;AN=2;DP=1112;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant9-variant11-variant14-variant15-variant16-variant17-variant20-variant22-variant24-variant25-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:14,21:35:99:516,0,340:6,8,10,11 chr2 99220707 . T C 345.25 PASS AC=1;AF=0.6;AN=2;DP=705;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant9-variant11-variant14-variant15-variant16-variant17-variant20-variant22-variant24-variant25-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:12,14:26:99:365,0,290:5,7,4,10 chr2 99224998 . C G 2120.75 PASS AC=1;AF=0.6;AN=2;DP=4822;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant9-variant11-variant14-variant15-variant16-variant17-variant20-variant22-variant24-variant25-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:104,106:210:99:3147,0,2757:39,65,33,73 chr2 99225168 . C T 1635.7 PASS AC=1;AF=0.6;AN=2;DP=3721;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant9-variant11-variant14-variant15-variant16-variant17-variant20-variant22-variant24-variant25-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:85,91:176:99:2195,0,1945:41,44,48,43 chr2 99225645 . T C 577.56 PASS AC=1;AF=0.6;AN=2;DP=1821;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant9-variant11-variant14-variant15-variant16-variant17-variant20-variant22-variant24-variant25-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:30,29:59:99:633,0,733:18,12,14,15 chr2 99225766 . TGATG T 1102.53 PASS AC=1;AF=0.6;AN=2;DP=1727;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant9-variant11-variant14-variant15-variant16-variant17-variant20-variant22-variant24-variant25-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:36,25:61:99:933,0,2098:18,18,11,14 chr2 99226021 . C T 528.44 PASS AC=1;AF=0.6;AN=2;DP=1218;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant9-variant11-variant14-variant15-variant16-variant17-variant20-variant22-variant24-variant25-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:29,25:54:99:762,0,840:15,14,10,15 chr2 99226173 . T A 849.42 PASS AC=1;AF=0.6;AN=2;DP=1905;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant9-variant11-variant14-variant15-variant16-variant17-variant20-variant22-variant24-variant25-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:37,44:81:99:1200,0,978:16,21,27,17 chr2 99234586 . A AT 234.77 PASS AC=1;AF=0.622;AN=2;DP=2188;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-filterInvariant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,22:54:99:360,0,616:22,10,18,4 chr2 99237439 . A G 2788.18 PASS AC=1;AF=0.6;AN=2;DP=6175;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant9-variant11-variant14-variant15-variant16-variant17-variant20-variant22-variant24-variant25-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:143,94:237:99:2349,0,3849:70,73,48,46 chr2 99237792 . C T 573.14 PASS AC=1;AF=0.604;AN=2;DP=1514;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant9-variant14-variant15-variant16-variant17-variant20-variant22-variant24-variant25-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:38,27:65:99:727,0,1040:17,21,15,12 chr2 99239164 . T C 557.63 PASS AC=1;AF=0.611;AN=2;DP=771;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant11-variant14-variant15-variant16-variant17-variant20-variant24-variant25-variant28-variant30-variant31-variant33-variant35-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:17,15:32:99:344,0,405:5,12,6,9 chr2 99239269 . C T 518.72 PASS AC=1;AF=0.611;AN=2;DP=529;MQ=60;set=variant2-variant5-variant11-variant14-variant15-variant16-variant17-variant20-variant24-variant25-variant28-variant30-variant31-variant33-variant35-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:9,5:14:99:127,0,240:5,4,2,3 chr2 99239497 . G A 72.4 PASS AC=1;AF=0.643;AN=2;DP=160;FractionInformativeReads=1;MQ=60;set=variant2-variant11-variant14-variant15-variant16-variant17-variant20-variant25-variant31-variant33-variant35-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:11,6:17:97:97,0,270:6,5,3,3 chr2 99239931 . C T 687.32 PASS AC=1;AF=0.611;AN=2;DP=1608;MQ=60;set=variant2-variant5-variant11-variant14-variant15-variant16-variant17-variant20-variant24-variant25-variant28-variant30-variant31-variant33-variant35-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:54,33:87:99:760,0,1386:29,25,17,16 chr2 99240243 . A T 1453.16 PASS AC=1;AF=0.611;AN=2;DP=3367;MQ=60;set=variant2-variant5-variant11-variant14-variant15-variant16-variant17-variant20-variant24-variant25-variant28-variant30-variant31-variant33-variant35-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:114,90:204:99:2055,0,2684:57,57,43,47 chr2 99272802 . G A 825.1 PASS AC=1;AF=0.658;AN=2;DP=1418;MQ=60;set=variant2-variant5-variant7-variant8-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant24-variant25-variant26-variant28-variant30-variant35-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:43,35:78:99:851,0,1072:25,18,22,13 chr2 99291196 . A T 289.62 PASS AC=1;AF=0.64;AN=2;DP=372;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant24-variant25-variant26-variant30-variant31-variant33-variant35-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,6:10:99:214,0,153:4,0,6,0 chr2 99449174 . C T 181.05 PASS AC=1;AF=0.682;AN=2;DP=800;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,10:25:99:363,0,538:7,8,8,2 chr2 99613924 . C T 6533.12 PASS AC=1;AF=0.586;AN=2;DP=7055;MQ=60;set=variant2-variant4-variant5-variant7-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:124,114:238:99:2839,0,2920:55,69,44,70 chr2 99614396 . G T 10339.2 PASS AC=1;AF=0.613;AN=2;DP=11319;MQ=60;set=variant2-variant4-variant5-variant7-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:166,207:373:99:4944,0,4251:78,88,101,106 chr2 99695097 . A G 2807.27 PASS AC=1;AF=0.6;AN=2;DP=2091;MQ=60;set=variant2-variant4-variant5-variant7-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:46,42:88:99:1141,0,1075:29,17,30,12 chr2 99721804 . CT C,CTT 88.02 PASS AC=1,0;AF=0.429,0.071;AN=2;DP=739;MQ=60;set=filterInvariant-filterInvariant2-filterInvariant6-variant7-filterInvariant9-filterInvariant11-filterInvariant16-filterInvariant17-filterInvariant26-variant31-variant32-filterInvariant34-filterInvariant35-variant38 GT:DP:GQ:SB 0/1:59:94:30,17,8,4 chr2 99725223 . A G 986.15 PASS AC=1;AF=0.705;AN=2;DP=692;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,12:17:99:400,0,165:5,0,10,2 chr2 99725479 . A AT 1904.54 PASS AC=1;AF=0.7;AN=2;DP=2172;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,36:75:99:1106,0,1228:14,25,10,26 chr2 99726043 . A G 4060.38 PASS AC=2;AF=1;AN=2;DP=5295;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,157:157:99:4682,469,0:0,0,59,98 chr2 99735052 . G T 2933.45 PASS AC=1;AF=0.684;AN=2;DP=2752;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,32:88:99:854,0,1494:38,18,25,7 chr2 99743419 . G A 6129.72 PASS AC=1;AF=0.684;AN=2;DP=7874;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:139,98:237:99:2193,0,3529:85,54,58,40 chr2 99758020 . G GCGCAGGCGCACGCCCA 4861.73 PASS AC=1;AF=0.684;AN=2;DP=5359;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:80,54:134:99:2291,0,4592:43,37,29,25 chr2 99766927 . CT C,CTT 78.44 PASS AC=1,0;AF=0.381,0.119;AN=2;DP=826;set=filterInvariant3-filterInvariant4-variant5-filterInvariant6-variant8-variant9-filterInvariant14-filterInvariant17-variant19-filterInvariant22-filterInvariant26-variant29-filterInvariant30-variant31-variant33-variant35-variant36-filterInvariant37-variant40-variant42-variant44 GT:DP:GQ:SB 0/1:49:99:10,9,19,11 chr2 99771268 . G C 4833.13 PASS AC=1;AF=0.7;AN=2;DP=5934;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:94,88:182:99:3429,0,5128:50,44,52,36 chr2 99771272 . C T 4906.66 PASS AC=1;AF=0.7;AN=2;DP=5961;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:93,90:183:99:3451,0,5125:49,44,53,37 chr2 99771533 . C T 3931.61 PASS AC=1;AF=0.705;AN=2;DP=6704;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:97,82:179:99:2061,0,2429:37,60,30,52 chr2 99771590 . G T 2184.61 PASS AC=1;AF=0.705;AN=2;DP=3193;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,31:76:99:820,0,1401:13,32,12,19 chr2 99771681 . G C 873.65 PASS AC=1;AF=0.588;AN=2;DP=564;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant7-variant13-variant14-variant15-variant16-variant19-variant21-variant23-variant25-variant28-variant31-variant32-variant33-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:15,22:37:99:655,0,447:6,9,12,10 chr2 99778985 . T C 3430.89 PASS AC=1;AF=0.705;AN=2;DP=4184;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:69,62:131:99:1682,0,1694:36,33,32,30 chr2 99779131 . T C 3448.7 PASS AC=1;AF=0.684;AN=2;DP=3755;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,79:129:99:2048,0,1188:24,26,34,45 chr2 99779654 . AC A 237.29 PASS AC=1;AF=0.5;AN=2;DP=3182;set=filterInvariant-variant3-filterInvariant4-variant6-filterInvariant11-filterInvariant12-variant17-variant22-variant24-filterInvariant35-filterInvariant36-variant37-filterInvariant39-filterInvariant41-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:215,35:250:84:84,0,6356:96,119,19,16 chr2 99779655 . C A 2817.42 PASS AC=1;AF=0.513;AN=2;DP=8555;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:187,63:250:99:743,0,4636:88,99,27,36 chr2 99802191 . G A 1661.66 PASS AC=1;AF=0.5;AN=2;DP=644;MQ=60;set=variant5-variant16-variant25-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:68,73:141:99:1670,0,1731:39,29,40,33 chr2 99802820 . A G 541.44 PASS AC=1;AF=0.711;AN=2;DP=492;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,4:10:99:143,0,234:1,5,1,3 chr2 99804642 . T C 2103.25 PASS AC=2;AF=0.93;AN=2;DP=2491;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,63:63:99:2050,188,0:0,0,36,27 chr2 99811894 . C T 2735.02 PASS AC=1;AF=0.7;AN=2;DP=2382;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,38:73:99:1079,0,986:25,10,28,10 chr2 99812070 . G A 5007.06 PASS AC=1;AF=0.7;AN=2;DP=7041;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:89,114:203:99:2581,0,2130:39,50,51,63 chr2 99813614 . T C 806.97 PASS AC=1;AF=0.7;AN=2;DP=774;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-filterInvariant13-variant14-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,5:20:76:76,0,385:6,9,3,2 chr2 99859863 . G A 1504.02 PASS AC=1;AF=0.575;AN=2;DP=1383;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant7-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant23-variant24-variant25-variant28-variant30-variant31-variant32-variant33-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:35,35:70:99:840,0,854:16,19,15,20 chr2 99859954 . CAGATAGATAGATAGAT CAGATAGATAGAT,CAGATAGATAGATAGATAGATAGAT,CAGATAGATAGATAGATAGAT,CAGATAGAT,C 212.98 PASS AC=0,0,2,0,0;AF=0.286,0.143,0.4,0.014,0.014;AN=2;DP=885;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 3/3:5:14:0,0,0,5 chr2 99870872 . AAGATAGTATTCTCACAGGCTC A 148.19 PASS AC=2;AF=0.625;AN=2;DP=134;MQ=60;set=variant3-variant6-variant9-variant11-variant13-variant22-variant23-variant26-variant27-variant31-variant35-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:13:183,13,0:0,0,0,4 chr2 99871370 . G A 54.21 PASS AC=2;AF=0.821;AN=2;DP=63;FS=0;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant6-variant15-variant20-variant22-variant23-variant25-variant31-variant35-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:178,15,0:0,0,3,2 chr2 99918077 . A G 106.77 PASS AC=2;AF=0.959;AN=2;DP=295;set=variant-variant2-variant3-variant5-variant6-filterInvariant7-variant9-variant11-variant13-variant14-variant15-variant16-filterInvariant17-variant19-filterInvariant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-filterInvariant30-variant31-variant32-variant33-variant35-filterInvariant36-variant37-variant38-variant39-variant40-filterInvariant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:273,21,0:0,0,7,0 chr2 99923088 . T C 1145.68 PASS AC=2;AF=0.919;AN=2;DP=1521;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:1840,165,0:0,0,43,12 chr2 99938942 . A G 690.78 PASS AC=2;AF=0.629;AN=2;DP=873;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:804,66,0:0,0,18,4 chr2 99939031 . A G 1240.93 PASS AC=2;AF=0.629;AN=2;DP=3276;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:2250,228,0:0,0,46,30 chr2 99954608 . A G 805.63 PASS AC=1;AF=0.609;AN=2;DP=1321;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant7-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant28-variant30-variant31-variant32-variant33-variant35-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:35,31:66:99:816,0,844:21,14,21,10 chr2 99954636 . GT G 1582.95 PASS AC=2;AF=0.93;AN=2;DP=3443;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,86:87:99:2529,232,0:0,1,54,32 chr2 99976564 . A G 61.77 PASS AC=2;AF=0.978;AN=2;DP=74;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.736;ReadPosRankSum=0.736;set=variant2-variant3-variant4-variant5-variant6-variant11-variant12-variant16-variant19-variant21-variant25-variant26-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:82,6,0:0,0,2,0 chr2 99978048 . G A 837.01 PASS AC=1;AF=0.571;AN=2;DP=461;MQ=60;set=variant3-variant6-variant9-variant11-variant22-variant23-variant26-variant27-variant35-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,16:31:99:421,0,416:8,7,8,8 chr2 99988453 . CA C 161.26 PASS AC=2;AF=0.708;AN=2;DP=442;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:342,30,0:0,0,0,10 chr2 99992822 . A C 388.73 PASS AC=2;AF=0.697;AN=2;DP=835;set=variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:713,60,0:0,0,16,4 chr2 99995458 . AT A,ATT 50.99 PASS AC=2,0;AF=0.594,0.016;AN=2;DP=456;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant44 GT:DP:GQ:SB 1/1:11:33:0,0,8,3 chr2 99995517 . C T 819.88 PASS AC=1;AF=0.614;AN=2;DP=785;MQ=60;set=variant2-variant5-variant7-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant28-variant30-variant31-variant32-variant33-variant35-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:16,17:33:99:356,0,375:9,7,10,7 chr2 99995804 . T C 1453.33 PASS AC=2;AF=0.692;AN=2;DP=6367;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,129:129:99:3779,386,0:0,0,58,71 chr2 99998561 . C T 356.54 PASS AC=2;AF=0.684;AN=2;DP=1004;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:872,75,0:0,0,18,7 chr2 100006620 . G T 794.64 PASS AC=2;AF=0.679;AN=2;DP=1494;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1640,138,0:0,0,36,10 chr2 100006890 . GT GTT,G 276.2 PASS AC=1,0;AF=0.473,0.027;AN=2;DP=3452;set=variant-variant2-variant3-filterInvariant4-variant5-variant6-variant7-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-filterInvariant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:DP:GQ:SB 0/1:82:69:7,5,36,34 chr2 100010685 . A G 742.42 PASS AC=1;AF=0.571;AN=2;DP=620;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant9-variant11-variant22-variant23-variant26-variant27-variant35-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,21:43:99:573,0,570:15,7,13,8 chr2 100016713 . G C 301.15 PASS AC=2;AF=0.629;AN=2;DP=985;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:628,60,0:0,0,8,12 chr2 100017906 . CAA C,CA,CAAA,CAAAA 30.23 PASS AC=0,0,1,0;AF=0.031,0.156,0.156,0.188;AN=2;DP=434;set=filterInvariant-variant4-filterInvariant6-variant7-variant8-variant10-variant11-variant18-variant21-variant23-variant24-variant27-variant35-variant39-variant40-variant42 GT:DP:GQ:SB 0/3:18:99:1,9,2,6 chr2 100019496 . A G 1470.76 PASS AC=2;AF=0.679;AN=2;DP=3017;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,78:78:99:2305,234,0:0,0,36,42 chr2 100019612 . TG T 617.48 PASS AC=2;AF=0.629;AN=2;DP=1106;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:1048,84,0:0,0,8,20 chr2 100021184 . A G 1393.87 PASS AC=2;AF=0.629;AN=2;DP=3196;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,121:121:99:4066,362,0:0,0,35,86 chr2 100022270 . G A 93.2 PASS AC=2;AF=0.661;AN=2;DP=284;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant35-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:356,27,0:0,0,8,1 chr2 100022772 . T C 1129.84 PASS AC=2;AF=0.629;AN=2;DP=3073;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,108:110:99:3481,295,0:1,1,73,35 chr2 100055506 . A G 868.59 PASS AC=2;AF=0.679;AN=2;DP=2415;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,66:66:99:2296,198,0:0,0,35,31 chr2 100058714 . CAAA CAAAAA,CAAAAAA,CAAAAAAA,CAAAA,CAA,C 42.4 PASS AC=2,0,0,0,0,0;AF=0.214,0.095,0.024,0.119,0.048,0.024;AN=2;DP=411;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant13-variant15-variant19-variant22-variant24-variant25-variant26-variant29-variant33-variant35-variant37-variant38-variant42-variant43 GT:DP:GQ:SB 1/1:11:6:1,0,7,3 chr2 100058870 . C T 1052.61 PASS AC=1;AF=0.609;AN=2;DP=2281;MQ=60;set=variant-variant2-variant5-variant7-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant28-variant30-variant31-variant32-variant33-variant35-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:47,43:90:99:1018,0,1069:22,25,22,21 chr2 100068069 . T C 143.08 PASS AC=2;AF=0.647;AN=2;DP=828;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:690,57,0:0,0,3,16 chr2 100081317 . T C 936.35 PASS AC=1;AF=0.591;AN=2;DP=684;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant9-variant11-variant22-variant23-variant35-variant37-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,31:72:99:815,0,996:27,14,19,12 chr2 100081323 . C T 538.4 PASS AC=2;AF=0.679;AN=2;DP=2536;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,78:78:99:2855,234,0:0,0,48,30 chr2 100081561 . A AAAGTC 524.02 PASS AC=2;AF=0.719;AN=2;DP=318;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant33-variant35-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:135,9,0:0,0,0,3 chr2 100106547 . C CCGGCCCCGCCCACGCCCCCTCCG,CCGGCCCCGCCCAGGCCCCCTCCG 184.98 PASS AC=2,0;AF=0.712,0.038;AN=2;DP=227;MQ=60;set=variant2-variant3-variant5-variant8-variant11-variant13-variant15-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant33-variant35-variant37-variant38-variant40-variant41-variant42-variant44 GT:DP:GQ:SB 1/1:10:34:0,0,4,6 chr2 100167615 . GGTGT G,GGTGTGT,GGT 121.6 PASS AC=1,0,0;AF=0.52,0.08,0.12;AN=2;DP=254;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant13-variant14-variant15-variant19-variant21-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant38-variant43 GT:DP:GQ:SB 0/1:8:99:3,2,2,1 chr2 100170728 . C G 1283.61 PASS AC=1;AF=0.5;AN=2;DP=108;FS=0.758;FractionInformativeReads=1;MQ=60;MQRankSum=-0.516;QD=11.89;ReadPosRankSum=2.538;SOR=0.569;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:55,53:108:99:1312,0,1456:37,18,34,19 chr2 100210074 . G C 554.28 PASS AC=1;AF=0.528;AN=2;DP=1732;MQ=60;set=variant-variant4-variant6-variant8-variant21-variant22-variant25-variant26-variant29-variant30-variant31-variant32-variant35-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,51:102:99:1327,0,1430:25,26,24,27 chr2 100210642 . T C 1949.96 PASS AC=1;AF=0.528;AN=2;DP=4351;MQ=60;set=variant-variant4-variant6-variant8-variant21-variant22-variant25-variant26-variant29-variant30-variant31-variant32-variant35-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:148,148:296:99:3774,0,3517:71,77,57,91 chr2 100218080 . G A 116.77 PASS AC=1;AF=0.579;AN=2;DP=834;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant19-variant21-variant28-variant32-variant33-variant35-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:22,18:40:99:444,0,532:8,14,6,12 chr2 100265936 . A G 91.72 PASS AC=1;AF=0.556;AN=2;DP=69;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant25-variant31-variant35-variant37-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,4:9:99:150,0,198:5,0,4,0 chr2 100288931 . G A 964.32 PASS AC=1;AF=0.633;AN=2;DP=2503;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant23-variant26-variant27-variant28-variant32-variant33-variant34-variant35-variant36-variant37-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:37,60:97:99:1583,0,795:22,15,36,24 chr2 100343557 . C T 3142.78 PASS AC=2;AF=1;AN=2;DP=4881;FS=0;MQ=60;MQRankSum=-0.917;ReadPosRankSum=1.703;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,111:111:99:3411,333,0:0,0,60,51 chr2 100360350 . T C 367.01 PASS AC=1;AF=0.533;AN=2;DP=347;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant6-variant8-variant9-variant10-variant12-variant14-variant16-variant17-variant28-variant29-variant35-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,11:20:99:391,0,264:6,3,8,3 chr2 100454072 . C CT 2365.07 PASS AC=2;AF=0.825;AN=2;DP=3134;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,61:61:99:2452,184,0:0,0,25,36 chr2 100721050 . A G 231.69 PASS AC=1;AF=0.685;AN=2;DP=296;set=variant-variant2-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant27-variant28-variant29-variant33-variant35-variant36-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,7:10:62:209,0,62:1,2,1,6 chr2 100891976 . C T 839.2 PASS AC=2;AF=0.86;AN=2;DP=1930;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1519,134,0:0,0,19,26 chr2 100892516 . C T 1930.17 PASS AC=1;AF=0.721;AN=2;DP=2937;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,35:64:99:1064,0,849:11,18,12,23 chr2 100893113 . C A 4496.03 PASS AC=1;AF=0.721;AN=2;DP=7617;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:78,111:189:99:2721,0,1883:30,48,50,61 chr2 100894114 . C G 1774.15 PASS AC=1;AF=0.707;AN=2;DP=2645;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,35:69:99:1328,0,1909:15,19,17,18 chr2 100894115 . T C 1774.15 PASS AC=1;AF=0.707;AN=2;DP=2661;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,35:70:99:1328,0,1909:16,19,17,18 chr2 100894802 . C G 3136.03 PASS AC=1;AF=0.709;AN=2;DP=4063;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,61:111:99:1686,0,1261:21,29,26,35 chr2 100894887 . C T 1658.4 PASS AC=1;AF=0.707;AN=2;DP=2238;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,38:65:99:1037,0,709:9,18,18,20 chr2 100895081 . G A 1553.35 PASS AC=1;AF=0.675;AN=2;DP=2450;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,28:58:99:696,0,747:17,13,16,12 chr2 100895784 . ACC AC,A 1255.44 PASS AC=2,0;AF=0.726,0.012;AN=2;DP=3418;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:79:99:3,0,36,40 chr2 100895872 . G A 2318.19 PASS AC=2;AF=0.725;AN=2;DP=3810;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,98:98:99:3287,293,0:0,0,44,54 chr2 100896110 . T C 3216.09 PASS AC=2;AF=0.725;AN=2;DP=2807;FractionInformativeReads=1;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:3139,211,0:0,0,30,40 chr2 100896112 . C T 3216.09 PASS AC=2;AF=0.725;AN=2;DP=2780;FractionInformativeReads=1;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:3139,211,0:0,0,30,40 chr2 100896242 . A G 1612.02 PASS AC=2;AF=0.725;AN=2;DP=2691;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:1478,143,0:0,0,23,25 chr2 100896311 . G T 1891.03 PASS AC=2;AF=0.725;AN=2;DP=2983;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:2166,213,0:0,0,36,35 chr2 100896376 . G C 1550.22 PASS AC=2;AF=0.725;AN=2;DP=2457;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,64:64:99:1912,192,0:0,0,31,33 chr2 100896415 . C T 1837.96 PASS AC=2;AF=0.725;AN=2;DP=2255;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1630,153,0:0,0,23,28 chr2 100896512 . G A 1501.15 PASS AC=2;AF=0.725;AN=2;DP=2041;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1098,114,0:0,0,16,22 chr2 100896964 . A G 331.77 PASS AC=2;AF=0.738;AN=2;DP=533;FractionInformativeReads=1;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:385,27,0:0,0,3,6 chr2 100896966 . G A 331.77 PASS AC=2;AF=0.725;AN=2;DP=498;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:27:385,27,0:0,0,2,6 chr2 100897008 . C T 112.51 PASS AC=2;AF=0.742;AN=2;DP=232;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:184,15,0:0,0,2,3 chr2 100897214 . G A 2117.35 PASS AC=2;AF=0.725;AN=2;DP=2072;FractionInformativeReads=1;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:1854,162,0:0,0,40,14 chr2 100897351 . T A 8594.84 PASS AC=2;AF=0.725;AN=2;DP=11946;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,338:338:99:9857,1012,0:0,0,181,157 chr2 100897573 . G A 8689 PASS AC=2;AF=0.725;AN=2;DP=12602;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,307:307:99:9371,920,0:0,0,134,173 chr2 100897674 . T A 5188.8 PASS AC=2;AF=0.744;AN=2;DP=6311;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,147:147:99:4863,440,0:0,0,55,92 chr2 100897739 . GTTTT G 5160.92 PASS AC=2;AF=0.725;AN=2;DP=5034;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,111:111:99:4805,334,0:0,0,51,60 chr2 100898081 . T C 478.93 PASS AC=2;AF=0.625;AN=2;DP=540;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant10-variant20-variant26-variant27-variant32-variant33-variant35-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:983,90,0:0,0,17,13 chr2 100898634 . G T 1281.89 PASS AC=2;AF=0.725;AN=2;DP=2012;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1388,119,0:0,0,16,24 chr2 100899258 . GAAAACTAAAAGAAAAATTAATAATATTATAA G 447.44 PASS AC=2;AF=0.75;AN=2;DP=4370;set=variant-variant2-variant3-variant5-filterInvariant6-variant7-variant8-variant9-variant10-variant11-filterInvariant12-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant22-filterInvariant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-filterInvariant37-variant38-filterInvariant39-variant40-filterInvariant41-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,18:19:94:893,94,0:1,0,2,16 chr2 100899292 . TCTTTATCTACTGAAACTAC T 453.26 PASS AC=2;AF=0.744;AN=2;DP=3750;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-filterInvariant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-filterInvariant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,18:19:99:933,100,0:1,0,2,16 chr2 100899328 . T TA 393.96 PASS AC=2;AF=0.744;AN=2;DP=2653;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,19:20:79:886,79,0:1,0,2,17 chr2 100899665 . G A 7126.25 PASS AC=2;AF=0.725;AN=2;DP=8954;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:4,226:230:99:6796,568,0:3,1,130,96 chr2 100899676 . T C 8273.52 PASS AC=2;AF=0.725;AN=2;DP=10125;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,244:246:99:7310,685,0:1,1,141,103 chr2 100900038 . AAT AATAT,A 2418.99 PASS AC=1,0;AF=0.488,0.012;AN=2;DP=6076;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-filterInvariant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:DP:GQ:SB 0/1:70:99:2,8,25,35 chr2 100900304 . T C 1813.59 PASS AC=2;AF=0.738;AN=2;DP=2595;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1534,150,0:0,0,27,23 chr2 100900379 . C T 836.36 PASS AC=2;AF=0.625;AN=2;DP=916;MQ=60;set=variant2-variant3-variant10-variant20-variant26-variant27-variant32-variant33-variant35-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,66:66:99:1954,197,0:0,0,33,33 chr2 100900406 . G A 1564.56 PASS AC=2;AF=0.744;AN=2;DP=3246;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:1958,195,0:0,0,29,36 chr2 100910578 . C T 1038.34 PASS AC=2;AF=0.607;AN=2;DP=1243;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant10-variant20-variant26-variant27-variant32-variant33-variant35-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,81:81:99:2619,243,0:0,0,56,25 chr2 100915629 . T C 1913.99 PASS AC=2;AF=0.726;AN=2;DP=2774;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:1994,186,0:0,0,41,21 chr2 100915772 . A G 2008.14 PASS AC=2;AF=0.726;AN=2;DP=2794;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,81:81:99:2501,243,0:0,0,31,50 chr2 100916051 . T C 160.45 PASS AC=2;AF=0.79;AN=2;DP=206;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant19-variant20-variant21-variant22-variant23-variant26-variant28-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:223,24,0:0,0,5,3 chr2 100916306 . A G 1103.52 PASS AC=2;AF=0.726;AN=2;DP=1913;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:1642,173,0:0,0,25,33 chr2 100938205 . G A 241.19 PASS AC=2;AF=0.636;AN=2;DP=170;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant10-variant20-variant26-variant27-variant32-variant33-variant35-variant39-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:80:944,80,0:0,0,10,17 chr2 100986964 . A C 1780.38 PASS AC=2;AF=0.762;AN=2;DP=1855;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,46:47:99:1566,107,0:1,0,13,33 chr2 101033756 . C T 306.41 PASS AC=2;AF=0.907;AN=2;DP=736;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,21:21:62:616,62,0:0,0,12,9 chr2 101089415 . C T 1113.69 PASS AC=1;AF=0.5;AN=2;DP=66;FS=4.023;FractionInformativeReads=1;MQ=60;MQRankSum=0.798;QD=16.87;ReadPosRankSum=-1.031;SOR=1.378;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:28,38:66:99:1142,0,775:9,19,8,30 chr2 101089919 . CTTTGA C 1874.51 PASS AC=1;AF=0.5;AN=2;DP=200;MQ=60;set=variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:40,49:89:99:1912,0,1893:11,29,22,27 chr2 101126124 . T A 7735.36 PASS AC=1;AF=0.898;AN=2;DP=11299;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:113,149:262:99:3814,0,2991:47,66,65,84 chr2 101436708 . C CGCGGCG,CGCG,CGCGGCGGCGGCGGCG 97.73 PASS AC=2,0,0;AF=0.587,0.065,0.043;AN=2;DP=207;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant11-variant12-variant13-variant14-variant16-variant20-variant23-variant25-variant31-variant34-variant35-variant36-variant37-variant38-variant39-variant43-variant44 GT:DP:GQ:SB 1/1:10:30:0,0,4,6 chr2 101520972 . A AT 432.93 PASS AC=2;AF=0.907;AN=2;DP=675;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:767,57,0:0,0,14,5 chr2 101521173 . ATTT AT,ATT,A,ATTTT 665.56 PASS AC=0,1,0,0;AF=0.337,0.302,0.012,0.012;AN=2;DP=2101;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-filterInvariant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:32:99:9,9,3,11 chr2 101541798 . C T 1986.79 PASS AC=2;AF=0.932;AN=2;DP=3552;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,97:97:99:2943,290,0:0,0,38,59 chr2 101564628 . A G,C 1270.53 PASS AC=2,0;AF=0.646,0.049;AN=2;DP=3877;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:88:99:0,0,54,34 chr2 101566070 . C T 670.34 PASS AC=2;AF=0.689;AN=2;DP=1749;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1509,135,0:0,0,16,29 chr2 101581246 . C T 2324.75 PASS AC=2;AF=0.898;AN=2;DP=3276;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,109:109:99:3434,327,0:0,0,67,42 chr2 101581934 . CA C 263.05 PASS AC=2;AF=0.75;AN=2;DP=1072;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:773,81,0:0,0,22,5 chr2 101581976 . A G 722.4 PASS AC=2;AF=0.786;AN=2;DP=1912;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1415,114,0:0,0,30,8 chr2 101591304 . A G 885.05 PASS AC=2;AF=0.75;AN=2;DP=4365;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,87:87:99:2639,260,0:0,0,42,45 chr2 101609827 . C T 1588.85 PASS AC=1;AF=0.62;AN=2;DP=5287;MQ=60;set=variant-variant4-variant5-variant8-variant11-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:145,110:255:99:2498,0,3488:74,71,61,49 chr2 101612568 . C T 1872.74 PASS AC=1;AF=0.64;AN=2;DP=2981;MQ=60;set=variant-variant4-variant5-variant8-variant11-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:73,53:126:99:1218,0,1914:40,33,30,23 chr2 101612584 . T A 1847.47 PASS AC=2;AF=0.655;AN=2;DP=3650;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,125:125:99:3283,374,0:0,0,71,54 chr2 101612615 . T C 3364.14 PASS AC=2;AF=0.788;AN=2;DP=5210;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,133:133:99:3911,398,0:0,0,70,63 chr2 101613409 . A T 49.76 PASS AC=2;AF=0.673;AN=2;DP=204;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant11-variant12-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant28-variant29-variant32-variant33-variant34-variant35-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:235,18,0:0,0,0,6 chr2 101618219 . A G 1033.54 PASS AC=1;AF=0.596;AN=2;DP=2511;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant24-variant25-variant26-variant27-variant28-variant33-variant35-variant36-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,42:98:99:981,0,1354:30,26,26,16 chr2 101619283 . C G 6194.7 PASS AC=2;AF=0.893;AN=2;DP=9830;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,247:248:99:7202,733,0:1,0,126,121 chr2 101619321 . T C 6491.53 PASS AC=2;AF=0.813;AN=2;DP=9996;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,276:276:99:7978,826,0:0,0,127,149 chr2 101619377 . C T 2086.95 PASS AC=1;AF=0.5;AN=2;DP=1055;MQ=60;set=variant2-variant3-variant9-variant33-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:89,95:184:99:2489,0,2238:31,58,30,65 chr2 101622728 . C T 3913.11 PASS AC=1;AF=0.64;AN=2;DP=8701;MQ=60;set=variant-variant4-variant5-variant8-variant11-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:207,155:362:99:3869,0,5390:100,107,71,84 chr2 101623227 . C T 3757.15 PASS AC=1;AF=0.5;AN=2;DP=1921;MQ=60;set=variant2-variant3-variant9-variant33-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:151,170:321:99:4276,0,4083:68,83,82,88 chr2 101623667 . C T 1713.83 PASS AC=1;AF=0.548;AN=2;DP=2995;MQ=60;set=variant-variant4-variant5-variant11-variant12-variant14-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant29-variant31-variant32-variant33-variant34-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:75,85:160:99:2099,0,1769:35,40,41,44 chr2 101623745 . T A 911.42 PASS AC=1;AF=0.64;AN=2;DP=1799;MQ=60;set=variant-variant4-variant5-variant8-variant11-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:44,45:89:99:1287,0,1183:15,29,15,30 chr2 101624471 . T C 3944.6 PASS AC=2;AF=0.788;AN=2;DP=8071;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,257:257:99:7782,770,0:0,0,140,117 chr2 101627925 . C T 496.85 PASS AC=1;AF=0.5;AN=2;DP=306;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant9-variant33-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:23,19:42:99:588,0,621:17,6,13,6 chr2 101634707 . T C 1344.06 PASS AC=1;AF=0.5;AN=2;DP=780;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant9-variant33-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:71,62:133:99:1455,0,1784:29,42,25,37 chr2 101634793 . GTTCA G 1279.27 PASS AC=1;AF=0.64;AN=2;DP=1485;MQ=60;set=variant-variant4-variant5-variant8-variant11-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:17,31:48:99:1251,0,580:5,12,9,22 chr2 101634830 . T A 206.17 PASS AC=1;AF=0.5;AN=2;DP=166;MQ=60;set=variant2-variant3-variant9-variant33-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:17,7:24:99:136,0,568:3,14,1,6 chr2 101635369 . G A 731.78 PASS AC=1;AF=0.5;AN=2;DP=402;MQ=60;set=variant2-variant3-variant9-variant33-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:29,37:66:99:940,0,668:17,12,23,14 chr2 101635538 . C T 707.23 PASS AC=1;AF=0.64;AN=2;DP=1769;set=variant-variant4-variant5-variant8-variant11-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:41,27:68:99:743,0,1146:17,24,14,13 chr2 101635989 . T A 2306.05 PASS AC=1;AF=0.5;AN=2;DP=1459;MQ=60;set=variant2-variant3-variant9-variant33-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:121,101:222:99:2245,0,3074:57,64,49,52 chr2 101638828 . C T 704.69 PASS AC=1;AF=0.5;AN=2;DP=603;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant9-variant33-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:62,69:131:99:1662,0,1448:32,30,36,33 chr2 101638888 . A G 2440.5 PASS AC=2;AF=0.825;AN=2;DP=4364;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,133:133:99:3997,398,0:0,0,72,61 chr2 101644855 . G A 1456.57 PASS AC=1;AF=0.64;AN=2;DP=3808;set=variant-variant2-variant4-variant5-variant8-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:91,94:185:99:2229,0,2084:53,38,52,42 chr2 101646359 . G C 38.97 PASS AC=1;AF=0.64;AN=2;DP=397;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant11-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,4:15:81:81,0,275:3,8,1,3 chr2 101652732 . C T 710.33 PASS AC=1;AF=0.654;AN=2;DP=1241;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant11-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:24,24:48:99:695,0,743:7,17,5,19 chr2 101656726 . T C 1386.51 PASS AC=2;AF=0.788;AN=2;DP=4498;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,127:127:99:3977,381,0:0,0,56,71 chr2 101675808 . A G 625.78 PASS AC=1;AF=0.643;AN=2;DP=1100;FractionInformativeReads=1;set=variant-variant2-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:18,16:34:99:459,0,478:11,7,10,6 chr2 101879023 . G A 1693.87 PASS AC=1;AF=0.5;AN=2;DP=800;FractionInformativeReads=1;MQ=60;set=variant3-variant13-variant35-variant36-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:64,65:129:99:1657,0,1487:35,29,38,27 chr2 101883027 . T C 247.6 PASS AC=1;AF=0.563;AN=2;DP=359;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant11-variant12-variant13-variant15-variant16-variant18-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,8:20:99:181,0,379:10,2,5,3 chr2 101883046 . A G 347.03 PASS AC=2;AF=0.672;AN=2;DP=605;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:911,72,0:0,0,17,7 chr2 101889938 . CTT CT,C,CTTT,CTTTTT 76.09 PASS AC=1,0,0,0;AF=0.393,0.036,0.054,0.036;AN=2;DP=1288;set=filterInvariant-variant2-filterInvariant3-filterInvariant4-filterInvariant5-variant6-variant7-filterInvariant8-variant10-filterInvariant12-filterInvariant13-variant14-filterInvariant17-filterInvariant19-variant21-filterInvariant24-filterInvariant25-filterInvariant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-filterInvariant37-variant41 GT:DP:GQ:SB 0/1:36:87:5,7,4,20 chr2 101893567 . C G 2169.77 PASS AC=1;AF=0.5;AN=2;DP=154;FS=2.309;FractionInformativeReads=1;MQ=60;MQRankSum=0.087;QD=14.09;ReadPosRankSum=-0.669;SOR=0.472;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:77,77:154:99:2198,0,2358:19,58,23,54 chr2 101898412 . G C 2408.65 PASS AC=2;AF=0.864;AN=2;DP=3273;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,84:84:99:2576,252,0:0,0,43,41 chr2 101925026 . T C 4044.61 PASS AC=1;AF=0.672;AN=2;DP=10006;MQ=60;set=variant2-variant3-variant5-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:178,168:346:99:4034,0,4541:74,104,73,95 chr2 101965113 . T C 1528.86 PASS AC=1;AF=0.738;AN=2;DP=1584;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,18:42:99:504,0,566:15,9,14,4 chr2 101965145 . T A 4320.57 PASS AC=1;AF=0.72;AN=2;DP=3232;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,43:79:99:1681,0,1455:21,15,30,13 chr2 101965146 . T A 4320.15 PASS AC=1;AF=0.762;AN=2;DP=3373;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,44:81:99:1681,0,1455:21,16,30,14 chr2 101965147 . A T 659.09 PASS AC=1;AF=0.5;AN=2;DP=1143;MQ=60;set=variant2-variant3-variant12-variant13-variant16-variant18-variant22-variant27-variant29-variant30-variant35-variant36-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:44,38:82:99:860,0,1728:30,14,22,16 chr2 101965367 . G A 9391 PASS AC=2;AF=0.909;AN=2;DP=9558;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,202:202:99:6787,606,0:0,0,90,112 chr2 101965448 . A T 7760.65 PASS AC=1;AF=0.738;AN=2;DP=7368;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:90,94:184:99:2414,0,2069:42,48,41,53 chr2 101965731 . C T 1052.57 PASS AC=1;AF=0.5;AN=2;DP=105;FS=0.727;FractionInformativeReads=1;MQ=60;MQRankSum=-1.618;QD=10.02;ReadPosRankSum=-2.563;SOR=0.597;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:57,48:105:99:1081,0,1451:30,27,24,24 chr2 101965861 . C T 1661.6 PASS AC=1;AF=0.5;AN=2;DP=1675;MQ=60;set=variant2-variant3-variant12-variant13-variant16-variant18-variant22-variant27-variant29-variant30-variant35-variant36-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:71,54:125:99:1583,0,2797:41,30,32,22 chr2 101965864 . C T 4487.28 PASS AC=1;AF=0.738;AN=2;DP=5296;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,71:126:99:2049,0,2076:32,23,41,30 chr2 101966038 . C A 3631.37 PASS AC=1;AF=0.577;AN=2;DP=8525;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant11-variant12-variant15-variant16-variant19-variant23-variant24-variant25-variant26-variant28-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:135,178:313:99:4235,0,3115:58,77,83,95 chr2 101967058 . TC T 7898.16 PASS AC=1;AF=0.738;AN=2;DP=13040;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:169,145:314:99:3119,0,5111:79,90,74,71 chr2 101967346 . C T 4429.85 PASS AC=1;AF=0.738;AN=2;DP=4374;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,71:124:99:1980,0,1429:29,24,45,26 chr2 102000210 . G A 727.75 PASS AC=1;AF=0.577;AN=2;DP=1118;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant11-variant12-variant15-variant16-variant19-variant23-variant24-variant25-variant26-variant28-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:18,40:58:99:1023,0,520:4,14,16,24 chr2 102003962 . T C 1046.36 PASS AC=1;AF=0.583;AN=2;DP=1109;MQ=60;set=variant3-variant5-variant6-variant9-variant11-variant12-variant15-variant16-variant19-variant23-variant24-variant25-variant26-variant28-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:30,21:51:99:616,0,890:9,21,7,14 chr2 102018878 . G A 1551.36 PASS AC=1;AF=0.565;AN=2;DP=3565;MQ=60;set=variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant16-variant19-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant33-variant35-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:93,77:170:99:1842,0,2136:46,47,39,38 chr2 102018908 . A G 4004.91 PASS AC=1;AF=0.681;AN=2;DP=4891;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,81:149:99:1965,0,1823:32,36,40,41 chr2 102026879 . A ACACT,ACACACT,ACT 389.32 PASS AC=1,0,0;AF=0.556,0.111,0.019;AN=2;DP=347;set=variant-variant2-variant4-variant5-variant7-variant9-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant29-variant31-variant33-variant34-variant35-variant37-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:19:99:8,1,9,1 chr2 102029273 . T C 333.9 PASS AC=1;AF=0.604;AN=2;DP=466;MQ=60;set=variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant16-variant19-variant22-variant24-variant25-variant26-variant27-variant28-variant30-variant33-variant35-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:18,12:30:99:322,0,529:13,5,10,2 chr2 102029548 . G A 653.41 PASS AC=1;AF=0.568;AN=2;DP=891;MQ=60;set=variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant16-variant19-variant23-variant24-variant25-variant26-variant28-variant30-variant33-variant35-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:20,26:46:99:852,0,541:6,14,6,20 chr2 102031176 . A G 1275.61 PASS AC=2;AF=0.989;AN=2;DP=1445;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1252,105,0:0,0,28,7 chr2 102031489 . C G 2040.65 PASS AC=2;AF=0.821;AN=2;DP=2442;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:2048,177,0:0,0,16,43 chr2 102033867 . T C 238.54 PASS AC=2;AF=0.988;AN=2;DP=240;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.72;ReadPosRankSum=0.72;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:342,24,0:0,0,7,1 chr2 102035192 . C T 1761.03 PASS AC=2;AF=0.821;AN=2;DP=2417;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,67:67:99:1873,200,0:0,0,35,32 chr2 102038849 . T A 5254.03 PASS AC=2;AF=0.989;AN=2;DP=7316;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,203:203:99:5754,607,0:0,0,92,111 chr2 102045328 . C T 1654.14 PASS AC=2;AF=0.742;AN=2;DP=1124;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1495,126,0:0,0,33,9 chr2 102066878 . A T 141.1 PASS AC=2;AF=0.866;AN=2;DP=341;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:543,45,0:0,0,14,1 chr2 102067083 . T C 1790.74 PASS AC=2;AF=0.857;AN=2;DP=2931;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,85:85:99:2619,254,0:0,0,36,49 chr2 102083183 . T C 2159.24 PASS AC=2;AF=0.73;AN=2;DP=1966;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:2003,186,0:0,0,42,20 chr2 102091075 . G A 1340.18 PASS AC=2;AF=0.716;AN=2;DP=3741;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,104:104:99:3029,310,0:0,0,53,51 chr2 102314391 . C CCCG 1387.15 PASS AC=1;AF=0.646;AN=2;DP=1176;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant33-variant35-variant36-variant37-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,24:63:99:889,0,1532:29,10,19,5 chr2 102314437 . T C 1986.88 PASS AC=2;AF=0.782;AN=2;DP=5584;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,146:146:99:4478,437,0:0,0,94,52 chr2 102314633 . G GGGCAGCC 1190.75 PASS AC=1;AF=0.559;AN=2;DP=1981;MQ=60;set=variant2-variant3-variant4-variant9-variant10-variant11-variant13-variant15-variant26-variant29-variant30-variant35-variant36-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,22:61:99:821,0,2442:12,27,5,17 chr2 102315057 . A G 285.44 PASS AC=1;AF=0.553;AN=2;DP=534;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant9-variant10-variant11-variant13-variant15-variant26-variant29-variant30-variant32-variant35-variant36-variant37-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,10:33:99:258,0,677:6,17,2,8 chr2 102440723 . G A 211.36 PASS AC=2;AF=0.888;AN=2;DP=394;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:283,27,0:0,0,4,5 chr2 102450648 . T C 73.75 PASS AC=1;AF=0.5;AN=2;DP=12;FS=28.987;FractionInformativeReads=1;MQ=60;MQRankSum=-0.529;QD=6.15;ReadPosRankSum=-2.793;SOR=3.584;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:7,5:12:99:102,0,325:0,7,5,0 chr2 102450652 . T C 70.79 PASS AC=1;AF=0.5;AN=2;DP=11;FS=25.185;FractionInformativeReads=1;MQ=60;MQRankSum=-0.278;QD=6.44;ReadPosRankSum=-2.52;SOR=3.22;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:7,4:11:99:99,0,341:0,7,4,0 chr2 102450690 . C CCCTCCCTT 211.66 PASS AC=1;AF=0.591;AN=2;DP=99;set=variant-variant2-variant5-variant8-variant12-variant14-variant21-variant26-variant33-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,5:10:99:195,0,247:1,4,2,3 chr2 102450731 . C A 752.2 PASS AC=1;AF=0.607;AN=2;DP=506;FractionInformativeReads=1;set=variant-variant2-variant5-variant8-variant12-variant14-variant21-variant24-variant26-variant33-variant35-variant36-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:19,15:34:99:454,0,657:13,6,10,5 chr2 102459268 . A G 748.21 PASS AC=1;AF=0.5;AN=2;DP=683;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant10-variant11-variant15-variant26-variant29-variant30-variant32-variant35-variant36-variant37-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,21:46:99:542,0,737:7,18,6,15 chr2 102472459 . A G 203.95 PASS AC=1;AF=0.607;AN=2;DP=799;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant8-variant12-variant14-variant21-variant24-variant26-variant33-variant35-variant36-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:45,25:70:99:544,0,1160:25,20,15,10 chr2 102483883 . T G 370.36 PASS AC=1;AF=0.528;AN=2;DP=274;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant9-variant10-variant11-variant13-variant15-variant26-variant29-variant30-variant32-variant35-variant36-variant37-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,6:16:99:175,0,336:1,9,1,5 chr2 102501512 . G C 181.57 PASS AC=1;AF=0.625;AN=2;DP=128;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant8-variant14-variant21-variant24-variant26-variant33-variant35-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:99:149,0,147:4,0,4,0 chr2 102501891 . A G 469.48 PASS AC=1;AF=0.528;AN=2;DP=611;MQ=60;set=variant3-variant4-variant9-variant10-variant11-variant13-variant15-variant26-variant29-variant30-variant32-variant35-variant36-variant37-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,14:29:99:403,0,427:4,11,3,11 chr2 102503486 . CAAAA C,CAA,CAAA,CA 89.22 PASS AC=0,0,0,1;AF=0.025,0.175,0.275,0.1;AN=2;DP=369;set=variant-variant2-variant4-variant5-variant8-variant12-variant14-variant19-variant20-variant22-variant24-variant27-variant29-variant33-variant34-variant35-variant36-variant39-variant40-variant43 GT:DP:GQ:SB 0/4:19:99:4,2,13,0 chr2 102508146 . G A 1369.39 PASS AC=2;AF=0.662;AN=2;DP=3709;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant21-variant22-variant23-variant24-variant26-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,83:83:99:2656,249,0:0,0,48,35 chr2 102508659 . A AT 2947.96 PASS AC=1;AF=0.594;AN=2;DP=4783;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant12-variant14-variant21-variant24-variant26-variant33-variant35-variant36-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:145,145:290:99:3146,0,3115:69,76,78,67 chr2 102509994 . G A 839.06 PASS AC=1;AF=0.5;AN=2;DP=392;MQ=60;set=variant30-variant32-variant35-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,30:84:99:851,0,1615:39,15,22,8 chr2 102608549 . AAG AAGAG,A 151.16 PASS AC=1,0;AF=0.367,0.233;AN=2;DP=162;MQ=60;set=variant4-variant6-variant10-variant12-variant13-variant16-variant22-variant25-variant27-variant32-variant35-variant38-variant39-variant42-variant44 GT:DP:GQ:SB 0/1:11:99:3,3,2,3 chr2 102632582 . T A 422.79 PASS AC=1;AF=0.649;AN=2;DP=915;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,15:22:99:524,0,201:2,5,2,13 chr2 102641264 . T A 653.09 PASS AC=1;AF=0.5;AN=2;DP=319;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant14-variant30-variant33-variant35-variant36-variant41 GT:AD:DP:GQ:PL:SB 0/1:21,19:40:99:451,0,601:8,13,6,13 chr2 102721116 . G A 716.55 PASS AC=1;AF=0.5;AN=2;DP=1098;FractionInformativeReads=1;MQ=60;set=variant2-variant11-variant14-variant15-variant17-variant18-variant19-variant22-variant23-variant24-variant26-variant32-variant35-variant36-variant41 GT:AD:DP:GQ:PL:SB 0/1:48,31:79:99:644,0,1157:23,25,17,14 chr2 102721214 . C A 638.28 PASS AC=1;AF=0.5;AN=2;DP=270;FractionInformativeReads=1;MQ=60;set=variant6-variant9-variant30-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:32,29:61:99:673,0,801:14,18,11,18 chr2 102721308 . G T 115.87 PASS AC=1;AF=0.5;AN=2;DP=374;MQ=60;set=variant2-variant4-variant8-variant11-variant14-variant15-variant17-variant18-variant19-variant22-variant23-variant24-variant26-variant32-variant35-variant36-variant41 GT:AD:DP:GQ:PL:SB 0/1:5,18:23:99:519,0,114:1,4,7,11 chr2 102759293 . A C 44.34 PASS AC=2;AF=0.825;AN=2;DP=562;FractionInformativeReads=1;MQ=60;set=filterInvariant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:479,36,0:0,0,11,1 chr2 102759381 . A T 1010.01 PASS AC=1;AF=0.641;AN=2;DP=1984;MQ=60;set=variant3-variant5-variant7-variant8-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,26:72:99:534,0,1154:29,17,14,12 chr2 102773999 . C T 617.44 PASS AC=1;AF=0.55;AN=2;DP=380;MQ=60;set=variant3-variant4-variant6-variant9-variant10-variant19-variant28-variant31-variant33-variant35 GT:AD:DP:GQ:PL:SB 0/1:14,15:29:99:438,0,402:10,4,12,3 chr2 102774054 . G A 635.91 PASS AC=1;AF=0.579;AN=2;DP=1047;MQ=60;set=variant-variant3-variant4-variant6-variant8-variant9-variant10-variant12-variant15-variant19-variant20-variant24-variant28-variant31-variant33-variant34-variant35-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:25,36:61:99:953,0,655:15,10,23,13 chr2 102782433 . T A 636.32 PASS AC=1;AF=0.596;AN=2;DP=678;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant7-variant14-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,11:24:99:301,0,379:10,3,8,3 chr2 102785158 . G T 385.46 PASS AC=1;AF=0.528;AN=2;DP=761;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant20-variant21-variant26-filterInvariant28-variant29-variant31-variant33-variant34-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:16,28:44:99:772,0,459:3,13,10,18 chr2 102788409 . G A 3296.81 PASS AC=2;AF=0.989;AN=2;DP=4160;MQ=60;MQRankSum=0.189;ReadPosRankSum=-0.456;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,87:87:99:2701,260,0:0,0,28,59 chr2 102792760 . A G 1815.58 PASS AC=1;AF=0.575;AN=2;DP=3271;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant15-variant19-variant20-variant21-variant26-variant28-variant29-variant31-variant33-variant34-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:86,59:145:99:1305,0,2024:46,40,29,30 chr2 102794282 . G A 1443.41 PASS AC=1;AF=0.6;AN=2;DP=3024;MQ=60;set=variant3-variant5-variant7-variant14-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant30-variant31-variant32-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,57:108:99:1323,0,1359:32,19,30,27 chr2 102804538 . A AACC 631.17 PASS AC=2;AF=0.667;AN=2;DP=1468;MQ=60;set=variant-variant3-variant5-variant7-variant8-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant30-variant31-variant32-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:2535,171,0:0,0,1,56 chr2 102817954 . A T 884.1 PASS AC=1;AF=0.587;AN=2;DP=961;MQ=60;set=variant3-variant5-variant7-variant14-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant30-variant31-variant32-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,16:33:99:496,0,532:11,6,11,5 chr2 102828378 . A ATT 52.25 PASS AC=1;AF=0.625;AN=2;DP=102;MQ=60;set=variant3-variant7-variant14-variant20-variant22-variant23-variant25-variant26-variant31-variant35-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,5:15:99:139,0,337:7,3,3,2 chr2 102828768 . G C 237.08 PASS AC=1;AF=0.595;AN=2;DP=171;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant14-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant30-variant31-variant32-variant35-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,6:8:63:202,0,63:0,2,1,5 chr2 102835706 . T C 382.95 PASS AC=1;AF=0.55;AN=2;DP=259;MQ=60;set=variant-variant7-variant8-variant15-variant17-variant20-variant28-variant34-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:17,11:28:99:313,0,554:3,14,2,9 chr2 102842467 . T C 1372.76 PASS AC=1;AF=0.55;AN=2;DP=1181;MQ=60;set=variant-variant7-variant8-variant15-variant17-variant20-variant28-variant34-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:78,73:151:99:1627,0,1684:37,41,39,34 chr2 102851243 . C T 208.39 PASS AC=1;AF=0.595;AN=2;DP=324;FractionInformativeReads=1;set=variant-variant4-variant6-variant8-variant12-variant13-variant15-variant17-variant19-variant20-variant22-variant24-variant27-variant28-variant33-variant34-variant35-variant36-variant37-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:9,7:16:99:264,0,360:9,0,7,0 chr2 102851708 . T C 429.51 PASS AC=1;AF=0.531;AN=2;DP=936;MQ=60;set=variant-variant4-variant6-variant8-variant12-variant13-variant15-variant17-variant20-variant24-variant28-variant33-variant34-variant35-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:19,51:70:99:1460,0,460:5,14,15,36 chr2 102957628 . CT CTT,C 69.62 PASS AC=1,0;AF=0.474,0.079;AN=2;DP=581;set=variant2-variant3-variant4-variant6-variant7-variant9-variant14-variant15-variant18-variant19-filterInvariant20-filterInvariant23-variant26-variant28-variant31-variant34-variant35-variant42-variant43 GT:DP:GQ:SB 0/1:42:99:16,7,16,3 chr2 102967928 . A G 412.18 PASS AC=1;AF=0.574;AN=2;DP=1360;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant15-variant18-variant19-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:16,25:41:99:744,0,582:16,0,18,7 chr2 102968007 . G A 1875.88 PASS AC=1;AF=0.574;AN=2;DP=4876;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant15-variant18-variant19-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:81,84:165:99:2142,0,2016:52,29,52,32 chr2 102968075 . T C 3179.6 PASS AC=1;AF=0.574;AN=2;DP=7488;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant15-variant18-variant19-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:148,150:298:99:3618,0,3411:76,72,83,67 chr2 102968211 . C A 2280.02 PASS AC=1;AF=0.574;AN=2;DP=3749;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant15-variant18-variant19-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:70,83:153:99:3265,0,2685:29,41,33,50 chr2 102968212 . A G 2280.02 PASS AC=1;AF=0.574;AN=2;DP=3715;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant15-variant18-variant19-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:70,83:153:99:3265,0,2685:29,41,34,49 chr2 102968285 . T C 738.69 PASS AC=1;AF=0.574;AN=2;DP=2166;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant15-variant18-variant19-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:48,43:91:99:1319,0,1350:18,30,16,27 chr2 102968356 . C T 1291.73 PASS AC=1;AF=0.574;AN=2;DP=1631;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant15-variant18-variant19-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:27,34:61:99:1312,0,1029:11,16,13,21 chr2 102968362 . T C 1354.47 PASS AC=1;AF=0.574;AN=2;DP=1635;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant15-variant18-variant19-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:28,33:61:99:1291,0,1049:11,17,12,21 chr2 102972499 . GGAGCGCCCCAGACTGA G 1225.03 PASS AC=1;AF=0.5;AN=2;DP=701;MQ=60;set=variant2-variant4-variant6-variant7-variant15-variant18-variant23-variant26-variant35-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:36,21:57:99:829,0,2172:18,18,10,11 chr2 102972534 . C T 1235.25 PASS AC=1;AF=0.5;AN=2;DP=603;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant7-variant15-variant18-variant23-variant26-variant35-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:36,22:58:99:796,0,2155:18,18,11,11 chr2 102972667 . CT CTT,C,CTTT 347.2 PASS AC=0,1,0;AF=0.47,0.045,0.015;AN=2;DP=1248;set=variant-variant3-variant5-variant6-variant7-filterInvariant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-filterInvariant16-variant17-variant18-variant21-variant22-variant24-filterInvariant26-variant29-variant31-variant32-variant33-variant34-filterInvariant35-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:36:74:19,10,5,2 chr2 102972799 . G C 825.4 PASS AC=1;AF=0.574;AN=2;DP=2097;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant15-variant18-variant19-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:36,43:79:99:1169,0,896:16,20,22,21 chr2 102984624 . C G 99.52 PASS AC=1;AF=0.574;AN=2;DP=391;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant15-variant18-variant19-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,6:14:99:216,0,320:1,7,0,6 chr2 102998279 . A G 190.6 PASS AC=1;AF=0.688;AN=2;DP=640;FractionInformativeReads=1;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant15-variant18-variant19-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:7,14:21:99:391,0,202:2,5,5,9 chr2 103006448 . C T 838.05 PASS AC=1;AF=0.671;AN=2;DP=2184;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:43,36:79:99:900,0,1131:23,20,21,15 chr2 103010912 . C T 678.2 PASS AC=1;AF=0.671;AN=2;DP=2194;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:39,42:81:99:887,0,908:22,17,25,17 chr2 103013408 . C T 999.65 PASS AC=1;AF=0.5;AN=2;DP=620;FractionInformativeReads=1;MQ=60;set=variant6-variant7-variant23-variant26-variant35-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:59,40:99:99:866,0,1554:28,31,19,21 chr2 103014696 . C T 907.78 PASS AC=1;AF=0.802;AN=2;DP=1567;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,20:37:99:635,0,395:11,6,10,10 chr2 103035044 . A G 982.81 PASS AC=1;AF=0.802;AN=2;DP=803;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,9:20:99:322,0,436:11,0,9,0 chr2 103035119 . T C 1136.58 PASS AC=1;AF=0.671;AN=2;DP=3175;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:49,45:94:99:1184,0,1205:31,18,32,13 chr2 103035455 . G A 627.11 PASS AC=1;AF=0.5;AN=2;DP=691;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant6-variant7-variant15-variant23-variant26-variant35-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:30,21:51:99:628,0,853:10,20,3,18 chr2 103039584 . A T 934.12 PASS AC=1;AF=0.802;AN=2;DP=1625;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,25:38:99:772,0,380:10,3,20,5 chr2 103040247 . T TG 895.2 PASS AC=1;AF=0.802;AN=2;DP=1071;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,14:26:99:534,0,817:10,2,12,2 chr2 103040249 . C T 904.24 PASS AC=1;AF=0.802;AN=2;DP=1119;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,14:26:99:534,0,817:10,2,12,2 chr2 103048738 . G A 545.31 PASS AC=1;AF=0.554;AN=2;DP=883;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant19-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant33-variant35-variant36-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:14,21:35:99:650,0,476:13,1,17,4 chr2 103057668 . G A 592.21 PASS AC=1;AF=0.554;AN=2;DP=1774;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant19-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant33-variant35-variant36-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:46,34:80:99:765,0,1092:27,19,18,16 chr2 103059613 . A G 3767.96 PASS AC=2;AF=1;AN=2;DP=4390;FS=0;MQ=60;MQRankSum=0.874;ReadPosRankSum=0.379;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,107:107:99:3356,321,0:0,0,53,54 chr2 103063369 . G A 926.41 PASS AC=1;AF=0.802;AN=2;DP=1369;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,18:37:99:452,0,488:12,7,12,6 chr2 103068787 . G A 1827.82 PASS AC=1;AF=0.802;AN=2;DP=3741;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,42:88:99:1060,0,1449:31,15,27,15 chr2 103068834 . T A 2485.08 PASS AC=1;AF=0.802;AN=2;DP=5482;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:88,63:151:99:1533,0,2280:51,37,41,22 chr2 103090041 . T C 415.64 PASS AC=1;AF=0.556;AN=2;DP=1129;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant19-variant21-variant22-variant25-variant26-variant27-variant29-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:18,26:44:99:627,0,433:7,11,13,13 chr2 103120179 . C T 1349.14 PASS AC=1;AF=0.55;AN=2;DP=1246;MQ=60;set=variant3-variant4-variant6-variant7-variant15-variant29-variant35-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:85,50:135:99:1243,0,2111:39,46,16,34 chr2 103120232 . G A 2821.58 PASS AC=1;AF=0.788;AN=2;DP=3321;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,38:99:99:1077,0,1476:27,34,10,28 chr2 103120311 . G A 1160.03 PASS AC=1;AF=0.8;AN=2;DP=1038;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,15:31:99:397,0,421:5,11,5,10 chr2 103120356 . C T 412.43 PASS AC=1;AF=0.816;AN=2;DP=386;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,7:14:99:221,0,251:0,7,2,5 chr2 103121533 . TAGGG T 515.38 PASS AC=1;AF=0.563;AN=2;DP=122;MQ=60;set=variant3-variant4-variant6-variant7-variant15-variant29-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:6,7:13:99:241,0,300:6,0,7,0 chr2 103125457 . A G 2991.22 PASS AC=1;AF=0.8;AN=2;DP=1736;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,23:48:99:856,0,1373:12,13,12,11 chr2 103125466 . T C 2921.46 PASS AC=1;AF=0.8;AN=2;DP=1656;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,21:45:99:799,0,1341:12,12,11,10 chr2 103128866 . T C 1254.92 PASS AC=1;AF=0.813;AN=2;DP=2029;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,21:47:99:543,0,694:9,17,8,13 chr2 103136309 . T C 2787 PASS AC=1;AF=0.813;AN=2;DP=5209;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,62:122:99:1380,0,1495:34,26,33,29 chr2 103136446 . T G 1408.49 PASS AC=1;AF=0.8;AN=2;DP=1951;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,25:49:99:627,0,764:5,19,7,18 chr2 103141651 . G C 658.03 PASS AC=1;AF=0.825;AN=2;DP=972;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,12:22:99:348,0,303:2,8,3,9 chr2 103142994 . G A 127.62 PASS AC=1;AF=0.55;AN=2;DP=166;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant6-variant7-variant15-variant29-variant35-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,7:11:99:282,0,150:0,4,1,6 chr2 103149210 . G A 1697 PASS AC=1;AF=0.556;AN=2;DP=795;MQ=60;set=variant3-variant4-variant6-variant7-variant15-variant29-variant35-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:49,41:90:99:1024,0,1258:25,24,23,18 chr2 103149520 . A T 1605.11 PASS AC=1;AF=0.545;AN=2;DP=1195;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant15-variant29-variant35-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:52,52:104:99:1547,0,1392:21,31,16,36 chr2 103236159 . C T 618.76 PASS AC=1;AF=0.5;AN=2;DP=161;FractionInformativeReads=1;MQ=60;set=variant8-variant35 GT:AD:DP:GQ:PL:SB 0/1:40,46:86:99:1135,0,1031:24,16,26,20 chr2 103281960 . A G 490.23 PASS AC=2;AF=0.988;AN=2;DP=497;FS=0;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:759,63,0:0,0,4,17 chr2 103299567 . G A 701.16 PASS AC=1;AF=0.5;AN=2;DP=213;FS=0;FractionInformativeReads=1;MQ=60;set=variant10-variant17-variant19-variant23-variant35-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:17,15:32:99:475,0,535:14,3,12,3 chr2 103299637 . T C 1092.31 PASS AC=1;AF=0.5;AN=2;DP=641;FractionInformativeReads=1;MQ=60;set=variant10-variant17-variant19-variant23-variant35-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:45,54:99:99:1374,0,1123:28,17,33,21 chr2 103300070 . G A 484.75 PASS AC=1;AF=0.5;AN=2;DP=306;MQ=60;set=variant10-variant17-variant19-variant23-variant35-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:19,33:52:99:861,0,515:5,14,13,20 chr2 103300407 . A G 466.97 PASS AC=1;AF=0.5;AN=2;DP=219;MQ=60;set=variant10-variant17-variant19-variant23-variant35-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:10,13:23:99:336,0,260:6,4,8,5 chr2 103300506 . A G 1152.38 PASS AC=1;AF=0.731;AN=2;DP=3614;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,38:84:99:943,0,1187:26,20,21,17 chr2 103327476 . A G 5756.43 PASS AC=1;AF=0.798;AN=2;DP=16188;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:218,182:400:99:4597,0,5393:113,105,95,87 chr2 103332590 . T G 1639.86 PASS AC=1;AF=0.621;AN=2;DP=4868;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant11-variant12-variant13-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:91,82:173:99:1863,0,2341:49,42,43,39 chr2 103333705 . A G 127.62 PASS AC=1;AF=0.821;AN=2;DP=450;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,2:10:60:60,0,280:7,1,2,0 chr2 103334969 . G A 2190.58 PASS AC=1;AF=0.607;AN=2;DP=5284;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant11-variant12-variant13-variant16-variant17-variant18-variant19-variant21-variant24-variant27-variant29-variant31-variant33-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:94,98:192:99:2364,0,2453:42,52,42,56 chr2 103335441 . A G 1787.38 PASS AC=1;AF=0.5;AN=2;DP=2805;MQ=60;set=variant2-variant3-variant6-variant8-variant17-variant21-variant27-variant31-variant35-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:181,129:310:99:2908,0,4272:94,87,65,64 chr2 103343234 . G C 194.35 PASS AC=2;AF=0.798;AN=2;DP=757;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:615,45,0:0,0,13,2 chr2 103343275 . GAA GA,GAAA,G 202.4 PASS AC=0,1,0;AF=0.143,0.357,0.029;AN=2;DP=1394;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant21-filterInvariant23-filterInvariant24-variant25-variant26-variant27-variant28-filterInvariant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:DP:GQ:SB 0/2:40:85:8,5,16,11 chr2 103431404 . T C 9578.13 PASS AC=2;AF=0.988;AN=2;DP=10956;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,257:257:99:7725,770,0:0,0,133,124 chr2 104995800 . C T 1239.65 PASS AC=1;AF=0.528;AN=2;DP=2296;FractionInformativeReads=1;MQ=60;set=variant5-variant7-variant8-variant10-variant11-variant12-variant15-variant17-variant18-variant19-variant27-variant30-variant33-variant35-variant36-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:85,66:151:99:1715,0,2377:39,46,34,32 chr2 105472055 . T C 399.59 PASS AC=2;AF=0.744;AN=2;DP=576;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:580,63,0:0,0,10,11 chr2 105473698 . G T 563.64 PASS AC=2;AF=0.697;AN=2;DP=1705;MQ=60;set=variant3-variant4-variant6-variant8-variant9-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1232,110,0:0,0,14,23 chr2 105475259 . C T 4590.64 PASS AC=2;AF=0.756;AN=2;DP=7778;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,175:175:99:5444,524,0:0,0,83,92 chr2 105475330 . A G 3980.46 PASS AC=2;AF=0.756;AN=2;DP=6118;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,155:155:99:4536,462,0:0,0,72,83 chr2 105475594 . G GT 3664.32 PASS AC=2;AF=0.768;AN=2;DP=4673;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,99:99:99:2998,297,0:0,0,63,36 chr2 105476225 . A G 3876.25 PASS AC=2;AF=0.756;AN=2;DP=4191;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,82:82:99:2542,246,0:0,0,36,46 chr2 105654446 . A G 891.84 PASS AC=1;AF=0.613;AN=2;DP=3159;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:63,40:103:99:889,0,1553:33,30,22,18 chr2 105654716 . C T 935.02 PASS AC=1;AF=0.613;AN=2;DP=3986;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:91,72:163:99:1607,0,2300:36,55,29,43 chr2 105654830 . G T 220.9 PASS AC=1;AF=0.613;AN=2;DP=748;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-filterInvariant8-variant9-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,10:24:99:331,0,508:1,13,1,9 chr2 105665808 . C T 984.3 PASS AC=1;AF=0.579;AN=2;DP=1746;MQ=60;set=variant2-variant3-variant5-variant10-variant12-variant13-variant16-variant18-variant21-variant25-variant27-variant30-variant34-variant35-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,44:99:99:1106,0,1373:24,31,21,23 chr2 105665921 . GA G 78.03 PASS AC=1;AF=0.588;AN=2;DP=264;MQ=60;set=variant2-variant3-variant5-variant10-variant12-variant16-variant21-variant25-variant27-variant30-variant34-variant35-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,11:16:99:311,0,115:0,5,0,11 chr2 105665941 . GTT G 70.64 PASS AC=1;AF=0.588;AN=2;DP=185;MQ=60;set=variant2-variant3-variant5-variant10-variant12-variant16-variant21-variant25-variant27-variant30-variant34-variant35-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,11:15:99:450,0,144:0,4,0,11 chr2 105705507 . C T 426.92 PASS AC=1;AF=0.579;AN=2;DP=1454;MQ=60;set=variant2-variant3-variant5-variant10-variant12-variant13-variant16-variant18-variant21-variant25-variant27-variant30-variant34-variant35-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,35:83:99:734,0,1145:25,23,14,21 chr2 105706584 . AAAAAC A 638.02 PASS AC=1;AF=0.579;AN=2;DP=761;MQ=60;set=variant2-variant3-variant5-variant10-variant12-variant13-variant16-variant18-variant21-variant25-variant27-variant30-variant34-variant35-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,14:26:99:553,0,503:4,8,4,10 chr2 105707766 . G A 702.28 PASS AC=1;AF=0.579;AN=2;DP=1823;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant10-variant12-variant13-variant16-variant18-variant21-variant25-variant27-variant30-variant34-variant35-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,51:89:99:1384,0,933:18,20,28,23 chr2 105709023 . T C 2141.59 PASS AC=2;AF=0.966;AN=2;DP=3513;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,69:69:99:2058,206,0:0,0,26,43 chr2 105713697 . A G 1124.67 PASS AC=1;AF=0.579;AN=2;DP=2397;MQ=60;set=variant2-variant3-variant5-variant10-variant12-variant13-variant16-variant18-variant21-variant25-variant27-variant30-variant34-variant35-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:71,54:125:99:1308,0,1797:33,38,29,25 chr2 105713868 . A G 905.22 PASS AC=1;AF=0.583;AN=2;DP=1605;set=variant-variant2-variant3-variant4-variant5-variant6-variant10-variant12-variant13-variant16-variant18-variant21-variant25-variant27-variant30-variant31-variant34-variant35-variant36-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,51:79:99:1943,0,1482:12,16,20,31 chr2 105713877 . T C 961.53 PASS AC=1;AF=0.579;AN=2;DP=1117;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant10-variant12-variant13-variant16-variant18-variant21-variant25-variant27-variant30-variant34-variant35-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,49:77:99:1887,0,1510:11,17,19,30 chr2 105716266 . A G 2189.1 PASS AC=1;AF=0.579;AN=2;DP=2962;MQ=60;set=variant2-variant3-variant5-variant10-variant12-variant13-variant16-variant18-variant21-variant25-variant27-variant30-variant34-variant35-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:66,77:143:99:1934,0,1601:40,26,44,33 chr2 105882061 . G A 3470.14 PASS AC=1;AF=0.556;AN=2;DP=3604;MQ=60;set=variant3-variant7-variant12-variant14-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant35-variant36-variant40 GT:AD:DP:GQ:PL:SB 0/1:116,108:224:99:2936,0,3146:62,54,50,58 chr2 105882601 . C T 760.24 PASS AC=1;AF=0.5;AN=2;DP=1232;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant8-variant10-variant13-variant15-variant16-variant18-variant19-variant35-variant36-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:56,56:112:99:1351,0,1318:28,28,29,27 chr2 105882683 . C T 894.25 PASS AC=1;AF=0.5;AN=2;DP=1370;MQ=60;set=variant-variant2-variant8-variant10-variant13-variant15-variant16-variant18-variant19-variant35-variant36-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:45,68:113:99:1691,0,960:22,23,32,36 chr2 105882761 . G A 892.62 PASS AC=1;AF=0.542;AN=2;DP=1510;MQ=60;set=variant-variant2-variant7-variant8-variant10-variant13-variant15-variant16-variant17-variant18-variant19-variant23-variant24-variant26-variant30-variant31-variant33-variant34-variant35-variant36-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:29,38:67:99:1011,0,681:11,18,13,25 chr2 105883624 . TTTCCATGTACATTCATAGAGCCTGGTCA T 2297.15 PASS AC=2;AF=0.81;AN=2;DP=3267;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:3532,246,0:0,0,40,39 chr2 105885961 . T C 696.16 PASS AC=1;AF=0.692;AN=2;DP=4577;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:80,71:151:99:1768,0,1984:39,41,39,32 chr2 105886219 . C A 324.35 PASS AC=1;AF=0.5;AN=2;DP=424;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant8-variant10-variant13-variant15-variant16-variant18-variant19-variant35-variant36-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,6:19:99:132,0,360:5,8,2,4 chr2 105889804 . C A 363.86 PASS AC=1;AF=0.5;AN=2;DP=377;MQ=60;set=variant-variant2-variant8-variant10-variant13-variant15-variant16-variant18-variant19-variant35-variant36-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,11:22:99:348,0,330:9,2,9,2 chr2 105897003 . G A 2422.52 PASS AC=1;AF=0.556;AN=2;DP=2932;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant12-variant14-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant35-variant36-variant40 GT:AD:DP:GQ:PL:SB 0/1:93,97:190:99:2320,0,2317:43,50,45,52 chr2 105897261 . C T 445.48 PASS AC=2;AF=0.955;AN=2;DP=1418;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1134,107,0:0,0,12,24 chr2 105900887 . G GA 1512.53 PASS AC=1;AF=0.5;AN=2;DP=323;MQ=60;set=variant2-variant18-variant35 GT:AD:DP:GQ:PL:SB 0/1:55,58:113:99:1712,0,1624:21,34,25,33 chr2 105915128 . G A 1040.89 PASS AC=1;AF=0.536;AN=2;DP=1320;MQ=60;set=variant-variant2-variant8-variant10-variant13-variant15-variant16-variant18-variant19-variant35-variant36-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:48,59:107:99:1678,0,1244:13,35,18,41 chr2 105924510 . A G 661.85 PASS AC=2;AF=0.677;AN=2;DP=3389;set=variant-variant2-variant3-variant4-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant33-variant35-variant36-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,123:123:99:4364,369,0:0,0,66,57 chr2 105946163 . C T 88.67 PASS AC=2;AF=0.882;AN=2;DP=109;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant8-variant18-variant19-variant21-variant22-variant24-variant26-variant27-variant29-variant35-variant36-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:477,51,0:0,0,10,7 chr2 105946474 . C T 732.37 PASS AC=1;AF=0.5;AN=2;DP=152;FractionInformativeReads=1;MQ=60;set=variant2-variant18-variant35 GT:AD:DP:GQ:PL:SB 0/1:45,22:67:99:368,0,1145:20,25,11,11 chr2 105953909 . G C 1871.29 PASS AC=1;AF=0.605;AN=2;DP=2231;MQ=60;set=variant3-variant4-variant7-variant12-variant14-variant17-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant33-variant35-variant36-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,70:124:99:1918,0,1313:31,23,35,35 chr2 105953938 . G GC 4643.38 PASS AC=2;AF=0.774;AN=2;DP=5759;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,148:148:99:5969,448,0:0,0,82,66 chr2 105961703 . G A 359.31 PASS AC=2;AF=0.677;AN=2;DP=1296;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant33-variant35-variant36-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1589,135,0:0,0,35,10 chr2 105963601 . CTG C 8452.08 PASS AC=1;AF=0.536;AN=2;DP=6228;MQ=60;set=variant-variant2-variant8-variant10-variant13-variant15-variant16-variant18-variant19-variant35-variant36-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:249,186:435:99:7012,0,10239:136,113,101,85 chr2 105964462 . T TTTC 5288.45 PASS AC=2;AF=0.774;AN=2;DP=6015;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,132:132:99:5819,396,0:0,0,42,90 chr2 105974978 . A G 797.55 PASS AC=1;AF=0.629;AN=2;DP=2885;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant12-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant37-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,45:87:99:1042,0,1192:20,22,21,24 chr2 105975456 . G A 1304.65 PASS AC=1;AF=0.536;AN=2;DP=955;MQ=60;set=variant3-variant7-variant12-variant14-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:57,49:106:99:1073,0,1494:25,32,22,27 chr2 105976344 . A G 1024.08 PASS AC=2;AF=0.762;AN=2;DP=1774;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1196,120,0:0,0,21,19 chr2 105977903 . G C 499.85 PASS AC=1;AF=0.536;AN=2;DP=1291;MQ=60;set=variant-variant2-variant8-variant10-variant13-variant15-variant16-variant18-variant19-variant35-variant36-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:65,46:111:99:1121,0,1774:28,37,21,25 chr2 105979730 . C A 526.87 PASS AC=1;AF=0.589;AN=2;DP=4644;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant9-variant12-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant35-variant37-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:69,76:145:99:1915,0,1715:40,29,43,33 chr2 105980168 . C T 56.47 PASS AC=1;AF=0.556;AN=2;DP=62;FS=0;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant12-variant14-variant24-variant27-variant28-variant29-variant35 GT:AD:DP:GQ:PL:SB 0/1:1,9:10:16:282,0,16:0,1,2,7 chr2 105994276 . T C 44.5 PASS AC=1;AF=0.692;AN=2;DP=231;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant17-variant19-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant35-variant36-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:2,7:9:60:275,0,60:1,1,5,2 chr2 105994564 . C CATCAA 3254.42 PASS AC=1;AF=0.567;AN=2;DP=1790;MQ=60;set=variant3-variant7-variant12-variant14-variant17-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:63,83:146:99:3240,0,4110:34,29,46,37 chr2 106013216 . T C 4622.78 PASS AC=1;AF=0.775;AN=2;DP=12929;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:203,183:386:99:4255,0,5224:111,92,95,88 chr2 106013248 . C T 4973.08 PASS AC=1;AF=0.609;AN=2;DP=11063;MQ=60;set=variant-variant3-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:214,191:405:99:4385,0,5305:111,103,88,103 chr2 106361471 . C G 105.43 PASS AC=1;AF=0.563;AN=2;DP=64;FractionInformativeReads=1;MQ=60;set=variant4-variant20-variant22-variant33-variant35-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:7,3:10:64:64,0,164:4,3,2,1 chr2 106361607 . T C 298.29 PASS AC=2;AF=0.943;AN=2;DP=918;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:731,78,0:0,0,14,12 chr2 106471327 . C A 831.02 PASS AC=2;AF=0.769;AN=2;DP=1126;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:840,78,0:0,0,19,7 chr2 106471393 . T C 2279.48 PASS AC=2;AF=0.942;AN=2;DP=3518;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,63:63:99:1862,189,0:0,0,38,25 chr2 106471825 . C CA,CAAA,CAA 466.05 PASS AC=2,0,0;AF=0.683,0.024,0.122;AN=2;DP=1104;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:24:45:0,1,6,17 chr2 106510191 . T TAAAG 4355.95 PASS AC=2;AF=0.953;AN=2;DP=4233;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,114:114:99:5334,360,0:0,0,68,46 chr2 106510455 . G GCA,GCACA 516.29 PASS AC=1,0;AF=0.343,0.386;AN=2;DP=1190;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant29-variant31-variant32-variant33-variant34-variant35-filterInvariant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:27:99:12,7,5,3 chr2 106510472 . CACACTA C 274.01 PASS AC=1;AF=0.528;AN=2;DP=638;set=variant2-variant4-variant7-variant8-variant11-variant17-variant18-variant19-variant22-variant27-variant28-variant29-variant30-variant33-variant35-variant36-variant37-variant42 GT:AD:DP:GQ:PL:SB 0/1:19,17:36:99:499,0,704:11,8,10,7 chr2 106679686 . C T 291.16 PASS AC=2;AF=0.633;AN=2;DP=393;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:351,33,0:0,0,8,3 chr2 106679971 . C T 1030.74 PASS AC=1;AF=0.5;AN=2;DP=785;MQ=60;set=variant-variant9-variant10-variant11-variant15-variant16-variant17-variant23-variant26-variant32-variant35 GT:AD:DP:GQ:PL:SB 0/1:52,29:81:99:663,0,1371:18,34,8,21 chr2 106680019 . G A 1557.64 PASS AC=2;AF=1;AN=2;DP=1437;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1501,123,0:0,0,8,33 chr2 106687456 . G C 1161.01 PASS AC=1;AF=0.5;AN=2;DP=1260;FractionInformativeReads=1;MQ=60;set=variant6-variant10-variant11-variant12-variant20-variant21-variant26-variant30-variant35-variant37-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:56,37:93:99:948,0,1499:22,34,13,24 chr2 106690542 . G A 204.13 PASS AC=1;AF=0.56;AN=2;DP=343;MQ=60;set=variant3-variant5-variant6-variant10-variant11-variant12-variant16-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant34-variant35-variant37-variant38-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:99:138,0,155:0,4,1,3 chr2 106709782 . A T 376.89 PASS AC=2;AF=1;AN=2;DP=623;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:480,51,0:0,0,10,7 chr2 106710108 . C T 7350.49 PASS AC=2;AF=1;AN=2;DP=8574;FS=0;MQ=60;MQRankSum=0.507;ReadPosRankSum=0.507;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,216:216:99:6400,646,0:0,0,132,84 chr2 106710668 . C CGCAGGAAGGAAGTGCCACCTT 1119.91 PASS AC=1;AF=0.826;AN=2;DP=2641;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,18:37:99:651,0,3267:4,15,2,16 chr2 106715342 . G A,T 938.63 PASS AC=2,0;AF=0.886,0.114;AN=2;DP=1762;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:DP:GQ:SB 1/1:40:99:0,0,11,29 chr2 106717171 . T C 218.84 PASS AC=1;AF=0.865;AN=2;DP=310;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:5,6:11:82:194,0,82:3,2,5,1 chr2 106717274 . A G 965.78 PASS AC=1;AF=0.818;AN=2;DP=1642;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:34,23:57:99:610,0,811:21,13,15,8 chr2 106717656 . G A 151.77 PASS AC=1;AF=0.814;AN=2;DP=552;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,5:14:99:124,0,311:2,7,1,4 chr2 106742139 . C T 1614.15 PASS AC=2;AF=1;AN=2;DP=3680;FS=0;MQ=60;MQRankSum=1.37;ReadPosRankSum=-0.806;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,73:73:99:2303,219,0:0,0,38,35 chr2 106742177 . T A 1567.96 PASS AC=2;AF=0.966;AN=2;DP=3248;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:1758,180,0:0,0,27,33 chr2 106754734 . A G 2276.93 PASS AC=2;AF=0.75;AN=2;DP=4377;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,150:150:99:4611,450,0:0,0,88,62 chr2 106780015 . C T 1328.64 PASS AC=2;AF=1;AN=2;DP=1426;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:938,90,0:0,0,20,10 chr2 106780055 . C CTG 2777.34 PASS AC=2;AF=1;AN=2;DP=1986;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1710,114,0:0,0,23,15 chr2 106782398 . C G 743.54 PASS AC=2;AF=1;AN=2;DP=1222;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1130,102,0:0,0,23,11 chr2 106810727 . A G 10418.4 PASS AC=2;AF=1;AN=2;DP=14860;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,373:373:99:10807,1113,0:0,0,147,226 chr2 106994382 . A G 295.24 PASS AC=2;AF=0.87;AN=2;DP=183;FractionInformativeReads=1;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant24-variant25-filterInvariant29-variant31-variant33-variant35-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:282,27,0:0,0,4,5 chr2 106994455 . C T 37.7 PASS AC=2;AF=0.87;AN=2;DP=123;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant17-variant19-variant20-variant25-filterInvariant29-variant31-variant35-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:261,18,0:0,0,0,6 chr2 106994468 . A G 40.7 PASS AC=2;AF=0.857;AN=2;DP=106;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant12-variant17-variant19-variant20-variant25-filterInvariant29-variant35-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:221,15,0:0,0,0,5 chr2 107002646 . G C 1098.23 PASS AC=2;AF=0.768;AN=2;DP=1324;FractionInformativeReads=1;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1295,108,0:0,0,28,8 chr2 107007576 . A T 811.98 PASS AC=2;AF=0.692;AN=2;DP=1514;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1466,138,0:0,0,15,31 chr2 107007994 . TA T,TAA 341.34 PASS AC=2,0;AF=0.675,0.013;AN=2;DP=1169;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:DP:GQ:SB 1/1:29:87:0,0,11,18 chr2 107008058 . A G 785.8 PASS AC=2;AF=0.852;AN=2;DP=283;FractionInformativeReads=1;set=variant2-variant3-variant5-filterInvariant6-filterInvariant9-variant11-variant13-variant16-filterInvariant18-variant19-variant22-filterInvariant23-filterInvariant24-filterInvariant25-variant26-filterInvariant27-variant28-filterInvariant29-filterInvariant31-filterInvariant33-filterInvariant35-variant36-variant37-variant38-filterInvariant39-variant40-filterInvariant41 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:190,21,0:0,0,3,4 chr2 107029053 . C T 169.55 PASS AC=1;AF=0.5;AN=2;DP=218;FractionInformativeReads=1;set=variant4-variant6-variant18-variant27-variant31-variant32-variant33-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:11,11:22:99:276,0,309:7,4,8,3 chr2 107029347 . T C 37.46 PASS AC=1;AF=0.667;AN=2;DP=10;FS=0;FractionInformativeReads=1;set=variant8-variant11-variant35 GT:AD:DP:GQ:PL:SB 0/1:1,2:3:32:77,0,32:0,1,0,2 chr2 107029365 . T G 73.79 PASS AC=2;AF=0.95;AN=2;DP=29;FS=0;FractionInformativeReads=1;MQRankSum=1.231;ReadPosRankSum=1.231;set=variant5-variant8-variant11-filterInvariant24-variant25-variant31-variant35-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:85,6,0:0,0,0,2 chr2 107032279 . T C 3636.03 PASS AC=2;AF=0.78;AN=2;DP=6543;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,159:159:99:4468,476,0:0,0,95,64 chr2 107032417 . A G 658.09 PASS AC=1;AF=0.5;AN=2;DP=1192;FractionInformativeReads=1;set=variant4-variant6-variant8-variant11-variant18-variant21-variant22-variant23-variant27-variant31-variant32-variant33-variant34-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:63,27:90:99:586,0,1723:22,41,8,19 chr2 107039428 . A G 230.45 PASS AC=1;AF=0.667;AN=2;DP=37;FractionInformativeReads=1;set=filterInvariant6-variant32-variant35 GT:AD:DP:GQ:PL:SB 0/1:10,7:17:99:175,0,259:8,2,5,2 chr2 107039817 . G A 243.32 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=521;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:73,22:95:99:294,0,1604:21,52,7,15 chr2 107040572 . T C 844.37 DRAGENHardSNP AC=2;AF=1;AN=2;DP=32;FS=0;FractionInformativeReads=1;MQ=23.13;QD=26.39;SOR=2.165;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:873,96,0:0,0,24,8 chr2 107040985 . T C 90.55 DRAGENHardSNP AC=2;AF=0.583;AN=2;DP=875;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1158,114,0:0,0,38,0 chr2 107049604 . T C 909.12 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=499;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:61,38:99:99:736,0,1281:29,32,15,23 chr2 107073469 . T A 2277.85 PASS AC=1;AF=0.692;AN=2;DP=3276;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:63,34:97:99:612,0,1337:35,28,19,15 chr2 107073501 . C T 2522.06 PASS AC=1;AF=0.692;AN=2;DP=3581;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:67,39:106:99:670,0,1336:33,34,20,19 chr2 107084739 . A G 2344.16 PASS AC=1;AF=0.591;AN=2;DP=3628;set=variant3-variant5-variant8-variant10-variant11-variant12-variant14-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant33-variant35-variant36-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:106,101:207:99:2416,0,2376:47,59,43,58 chr2 107084845 . G C 883 PASS AC=1;AF=0.5;AN=2;DP=279;FractionInformativeReads=1;set=variant8-variant11-variant21-variant22-variant23-variant35 GT:AD:DP:GQ:PL:SB 0/1:26,29:55:99:907,0,797:5,21,7,22 chr2 107092169 . A C 109.21 PASS AC=1;AF=0.5;AN=2;DP=24;FS=2.644;FractionInformativeReads=1;MQ=41.35;MQRankSum=1.066;QD=4.55;ReadPosRankSum=-0.924;SOR=1.911;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:19,5:24:99:137,0,550:14,5,5,0 chr2 107107694 . A G 687.7 PASS AC=2;AF=1;AN=2;DP=1266;FS=0;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1339,102,0:0,0,4,30 chr2 107112773 . T C 96.86 PASS AC=1;AF=0.5;AN=2;DP=80;FractionInformativeReads=1;set=variant4-variant20-filterInvariant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:10,3:13:63:63,0,1088:2,8,3,0 chr2 107112777 . T C 96.86 PASS AC=1;AF=0.5;AN=2;DP=92;set=variant4-variant20-variant29-filterInvariant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:11,3:14:60:60,0,1185:2,9,3,0 chr2 107118896 . T C 160.68 PASS AC=2;AF=1;AN=2;DP=1208;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:989,75,0:0,0,18,7 chr2 107118897 . G A 161.37 PASS AC=1;AF=0.5;AN=2;DP=42;FractionInformativeReads=1;set=variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:17,8:25:99:190,0,544:13,4,5,3 chr2 107119136 . G C 176.5 PASS AC=2;AF=1;AN=2;DP=1122;FS=0;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:835,69,0:0,0,6,17 chr2 107121040 . T TA 1711.54 PASS AC=2;AF=1;AN=2;DP=1657;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,27:28:78:767,78,0:1,0,13,14 chr2 107419088 . T C 4665.94 PASS AC=1;AF=0.5;AN=2;DP=4983;MQ=60;set=variant6-variant12-variant13-variant18-variant24-variant25-variant26-variant27-variant32-variant33-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:200,189:389:99:4716,0,5075:102,98,94,95 chr2 107420068 . TAACAACAAC TAAC,TAACAAC,T 59.04 PASS AC=1,1,0;AF=0.134,0.646,0.012;AN=2;DP=651;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/2:8:99:0,0,2,6 chr2 107421297 . CAA CAAA,CAAAA,CAAAAA,C 1002.71 PASS AC=1,0,0,0;AF=0.269,0.295,0.051,0.038;AN=2;DP=1516;set=variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:DP:GQ:SB 0/1:47:99:14,1,23,9 chr2 107446430 . T C 863.3 PASS AC=1;AF=0.852;AN=2;DP=1367;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:12,13:25:99:419,0,348:8,4,10,3 chr2 107459919 . C T 2063.3 PASS AC=1;AF=0.5;AN=2;DP=353;FractionInformativeReads=1;MQ=60;set=variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:116,83:199:99:2092,0,3123:57,59,42,41 chr2 107502682 . T C 1938.92 PASS AC=1;AF=0.6;AN=2;DP=1057;MQ=60;set=variant2-variant14-variant17-variant20-variant22-variant31-variant33-variant35-variant36-variant41 GT:AD:DP:GQ:PL:SB 0/1:63,47:110:99:1087,0,1510:30,33,21,26 chr2 107502705 . G A 1707.29 PASS AC=1;AF=0.6;AN=2;DP=916;MQ=60;set=variant2-variant14-variant17-variant20-variant22-variant31-variant33-variant35-variant36-variant41 GT:AD:DP:GQ:PL:SB 0/1:65,40:105:99:965,0,1497:31,34,16,24 chr2 107503324 . C T 587.2 PASS AC=1;AF=0.789;AN=2;DP=954;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,19:41:99:449,0,561:12,10,11,8 chr2 107503363 . G T 568.09 PASS AC=1;AF=0.5;AN=2;DP=87;FractionInformativeReads=1;MQ=60;set=variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:29,24:53:99:596,0,734:16,13,15,9 chr2 107503532 . A G 2113.09 PASS AC=1;AF=0.6;AN=2;DP=1665;MQ=60;set=variant2-variant14-variant17-variant20-variant22-variant31-variant33-variant35-variant36-variant41 GT:AD:DP:GQ:PL:SB 0/1:90,110:200:99:2663,0,2030:50,40,63,47 chr2 108443325 . T C 950.21 PASS AC=1;AF=0.75;AN=2;DP=1380;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,14:31:99:534,0,1005:11,6,9,5 chr2 108443328 . A T 950.21 PASS AC=1;AF=0.738;AN=2;DP=1421;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,14:31:99:537,0,983:11,6,9,5 chr2 108443511 . C G 2043.16 PASS AC=1;AF=0.75;AN=2;DP=6169;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,81:135:99:2934,0,1868:25,29,45,36 chr2 108443567 . G A 2302.57 PASS AC=1;AF=0.738;AN=2;DP=5097;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,74:125:99:2934,0,1989:19,32,32,42 chr2 108443591 . A C 2109.33 PASS AC=1;AF=0.75;AN=2;DP=3983;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,64:110:99:2633,0,1686:19,27,27,37 chr2 108443598 . G C 1875.42 PASS AC=1;AF=0.738;AN=2;DP=3677;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,62:105:99:2454,0,1602:17,26,26,36 chr2 108443647 . C G 511.77 PASS AC=2;AF=0.81;AN=2;DP=1404;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,45:46:99:1848,117,0:1,0,7,38 chr2 108475958 . A G 4452.92 PASS AC=1;AF=0.679;AN=2;DP=9857;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant4-variant5-filterInvariant6-variant8-variant9-variant10-variant11-filterInvariant12-filterInvariant13-filterInvariant14-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant19-variant20-variant21-filterInvariant22-filterInvariant23-variant24-variant25-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-filterInvariant35-variant36-variant37-filterInvariant38-variant39-filterInvariant40-variant41-variant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:89,135:224:99:2898,0,1713:44,45,61,74 chr2 108479432 . G A 1634.17 DRAGENHardSNP AC=1;AF=0.738;AN=2;DP=3449;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:63,38:101:99:701,0,1435:21,42,16,22 chr2 108479487 . A T 835.5 PASS AC=1;AF=0.738;AN=2;DP=1538;FractionInformativeReads=1;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant13-filterInvariant14-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-filterInvariant35-variant36-filterInvariant37-filterInvariant38-filterInvariant39-filterInvariant40-filterInvariant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:24,19:43:99:443,0,593:7,17,4,15 chr2 108487330 . A G 3988.11 PASS AC=1;AF=0.769;AN=2;DP=5445;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:103,79:182:99:1764,0,2492:48,55,31,48 chr2 108487877 . T C 178.42 PASS AC=2;AF=0.929;AN=2;DP=355;FractionInformativeReads=1;set=filterInvariant7-variant11-variant30-variant33-variant35-filterInvariant39-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:600,57,0:0,0,2,17 chr2 108496435 . T A 1775.19 PASS AC=1;AF=0.75;AN=2;DP=2461;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,29:59:99:753,0,843:22,8,20,9 chr2 108499667 . C T 443.35 PASS AC=2;AF=0.846;AN=2;DP=424;FractionInformativeReads=1;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant13-filterInvariant14-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant26-variant27-filterInvariant28-filterInvariant30-filterInvariant32-filterInvariant33-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant38-variant39-filterInvariant40-filterInvariant41-filterInvariant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:338,36,0:0,0,8,4 chr2 108618128 . CA CAA,CAAAA,C,CAAA 96.4 PASS AC=1,0,0,0;AF=0.231,0.077,0.115,0.154;AN=2;DP=122;set=variant2-variant8-variant9-variant11-filterInvariant21-variant23-variant24-variant25-variant35-variant37-variant38-variant39-variant43 GT:DP:GQ:SB 0/1:6:99:4,0,2,0 chr2 108618146 . G A 102.31 PASS AC=1;AF=0.625;AN=2;DP=199;FractionInformativeReads=1;set=variant-variant2-variant4-variant8-variant11-variant15-variant19-variant31-variant32-variant35-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,12:20:99:341,0,267:7,1,10,2 chr2 108618540 . G A 1739.68 PASS AC=1;AF=0.635;AN=2;DP=1400;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant8-variant11-variant13-variant14-variant15-variant17-variant19-variant21-variant22-variant24-variant25-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:27,28:55:99:801,0,716:12,15,9,19 chr2 108622812 . TTA T 752.81 PASS AC=2;AF=0.875;AN=2;DP=1875;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1607,114,0:0,0,6,32 chr2 108627917 . G A 8271.95 PASS AC=2;AF=0.875;AN=2;DP=27575;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,646:646:99:19780,1934,0:0,0,315,331 chr2 108628585 . T G 2309.04 PASS AC=1;AF=0.676;AN=2;DP=4031;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:71,51:122:99:1886,0,4009:41,30,32,19 chr2 108628586 . G T 2309.04 PASS AC=1;AF=0.676;AN=2;DP=4038;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:71,51:122:99:1886,0,4009:41,30,31,20 chr2 108629104 . G A 2133.31 PASS AC=2;AF=0.875;AN=2;DP=6417;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,150:150:99:4685,447,0:0,0,82,68 chr2 108629260 . A C 5300.64 PASS AC=1;AF=0.676;AN=2;DP=13810;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:148,159:307:99:3793,0,3615:81,67,84,75 chr2 108863767 . A C 1599.65 PASS AC=1;AF=0.757;AN=2;DP=4596;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:49,68:117:99:1789,0,1123:23,26,28,40 chr2 108863898 . C T 454.19 PASS AC=1;AF=0.567;AN=2;DP=396;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant13-variant24-variant26-variant27-variant29-variant35-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:10,14:24:99:450,0,282:2,8,2,12 chr2 108875093 . T A 506.59 PASS AC=1;AF=0.567;AN=2;DP=587;MQ=60;set=variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant13-variant24-variant26-variant27-variant29-variant35-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:22,20:42:99:507,0,650:18,4,16,4 chr2 108875198 . G A 1431.08 PASS AC=1;AF=0.567;AN=2;DP=1609;MQ=60;set=variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant13-variant24-variant26-variant27-variant29-variant35-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:59,59:118:99:1402,0,1601:34,25,33,26 chr2 108875244 . T C 1560.09 PASS AC=1;AF=0.619;AN=2;DP=2735;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant24-variant26-variant27-variant29-variant31-variant33-variant35-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:74,77:151:99:1868,0,1891:39,35,38,39 chr2 108875471 . G T 1798.39 PASS AC=1;AF=0.619;AN=2;DP=3610;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant24-variant26-variant27-variant29-variant31-variant33-variant35-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:98,97:195:99:2308,0,2279:44,54,44,53 chr2 108876948 . C T 70.21 PASS AC=1;AF=0.722;AN=2;DP=449;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,9:13:99:236,0,144:2,2,6,3 chr2 108877062 . T A 680.67 PASS AC=1;AF=0.722;AN=2;DP=3057;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:46,42:88:99:1088,0,1106:30,16,27,15 chr2 108905030 . C T 421.42 PASS AC=2;AF=0.72;AN=2;DP=254;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant16-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:423,36,0:0,0,10,2 chr2 108905396 . G GC 834.05 PASS AC=1;AF=0.5;AN=2;DP=108;MQ=60;set=variant11-variant35 GT:AD:DP:GQ:PL:SB 0/1:26,28:54:99:727,0,666:12,14,10,18 chr2 108915136 . T C 408.15 PASS AC=1;AF=0.703;AN=2;DP=1461;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,30:55:99:621,0,502:13,12,15,15 chr2 108915263 . C T 306.94 PASS AC=1;AF=0.716;AN=2;DP=1009;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-filterInvariant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,7:21:99:233,0,349:6,8,1,6 chr2 108921161 . G A 690.1 PASS AC=1;AF=0.5;AN=2;DP=61;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=3.098;QD=11.31;ReadPosRankSum=-2.029;SOR=0.685;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:32,29:61:99:718,0,830:11,21,10,19 chr2 108925780 . T C 1255.78 PASS AC=1;AF=0.756;AN=2;DP=1582;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,21:37:99:616,0,427:7,9,7,14 chr2 108925825 . C G 342.07 PASS AC=1;AF=0.5;AN=2;DP=34;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.277;QD=10.06;ReadPosRankSum=-0.59;SOR=0.716;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:19,15:34:99:370,0,426:9,10,7,8 chr2 108999483 . CAA CA,C 36.29 PASS AC=1,0;AF=0.452,0.048;AN=2;DP=738;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-filterInvariant28-variant33-filterInvariant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43 GT:DP:GQ:SB 0/1:19:74:4,4,9,2 chr2 109004251 . ATT AT,A,ATTT 119.25 PASS AC=0,0,1;AF=0.31,0.095,0.119;AN=2;DP=558;MQ=60;set=variant-variant2-filterInvariant3-variant5-variant6-variant11-variant12-filterInvariant14-variant16-filterInvariant19-variant28-variant30-variant32-variant35-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:DP:GQ:SB 0/3:13:65:0,5,4,4 chr2 109006665 . T A 904.34 PASS AC=1;AF=0.556;AN=2;DP=1226;FractionInformativeReads=1;MQ=60;set=variant7-variant8-variant11-variant12-variant15-variant17-variant18-variant20-variant24-variant27-variant28-variant30-variant34-variant35-variant36-variant37-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,23:63:99:639,0,909:16,24,5,18 chr2 109065123 . C T 1774.33 PASS AC=1;AF=0.674;AN=2;DP=3968;MQ=60;set=variant2-variant6-variant8-variant11-variant12-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant27-variant28-variant29-variant30-variant34-variant35-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:119,97:216:99:2223,0,2971:51,68,45,52 chr2 109065481 . C CA 1690.71 PASS AC=1;AF=0.674;AN=2;DP=2646;MQ=60;set=variant2-variant6-variant8-variant11-variant12-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant27-variant28-variant29-variant30-variant34-variant35-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:73,65:138:99:2028,0,2302:40,33,37,28 chr2 109065858 . T C 1330.13 PASS AC=1;AF=0.717;AN=2;DP=2535;MQ=60;set=variant2-variant4-variant6-variant7-variant8-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,50:98:99:1251,0,1288:15,33,21,29 chr2 109065919 . T C 1054.47 PASS AC=1;AF=0.674;AN=2;DP=1445;MQ=60;set=variant2-variant6-variant8-variant11-variant12-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant27-variant28-variant29-variant30-variant34-variant35-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,32:62:99:832,0,918:11,19,17,15 chr2 109067337 . C T 148.64 PASS AC=1;AF=0.682;AN=2;DP=390;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant8-variant11-variant12-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant27-variant28-variant29-variant30-variant34-variant35-variant37-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,6:15:99:216,0,228:7,2,6,0 chr2 109067359 . G A 293.44 PASS AC=1;AF=0.674;AN=2;DP=702;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant8-variant11-variant12-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant27-variant28-variant29-variant30-variant34-variant35-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,11:30:99:405,0,879:13,6,10,1 chr2 109067360 . T A 293.44 PASS AC=1;AF=0.674;AN=2;DP=716;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant8-variant11-variant12-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant27-variant28-variant29-variant30-variant34-variant35-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,11:30:99:405,0,879:13,6,10,1 chr2 109069008 . T C 535.67 PASS AC=1;AF=0.717;AN=2;DP=1271;MQ=60;set=variant2-variant4-variant6-variant7-variant8-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,25:55:99:629,0,715:13,17,11,14 chr2 109085373 . A G 1707.71 PASS AC=1;AF=0.674;AN=2;DP=2895;set=variant2-variant6-variant8-variant11-variant12-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant27-variant28-variant29-variant30-variant34-variant35-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:76,74:150:99:1817,0,1892:40,36,42,32 chr2 109089404 . C G 560.22 PASS AC=1;AF=0.717;AN=2;DP=1066;MQ=60;set=variant2-variant4-variant6-variant7-variant8-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,25:39:99:643,0,400:3,11,10,15 chr2 109092121 . G A 765.17 PASS AC=1;AF=0.682;AN=2;DP=966;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant8-variant11-variant12-variant15-variant17-variant20-variant21-variant23-variant24-variant27-variant28-variant29-variant30-variant34-variant35-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,25:42:99:544,0,416:8,9,12,13 chr2 109098994 . T C 205.39 PASS AC=1;AF=0.674;AN=2;DP=376;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant8-variant11-variant12-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant27-variant28-variant29-variant30-variant34-variant35-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,15:20:99:493,0,118:1,4,3,12 chr2 109099477 . A G 671.97 PASS AC=1;AF=0.717;AN=2;DP=1685;MQ=60;set=variant2-variant4-variant6-variant7-variant8-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,46:87:99:1151,0,868:22,19,26,20 chr2 109099572 . C G 1810.75 PASS AC=2;AF=0.989;AN=2;DP=2010;MQ=60;MQRankSum=-1.092;ReadPosRankSum=-0.705;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1666,159,0:0,0,21,32 chr2 109103108 . C T 883.77 PASS AC=1;AF=0.674;AN=2;DP=1876;MQ=60;set=variant2-variant6-variant8-variant11-variant12-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant27-variant28-variant29-variant30-variant34-variant35-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,36:79:99:1006,0,1188:16,27,13,23 chr2 109106381 . A G 1139.85 PASS AC=1;AF=0.674;AN=2;DP=1870;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant8-variant11-variant12-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant27-variant28-variant29-variant30-variant34-variant35-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,44:80:99:1026,0,905:20,16,27,17 chr2 109116613 . CAT C 551.74 PASS AC=1;AF=0.722;AN=2;DP=779;set=variant2-variant4-variant6-variant7-variant8-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant34-variant35-variant37-variant38-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:18,12:30:99:413,0,676:8,10,6,6 chr2 109123950 . T A 167.47 PASS AC=1;AF=0.684;AN=2;DP=191;FractionInformativeReads=1;set=variant2-variant6-variant8-variant11-variant15-variant20-variant21-variant23-variant24-variant27-variant28-variant29-variant34-variant35-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:77:117,0,77:2,1,3,0 chr2 109123988 . C CT,CTT 180.8 PASS AC=1,0;AF=0.548,0.119;AN=2;DP=544;set=variant2-variant6-variant8-variant11-variant12-variant15-variant20-variant21-variant23-variant24-variant27-variant28-variant29-variant30-variant34-variant35-variant37-variant38-variant39-variant41-variant44 GT:DP:GQ:SB 0/1:20:99:8,4,7,1 chr2 109277239 . C T 865.51 PASS AC=1;AF=0.674;AN=2;DP=1530;set=variant2-variant6-variant8-variant11-variant12-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant27-variant28-variant29-variant30-variant34-variant35-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,41:77:99:925,0,829:19,17,18,23 chr2 109292280 . T C 4280.65 PASS AC=2;AF=0.943;AN=2;DP=8245;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,211:211:99:6528,631,0:0,0,139,72 chr2 109294588 . A T 1412.03 PASS AC=1;AF=0.679;AN=2;DP=3083;set=variant2-variant4-variant6-variant7-variant8-variant11-variant12-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,55:104:99:1256,0,1334:13,36,20,35 chr2 109296984 . C A 157.99 PASS AC=1;AF=0.821;AN=2;DP=73;set=variant7-variant11-variant15-variant19-variant20-variant21-variant23-variant24-variant27-variant28-variant33-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:1,3:4:34:123,0,34:1,0,3,0 chr2 109297016 . AAAAAG A 117.55 PASS AC=1;AF=0.571;AN=2;DP=113;set=variant6-variant17-variant18-variant28-variant35-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,10:14:99:309,0,139:4,0,7,3 chr2 109301074 . C A 5166.51 PASS AC=1;AF=0.726;AN=2;DP=4552;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant22-variant25-variant26-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:79,79:158:99:1774,0,1672:40,39,40,39 chr2 109301115 . T TA 2873.56 PASS AC=1;AF=0.679;AN=2;DP=4217;MQ=60;set=variant2-variant4-variant6-variant7-variant8-variant11-variant12-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:80,82:162:99:2851,0,2752:40,40,39,43 chr2 109301398 . C A 18992 PASS AC=2;AF=1;AN=2;DP=22080;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,469:470:99:15078,1390,0:1,0,254,215 chr2 109301687 . G C 8073.57 PASS AC=1;AF=0.726;AN=2;DP=6488;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant22-variant25-variant26-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:124,102:226:99:2571,0,3115:72,52,57,45 chr2 109301841 . G A 4825.37 PASS AC=1;AF=0.679;AN=2;DP=8952;MQ=60;set=variant2-variant4-variant6-variant7-variant8-variant11-variant12-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:156,183:339:99:4604,0,3796:72,84,87,96 chr2 109301889 . G GT 2840.64 PASS AC=1;AF=0.619;AN=2;DP=5978;set=variant2-variant5-variant6-variant8-variant9-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant22-variant26-variant31-variant32-variant35-variant36-variant38-variant-variant42 GT:AD:DP:GQ:PL:SB 0/1:149,110:259:99:2105,0,3668:62,87,49,61 chr2 109302388 . G A 6863.97 PASS AC=1;AF=0.726;AN=2;DP=5083;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant22-variant25-variant26-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:70,80:150:99:1997,0,2013:21,49,28,52 chr2 109302699 . C T 315.3 PASS AC=1;AF=0.768;AN=2;DP=246;MQ=60;set=variant-variant3-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant22-variant25-variant26-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,4:9:99:109,0,180:5,0,3,1 chr2 109345484 . G A 251.82 PASS AC=1;AF=0.604;AN=2;DP=640;FractionInformativeReads=1;set=variant2-variant7-variant8-variant9-variant10-variant12-variant13-variant16-variant18-variant19-variant23-variant24-variant25-variant31-variant32-variant33-variant34-variant35-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,15:27:99:422,0,282:7,5,10,5 chr2 109347947 . T G 786.91 PASS AC=1;AF=0.625;AN=2;DP=1251;FractionInformativeReads=1;set=variant2-variant7-variant8-variant9-variant10-variant12-variant13-variant16-variant18-variant19-variant23-variant24-variant25-variant31-variant32-variant33-variant34-variant35-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,26:37:99:655,0,206:4,7,10,16 chr2 109351914 . C G 628.14 PASS AC=1;AF=0.604;AN=2;DP=1115;set=variant2-variant7-variant8-variant9-variant10-variant12-variant13-variant16-variant18-variant19-variant23-variant24-variant25-variant31-variant32-variant33-variant34-variant35-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,18:33:99:535,0,443:14,1,15,3 chr2 109352503 . A G 377.77 PASS AC=1;AF=0.63;AN=2;DP=520;FractionInformativeReads=1;set=variant2-variant7-variant8-variant9-variant10-variant12-variant13-variant16-variant18-variant19-variant23-variant24-variant25-variant31-variant32-variant33-variant34-variant35-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,7:17:99:187,0,403:10,0,6,1 chr2 109352542 . G A 401.28 PASS AC=1;AF=0.625;AN=2;DP=1005;FractionInformativeReads=1;set=variant2-variant7-variant8-variant9-variant10-variant12-variant13-variant16-variant18-variant19-variant23-variant24-variant25-variant31-variant32-variant33-variant34-variant35-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,9:40:99:171,0,1013:24,7,8,1 chr2 109352744 . C T 558.67 PASS AC=1;AF=0.528;AN=2;DP=1240;set=variant2-variant7-variant8-variant9-variant12-variant16-variant18-variant19-variant23-variant24-variant25-variant31-variant32-variant34-variant35-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:30,34:64:99:973,0,898:6,24,7,27 chr2 109357252 . T TTAAAA 281.3 PASS AC=1;AF=0.63;AN=2;DP=435;set=variant2-variant7-variant8-filterInvariant9-variant10-variant12-variant13-variant16-variant18-variant19-variant23-variant24-variant25-variant31-variant32-variant33-variant34-variant35-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,6:19:99:213,0,952:3,10,0,6 chr2 109369720 . G T 155.96 PASS AC=1;AF=0.604;AN=2;DP=607;set=variant2-variant7-variant8-variant9-variant10-variant12-variant13-variant16-variant18-variant19-variant23-variant24-variant25-variant31-variant32-variant33-variant34-variant35-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,9:21:99:287,0,376:5,7,4,5 chr2 109374952 . A G 1016.41 PASS AC=1;AF=0.625;AN=2;DP=2142;set=variant2-variant7-variant8-variant9-variant10-variant12-variant13-variant16-variant18-variant19-variant23-variant24-variant25-variant31-variant32-variant33-variant34-variant35-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,37:97:99:657,0,1420:27,33,18,19 chr2 109375074 . G A 62.99 PASS AC=1;AF=0.667;AN=2;DP=85;FS=0;FractionInformativeReads=1;set=variant9-variant10-variant13-variant16-variant19-variant24-variant25-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,5:18:99:125,0,485:0,13,0,5 chr2 109388846 . G A 343.58 PASS AC=1;AF=0.604;AN=2;DP=743;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant8-variant9-variant10-variant12-variant13-variant16-variant18-variant19-variant23-variant24-variant25-variant31-variant32-variant33-variant34-variant35-variant38-variant40-variant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:11,13:24:99:382,0,305:8,3,8,5 chr2 109389124 . A T 48 PASS AC=1;AF=0.609;AN=2;DP=348;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant8-variant9-variant10-variant12-variant13-variant16-variant18-variant19-variant23-variant24-variant25-variant31-variant32-variant33-variant34-variant35-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,7:17:99:220,0,312:4,6,2,5 chr2 109389463 . G A 3157.69 PASS AC=2;AF=1;AN=2;DP=5158;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,111:111:99:3278,333,0:0,0,48,63 chr2 109393522 . TG T 961.97 PASS AC=2;AF=1;AN=2;DP=1458;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1250,111,0:0,0,26,11 chr2 109393766 . A T 509.3 PASS AC=1;AF=0.604;AN=2;DP=982;MQ=60;set=variant2-variant7-variant8-variant9-variant10-variant12-variant13-variant16-variant18-variant19-variant23-variant24-variant25-variant31-variant32-variant33-variant34-variant35-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,21:44:99:729,0,6898:4,19,4,17 chr2 109393767 . TATAAC T 500.26 PASS AC=1;AF=0.604;AN=2;DP=866;MQ=60;set=variant2-variant7-variant8-variant9-variant10-variant12-variant13-variant16-variant18-variant19-variant23-variant24-variant25-variant31-variant32-variant33-variant34-variant35-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,18:40:99:729,0,6898:4,18,1,17 chr2 109393774 . A T 439.37 PASS AC=1;AF=0.604;AN=2;DP=778;MQ=60;set=variant2-variant7-variant8-variant9-variant10-variant12-variant13-variant16-variant18-variant19-variant23-variant24-variant25-variant31-variant32-variant33-variant34-variant35-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,16:33:99:660,0,6591:3,14,1,15 chr2 109393779 . A T 448.4 PASS AC=1;AF=0.604;AN=2;DP=701;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant8-variant9-variant10-variant12-variant13-variant16-variant18-variant19-variant23-variant24-variant25-variant31-variant32-variant33-variant34-variant35-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,12:26:99:495,0,6658:2,12,1,11 chr2 109393780 . G T 448.4 PASS AC=1;AF=0.604;AN=2;DP=693;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant8-variant9-variant10-variant12-variant13-variant16-variant18-variant19-variant23-variant24-variant25-variant31-variant32-variant33-variant34-variant35-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,12:26:99:498,0,6522:2,12,1,11 chr2 109393781 . A T 451.41 PASS AC=1;AF=0.604;AN=2;DP=687;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant8-variant9-variant10-variant12-variant13-variant16-variant18-variant19-variant23-variant24-variant25-variant31-variant32-variant33-variant34-variant35-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,12:26:99:462,0,6281:2,12,1,11 chr2 109393786 . TC T 400.38 PASS AC=1;AF=0.604;AN=2;DP=615;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant8-variant9-variant10-variant12-variant13-variant16-variant18-variant19-variant23-variant24-variant25-variant31-variant32-variant33-variant34-variant35-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,10:22:99:378,0,6287:2,10,1,9 chr2 109393789 . TCCCTTACCCCCC T 400.38 PASS AC=1;AF=0.604;AN=2;DP=592;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant8-variant9-variant10-variant12-variant13-variant16-variant18-variant19-variant23-variant24-variant25-variant31-variant32-variant33-variant34-variant35-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,9:21:99:384,0,5877:2,10,1,8 chr2 109393803 . GT G 430.49 PASS AC=1;AF=0.604;AN=2;DP=510;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant8-variant9-variant10-variant12-variant13-variant16-variant18-variant19-variant23-variant24-variant25-variant31-variant32-variant33-variant34-variant35-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,7:18:99:261,0,5532:1,10,0,7 chr2 109393807 . G GTTTAGT 439.52 PASS AC=1;AF=0.604;AN=2;DP=472;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant8-variant9-variant10-variant12-variant13-variant16-variant18-variant19-variant23-variant24-variant25-variant31-variant32-variant33-variant34-variant35-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,7:17:99:261,0,5532:1,9,0,7 chr2 109401259 . C T 4323.12 PASS AC=1;AF=0.625;AN=2;DP=8960;MQ=60;set=variant2-variant7-variant8-variant9-variant10-variant12-variant13-variant16-variant18-variant19-variant23-variant24-variant25-variant31-variant32-variant33-variant34-variant35-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:181,188:369:99:4670,0,4350:95,86,88,100 chr2 109401291 . T TTCTAG 7307.43 PASS AC=1;AF=0.625;AN=2;DP=9143;MQ=60;set=variant2-variant7-variant8-variant9-variant10-variant12-variant13-variant16-variant18-variant19-variant23-variant24-variant25-variant31-variant32-variant33-variant34-variant35-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:193,195:388:99:4879,0,10947:102,91,94,101 chr2 109403101 . G C 320.6 PASS AC=1;AF=0.604;AN=2;DP=1899;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant8-variant9-variant10-variant12-variant13-variant16-variant18-variant19-variant23-variant24-variant25-variant31-variant32-variant33-variant34-variant35-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,18:67:99:666,0,2945:32,17,12,6 chr2 109403112 . T C 415.15 PASS AC=1;AF=0.528;AN=2;DP=1476;MQ=60;set=variant2-variant7-variant8-variant9-variant12-variant16-variant18-variant19-variant23-variant24-variant25-variant31-variant32-variant34-variant35-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:51,23:74:99:760,0,2962:33,18,16,7 chr2 109404474 . C CT 137.61 PASS AC=1;AF=0.614;AN=2;DP=681;MQ=60;set=variant2-variant7-variant9-variant10-variant12-variant13-variant16-variant19-variant23-variant24-variant25-variant31-variant32-variant33-variant34-variant35-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,9:24:99:168,0,345:10,5,4,5 chr2 109408208 . G A 513.65 PASS AC=1;AF=0.604;AN=2;DP=1298;FractionInformativeReads=1;set=variant2-variant7-variant8-variant9-variant10-variant12-variant13-variant16-variant18-variant19-variant23-variant24-variant25-variant31-variant32-variant33-variant34-variant35-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,32:57:99:768,0,652:9,16,12,20 chr2 109411248 . GAATAT G 450.49 PASS AC=1;AF=0.756;AN=2;DP=690;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,12:15:99:495,0,152:0,3,0,12 chr2 109429146 . T A 2799.86 PASS AC=1;AF=0.763;AN=2;DP=2774;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,30:68:99:797,0,1018:27,11,16,14 chr2 109490104 . A G 535.17 PASS AC=2;AF=1;AN=2;DP=484;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:466,33,0:0,0,2,9 chr2 109492907 . A G 1650.3 PASS AC=1;AF=0.932;AN=2;DP=6774;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:64,102:166:99:2457,0,1382:29,35,46,56 chr2 109493002 . T A 537.21 PASS AC=1;AF=0.78;AN=2;DP=1939;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,30:43:99:809,0,330:3,10,12,18 chr2 109510937 . G A 76.69 PASS AC=1;AF=0.714;AN=2;DP=430;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,7:8:18:197,0,18:1,0,4,3 chr2 109511765 . A G 3848.09 PASS AC=1;AF=0.774;AN=2;DP=12710;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:181,171:352:99:4010,0,4390:86,95,84,87 chr2 109512234 . T C 288.11 PASS AC=1;AF=0.786;AN=2;DP=2106;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,31:61:99:830,0,869:11,19,14,17 chr2 109513321 . C A 866.01 PASS AC=1;AF=0.864;AN=2;DP=5660;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:88,75:163:99:1877,0,2156:46,42,35,40 chr2 109513654 . G A 69.16 PASS AC=1;AF=0.774;AN=2;DP=4278;MQ=60;set=filterInvariant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,55:103:99:1322,0,1186:17,31,22,33 chr2 109513786 . A T 125.53 PASS AC=1;AF=0.8;AN=2;DP=354;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant14-variant15-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,5:8:71:160,0,71:1,2,1,4 chr2 109522720 . G A 646.44 PASS AC=1;AF=0.774;AN=2;DP=2184;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,20:55:99:431,0,844:20,15,13,7 chr2 109524105 . CA C 286.67 PASS AC=1;AF=0.833;AN=2;DP=912;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,12:26:99:256,0,297:10,4,9,3 chr2 109526969 . G A 1694.17 PASS AC=1;AF=0.864;AN=2;DP=8474;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:120,105:225:99:2461,0,3007:64,56,55,50 chr2 109527087 . G A 1579.31 PASS AC=1;AF=0.762;AN=2;DP=4645;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,70:135:99:1708,0,1657:26,39,31,39 chr2 109527373 . A G 1538.26 PASS AC=1;AF=0.864;AN=2;DP=6192;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:93,86:179:99:2045,0,2323:46,47,46,40 chr2 109539653 . A G 624.2 PASS AC=1;AF=0.864;AN=2;DP=2304;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:21,26:47:99:799,0,609:16,5,19,7 chr2 109605767 . G A 938.64 PASS AC=1;AF=0.536;AN=2;DP=822;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant7-variant11-variant24-variant27-variant28-variant29-variant31-variant34-variant35-variant36-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:43,28:71:99:703,0,1061:19,24,12,16 chr2 109745176 . G A 534.65 PASS AC=2;AF=0.989;AN=2;DP=959;MQ=60;MQRankSum=0.953;ReadPosRankSum=2.307;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:866,69,0:0,0,21,2 chr2 109745782 . TGGCCGGTCCCCGCCACGCA T 2907.5 PASS AC=2;AF=0.989;AN=2;DP=4378;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:2575,186,0:0,0,23,35 chr2 109745929 . C G 797.11 PASS AC=1;AF=0.5;AN=2;DP=724;MQ=60;set=variant7-variant21-variant27-variant28-variant31-variant34-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:37,49:86:99:1249,0,987:22,15,27,22 chr2 109746039 . G A 1656.61 PASS AC=1;AF=0.553;AN=2;DP=1819;MQ=60;set=variant2-variant6-variant8-variant9-variant11-variant12-variant13-variant14-variant17-variant18-variant21-variant24-variant25-variant26-variant27-variant30-variant35-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:59,59:118:99:1638,0,1452:31,28,33,26 chr2 109758196 . C T 540.9 PASS AC=1;AF=0.571;AN=2;DP=886;MQ=60;set=variant2-variant6-variant8-variant9-variant11-variant12-variant13-variant14-variant17-variant18-variant21-variant24-variant25-variant26-variant27-variant28-variant30-variant35-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:20,28:48:99:895,0,558:5,15,6,22 chr2 109929958 . A G 913.86 PASS AC=1;AF=0.672;AN=2;DP=1609;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,34:58:99:931,0,730:17,7,20,14 chr2 109988215 . C G 64.98 PASS AC=1;AF=0.671;AN=2;DP=552;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,6:14:99:225,0,282:1,7,1,5 chr2 110053209 . T G 950.33 PASS AC=1;AF=0.689;AN=2;DP=2835;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,58:119:99:1493,0,1359:34,27,31,27 chr2 110053248 . C T 1083.28 PASS AC=1;AF=0.575;AN=2;DP=1706;MQ=60;set=variant-variant3-variant4-variant7-variant10-variant11-variant13-variant18-variant20-variant22-variant27-variant28-variant30-variant32-variant33-variant35-variant36-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,64:128:99:1717,0,1596:37,27,34,30 chr2 110260993 . C T 2088.05 PASS AC=2;AF=0.932;AN=2;DP=2609;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:2806,231,0:0,0,20,57 chr2 110332020 . TAAAA TAA,T 42.58 PASS AC=0,2;AF=0.5,0.5;AN=2;DP=7;FS=0;MQ=60;set=variant33-variant35 GT:DP:GQ:SB 2/2:2:6:0,0,2,0 chr2 110343448 . T TA 483.26 PASS AC=1;AF=0.5;AN=2;DP=50;FS=2.415;FractionInformativeReads=0.96;MQ=60;MQRankSum=-2.002;QD=9.67;ReadPosRankSum=-0.681;SOR=1.078;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:25,23:48:99:521,0,607:12,13,9,14 chr2 110371622 . C G 3335.51 PASS AC=2;AF=1;AN=2;DP=5137;FS=0;MQ=60;MQRankSum=1.338;ReadPosRankSum=-0.157;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,111:111:99:3712,332,0:0,0,73,38 chr2 110372192 . A G 2494.64 PASS AC=2;AF=1;AN=2;DP=3780;FS=0;MQ=60;MQRankSum=0.197;ReadPosRankSum=-0.945;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,91:91:99:2725,273,0:0,0,55,36 chr2 110375592 . CAAAAA C,CAAAA,CAAA 384.22 PASS AC=0,1,0;AF=0.266,0.203,0.063;AN=2;DP=835;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-filterInvariant35-variant36-variant39-variant40-variant41-variant44 GT:DP:GQ:SB 0/2:19:70:11,2,6,0 chr2 110855123 . G T 1199.86 PASS AC=2;AF=0.966;AN=2;DP=5600;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,127:127:99:3754,380,0:0,0,72,55 chr2 110873470 . GA GAA,G 746.48 PASS AC=1,0;AF=0.382,0.132;AN=2;DP=3712;set=variant2-filterInvariant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant15-filterInvariant18-variant19-variant21-filterInvariant22-variant23-variant24-variant25-variant26-variant27-filterInvariant28-variant30-variant31-variant32-variant33-variant34-variant35-filterInvariant36-filterInvariant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:136:99:32,39,34,31 chr2 110880187 . C T 2550.5 PASS AC=2;AF=1;AN=2;DP=3873;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,99:99:99:3140,297,0:0,0,60,39 chr2 110882699 . A G 672.67 PASS AC=1;AF=0.62;AN=2;DP=1569;MQ=60;set=variant2-variant5-variant7-variant9-variant10-variant11-variant12-variant15-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,41:80:99:1071,0,935:24,15,26,15 chr2 110886686 . A AGACCAGAT 831.82 PASS AC=1;AF=0.62;AN=2;DP=1472;MQ=60;set=variant2-variant5-variant7-variant9-variant10-variant11-variant12-variant15-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,23:60:99:896,0,3549:21,16,14,9 chr2 110889108 . C T 142.15 PASS AC=1;AF=0.625;AN=2;DP=305;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant7-variant9-variant10-variant12-variant15-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,11:13:48:365,0,48:2,0,9,2 chr2 110905664 . G A 387.05 PASS AC=1;AF=0.62;AN=2;DP=638;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant7-variant9-variant10-variant11-variant12-variant15-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,14:26:99:430,0,373:3,9,4,10 chr2 110919041 . A G 330.23 PASS AC=1;AF=0.708;AN=2;DP=431;FractionInformativeReads=1;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant28-variant29-variant30-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,5:8:99:191,0,104:3,0,4,1 chr2 110919321 . C T 490 PASS AC=1;AF=0.62;AN=2;DP=761;MQ=60;set=variant2-variant5-variant7-variant9-variant10-variant11-variant12-variant15-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,9:20:99:223,0,283:3,8,3,6 chr2 110920729 . C T 909.94 PASS AC=1;AF=0.5;AN=2;DP=299;FractionInformativeReads=1;MQ=60;set=variant-variant14-variant35 GT:AD:DP:GQ:PL:SB 0/1:66,45:111:99:1014,0,1921:28,38,18,27 chr2 110922703 . C T 1321.18 PASS AC=1;AF=0.62;AN=2;DP=3178;MQ=60;set=variant2-variant5-variant7-variant9-variant10-variant11-variant12-variant15-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,67:127:99:1487,0,1366:29,31,35,32 chr2 110935867 . A G 2352.4 PASS AC=1;AF=0.62;AN=2;DP=6449;set=variant2-variant5-variant7-variant9-variant10-variant11-variant12-variant15-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:125,108:233:99:2635,0,3070:58,67,50,58 chr2 110959898 . C G 1027.84 PASS AC=1;AF=0.62;AN=2;DP=2402;MQ=60;set=variant2-variant5-variant7-variant9-variant10-variant11-variant12-variant15-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,46:102:99:1266,0,1394:34,22,32,14 chr2 111406724 . T TCA,TCACA 256.11 PASS AC=1,0;AF=0.463,0.093;AN=2;DP=517;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant15-variant16-variant17-variant20-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant43 GT:DP:GQ:SB 0/1:13:31:2,0,7,4 chr2 111598958 . C T 525.5 PASS AC=1;AF=0.5;AN=2;DP=559;FractionInformativeReads=1;MQ=60;set=variant12-variant16-variant22-variant30-variant32-variant34-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:54,26:80:99:679,0,1432:30,24,18,8 chr2 111721142 . ATGTGTGTGTGTGTGTGTGTG ATGTGTGTGTGTGTG,ATGTGTGTGTGTGTGTG,A,ATGTGTGTGTGTGTGTGTGTGTGTG,ATGTGTGTGTGTGTGTGTG,ATGTGTGTGTGTG 1279.5 PASS AC=0,0,1,0,0,0;AF=0.281,0.109,0.188,0.016,0.016,0.016;AN=2;DP=2653;set=variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant18-filterInvariant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:DP:GQ:SB 0/3:111:99:27,17,38,29 chr2 111721171 . TGTGTGTGTG TTGTGTGTG,T 1916.42 PASS AC=1,0;AF=0.464,0.036;AN=2;DP=1371;MQ=60;set=variant-variant2-variant5-variant9-variant11-variant14-variant24-variant27-variant34-variant35-variant36-variant41-variant42-variant44 GT:DP:GQ:SB 0/1:130:99:47,35,28,20 chr2 111721173 . TGTGTGTG T 1910.96 PASS AC=1;AF=0.5;AN=2;DP=1323;MQ=60;set=variant-variant2-variant5-variant9-variant11-variant14-variant24-variant27-variant34-variant35-variant36-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:84,34:118:99:667,0,3203:48,36,23,11 chr2 111744435 . A C 46.72 PASS AC=1;AF=0.605;AN=2;DP=186;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant8-variant12-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant35-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,4:9:99:101,0,147:4,1,2,2 chr2 111753449 . G C 1433.35 PASS AC=1;AF=0.591;AN=2;DP=4156;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant30-variant32-variant33-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,54:106:99:1192,0,1203:32,20,32,22 chr2 111875799 . GA G 48.25 PASS AC=1;AF=0.741;AN=2;DP=711;MQ=60;set=variant2-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant20-variant21-variant22-variant23-variant25-variant27-variant30-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,15:21:98:345,0,98:3,3,6,9 chr2 111878556 . TGCCGCCGCCGCC TGCCGCCGCC,TGCCGCCGCCGCCGCCGCCGCCGCCGCC,T,TGCCGCCGCCGCCGCC,TGCC 1561.47 PASS AC=1,0,1,0,0;AF=0.762,0.012,0.071,0.036,0.012;AN=2;DP=7143;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 3/1:200:99:0,0,112,88 chr2 111878565 . C T 1298.09 PASS AC=1;AF=0.808;AN=2;DP=6642;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:102,90:192:99:3432,0,3956:55,47,53,37 chr2 111878574 . C T 2947.16 PASS AC=1;AF=0.5;AN=2;DP=1120;set=variant14-variant18-variant23-variant29-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:106,106:212:99:4001,0,4037:61,45,57,49 chr2 111881810 . C T 518.18 PASS AC=2;AF=0.55;AN=2;DP=753;MQ=60;set=variant13-variant14-variant18-variant24-variant29-variant34-variant35-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2142,210,0:0,0,35,35 chr2 111886180 . CTT CT,CTTT,CTTTT,C 229.91 PASS AC=1,0,0,1;AF=0.388,0.138,0.013,0.013;AN=2;DP=2417;set=variant-filterInvariant2-variant3-variant4-variant5-variant6-filterInvariant7-variant9-variant10-filterInvariant11-variant12-variant13-variant14-variant15-filterInvariant16-variant17-variant18-variant19-variant20-variant21-variant22-filterInvariant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:DP:GQ:SB 4/1:65:99:6,0,50,9 chr2 111887703 . T A 522.91 PASS AC=2;AF=0.793;AN=2;DP=463;set=variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant18-variant20-variant21-variant22-variant24-variant25-variant27-variant29-variant30-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,15:16:38:391,38,0:1,0,6,9 chr2 111899881 . G A 701.34 PASS AC=2;AF=0.55;AN=2;DP=617;FractionInformativeReads=1;MQ=60;set=variant6-variant13-variant14-variant18-variant24-variant29-variant34-variant35-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,61:61:99:1904,183,0:0,0,33,28 chr2 111907691 . T C 1060.81 PASS AC=2;AF=0.8;AN=2;DP=2310;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:2268,216,0:0,0,48,24 chr2 111921438 . CTTTT CTT,C,CT 59.75 PASS AC=2,0,0;AF=0.333,0.083,0.167;AN=2;DP=45;MQ=60;set=variant5-variant12-variant14-variant31-variant35-variant42 GT:DP:GQ:SB 1/1:5:15:0,0,3,2 chr2 111923630 . T G 2599.99 PASS AC=2;AF=0.781;AN=2;DP=3485;MQ=60;set=variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,100:100:99:2947,299,0:0,0,59,41 chr2 111925731 . CTTATGTT C 2712.57 PASS AC=2;AF=0.55;AN=2;DP=1551;MQ=60;set=variant6-variant13-variant14-variant18-variant24-variant29-variant34-variant35-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,130:130:99:5830,394,0:0,0,65,65 chr2 112526866 . G A 610.17 DRAGENHardSNP AC=1;AF=0.526;AN=2;DP=1660;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:29,52:81:99:1136,0,532:11,18,23,29 chr2 112536264 . G T 140.39 PASS AC=2;AF=1;AN=2;DP=473;FS=0;MQRankSum=-1.156;ReadPosRankSum=-0.771;set=variant-variant2-variant3-filterInvariant4-variant5-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-variant10-filterInvariant11-variant12-variant13-variant14-variant15-filterInvariant16-filterInvariant17-variant18-filterInvariant19-filterInvariant20-filterInvariant21-variant22-variant23-variant24-filterInvariant25-filterInvariant26-variant27-variant28-filterInvariant29-variant30-filterInvariant31-variant32-filterInvariant33-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant37-variant38-variant39-filterInvariant40-filterInvariant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:307,27,0:0,0,9,0 chr2 112551673 . G A 100.57 PASS AC=1;AF=0.727;AN=2;DP=76;FractionInformativeReads=1;set=filterInvariant3-variant7-filterInvariant9-filterInvariant11-variant13-filterInvariant19-filterInvariant27-variant31-filterInvariant33-variant35-filterInvariant40 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:77:82,0,77:2,1,3,0 chr2 112552427 . C T 178.97 PASS AC=1;AF=0.55;AN=2;DP=73;FractionInformativeReads=1;set=variant3-variant13-filterInvariant14-variant16-filterInvariant19-variant33-variant35-variant39-filterInvariant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:5,4:9:99:126,0,114:2,3,0,4 chr2 112566517 . C T 208.22 DRAGENHardSNP AC=1;AF=0.567;AN=2;DP=171;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:4,8:12:80:170,0,80:1,3,3,5 chr2 112578794 . T C 30.28 PASS AC=1;AF=0.583;AN=2;DP=97;FractionInformativeReads=1;set=filterInvariant3-variant9-filterInvariant16-filterInvariant19-filterInvariant25-filterInvariant27-filterInvariant28-filterInvariant32-filterInvariant33-filterInvariant35-filterInvariant39-filterInvariant41 GT:AD:DP:GQ:PL:SB 0/1:6,3:9:78:78,0,132:4,2,3,0 chr2 112582523 . G A 685.13 PASS AC=1;AF=0.66;AN=2;DP=1460;FractionInformativeReads=1;set=variant2-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant13-variant15-variant18-variant22-variant23-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,32:62:99:792,0,720:17,13,17,15 chr2 112582766 . CTT C 424.5 PASS AC=1;AF=0.553;AN=2;DP=464;set=variant-variant3-variant8-variant9-variant13-variant14-variant16-variant19-variant25-variant27-variant28-variant32-variant33-variant35-variant37-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:7,7:14:99:273,0,309:1,6,1,6 chr2 112583476 . C T 323.26 PASS AC=1;AF=0.526;AN=2;DP=685;FractionInformativeReads=1;set=variant-variant3-variant8-variant9-variant13-variant14-variant16-variant19-variant25-variant27-variant28-variant32-variant33-variant35-variant37-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:18,16:34:99:409,0,497:6,12,6,10 chr2 112588751 . C T 303.14 PASS AC=2;AF=0.75;AN=2;DP=669;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant22-variant23-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:531,51,0:0,0,12,5 chr2 112589080 . G A 139.26 PASS AC=1;AF=0.567;AN=2;DP=111;FractionInformativeReads=1;set=variant-variant3-variant8-filterInvariant14-filterInvariant16-variant19-variant27-filterInvariant28-variant32-filterInvariant33-filterInvariant35-variant37-variant39-filterInvariant40-filterInvariant41 GT:AD:DP:GQ:PL:SB 0/1:2,5:7:38:139,0,38:0,2,1,4 chr2 112590989 . A T 311.09 PASS AC=2;AF=0.763;AN=2;DP=1183;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant22-variant23-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1128,102,0:0,0,9,25 chr2 112591057 . CA C 48.85 PASS AC=1;AF=0.571;AN=2;DP=64;set=variant7-variant15-variant22-variant35-variant37-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,4:9:99:116,0,150:1,4,0,4 chr2 112592109 . ACAAGGT A 133.03 PASS AC=2;AF=1;AN=2;DP=30;FS=0;set=variant7-variant11-variant18-variant27-variant31-variant34-variant35-variant36-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:90,6,0:0,0,0,2 chr2 112592117 . CCTAT C 133.03 PASS AC=2;AF=1;AN=2;DP=32;FS=0;set=variant7-variant11-variant18-variant27-variant31-variant34-variant35-variant36-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:90,6,0:0,0,0,2 chr2 112605302 . C T 270.87 PASS AC=2;AF=0.771;AN=2;DP=360;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant22-variant23-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:476,39,0:0,0,10,3 chr2 112605465 . T C 797.01 PASS AC=2;AF=1;AN=2;DP=1426;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1323,129,0:0,0,19,24 chr2 112614429 . G A 43.85 PASS AC=1;AF=0.5;AN=2;DP=60;FractionInformativeReads=1;set=variant6-variant30-filterInvariant35 GT:AD:DP:GQ:PL:SB 0/1:21,6:27:68:68,0,578:9,12,3,3 chr2 112614585 . T A 88.71 PASS AC=2;AF=0.891;AN=2;DP=101;FS=0;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant7-variant9-variant11-variant14-variant19-variant22-variant23-variant27-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:135,9,0:0,0,1,2 chr2 112614589 . A C 91.72 PASS AC=2;AF=0.891;AN=2;DP=89;FS=0;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant7-variant9-variant11-variant14-variant19-variant22-variant23-variant27-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:135,9,0:0,0,1,2 chr2 112616059 . C T 302.38 PASS AC=1;AF=0.55;AN=2;DP=195;FractionInformativeReads=1;set=variant7-variant13-variant15-variant18-variant22-variant30-variant31-variant35-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,10:21:99:258,0,285:1,10,1,9 chr2 112621498 . GA G 349.93 PASS AC=2;AF=0.66;AN=2;DP=483;set=variant3-variant7-variant9-variant13-variant14-variant15-variant16-variant18-variant19-variant22-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:46:374,46,0:0,0,3,13 chr2 112622642 . C T 253.66 PASS AC=1;AF=0.7;AN=2;DP=383;set=variant2-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant15-variant16-variant18-variant22-variant23-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,6:19:99:163,0,302:5,8,1,5 chr2 112622643 . A G 293.15 PASS AC=2;AF=0.77;AN=2;DP=553;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant22-variant23-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:850,57,0:0,0,6,13 chr2 112622650 . T C 166.67 PASS AC=2;AF=0.77;AN=2;DP=456;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant22-variant23-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:54:810,54,0:0,0,6,11 chr2 112625575 . T C 159.5 PASS AC=2;AF=0.8;AN=2;DP=348;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant22-variant23-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:342,39,0:0,0,7,6 chr2 112630412 . A C 241.5 PASS AC=2;AF=0.743;AN=2;DP=358;FractionInformativeReads=1;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-filterInvariant14-filterInvariant16-variant18-variant19-variant22-filterInvariant23-variant27-variant28-variant30-variant31-filterInvariant32-variant33-variant34-filterInvariant35-variant36-variant37-filterInvariant38-variant39-variant40-variant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:183,18,0:0,0,1,5 chr2 112636685 . G A 209.71 PASS AC=2;AF=0.786;AN=2;DP=309;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant22-variant23-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:210,15,0:0,0,0,5 chr2 112641149 . G C 622.5 PASS AC=1;AF=0.55;AN=2;DP=1608;MQ=60;set=variant-variant3-variant8-variant9-variant13-variant14-variant16-variant19-variant21-variant25-variant27-variant28-variant32-variant33-variant35-variant37-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:53,41:94:99:938,0,1226:26,27,18,23 chr2 112641256 . G A 831.08 PASS AC=2;AF=1;AN=2;DP=1569;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1735,117,0:0,0,11,28 chr2 112641257 . A G 422.73 PASS AC=2;AF=0.769;AN=2;DP=1376;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1735,117,0:0,0,10,28 chr2 112641266 . G C 350.34 PASS AC=1;AF=0.525;AN=2;DP=612;MQ=60;set=variant-variant3-variant8-variant9-variant13-variant14-variant16-variant19-variant21-variant25-variant27-variant28-variant32-variant33-variant35-variant37-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:16,21:37:99:591,0,460:3,13,6,15 chr2 112641283 . A G 362.35 PASS AC=2;AF=0.756;AN=2;DP=942;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:1253,90,0:0,0,8,22 chr2 112641666 . T C 295.98 PASS AC=1;AF=0.667;AN=2;DP=1841;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant21-variant23-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:21,28:49:99:728,0,506:13,8,18,10 chr2 112641854 . C T 1095.53 PASS AC=2;AF=0.643;AN=2;DP=4484;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,154:154:99:4709,460,0:0,0,84,70 chr2 112641909 . C T 1108.61 PASS AC=2;AF=0.737;AN=2;DP=5205;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,180:180:99:5142,539,0:0,0,91,89 chr2 112656372 . A T 1361.79 PASS AC=1;AF=0.5;AN=2;DP=850;MQ=60;set=variant9-variant10-variant20-variant25-variant28-variant35-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:50,61:111:99:1423,0,1177:19,31,22,39 chr2 112704846 . T TCCC,TC,TCCCCC 544.6 PASS AC=0,1,0;AF=0.1,0.3,0.1;AN=2;DP=125;set=variant4-variant13-variant34-variant35-variant36 GT:DP:GQ:SB 0/2:14:99:1,3,10,0 chr2 112704851 . A C 247.17 PASS AC=1;AF=0.5;AN=2;DP=392;set=variant2-filterInvariant4-variant8-variant9-variant12-variant13-variant14-variant16-variant18-variant19-variant22-variant25-variant31-variant34-variant35-variant36-variant37-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:8,12:20:99:391,0,143:2,6,12,0 chr2 112704855 . G C 87.22 PASS AC=1;AF=0.5;AN=2;DP=432;set=variant-variant2-variant4-variant8-variant9-variant12-variant13-variant14-variant16-variant18-variant22-variant25-variant31-variant34-variant35-variant36-variant37-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,10:23:99:201,0,882:7,6,10,0 chr2 112704862 . A G,C 180.71 PASS AC=0,1;AF=0.605,0.132;AN=2;DP=907;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:33:99:13,9,11,0 chr2 112705157 . T C 360.92 PASS AC=1;AF=0.769;AN=2;DP=1460;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,10:35:99:253,0,721:7,18,4,6 chr2 112725684 . A ATGTGTG 1432.82 PASS AC=1;AF=0.769;AN=2;DP=4161;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,44:91:99:1756,0,2973:32,15,35,9 chr2 112740373 . G A 309.33 PASS AC=1;AF=0.769;AN=2;DP=1046;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,9:35:99:179,0,742:18,8,5,4 chr2 112751928 . G A 1279.96 PASS AC=1;AF=0.769;AN=2;DP=5457;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:86,66:152:99:1447,0,2305:52,34,37,29 chr2 112752142 . A C 246.31 PASS AC=1;AF=0.769;AN=2;DP=1773;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,19:51:99:523,0,1068:5,27,5,14 chr2 112752880 . G A 1422.91 PASS AC=1;AF=0.769;AN=2;DP=3735;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,50:101:99:1439,0,1349:28,23,23,27 chr2 112753097 . A C 1716.33 PASS AC=1;AF=0.769;AN=2;DP=4898;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:72,66:138:99:1622,0,1684:28,44,26,40 chr2 112753781 . TA T 1610.55 PASS AC=1;AF=0.769;AN=2;DP=3665;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,37:85:99:1065,0,1450:24,24,19,18 chr2 112753883 . C T 998.7 PASS AC=1;AF=0.769;AN=2;DP=2167;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,33:59:99:890,0,772:12,14,16,17 chr2 112754229 . T C 1127.46 PASS AC=1;AF=0.5;AN=2;DP=809;MQ=60;set=variant9-variant10-variant20-variant25-variant28-variant35-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:64,62:126:99:1526,0,1654:30,34,29,33 chr2 112755001 . A G 1207.29 PASS AC=1;AF=0.769;AN=2;DP=4790;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:66,57:123:99:1430,0,1620:26,40,20,37 chr2 112761369 . G A 457.74 PASS AC=1;AF=0.5;AN=2;DP=343;FractionInformativeReads=1;MQ=60;set=variant9-variant10-variant20-variant25-variant28-variant35-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:23,22:45:99:681,0,690:15,8,17,5 chr2 112761653 . C G 582.43 PASS AC=1;AF=0.769;AN=2;DP=1425;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,24:41:99:813,0,506:4,13,3,21 chr2 112765973 . A G 1065.66 PASS AC=1;AF=0.769;AN=2;DP=3859;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,53:112:99:1207,0,1487:36,23,29,24 chr2 112766262 . A G 659.15 PASS AC=1;AF=0.769;AN=2;DP=2009;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,33:70:99:844,0,1001:18,19,18,15 chr2 112770770 . A G 503.26 PASS AC=1;AF=0.769;AN=2;DP=2758;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,40:79:99:1030,0,898:24,15,19,21 chr2 112770798 . T C 1007.34 PASS AC=1;AF=0.769;AN=2;DP=3123;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,47:94:99:1115,0,1092:25,22,21,26 chr2 112773366 . A G 813.81 PASS AC=1;AF=0.769;AN=2;DP=2280;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,30:49:99:705,0,466:11,8,17,13 chr2 112773528 . TCTTGTAC T 1456.67 PASS AC=1;AF=0.769;AN=2;DP=2466;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,17:62:99:544,0,3050:22,23,6,11 chr2 112779286 . A ATC 407.07 PASS AC=1;AF=0.782;AN=2;DP=898;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,6:15:99:207,0,319:4,5,2,4 chr2 112779732 . G T 705.24 PASS AC=1;AF=0.5;AN=2;DP=277;FractionInformativeReads=1;MQ=60;set=variant9-variant10-variant20-variant25-variant28-variant35-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:23,15:38:99:428,0,910:16,7,12,3 chr2 112779734 . A G 298.23 PASS AC=1;AF=0.5;AN=2;DP=381;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant7-variant18-variant31-variant34-variant35-variant36-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,23:41:99:613,0,638:14,4,16,7 chr2 112785775 . T C 153.09 PASS AC=1;AF=0.683;AN=2;DP=499;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,11:17:99:309,0,139:4,2,8,3 chr2 112812842 . T C 441.34 PASS AC=2;AF=0.817;AN=2;DP=2970;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:2596,237,0:0,0,54,25 chr2 112813005 . G A 1265.54 PASS AC=1;AF=0.5;AN=2;DP=503;MQ=60;set=variant10-variant20-variant25-variant28-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:55,43:98:99:1082,0,1498:22,33,20,23 chr2 112813190 . G C 676.17 PASS AC=1;AF=0.5;AN=2;DP=381;MQ=60;set=variant10-variant20-variant25-variant28-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:33,48:81:99:1547,0,902:22,11,36,12 chr2 112813391 . C G 2136.74 PASS AC=2;AF=0.817;AN=2;DP=6712;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,179:179:99:5239,536,0:0,0,71,108 chr2 112817458 . A T 593.24 PASS AC=2;AF=0.533;AN=2;DP=1041;MQ=60;set=variant6-variant7-variant10-variant20-variant25-variant27-variant28-variant31-variant34-variant35-variant36-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:2089,229,0:0,0,41,36 chr2 112832535 . CAAT C 1582.53 PASS AC=1;AF=0.694;AN=2;DP=2096;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant15-variant17-variant18-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,32:65:99:1244,0,1701:17,16,20,12 chr2 112832684 . G A 518.67 PASS AC=2;AF=1;AN=2;DP=811;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,18:18:53:581,53,0:0,0,4,14 chr2 112847088 . A C 836.26 PASS AC=1;AF=0.5;AN=2;DP=269;MQ=60;set=variant10-variant16-variant20-variant25-variant35 GT:AD:DP:GQ:PL:SB 0/1:20,29:49:99:700,0,600:17,3,18,11 chr2 112847164 . C T 1452.68 PASS AC=1;AF=0.688;AN=2;DP=3800;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant15-variant17-variant18-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,47:105:99:1120,0,1445:33,25,31,16 chr2 112854931 . C G 150.21 PASS AC=1;AF=0.5;AN=2;DP=133;FractionInformativeReads=1;MQ=60;set=variant10-variant16-variant20-variant25-variant35 GT:AD:DP:GQ:PL:SB 0/1:29,11:40:99:244,0,813:9,20,4,7 chr2 112856165 . C A 714.4 PASS AC=2;AF=0.782;AN=2;DP=3249;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,90:90:99:2716,269,0:0,0,53,37 chr2 112856334 . C A 509.05 PASS AC=1;AF=0.5;AN=2;DP=278;MQ=60;set=variant4-variant7-variant31-variant34-variant35-variant36-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,9:33:99:247,0,827:6,18,1,8 chr2 112858122 . C T 175.15 PASS AC=1;AF=0.694;AN=2;DP=647;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant15-variant17-variant18-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,5:16:99:133,0,329:8,3,4,1 chr2 112863827 . A G 358.93 PASS AC=1;AF=0.5;AN=2;DP=48;FractionInformativeReads=1;MQ=60;set=variant10-variant16-variant20-variant25-variant35 GT:AD:DP:GQ:PL:SB 0/1:4,3:7:99:105,0,154:0,4,0,3 chr2 112865517 . G C 2143.62 PASS AC=2;AF=1;AN=2;DP=2836;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:2373,230,0:0,0,33,44 chr2 112874171 . G T 2131.22 PASS AC=1;AF=0.5;AN=2;DP=1121;FractionInformativeReads=1;MQ=60;set=variant10-variant16-variant20-variant25-variant35 GT:AD:DP:GQ:PL:SB 0/1:122,96:218:99:2257,0,2979:60,62,44,52 chr2 112874281 . A C 383.61 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=2778;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:92,21:113:99:373,0,5188:9,83,21,0 chr2 112875039 . A G 2705.21 PASS AC=1;AF=0.764;AN=2;DP=7309;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant15-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:100,87:187:99:2309,0,2679:52,48,40,47 chr2 112875614 . C CT 498.95 PASS AC=1;AF=0.5;AN=2;DP=106;FractionInformativeReads=1;MQ=60;set=variant9-variant16-variant20-variant25-variant35 GT:AD:DP:GQ:PL:SB 0/1:6,10:16:99:356,0,187:1,5,7,3 chr2 112876039 . T C 3270.31 PASS AC=1;AF=0.5;AN=2;DP=2617;MQ=60;set=variant4-variant6-variant7-variant31-variant34-variant35-variant36-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:128,139:267:99:3291,0,2960:61,67,67,72 chr2 112896309 . TCAGTGTCCCTCCCGCCTCTCTCCAGGC T 531.82 PASS AC=2;AF=1;AN=2;DP=74;FS=0;FractionInformativeReads=0.216;MQ=58.88;QD=7.19;SOR=2.584;set=variant35 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:17:569,17,0:0,0,3,13 chr2 112917102 . G C 250.13 PASS AC=1;AF=0.694;AN=2;DP=1249;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,21:44:99:718,0,659:19,4,19,2 chr2 112939115 . T G 106.77 PASS AC=2;AF=0.778;AN=2;DP=100;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant6-variant7-variant8-variant9-variant14-variant19-variant28-variant29-variant31-variant35-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:320,30,0:0,0,6,4 chr2 112939209 . G A 209.13 PASS AC=2;AF=0.6;AN=2;DP=124;FractionInformativeReads=1;MQ=60;set=variant6-variant7-variant8-variant25-variant31-variant35-variant36-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:676,69,0:0,0,15,8 chr2 112945220 . G A 1329.53 PASS AC=2;AF=0.575;AN=2;DP=2127;set=variant-variant2-variant4-variant6-variant7-variant13-variant16-variant18-variant22-variant23-variant25-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,136:136:99:4268,406,0:0,0,62,74 chr2 112995810 . A G 214.45 PASS AC=2;AF=0.595;AN=2;DP=184;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant13-variant16-variant18-variant19-variant22-variant23-variant25-variant33-variant34-variant35-variant36-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:133,12,0:0,0,4,0 chr2 113007757 . C T 1024.89 PASS AC=2;AF=0.556;AN=2;DP=602;FractionInformativeReads=1;MQ=60;set=variant6-variant7-variant25-variant34-variant35-variant36-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,63:63:99:1901,188,0:0,0,35,28 chr2 113074775 . C CT,CTT 289.06 PASS AC=1,0;AF=0.522,0.022;AN=2;DP=872;set=variant3-variant4-variant6-variant7-variant8-variant10-filterInvariant17-variant19-variant20-variant22-variant23-variant25-variant27-variant28-variant29-variant31-variant34-variant35-variant36-variant37-variant39-variant40-variant44 GT:DP:GQ:SB 0/1:27:42:4,2,13,8 chr2 113079576 . C A 36.43 PASS AC=2;AF=0.679;AN=2;DP=77;FS=0;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant22-variant23-variant25-variant27-variant29-variant31-variant32-variant35-variant37-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:280,21,0:0,0,3,4 chr2 113082250 . CT C 950.89 PASS AC=2;AF=0.596;AN=2;DP=2353;MQ=60;set=variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant17-variant19-variant20-variant22-variant23-variant25-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,82:82:99:2577,245,0:0,0,22,60 chr2 113089267 . T C 1079.74 PASS AC=2;AF=0.671;AN=2;DP=2936;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:2466,237,0:0,0,38,41 chr2 113090047 . T C 2578.65 PASS AC=2;AF=0.671;AN=2;DP=8134;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,239:239:99:6796,715,0:0,0,119,120 chr2 113091340 . A G 3849.67 PASS AC=2;AF=0.596;AN=2;DP=7115;MQ=60;set=variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant17-variant19-variant20-variant22-variant23-variant25-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,254:254:99:7460,761,0:0,0,139,115 chr2 113091685 . T G 3580.08 PASS AC=2;AF=0.596;AN=2;DP=4367;MQ=60;set=variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant17-variant19-variant20-variant22-variant23-variant25-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,174:174:99:5501,520,0:0,0,60,114 chr2 113092433 . C A 5841.61 PASS AC=2;AF=0.596;AN=2;DP=9558;MQ=60;set=variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant17-variant19-variant20-variant22-variant23-variant25-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,394:394:99:12032,1180,0:0,0,208,186 chr2 113093928 . C T 1120.65 PASS AC=2;AF=0.596;AN=2;DP=1629;MQ=60;set=variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant17-variant19-variant20-variant22-variant23-variant25-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:2449,212,0:0,0,36,35 chr2 113094793 . G A 1574.45 PASS AC=2;AF=0.596;AN=2;DP=3210;MQ=60;set=variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant17-variant19-variant20-variant22-variant23-variant25-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,106:106:99:3300,318,0:0,0,44,62 chr2 113094921 . A G 283.47 PASS AC=2;AF=0.596;AN=2;DP=536;MQ=60;set=variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant17-variant19-variant20-variant22-variant23-variant25-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:616,54,0:0,0,4,14 chr2 113096406 . C CTA 34.62 PASS AC=2;AF=0.769;AN=2;DP=101;MQ=60;set=variant-variant4-variant6-variant10-variant13-variant18-variant25-variant27-variant35-variant36-variant37-variant38-variant39 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:168,12,0:0,0,0,4 chr2 113096432 . G A 55.57 PASS AC=2;AF=0.917;AN=2;DP=15;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.736;ReadPosRankSum=0.736;set=variant10-variant25-variant35-variant36-variant37-variant39 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:90,6,0:0,0,0,2 chr2 113096857 . G C 2270.29 PASS AC=2;AF=0.596;AN=2;DP=4121;set=variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant17-variant19-variant20-variant22-variant23-variant25-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,150:152:99:4406,403,0:1,1,89,61 chr2 113097699 . T G 397.85 PASS AC=2;AF=0.596;AN=2;DP=672;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant17-variant19-variant20-variant22-variant23-variant25-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:668,63,0:0,0,5,16 chr2 113138227 . CA CAAA,CAAAA,C,CAAAAA,CAA 61.62 PASS AC=0,0,0,1,0;AF=0.125,0.15,0.1,0.075,0.075;AN=2;DP=323;set=variant-variant3-variant6-variant7-variant9-variant10-variant12-variant13-variant15-variant17-variant19-filterInvariant21-variant30-variant31-variant32-variant34-variant35-variant36-variant40-variant42 GT:DP:GQ:SB 0/4:20:76:4,0,14,2 chr2 113138346 . A G 115.11 PASS AC=2;AF=0.773;AN=2;DP=896;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant4-variant6-variant7-filterInvariant8-filterInvariant12-filterInvariant16-filterInvariant19-variant23-filterInvariant27-variant29-variant31-filterInvariant32-filterInvariant35-variant36-variant37-variant38-variant39-filterInvariant40-filterInvariant44 GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:578,57,0:0,0,3,16 chr2 113145814 . C T 2045.82 DRAGENHardSNP AC=2;AF=1;AN=2;DP=1388;FS=0;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:899,108,0:0,0,20,16 chr2 113147159 . G A 1680.82 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=13290;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:388,63:451:99:247,0,8394:161,227,26,37 chr2 113239833 . C T 544.96 PASS AC=2;AF=0.6;AN=2;DP=531;FractionInformativeReads=1;MQ=60;set=variant6-variant7-variant8-variant9-variant10-variant21-variant25-variant30-variant34-variant35-variant36-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,52:52:99:1793,155,0:0,0,41,11 chr2 113240183 . T C 626.25 PASS AC=2;AF=0.611;AN=2;DP=1149;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant16-variant19-variant21-variant22-variant23-variant25-variant30-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1715,135,0:0,0,7,38 chr2 113286562 . A G 1958.33 PASS AC=2;AF=0.977;AN=2;DP=3894;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,100:100:99:3186,300,0:0,0,52,48 chr2 113287329 . C G 850.02 PASS AC=2;AF=0.966;AN=2;DP=1439;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1472,147,0:0,0,24,25 chr2 113287964 . A G 237.91 PASS AC=2;AF=0.83;AN=2;DP=1218;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,26:26:77:853,77,0:0,0,13,13 chr2 113288580 . G A 340.19 PASS AC=2;AF=0.985;AN=2;DP=135;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.731;ReadPosRankSum=0.731;set=variant-variant4-variant6-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:172,12,0:0,0,3,1 chr2 113289701 . T G 2268.96 PASS AC=2;AF=0.977;AN=2;DP=3347;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,93:93:99:2814,278,0:0,0,44,49 chr2 113300330 . G A 827.87 PASS AC=2;AF=0.744;AN=2;DP=1321;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1444,108,0:0,0,1,35 chr2 113305150 . G C 3445.72 PASS AC=2;AF=0.689;AN=2;DP=3576;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,116:116:99:3668,346,0:0,0,46,70 chr2 113308516 . T A 3408.64 PASS AC=2;AF=0.75;AN=2;DP=4681;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,118:118:99:3336,353,0:0,0,55,63 chr2 113308622 . C T 943.39 PASS AC=2;AF=0.75;AN=2;DP=1169;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:1006,81,0:0,0,3,24 chr2 113309473 . C T 4962.05 PASS AC=2;AF=0.681;AN=2;DP=6137;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,187:187:99:5609,561,0:0,0,103,84 chr2 113310197 . CT C 1061.63 PASS AC=2;AF=0.738;AN=2;DP=2142;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,32:33:72:860,72,0:1,0,25,7 chr2 113315735 . CT C 441.42 PASS AC=1;AF=0.62;AN=2;DP=415;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant11-variant12-variant14-variant15-variant17-variant19-variant21-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant35-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,4:11:97:97,0,185:1,6,2,2 chr2 113321900 . T C 3980.36 PASS AC=1;AF=0.607;AN=2;DP=3305;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant35-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:85,52:137:99:1196,0,2299:51,34,32,20 chr2 113326281 . C G 1264.6 PASS AC=2;AF=0.837;AN=2;DP=1918;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:1471,141,0:0,0,30,17 chr2 113326502 . C T 2296.48 PASS AC=2;AF=0.837;AN=2;DP=3117;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,88:88:99:2822,264,0:0,0,33,55 chr2 113334178 . A T 67.44 PASS AC=1;AF=0.5;AN=2;DP=349;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant6-variant7-variant9-variant10-variant12-variant14-variant16-variant18-variant19-variant21-variant22-variant27-variant29-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,6:15:99:213,0,355:0,9,0,6 chr2 113334357 . G A 849.52 PASS AC=1;AF=0.6;AN=2;DP=464;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant35-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,11:23:99:342,0,428:11,1,9,2 chr2 113341914 . C G 93.19 PASS AC=1;AF=0.5;AN=2;DP=157;MQ=60;set=variant2-variant6-variant7-variant9-variant14-variant16-variant18-variant21-variant34-variant35-variant36-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,12:17:99:361,0,135:4,1,8,4 chr2 113343488 . A T 321.38 PASS AC=1;AF=0.7;AN=2;DP=394;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant35-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,11:23:99:250,0,303:8,4,8,3 chr2 113344047 . T C 5181.59 PASS AC=2;AF=0.826;AN=2;DP=8777;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,240:240:99:7260,719,0:0,0,108,132 chr2 113344176 . T A 874.57 PASS AC=1;AF=0.5;AN=2;DP=1432;MQ=60;set=variant2-variant6-variant7-variant9-variant10-variant14-variant16-variant18-variant21-variant34-variant35-variant36-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,56:113:99:1469,0,1473:22,35,21,35 chr2 113345588 . C T 167.43 PASS AC=1;AF=0.5;AN=2;DP=255;MQ=60;set=variant6-variant7-variant9-variant14-variant18-variant21-variant34-variant35-variant36-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,23:32:99:622,0,232:3,6,8,15 chr2 113346413 . C G 1256.95 PASS AC=1;AF=0.607;AN=2;DP=1385;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant35-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,20:57:99:537,0,1023:18,19,10,10 chr2 113346480 . G A 526.1 PASS AC=1;AF=0.611;AN=2;DP=463;FractionInformativeReads=1;MQ=60;set=variant5-variant8-variant9-variant13-variant17-variant25-variant26-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:39,20:59:99:542,0,998:18,21,13,7 chr2 113346512 . A C 1090.52 PASS AC=2;AF=0.833;AN=2;DP=2140;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:1853,164,0:0,0,30,25 chr2 113403662 . T C 613.4 PASS AC=2;AF=0.895;AN=2;DP=3669;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,98:98:99:3031,293,0:0,0,46,52 chr2 113404708 . G A 1773.12 PASS AC=2;AF=0.721;AN=2;DP=5388;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,150:150:99:4569,449,0:0,0,63,87 chr2 113418276 . A AG 97.73 PASS AC=2;AF=0.927;AN=2;DP=367;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:621,42,0:0,0,3,11 chr2 113418277 . T TG 97.73 PASS AC=2;AF=0.927;AN=2;DP=353;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:42:621,42,0:0,0,3,10 chr2 113421334 . G A 244.19 PASS AC=2;AF=0.895;AN=2;DP=1002;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,31:31:93:1071,93,0:0,0,8,23 chr2 113479745 . AC A 1816.51 PASS AC=2;AF=0.977;AN=2;DP=4991;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,124:124:99:3938,373,0:0,0,55,69 chr2 113480491 . T C 196.77 PASS AC=2;AF=0.977;AN=2;DP=454;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:359,24,0:0,0,5,3 chr2 113480493 . G GCCCC 187.73 PASS AC=2;AF=0.988;AN=2;DP=405;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.729;ReadPosRankSum=-1.307;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:360,24,0:0,0,5,3 chr2 113480495 . A AATCCTGC 187.73 PASS AC=2;AF=0.988;AN=2;DP=392;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.001;ReadPosRankSum=-0.573;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:360,24,0:0,0,5,3 chr2 113480498 . C CTGGTGCTGCCCCCAAGGGGTG 97.73 PASS AC=2;AF=0.988;AN=2;DP=388;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.633;ReadPosRankSum=-1.036;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:30:449,30,0:0,0,5,3 chr2 113480556 . GC G 170.96 PASS AC=2;AF=0.714;AN=2;DP=408;MQ=60;set=variant2-variant3-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant16-variant17-variant21-variant22-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:517,45,0:0,0,11,4 chr2 113480938 . G GCACACA,GCACACACACACA,GCACACACA,GCACACACACACACA,GCACACACACACACACACA,GCACACACACA,GCACACACACACACACA,GCA,GCACA 330.45 PASS AC=0,0,0,2,0,0,0,0,0;AF=0.262,0.286,0.06,0.19,0.024,0.036,0.036,0.024,0.048;AN=2;DP=819;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 4/4:20:59:0,0,12,8 chr2 113481547 . A G 2005.43 PASS AC=2;AF=0.977;AN=2;DP=3981;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,85:85:99:2743,255,0:0,0,42,43 chr2 113482779 . A C 2935.79 PASS AC=2;AF=0.989;AN=2;DP=6794;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,176:176:99:5309,528,0:0,0,86,90 chr2 113484319 . G A 1951.79 PASS AC=2;AF=1;AN=2;DP=5751;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,161:161:99:4677,481,0:0,0,67,94 chr2 113484353 . A G 1580.23 PASS AC=2;AF=1;AN=2;DP=4206;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,121:122:99:3679,345,0:1,0,44,77 chr2 113494250 . T C 10451.1 PASS AC=2;AF=0.977;AN=2;DP=12447;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,298:298:99:9158,893,0:0,0,113,185 chr2 113495785 . T C 4091.71 PASS AC=2;AF=0.977;AN=2;DP=4670;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,119:119:99:4163,357,0:0,0,61,58 chr2 113498566 . A G 197.62 PASS AC=2;AF=0.688;AN=2;DP=1310;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant16-variant17-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:1577,144,0:0,0,17,31 chr2 113513825 . T C 5415.05 PASS AC=2;AF=0.977;AN=2;DP=6127;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,158:158:99:5019,473,0:0,0,83,75 chr2 113531715 . T TTGAA 7611.35 PASS AC=1;AF=0.732;AN=2;DP=6534;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:75,86:161:99:3300,0,4260:32,43,37,49 chr2 113532083 . A G 2765.06 PASS AC=1;AF=0.595;AN=2;DP=2417;MQ=60;set=variant2-variant8-variant9-variant11-variant12-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant30-variant31-variant32-variant35-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:84,47:131:99:1081,0,2197:51,33,31,16 chr2 113532236 . T C 6650.48 PASS AC=1;AF=0.591;AN=2;DP=5264;MQ=60;set=variant2-variant8-variant9-variant11-variant12-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant30-variant31-variant32-variant35-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:116,145:261:99:3483,0,3018:59,57,74,71 chr2 113532885 . G T 2732.22 PASS AC=1;AF=0.732;AN=2;DP=3993;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:63,35:98:99:831,0,1598:25,38,12,23 chr2 113535395 . G T 652.2 PASS AC=1;AF=0.732;AN=2;DP=933;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,7:21:99:168,0,411:10,4,5,2 chr2 113535438 . C T 719.71 PASS AC=1;AF=0.595;AN=2;DP=788;MQ=60;set=variant2-variant8-variant9-variant11-variant12-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant30-variant31-variant32-variant35-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,13:38:99:275,0,625:16,9,9,4 chr2 113537223 . C A 1712.87 PASS AC=1;AF=0.595;AN=2;DP=1214;MQ=60;set=variant2-variant8-variant9-variant11-variant12-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant30-variant31-variant32-variant35-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,39:69:99:1070,0,874:7,23,12,27 chr2 113540084 . G A 743.66 PASS AC=1;AF=0.744;AN=2;DP=764;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,6:15:99:173,0,237:6,3,4,2 chr2 113540177 . C T 1380.42 PASS AC=1;AF=0.591;AN=2;DP=1165;FractionInformativeReads=1;MQ=60;set=variant2-variant8-variant9-variant11-variant12-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant30-variant31-variant32-variant35-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,22:57:99:644,0,943:22,13,17,5 chr2 113540205 . G T 2531.26 PASS AC=1;AF=0.732;AN=2;DP=2701;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,28:64:99:762,0,901:22,14,19,9 chr2 113541925 . G A 197.26 PASS AC=2;AF=0.719;AN=2;DP=115;FractionInformativeReads=1;MQ=60;set=variant2-variant8-variant9-variant11-variant12-variant19-variant20-variant21-variant22-variant23-variant24-variant30-variant31-variant32-variant35-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:94,9,0:0,0,2,1 chr2 113588302 . C T 237.96 PASS AC=1;AF=0.536;AN=2;DP=321;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant26-variant27-variant29-variant31-variant33-variant35-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,3:8:70:70,0,204:0,5,1,2 chr2 113590467 . C T 388.06 PASS AC=1;AF=0.536;AN=2;DP=1149;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant26-variant27-variant29-variant31-variant33-variant35-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:26,32:58:99:853,0,691:7,19,9,23 chr2 113594387 . G A 357.73 PASS AC=1;AF=0.711;AN=2;DP=1016;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,12:26:99:308,0,306:6,8,4,8 chr2 113671303 . T C 3199.29 PASS AC=2;AF=0.775;AN=2;DP=4049;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,80:80:99:2510,240,0:0,0,41,39 chr2 113671378 . G T 2495.75 PASS AC=2;AF=0.775;AN=2;DP=4089;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,84:84:99:2585,252,0:0,0,43,41 chr2 113671410 . A G 1817.15 PASS AC=2;AF=0.775;AN=2;DP=3154;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:2232,216,0:0,0,33,39 chr2 113671518 . G A 278.65 PASS AC=2;AF=0.782;AN=2;DP=652;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:627,54,0:0,0,5,13 chr2 113675959 . G T 368.27 PASS AC=2;AF=0.977;AN=2;DP=368;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:120,15,0:0,0,3,2 chr2 113676659 . T C 2325.36 PASS AC=2;AF=0.932;AN=2;DP=2540;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:2423,204,0:0,0,13,55 chr2 113742734 . G A 1034.35 PASS AC=1;AF=0.756;AN=2;DP=1747;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,14:35:99:429,0,551:9,12,5,9 chr2 113763463 . A C 1790.93 PASS AC=1;AF=0.577;AN=2;DP=3881;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant17-variant20-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant32-variant34-variant35-variant36-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:95,69:164:99:1678,0,2494:51,44,40,29 chr2 113763575 . A G 3801.07 PASS AC=1;AF=0.756;AN=2;DP=5712;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:97,63:160:99:1564,0,2611:47,50,25,38 chr2 113779875 . G A 5514.73 PASS AC=1;AF=0.658;AN=2;DP=7025;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:101,102:203:99:2375,0,2506:59,42,51,51 chr2 113783570 . C T 926.59 PASS AC=1;AF=0.658;AN=2;DP=1004;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,15:21:99:556,0,162:5,1,13,2 chr2 113783909 . A T 1677.15 PASS AC=1;AF=0.788;AN=2;DP=1946;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,19:38:99:508,0,590:6,13,5,14 chr2 113785020 . A G 7717.19 PASS AC=1;AF=0.697;AN=2;DP=8983;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:122,111:233:99:2907,0,3322:80,42,69,42 chr2 113785202 . G A 9009.99 PASS AC=1;AF=0.671;AN=2;DP=10359;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:140,161:301:99:4268,0,3657:61,79,63,98 chr2 113785727 . A G 683.69 PASS AC=2;AF=0.977;AN=2;DP=1048;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:802,72,0:0,0,9,15 chr2 113789316 . C T 222.57 PASS AC=1;AF=0.73;AN=2;DP=926;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:17,12:29:99:250,0,416:10,7,5,7 chr2 113816090 . T A 45.95 PASS AC=1;AF=0.789;AN=2;DP=491;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,7:12:99:157,0,189:5,0,4,3 chr2 113816940 . C G 1132.93 PASS AC=1;AF=0.636;AN=2;DP=2843;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,41:89:99:1543,0,2332:27,21,27,14 chr2 113816942 . A C 1132.93 PASS AC=1;AF=0.636;AN=2;DP=2868;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,40:90:99:1543,0,2332:28,22,27,13 chr2 113818632 . G A 622.22 PASS AC=1;AF=0.689;AN=2;DP=1872;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,27:53:99:759,0,835:5,21,8,19 chr2 113818702 . G C 146.08 PASS AC=1;AF=0.703;AN=2;DP=543;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,10:22:99:329,0,435:2,10,1,9 chr2 113819614 . T C 683.09 PASS AC=1;AF=0.689;AN=2;DP=2617;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,47:89:99:1301,0,1031:28,14,35,12 chr2 113820476 . T C 535.79 PASS AC=1;AF=0.689;AN=2;DP=1577;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,26:57:99:658,0,804:15,16,14,12 chr2 113820530 . A G 502.35 PASS AC=1;AF=0.689;AN=2;DP=1880;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,36:68:99:908,0,706:15,17,18,18 chr2 113820580 . C A 584.43 PASS AC=1;AF=0.689;AN=2;DP=2055;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,32:50:99:981,0,561:9,9,18,14 chr2 113820655 . A T 1016.38 PASS AC=1;AF=0.689;AN=2;DP=2664;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,31:60:99:786,0,755:18,11,17,14 chr2 113820672 . A G 1136.43 PASS AC=1;AF=0.689;AN=2;DP=2876;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,35:68:99:946,0,932:21,12,20,15 chr2 113820732 . T C 1427.08 PASS AC=1;AF=0.689;AN=2;DP=3466;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,48:98:99:1372,0,1245:28,22,27,21 chr2 113820814 . C G 1560.23 PASS AC=1;AF=0.689;AN=2;DP=3975;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,49:106:99:1271,0,1467:27,30,28,21 chr2 113821117 . C T 1314.13 PASS AC=1;AF=0.756;AN=2;DP=5923;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:103,65:168:99:1384,0,2441:56,47,36,29 chr2 113821200 . T C 1528.48 PASS AC=1;AF=0.689;AN=2;DP=6398;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:102,68:170:99:1658,0,2578:49,53,38,30 chr2 113821653 . T C 251.41 PASS AC=1;AF=0.689;AN=2;DP=1371;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,22:43:99:525,0,535:10,11,8,14 chr2 113825386 . C A 41.46 PASS AC=1;AF=0.788;AN=2;DP=155;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant35-variant36-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,2:5:75:75,0,76:2,1,2,0 chr2 113829869 . G T 125.48 PASS AC=1;AF=0.652;AN=2;DP=536;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant33-variant34-variant35-variant37-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:3,11:14:82:306,0,82:3,0,9,2 chr2 113830201 . T G 1912.71 PASS AC=1;AF=0.711;AN=2;DP=4031;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,78:142:99:2163,0,1774:34,30,43,35 chr2 113830563 . G A 657.83 PASS AC=1;AF=0.689;AN=2;DP=1908;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,28:61:99:789,0,971:11,22,8,20 chr2 113830582 . A C 634.67 PASS AC=1;AF=0.718;AN=2;DP=1473;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,24:53:99:669,0,794:8,21,6,18 chr2 113830688 . G A 106.77 PASS AC=1;AF=0.758;AN=2;DP=245;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant30-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,5:11:99:150,0,200:2,4,1,4 chr2 113832153 . A C 966.88 PASS AC=1;AF=0.5;AN=2;DP=114;FractionInformativeReads=1;MQ=60;set=variant32-variant35 GT:AD:DP:GQ:PL:SB 0/1:28,33:61:99:906,0,797:15,13,22,11 chr2 113832312 . T C 1311.79 PASS AC=1;AF=0.736;AN=2;DP=4030;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:87,61:148:99:1274,0,2161:41,46,27,34 chr2 113832333 . C A 1165.89 PASS AC=1;AF=0.75;AN=2;DP=3516;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:74,51:125:99:1194,0,1795:32,42,20,31 chr2 113870725 . T G 151.64 PASS AC=1;AF=0.667;AN=2;DP=538;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant11-variant13-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant26-variant28-variant29-variant30-variant35-variant37-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,9:20:99:205,0,304:4,7,3,6 chr2 113877495 . G T 584.72 PASS AC=2;AF=0.886;AN=2;DP=1149;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:842,75,0:0,0,16,9 chr2 113888900 . T A 488.01 PASS AC=1;AF=0.72;AN=2;DP=1490;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,10:30:99:319,0,660:3,17,1,9 chr2 113890304 . T C 557.13 PASS AC=1;AF=0.542;AN=2;DP=3020;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant7-variant9-variant11-variant12-variant14-variant17-variant19-variant20-variant22-variant23-variant24-variant28-variant29-variant31-variant32-variant33-variant35-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,85:149:99:2093,0,1494:36,28,48,37 chr2 113890586 . C G 537.18 PASS AC=1;AF=0.542;AN=2;DP=2126;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant7-variant9-variant11-variant12-variant14-variant17-variant19-variant20-variant22-variant23-variant24-variant28-variant29-variant31-variant32-variant33-variant35-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,44:102:99:1052,0,1627:23,35,22,22 chr2 113953401 . A G 814.17 PASS AC=2;AF=1;AN=2;DP=3820;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,93:93:99:2834,278,0:0,0,41,52 chr2 113953657 . A C 2274.28 PASS AC=1;AF=0.621;AN=2;DP=3825;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,67:118:99:1718,0,1347:27,24,39,28 chr2 113953952 . T C 775.97 PASS AC=1;AF=0.621;AN=2;DP=1380;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,27:62:99:753,0,852:13,22,7,20 chr2 113953973 . A AT 580.73 PASS AC=1;AF=0.621;AN=2;DP=989;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,19:44:99:718,0,1290:7,18,3,16 chr2 113953974 . GACA G 580.73 PASS AC=1;AF=0.621;AN=2;DP=953;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,19:44:99:718,0,1290:7,18,3,16 chr2 113954006 . A G 362.08 PASS AC=1;AF=0.625;AN=2;DP=495;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,8:21:99:254,0,376:2,11,2,6 chr2 113954879 . A C 3799.47 PASS AC=1;AF=0.621;AN=2;DP=3105;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,37:89:99:863,0,1386:26,26,20,17 chr2 113955074 . G A 3815.33 PASS AC=1;AF=0.621;AN=2;DP=4373;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:80,59:139:99:1387,0,2175:45,35,27,32 chr2 113956371 . G C 5454.3 PASS AC=1;AF=0.621;AN=2;DP=6874;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:128,119:247:99:3032,0,3335:70,58,65,54 chr2 113956821 . C G 2597.97 PASS AC=1;AF=0.621;AN=2;DP=3416;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,50:115:99:1237,0,1819:21,44,17,33 chr2 113959452 . A G 2238 PASS AC=2;AF=1;AN=2;DP=3425;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,106:106:99:3318,318,0:0,0,60,46 chr2 113973632 . G A 869.92 PASS AC=1;AF=0.621;AN=2;DP=1280;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,22:61:99:391,0,1002:21,18,10,12 chr2 113973801 . T C 1286.45 PASS AC=1;AF=0.726;AN=2;DP=2385;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,38:71:99:981,0,743:16,17,24,14 chr2 113973964 . T C 1544.39 PASS AC=1;AF=0.621;AN=2;DP=2203;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,40:84:99:1048,0,1014:25,19,16,24 chr2 113975110 . A G 2596.78 PASS AC=1;AF=0.543;AN=2;DP=1135;MQ=60;set=variant3-variant4-variant8-variant9-variant11-variant15-variant16-variant17-variant18-variant19-variant21-variant25-variant27-variant28-variant29-variant30-variant35-variant36-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,21:47:99:589,0,709:18,8,10,11 chr2 113976146 . T C 1060.87 PASS AC=1;AF=0.5;AN=2;DP=69;FS=2.066;FractionInformativeReads=1;MQ=60;MQRankSum=-0.719;QD=15.37;ReadPosRankSum=-1.924;SOR=1.036;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:27,42:69:99:1089,0,536:14,13,25,17 chr2 113977454 . G A 1089.45 PASS AC=1;AF=0.58;AN=2;DP=634;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant8-variant9-variant11-variant14-variant16-variant17-variant18-variant19-variant21-variant25-variant27-variant28-variant29-variant30-variant35-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,18:25:99:518,0,196:6,1,13,5 chr2 113977862 . T G 201.22 PASS AC=2;AF=1;AN=2;DP=593;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.552;ReadPosRankSum=1.552;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:310,33,0:0,0,4,7 chr2 113994417 . G T 158.3 PASS AC=1;AF=0.611;AN=2;DP=1450;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,19:40:99:517,0,535:6,15,7,12 chr2 113994461 . G A 502.91 PASS AC=1;AF=0.5;AN=2;DP=352;MQ=60;set=variant3-variant4-variant8-variant9-variant11-variant17-variant18-variant19-variant21-variant25-variant27-variant28-variant29-variant30-variant35-variant36-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,11:25:99:284,0,439:3,11,3,8 chr2 113996647 . C CT,CTT 916.32 PASS AC=1,0;AF=0.5,0.018;AN=2;DP=4022;set=variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant14-variant16-variant17-variant18-variant19-variant21-filterInvariant23-variant24-variant25-variant27-variant28-variant29-variant30-variant34-variant35-variant36-variant37-variant39-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:99:99:19,30,17,33 chr2 113999534 . G C 2336.06 PASS AC=1;AF=0.5;AN=2;DP=2272;MQ=60;set=variant3-variant4-variant8-variant9-variant11-variant17-variant18-variant19-variant25-variant27-variant28-variant29-variant30-variant35-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:74,76:150:99:1767,0,1843:38,36,34,42 chr2 113999736 . G T 327.17 PASS AC=1;AF=0.52;AN=2;DP=629;set=variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant14-variant16-variant17-variant18-variant19-variant24-variant25-variant27-variant28-variant29-variant30-variant34-variant35-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,11:29:99:302,0,579:5,13,4,7 chr2 114000458 . C A 1227.62 PASS AC=2;AF=1;AN=2;DP=2052;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:2426,230,0:0,0,27,50 chr2 114020848 . T G 916.27 PASS AC=2;AF=0.679;AN=2;DP=2384;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:1865,179,0:0,0,39,21 chr2 114036436 . G C 2992.08 PASS AC=2;AF=0.989;AN=2;DP=4786;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:2,112:114:99:3301,292,0:1,1,59,53 chr2 114210662 . A G 344.77 PASS AC=1;AF=0.5;AN=2;DP=54;FS=6.818;FractionInformativeReads=1;MQ=36.52;MQRankSum=2.086;QD=6.38;ReadPosRankSum=0.29;SOR=1.84;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:39,15:54:99:373,0,969:23,16,12,3 chr2 114213299 . AT A 30.94 PASS AC=1;AF=0.5;AN=2;DP=772;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant4-variant6-variant7-variant9-variant11-variant13-variant14-variant15-filterInvariant19-variant20-variant21-variant22-variant25-variant27-variant29-variant31-variant33-variant34-variant35-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,8:22:99:103,0,257:2,12,1,7 chr2 114257401 . A G 1698.83 PASS AC=1;AF=0.5;AN=2;DP=320;FractionInformativeReads=1;set=variant25-variant30-variant35 GT:AD:DP:GQ:PL:SB 0/1:58,66:124:99:1842,0,1392:22,36,21,45 chr2 114335380 . A G 43.71 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=342;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:9,5:14:84:84,0,185:4,5,2,3 chr2 114335753 . T G 183.34 PASS AC=1;AF=0.8;AN=2;DP=358;set=variant-variant2-variant3-variant4-variant5-variant10-variant13-variant17-variant19-variant25-variant31-filterInvariant35-variant39-filterInvariant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:42,6:48:98:98,0,1006:24,18,0,6 chr2 114340433 . A G 119.88 PASS AC=1;AF=0.5;AN=2;DP=684;set=variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant11-filterInvariant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,5:17:99:120,0,290:8,4,2,3 chr2 114340494 . G A 64.66 PASS AC=1;AF=0.5;AN=2;DP=1755;FractionInformativeReads=1;set=variant-variant2-variant3-variant5-variant6-variant8-filterInvariant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-filterInvariant17-variant18-variant19-variant20-filterInvariant22-variant23-variant24-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,11:41:99:212,0,672:15,15,7,4 chr2 114340663 . G A 262.84 PASS AC=1;AF=0.5;AN=2;DP=1814;set=variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,13:35:99:480,0,892:9,13,5,8 chr2 114340677 . C A 237.1 PASS AC=1;AF=0.5;AN=2;DP=1576;set=variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,14:35:99:501,0,884:9,12,5,9 chr2 114340706 . A G 310.29 PASS AC=1;AF=0.5;AN=2;DP=926;set=variant3-filterInvariant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,7:24:99:158,0,391:6,11,1,6 chr2 114346484 . C T 80.75 DRAGENHardSNP AC=1;AF=0.654;AN=2;DP=583;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:8,4:12:74:74,0,165:5,3,4,0 chr2 114346531 . A G 358.79 DRAGENHardSNP AC=1;AF=0.602;AN=2;DP=1769;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:22,15:37:99:273,0,451:15,7,10,5 chr2 114346567 . G A 382.72 DRAGENHardSNP AC=1;AF=0.535;AN=2;DP=2778;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:35,24:59:99:406,0,695:21,14,13,11 chr2 114346582 . A G 822.49 DRAGENHardSNP AC=1;AF=0.602;AN=2;DP=3232;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:40,25:65:99:426,0,773:22,18,13,12 chr2 114346668 . ACC A 1177.76 PASS AC=1;AF=0.602;AN=2;DP=2213;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:22,13:35:99:480,0,866:9,13,4,9 chr2 114346710 . G C 797.73 DRAGENHardSNP AC=1;AF=0.607;AN=2;DP=1168;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:13,5:18:99:148,0,563:6,7,2,3 chr2 114346716 . G C 795.74 DRAGENHardSNP AC=1;AF=0.619;AN=2;DP=1062;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:12,4:16:99:129,0,540:7,5,1,3 chr2 114352750 . G C 77.97 PASS AC=1;AF=0.5;AN=2;DP=820;FractionInformativeReads=1;set=filterInvariant-filterInvariant2-filterInvariant4-filterInvariant5-filterInvariant6-variant7-variant9-filterInvariant10-filterInvariant11-variant13-filterInvariant14-variant16-variant17-variant21-filterInvariant22-variant23-filterInvariant25-filterInvariant26-variant28-filterInvariant32-variant34-variant35-variant38-filterInvariant40 GT:AD:DP:GQ:PL:SB 0/1:16,11:27:99:193,0,357:8,8,6,5 chr2 114352806 . T C 209.36 PASS AC=1;AF=0.5;AN=2;DP=1138;set=filterInvariant-filterInvariant2-variant3-filterInvariant4-variant5-variant6-variant7-variant9-filterInvariant10-variant11-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-filterInvariant40-variant41-filterInvariant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,11:31:99:263,0,452:9,11,6,5 chr2 114352837 . C T 31.38 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=53;FS=0;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:25,6:31:59:59,0,749:13,12,3,3 chr2 114353282 . G T 32.12 PASS AC=1;AF=0.5;AN=2;DP=8030;set=filterInvariant-filterInvariant2-filterInvariant4-filterInvariant5-filterInvariant6-variant7-filterInvariant8-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant13-filterInvariant14-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant20-filterInvariant22-filterInvariant24-variant25-filterInvariant26-variant27-filterInvariant28-filterInvariant29-filterInvariant31-filterInvariant32-filterInvariant33-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant38-filterInvariant39-variant40-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:197,34:231:99:594,0,4630:99,98,17,17 chr2 114353351 . C T 1495.73 PASS AC=1;AF=0.5;AN=2;DP=3564;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant13-variant19-variant20-variant21-variant27-variant30-variant31-variant34-variant35-variant36-filterInvariant37-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:107,60:167:99:1159,0,2342:42,65,29,31 chr2 114354996 . G A 81.2 PASS AC=1;AF=0.5;AN=2;DP=49;FractionInformativeReads=1;set=filterInvariant9-filterInvariant13-variant15-filterInvariant26-filterInvariant35-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:83:85,0,83:3,1,3,1 chr2 114355167 . A G 96.17 PASS AC=1;AF=0.5;AN=2;DP=846;FractionInformativeReads=1;set=filterInvariant2-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant12-filterInvariant13-variant15-filterInvariant18-filterInvariant19-filterInvariant21-filterInvariant22-filterInvariant23-variant24-filterInvariant26-filterInvariant27-variant28-filterInvariant30-filterInvariant31-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant38-filterInvariant39-variant40-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:20,11:31:99:184,0,391:9,11,5,6 chr2 114355200 . A G 39.98 PASS AC=1;AF=0.5;AN=2;DP=233;set=filterInvariant-filterInvariant4-filterInvariant13-filterInvariant19-filterInvariant20-filterInvariant21-variant27-filterInvariant35-filterInvariant39-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:17,8:25:99:123,0,385:7,10,4,4 chr2 114355998 . C G 130.79 PASS AC=1;AF=0.5;AN=2;DP=2885;set=filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant11-variant14-filterInvariant15-filterInvariant18-variant19-filterInvariant20-variant21-variant23-filterInvariant24-variant26-filterInvariant27-filterInvariant28-filterInvariant29-filterInvariant31-filterInvariant33-filterInvariant34-filterInvariant35-filterInvariant36-variant38-filterInvariant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:59,13:72:99:140,0,1436:31,28,10,3 chr2 114356059 . G A 1789.37 PASS AC=1;AF=0.5;AN=2;DP=3257;set=filterInvariant-variant2-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant7-variant9-filterInvariant10-filterInvariant13-variant16-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant27-filterInvariant30-filterInvariant31-filterInvariant34-variant35-filterInvariant36-filterInvariant37-filterInvariant39-variant41-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:91,25:116:99:326,0,2113:45,46,11,14 chr2 114357350 . T C 828.98 PASS AC=1;AF=0.611;AN=2;DP=1289;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant13-variant14-variant16-variant19-variant20-variant21-variant23-variant27-variant30-variant31-filterInvariant33-variant34-variant35-variant36-variant37-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,14:42:99:375,0,926:24,4,14,0 chr2 114357862 . C T 735.31 PASS AC=1;AF=0.667;AN=2;DP=1823;set=variant-variant2-variant4-filterInvariant5-variant6-variant7-variant9-filterInvariant10-filterInvariant13-variant16-filterInvariant19-variant20-filterInvariant21-variant22-variant25-variant26-filterInvariant27-variant30-variant31-variant34-variant35-variant36-filterInvariant37-variant39-variant41-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:79,19:98:99:290,0,2089:28,51,6,13 chr2 114357926 . CCT C 1213.23 PASS AC=1;AF=0.604;AN=2;DP=1334;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant13-variant16-variant19-variant20-variant21-variant27-variant30-variant31-variant34-variant35-variant36-variant37-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,26:74:99:938,0,2035:16,32,11,15 chr2 114358139 . TA T 406.68 PASS AC=1;AF=0.661;AN=2;DP=1160;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant13-variant16-variant17-variant19-variant20-variant21-variant22-variant25-variant26-variant27-variant30-variant31-variant34-variant35-variant36-variant37-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,18:63:99:485,0,1492:29,16,14,4 chr2 114358432 . TGGG T 1087.85 PASS AC=1;AF=0.583;AN=2;DP=1205;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant13-variant16-variant19-variant20-variant21-variant27-variant30-variant31-variant34-variant35-variant36-variant37-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,28:59:99:1081,0,3334:11,20,9,19 chr2 114358437 . C T 1106.39 PASS AC=1;AF=0.583;AN=2;DP=1175;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant13-variant16-variant19-variant20-variant21-variant27-variant30-variant31-variant34-variant35-variant36-variant37-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,28:58:99:1084,0,3307:11,19,9,19 chr2 114358438 . CA C 1097.35 PASS AC=1;AF=0.583;AN=2;DP=1176;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant13-variant16-variant19-variant20-variant21-variant27-variant30-variant31-variant34-variant35-variant36-variant37-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,27:57:99:1084,0,3307:11,19,8,19 chr2 114358772 . G A 1547.26 PASS AC=1;AF=0.604;AN=2;DP=1480;FractionInformativeReads=1;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant13-variant16-variant19-variant20-variant21-variant27-filterInvariant30-variant31-variant34-variant35-variant36-variant37-variant39-variant41-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:44,24:68:99:417,0,970:22,22,12,12 chr2 114369542 . G A 97.42 DRAGENHardSNP AC=2;AF=0.75;AN=2;DP=13;FS=0;FractionInformativeReads=1;MQRankSum=-0.684;ReadPosRankSum=0.684;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:126,15,0:0,0,3,2 chr2 114369646 . C A 79.75 PASS AC=2;AF=0.967;AN=2;DP=136;FS=0;set=filterInvariant2-filterInvariant4-filterInvariant6-variant10-filterInvariant13-filterInvariant21-filterInvariant22-filterInvariant26-filterInvariant28-filterInvariant31-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant39-filterInvariant43 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:135,9,0:0,0,3,0 chr2 114369669 . A G 114.53 DRAGENHardSNP AC=2;AF=0.972;AN=2;DP=151;MQRankSum=-3.624;ReadPosRankSum=2.219;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:163,12,0:0,0,4,0 chr2 114369746 . CT C 227.11 PASS AC=1;AF=0.542;AN=2;DP=738;set=variant3-variant4-variant6-variant8-variant11-variant14-variant15-variant17-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:16,5:21:99:139,0,657:9,7,2,3 chr2 114369771 . C T 296.37 PASS AC=1;AF=0.543;AN=2;DP=719;set=filterInvariant-variant2-filterInvariant4-filterInvariant6-variant7-variant9-variant10-variant13-variant16-variant19-filterInvariant20-variant21-filterInvariant26-filterInvariant27-variant31-filterInvariant34-variant35-filterInvariant36-filterInvariant37-filterInvariant39-variant41-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,17:22:99:345,0,159:2,3,9,8 chr2 114386172 . A G 148.75 PASS AC=1;AF=0.643;AN=2;DP=88;FractionInformativeReads=1;set=variant8-variant15-variant22-variant23-variant25-variant26-filterInvariant28-filterInvariant30-variant31-variant32-variant34-variant35-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:2,2:4:77:77,0,77:2,0,2,0 chr2 114386338 . G A 1005.17 PASS AC=1;AF=0.6;AN=2;DP=895;FractionInformativeReads=1;set=variant-variant2-variant4-variant6-variant7-variant9-variant10-variant13-variant16-variant19-variant20-variant21-variant26-variant27-variant30-variant31-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,19:34:99:495,0,361:9,6,11,8 chr2 114386461 . T C 419.22 PASS AC=1;AF=0.583;AN=2;DP=324;FractionInformativeReads=1;set=variant4-variant6-variant8-variant14-variant17-variant22-variant25-variant28-variant30-variant34-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:14,11:25:99:381,0,478:1,13,0,11 chr2 114387907 . C T 1981.3 PASS AC=1;AF=0.543;AN=2;DP=4679;set=variant4-variant6-variant8-variant11-variant14-variant15-variant17-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:131,122:253:99:2896,0,3337:51,80,43,79 chr2 114387950 . G A 1037.43 PASS AC=1;AF=0.543;AN=2;DP=2432;set=variant4-variant6-variant8-variant11-variant14-variant15-variant17-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:74,57:131:99:1501,0,2127:21,53,16,41 chr2 114391721 . T C 2073.62 PASS AC=1;AF=0.577;AN=2;DP=2037;set=variant4-variant6-variant8-variant14-variant17-variant19-variant22-variant25-variant28-variant30-variant34-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:99,79:178:99:1797,0,2385:47,52,37,42 chr2 114392716 . C T 1182.88 PASS AC=1;AF=0.543;AN=2;DP=2311;set=variant4-variant6-variant8-variant11-variant14-variant15-variant17-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:61,49:110:99:1067,0,1501:21,40,15,34 chr2 114400526 . C T 206.89 PASS AC=1;AF=0.577;AN=2;DP=249;FractionInformativeReads=1;set=variant4-variant6-variant8-variant14-variant17-variant19-variant22-variant25-variant28-variant30-variant34-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:11,12:23:99:297,0,331:9,2,8,4 chr2 114425425 . C A 577.5 PASS AC=1;AF=0.63;AN=2;DP=636;FractionInformativeReads=1;set=variant-variant2-variant4-variant5-variant6-filterInvariant7-variant8-variant9-variant10-variant13-variant16-variant19-variant20-variant21-variant26-variant27-variant30-variant31-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,11:22:99:315,0,336:10,1,11,0 chr2 114426115 . T C 1269.78 PASS AC=2;AF=0.688;AN=2;DP=4356;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant19-variant20-variant21-variant22-variant25-variant26-variant27-variant28-variant30-variant31-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,132:132:99:3763,395,0:0,0,76,56 chr2 114429573 . C T 2106.12 PASS AC=1;AF=0.5;AN=2;DP=1088;set=variant11-variant14-variant22-variant25-variant28-variant30-variant34-variant35 GT:AD:DP:GQ:PL:SB 0/1:75,79:154:99:1851,0,1875:32,43,34,45 chr2 114470778 . G A 5384.82 PASS AC=1;AF=0.817;AN=2;DP=8326;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:102,126:228:99:3055,0,2334:54,48,62,64 chr2 114471061 . T C 14208.2 PASS AC=1;AF=0.614;AN=2;DP=8649;MQ=60;set=variant-variant2-variant6-variant7-variant9-variant10-variant13-variant16-variant20-variant21-variant26-variant27-variant31-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:182,200:382:99:4910,0,4411:97,85,103,97 chr2 114471346 . A AGAG,AAGAG,AAAGAG,AAAAGAG,AG 2043.1 PASS AC=1,0,0,0,0;AF=0.179,0.375,0.125,0.018,0.018;AN=2;DP=2002;set=variant-variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant16-variant19-variant20-variant21-variant22-variant26-variant27-variant30-variant31-variant32-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43 GT:DP:GQ:SB 0/1:50:99:13,17,7,13 chr2 114471782 . C T 3559 PASS AC=1;AF=0.614;AN=2;DP=2387;MQ=60;set=variant-variant2-variant6-variant7-variant9-variant10-variant13-variant16-variant20-variant21-variant26-variant27-variant31-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,40:75:99:1080,0,980:13,22,16,24 chr2 114471932 . G C 1630.12 PASS AC=1;AF=0.697;AN=2;DP=2323;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant19-variant20-variant21-variant22-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,22:55:99:568,0,864:17,16,11,11 chr2 114476582 . C A 568.49 PASS AC=1;AF=0.703;AN=2;DP=663;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant19-variant20-variant21-variant22-variant26-variant27-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,15:26:99:435,0,257:7,4,11,4 chr2 114480812 . A AAAC 446.07 PASS AC=1;AF=0.825;AN=2;DP=880;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,7:16:99:267,0,357:2,7,1,6 chr2 114486880 . GA G 82.85 PASS AC=1;AF=0.654;AN=2;DP=95;FS=0;MQ=60;set=variant-variant2-variant7-variant10-variant21-variant26-variant27-variant31-variant35-variant36-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,3:7:69:69,0,95:4,0,3,0 chr2 114486907 . T C 151.77 PASS AC=1;AF=0.724;AN=2;DP=276;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant19-variant21-variant22-variant26-variant27-variant30-variant31-variant32-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,6:15:99:175,0,351:9,0,5,1 chr2 114492135 . C T 1855.07 PASS AC=1;AF=0.697;AN=2;DP=2174;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant19-variant20-variant21-variant22-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,31:78:99:641,0,1185:26,21,15,16 chr2 114493524 . C T 1427.42 PASS AC=1;AF=0.697;AN=2;DP=1985;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant19-variant20-variant21-variant22-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,30:74:99:677,0,1035:20,24,13,17 chr2 114499605 . A C 13338.8 PASS AC=1;AF=0.697;AN=2;DP=13575;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant19-variant20-variant21-variant22-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:226,190:416:99:4215,0,5520:114,112,103,87 chr2 114500131 . C A 10078.3 PASS AC=1;AF=0.697;AN=2;DP=9217;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant19-variant20-variant21-variant22-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:162,113:275:99:2796,0,4102:69,93,42,71 chr2 114501242 . T C 2470.53 PASS AC=1;AF=0.614;AN=2;DP=1689;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant7-variant9-variant10-variant13-variant16-variant20-variant21-variant26-variant27-variant31-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,30:61:99:640,0,765:21,10,15,15 chr2 114513386 . C T 2064.95 PASS AC=1;AF=0.697;AN=2;DP=2493;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant19-variant20-variant21-variant22-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,23:71:99:611,0,1155:28,20,14,9 chr2 114513787 . C G 4230.46 PASS AC=2;AF=0.919;AN=2;DP=7300;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,181:181:99:5728,541,0:0,0,105,76 chr2 114514098 . A C 2778.48 PASS AC=1;AF=0.697;AN=2;DP=3999;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant19-variant20-variant21-variant22-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,81:140:99:2164,0,1419:27,32,35,46 chr2 114514298 . C T 954.55 PASS AC=1;AF=0.579;AN=2;DP=1927;MQ=60;set=variant-variant2-variant6-variant7-variant9-variant10-variant13-variant16-variant21-variant26-variant27-variant31-variant34-variant35-variant37-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:62,58:120:99:1288,0,1416:29,33,32,26 chr2 114514338 . T G 1882.93 PASS AC=1;AF=0.697;AN=2;DP=3645;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant19-variant20-variant21-variant22-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:70,67:137:99:1629,0,1754:35,35,32,35 chr2 114514391 . T G 1683.92 PASS AC=1;AF=0.817;AN=2;DP=4067;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:62,58:120:99:1373,0,1457:30,32,26,32 chr2 114647551 . G C 247.9 PASS AC=1;AF=0.5;AN=2;DP=53;MQ=60;set=variant35-variant36-variant41 GT:AD:DP:GQ:PL:SB 0/1:15,8:23:99:276,0,524:11,4,7,1 chr2 114648081 . C T 403.3 PASS AC=1;AF=0.563;AN=2;DP=170;FractionInformativeReads=1;MQ=60;set=variant10-variant14-variant15-variant16-variant25-variant28-variant30-variant35 GT:AD:DP:GQ:PL:SB 0/1:17,11:28:99:274,0,459:10,7,5,6 chr2 114689047 . C CT 83.76 PASS AC=1;AF=0.571;AN=2;DP=177;MQ=60;set=variant10-variant15-variant16-filterInvariant25-variant28-variant30-variant35 GT:AD:DP:GQ:PL:SB 0/1:6,12:18:99:259,0,103:2,4,4,8 chr2 114709476 . A T 855.18 PASS AC=1;AF=0.563;AN=2;DP=464;FractionInformativeReads=1;MQ=60;set=variant10-variant14-variant15-variant16-variant25-variant28-variant30-variant35 GT:AD:DP:GQ:PL:SB 0/1:26,29:55:99:688,0,681:7,19,10,19 chr2 114715533 . G A 1215.25 PASS AC=1;AF=0.738;AN=2;DP=2312;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,26:46:99:578,0,489:10,10,14,12 chr2 114716178 . GT G,GTT 109.7 PASS AC=1,0;AF=0.429,0.143;AN=2;DP=373;MQ=60;set=variant10-variant14-variant15-variant16-variant23-variant25-variant28-variant29-variant30-variant31-variant35-variant38-variant41-variant42 GT:DP:GQ:SB 0/1:33:99:14,6,10,3 chr2 114716365 . G A 2187.59 PASS AC=1;AF=0.545;AN=2;DP=1795;FractionInformativeReads=1;MQ=60;set=variant10-variant14-variant15-variant16-variant25-variant28-variant29-variant30-variant35-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:91,94:185:99:2316,0,2086:44,47,49,45 chr2 114719451 . A G 12648.4 PASS AC=1;AF=0.738;AN=2;DP=14420;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:172,193:365:99:5071,0,4415:84,88,101,92 chr2 115919301 . G A 666.15 PASS AC=2;AF=0.667;AN=2;DP=1421;MQ=60;set=variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,47:48:99:1315,132,0:1,0,19,28 chr2 115919677 . C G 2250.7 PASS AC=2;AF=1;AN=2;DP=2686;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,83:83:99:3695,250,0:0,0,53,30 chr2 115919678 . T C 2250.7 PASS AC=2;AF=1;AN=2;DP=2711;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,83:83:99:3695,250,0:0,0,53,30 chr2 116066984 . G A 1899.03 PASS AC=2;AF=0.857;AN=2;DP=2023;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1829,158,0:0,0,14,39 chr2 116099725 . A T 4300.01 PASS AC=2;AF=0.93;AN=2;DP=4811;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,114:114:99:3448,341,0:0,0,49,65 chr2 116099765 . A ATGTG 752.33 PASS AC=1;AF=0.5;AN=2;DP=56;FS=3.75;FractionInformativeReads=0.643;MQ=60;MQRankSum=1.703;QD=13.43;ReadPosRankSum=-0.334;SOR=1.802;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:16,20:36:99:790,0,610:5,11,3,17 chr2 116447277 . G A 445.43 PASS AC=1;AF=0.583;AN=2;DP=299;FractionInformativeReads=1;MQ=60;set=variant18-variant23-variant32-variant33-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,30:48:99:858,0,405:9,9,21,9 chr2 116447606 . T C 431.39 PASS AC=1;AF=0.583;AN=2;DP=260;FractionInformativeReads=1;MQ=60;set=variant18-variant23-variant32-variant33-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,20:38:99:583,0,448:6,12,6,14 chr2 116497479 . A G 2797.89 PASS AC=2;AF=1;AN=2;DP=3446;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,74:74:99:2545,222,0:0,0,20,54 chr2 116497528 . A G 1419.36 PASS AC=2;AF=1;AN=2;DP=1510;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1382,120,0:0,0,10,30 chr2 116503671 . G A 1032.41 PASS AC=1;AF=0.6;AN=2;DP=592;FractionInformativeReads=1;MQ=60;set=variant23-variant32-variant33-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,75:133:99:1657,0,1339:31,27,40,35 chr2 116525960 . G A 3394.71 PASS AC=2;AF=1;AN=2;DP=5503;FS=0;MQ=60;MQRankSum=0.66;ReadPosRankSum=0.561;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,137:137:99:4081,409,0:0,0,73,64 chr2 116534922 . A G 1492.84 PASS AC=1;AF=0.618;AN=2;DP=1916;MQ=60;set=variant3-variant4-variant7-variant8-variant10-variant17-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant30-variant35-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:57,60:117:99:1524,0,1456:24,33,26,34 chr2 116535086 . T C 453.85 PASS AC=2;AF=1;AN=2;DP=577;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:708,54,0:0,0,3,15 chr2 116539846 . GA G 348.25 PASS AC=1;AF=0.583;AN=2;DP=520;MQ=60;set=variant3-variant7-variant8-variant10-variant17-variant19-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant30-variant35-variant36-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:13,20:33:99:520,0,313:11,2,14,6 chr2 116539911 . A G 839.57 PASS AC=1;AF=0.583;AN=2;DP=558;MQ=60;set=variant18-variant23-variant32-variant33-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,49:102:99:1207,0,1174:28,25,33,16 chr2 116548526 . A G 509.76 PASS AC=1;AF=0.919;AN=2;DP=605;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,5:8:99:160,0,104:3,0,4,1 chr2 116548820 . C T 2849.35 PASS AC=1;AF=0.919;AN=2;DP=3525;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,22:73:99:449,0,1222:22,29,11,11 chr2 116593675 . ATG A 438.21 PASS AC=2;AF=0.925;AN=2;DP=457;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:277,24,0:0,0,5,3 chr2 116598431 . C T 911.8 PASS AC=1;AF=0.583;AN=2;DP=440;FractionInformativeReads=1;MQ=60;set=variant18-variant23-variant32-variant33-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,40:76:99:1030,0,822:15,21,16,24 chr2 116598546 . G A 461.7 PASS AC=2;AF=0.977;AN=2;DP=627;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:457,36,0:0,0,1,11 chr2 116599659 . A T 1435.05 PASS AC=2;AF=0.966;AN=2;DP=1738;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1277,123,0:0,0,28,13 chr2 116599927 . T C 11398.5 PASS AC=2;AF=0.989;AN=2;DP=14420;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,317:317:99:10142,950,0:0,0,182,135 chr2 116600118 . G A 1672.81 PASS AC=1;AF=0.5;AN=2;DP=656;MQ=60;set=variant4-variant7-variant25-variant28-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:61,58:119:99:1817,0,1892:18,43,14,44 chr2 116601843 . T C 1404.43 PASS AC=1;AF=0.583;AN=2;DP=775;FractionInformativeReads=1;MQ=60;set=variant23-variant32-variant33-variant34-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:73,77:150:99:1809,0,1588:32,41,37,40 chr2 116602353 . T A 3823.16 PASS AC=2;AF=1;AN=2;DP=5850;FS=0;MQ=60;MQRankSum=0.323;ReadPosRankSum=1.243;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,137:137:99:4841,411,0:0,0,59,78 chr2 116602671 . C T 3824.15 PASS AC=1;AF=0.583;AN=2;DP=2497;MQ=60;set=variant23-variant32-variant33-variant34-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:238,225:463:99:5420,0,5982:112,126,107,118 chr2 118572471 . A C,T 3108.6 PASS AC=1,0;AF=0.643,0.014;AN=2;DP=9408;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:DP:GQ:SB 0/1:271:99:54,82,52,83 chr2 118575414 . C T 759.35 PASS AC=1;AF=0.5;AN=2;DP=264;MQ=60;set=variant7-variant8-variant14-variant16-variant35 GT:AD:DP:GQ:PL:SB 0/1:20,19:39:99:435,0,521:6,14,6,13 chr2 118577153 . CT C 117.03 PASS AC=1;AF=0.5;AN=2;DP=81;FractionInformativeReads=1;MQ=60;set=variant7-variant8-variant14-variant16-variant35 GT:AD:DP:GQ:PL:SB 0/1:12,8:20:99:264,0,424:8,4,5,3 chr2 118578691 . TA T 284.1 PASS AC=2;AF=0.898;AN=2;DP=1810;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1151,117,0:0,0,19,20 chr2 118582682 . GTGA G 851.24 PASS AC=1;AF=0.5;AN=2;DP=403;MQ=60;set=variant7-variant8-variant14-variant16-variant35 GT:AD:DP:GQ:PL:SB 0/1:51,28:79:99:1023,0,2268:26,25,10,18 chr2 118582817 . G C 627.6 PASS AC=1;AF=0.5;AN=2;DP=265;MQ=60;set=variant7-variant8-variant14-variant16-variant35 GT:AD:DP:GQ:PL:SB 0/1:25,23:48:99:694,0,843:12,13,10,13 chr2 118582936 . A ATAAAG 2531.88 PASS AC=2;AF=0.898;AN=2;DP=5707;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,127:127:99:5810,393,0:0,0,71,56 chr2 118583100 . G A 1158.95 PASS AC=1;AF=0.5;AN=2;DP=508;FractionInformativeReads=1;MQ=60;set=variant7-variant8-variant14-variant16-variant35 GT:AD:DP:GQ:PL:SB 0/1:54,46:100:99:1367,0,1330:28,26,18,28 chr2 118583940 . C T 669.38 PASS AC=1;AF=0.662;AN=2;DP=2232;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,31:72:99:733,0,1021:24,17,20,11 chr2 118588640 . C T 1931.52 PASS AC=2;AF=0.898;AN=2;DP=5976;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,174:174:99:5438,522,0:0,0,68,106 chr2 118675004 . C T 684.56 PASS AC=1;AF=0.5;AN=2;DP=179;FractionInformativeReads=1;MQ=60;set=variant2-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,25:60:99:579,0,935:19,16,14,11 chr2 118688754 . T C 2379.45 PASS AC=2;AF=0.989;AN=2;DP=2728;MQ=60;MQRankSum=0.12;ReadPosRankSum=2.065;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,67:67:99:2100,200,0:0,0,25,42 chr2 118698932 . T C 1192.47 PASS AC=1;AF=0.5;AN=2;DP=349;FractionInformativeReads=1;MQ=60;set=variant2-variant35-variant44 GT:AD:DP:GQ:PL:SB 0/1:71,73:144:99:1792,0,1851:28,43,28,45 chr2 118704478 . T G 2182.25 PASS AC=2;AF=1;AN=2;DP=2211;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1441,129,0:0,0,14,29 chr2 118704503 . A G 1391.48 PASS AC=2;AF=0.763;AN=2;DP=1360;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:1182,96,0:0,0,6,26 chr2 118705570 . A G 2569.3 PASS AC=2;AF=0.989;AN=2;DP=3110;MQRankSum=0.542;ReadPosRankSum=1.075;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,69:69:99:2214,207,0:0,0,45,24 chr2 118706879 . A G 2778.79 PASS AC=2;AF=0.989;AN=2;DP=3528;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,84:84:99:2433,251,0:0,0,42,42 chr2 118731573 . G A 2247.44 PASS AC=2;AF=0.706;AN=2;DP=3780;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,105:105:99:3051,313,0:0,0,48,57 chr2 118732975 . T C 1455.63 PASS AC=2;AF=0.989;AN=2;DP=3368;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:2493,231,0:0,0,25,52 chr2 118735395 . G A 944.04 PASS AC=2;AF=0.989;AN=2;DP=1147;FS=0;MQ=60;MQRankSum=0.228;ReadPosRankSum=-0.152;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1214,110,0:0,0,26,11 chr2 118743736 . CTTT CTTTTT,CT,CTTTTTT,C,CTT,CTTTT 147.39 PASS AC=1,0,0,0,0,0;AF=0.306,0.028,0.028,0.056,0.028,0.139;AN=2;DP=534;set=variant4-variant5-variant7-filterInvariant8-variant11-variant12-filterInvariant19-variant22-variant25-filterInvariant26-variant27-variant28-variant29-variant34-variant35-variant36-variant37-variant40 GT:DP:GQ:SB 0/1:15:99:1,6,1,7 chr2 118753097 . C T 464.73 PASS AC=2;AF=0.676;AN=2;DP=1293;MQ=60;set=variant-variant2-variant4-variant11-variant15-variant22-variant23-variant24-variant25-variant27-variant28-variant33-variant35-variant36-variant37-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2176,209,0:0,0,28,42 chr2 118753148 . A ATC 1078.68 PASS AC=2;AF=0.989;AN=2;DP=1836;MQ=60;MQRankSum=0.716;ReadPosRankSum=-1.273;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1935,129,0:0,0,13,30 chr2 118764242 . C CA 3387.83 PASS AC=1;AF=0.682;AN=2;DP=2603;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:42,33:75:99:1039,0,1345:25,17,21,12 chr2 118766024 . A G 1620.32 PASS AC=2;AF=0.989;AN=2;DP=2035;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1470,126,0:0,0,31,11 chr2 118771663 . A G 4128.67 PASS AC=2;AF=0.989;AN=2;DP=6324;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,201:201:99:5998,600,0:0,0,92,109 chr2 118850654 . AGATGATGAT A 71.48 PASS AC=1;AF=0.655;AN=2;DP=1569;set=filterInvariant-variant2-filterInvariant3-variant4-variant7-variant8-variant11-filterInvariant13-variant14-variant16-variant17-variant19-variant21-variant24-variant25-variant27-variant28-variant29-variant31-filterInvariant32-variant33-variant34-variant35-variant36-variant37-variant39-filterInvariant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,15:19:46:611,0,46:3,1,1,14 chr2 118851073 . AGATGATGATGATGAT AGAT,AGATGATGAT,A,AGATGATGATGATGATGATGAT 516.41 PASS AC=2,0,0,0;AF=0.5,0.184,0.132,0.079;AN=2;DP=213;FS=0;set=variant4-variant6-variant8-variant10-variant13-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant34-variant35-variant37-variant39 GT:DP:GQ:SB 1/1:9:27:0,0,9,0 chr2 118851167 . T G 1410.16 PASS AC=2;AF=0.789;AN=2;DP=605;set=variant6-variant7-variant8-variant9-variant12-variant13-variant16-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant28-variant29-variant33-variant2-variant35 GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1653,123,0:0,0,31,9 chr2 118851236 . T TGAG,TGAGGAG 3597.94 PASS AC=1,0;AF=0.4,0.1;AN=2;DP=1734;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant13-variant16-variant25-variant28-variant29-variant32-variant35-variant40 GT:DP:GQ:SB 0/1:119:99:29,14,40,36 chr2 118851239 . T G 3711.38 PASS AC=1;AF=0.5;AN=2;DP=1751;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant13-variant25-variant28-variant29-variant32-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:47,101:148:99:3759,0,1695:30,17,53,48 chr2 118851294 . G A 332.46 PASS AC=1;AF=0.5;AN=2;DP=3385;set=filterInvariant2-filterInvariant3-variant4-variant7-variant8-variant9-variant11-variant12-variant16-variant19-variant24-variant25-variant28-variant29-filterInvariant32-variant33-variant35-variant36-variant37-filterInvariant38-filterInvariant42 GT:AD:DP:GQ:PL:SB 0/1:146,62:208:99:867,0,4989:72,74,30,32 chr2 118851371 . T A 481.43 PASS AC=1;AF=0.5;AN=2;DP=2963;set=variant-filterInvariant2-filterInvariant4-filterInvariant8-variant10-filterInvariant11-filterInvariant14-variant18-filterInvariant24-filterInvariant28-filterInvariant29-filterInvariant31-filterInvariant32-variant33-filterInvariant35-filterInvariant37 GT:AD:DP:GQ:PL:SB 0/1:151,112:263:99:520,0,5862:67,84,50,62 chr2 118851381 . TGAA T 2736.95 PASS AC=1;AF=0.5;AN=2;DP=5389;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:108,132:240:99:5278,0,730:48,60,61,71 chr2 118851809 . AGAT AGATGAT,AGATGATGAT,AGATGATGATGAT,AGATGATGATGATGAT,A 1256.93 PASS AC=1,0,0,0,0;AF=0.663,0.188,0.025,0.013,0.013;AN=2;DP=3731;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:DP:GQ:SB 0/1:67:28:4,2,35,26 chr2 118866033 . G GA 778.04 PASS AC=2;AF=0.69;AN=2;DP=1668;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant9-variant11-variant13-variant14-variant15-variant17-variant19-variant23-variant24-variant25-variant27-variant28-variant29-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1682,138,0:0,0,12,34 chr2 118866963 . C T 7396.24 PASS AC=2;AF=1;AN=2;DP=8655;FS=0;MQRankSum=0.871;ReadPosRankSum=0.38;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,206:206:99:6314,618,0:0,0,119,87 chr2 119600067 . C CT 639.55 PASS AC=1;AF=0.869;AN=2;DP=566;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,3:7:97:97,0,136:3,1,2,1 chr2 119605301 . T TG 875.93 PASS AC=1;AF=0.538;AN=2;DP=475;set=variant8-variant11-variant12-variant15-variant18-filterInvariant21-variant22-variant25-variant28-variant34-variant35-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,7:13:99:174,0,177:1,5,0,7 chr2 119605303 . T G 1211.8 PASS AC=1;AF=0.704;AN=2;DP=859;set=variant-variant2-variant3-variant5-variant7-variant9-variant12-variant13-variant16-variant17-variant18-variant19-variant26-variant27-filterInvariant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant40-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,7:14:99:177,0,177:0,7,1,6 chr2 119605315 . T G 381.27 PASS AC=1;AF=0.5;AN=2;DP=182;set=variant8-variant11-variant15-variant18-variant23-variant28-variant34-variant35-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,7:14:99:174,0,177:1,6,0,7 chr2 119605317 . T G 111.71 PASS AC=1;AF=0.605;AN=2;DP=353;set=variant2-variant3-variant5-variant9-variant16-variant17-variant18-variant19-variant21-variant26-variant28-variant32-variant33-variant34-variant35-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,6:13:99:177,0,177:0,7,0,6 chr2 119700096 . T C 1538.16 PASS AC=2;AF=0.707;AN=2;DP=1862;set=variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:977,78,0:0,0,5,21 chr2 119732042 . T C 1468.96 PASS AC=1;AF=0.583;AN=2;DP=3775;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant35-variant36-variant38-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:63,57:120:99:1497,0,1749:27,36,22,35 chr2 119739269 . C T 996.43 PASS AC=1;AF=0.583;AN=2;DP=2579;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant11-variant12-variant13-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,43:84:99:968,0,908:19,22,19,24 chr2 119740290 . C T 82.69 PASS AC=2;AF=0.729;AN=2;DP=399;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:26:307,26,0:0,0,4,5 chr2 119749477 . T G 2231.23 PASS AC=2;AF=0.872;AN=2;DP=7013;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,179:179:99:5509,536,0:0,0,78,101 chr2 119749611 . C T 420.59 PASS AC=1;AF=0.625;AN=2;DP=1022;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,26:43:99:739,0,472:5,12,6,20 chr2 119749858 . A G 125.14 PASS AC=1;AF=0.688;AN=2;DP=390;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,3:8:99:108,0,161:5,0,3,0 chr2 119750894 . C T 819.07 PASS AC=1;AF=0.5;AN=2;DP=68;FS=1.081;FractionInformativeReads=1;MQ=60;MQRankSum=-0.682;QD=12.05;ReadPosRankSum=0.866;SOR=1.013;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:36,32:68:99:847,0,997:10,26,7,25 chr2 119751769 . AAAC A,AAACAAC 340.72 PASS AC=1,0;AF=0.671,0.073;AN=2;DP=949;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:22:99:7,1,12,2 chr2 119914101 . T G 1210.36 PASS AC=2;AF=0.769;AN=2;DP=2408;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:2340,228,0:0,0,41,35 chr2 119915132 . CG C 943.22 PASS AC=2;AF=0.966;AN=2;DP=2073;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1308,120,0:0,0,31,9 chr2 119915249 . T C 793.2 PASS AC=2;AF=0.805;AN=2;DP=6778;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,181:181:99:5340,542,0:0,0,98,83 chr2 119915988 . A G 492.14 PASS AC=2;AF=0.805;AN=2;DP=1552;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1500,153,0:0,0,27,24 chr2 119981523 . G T 358.59 PASS AC=1;AF=0.672;AN=2;DP=1197;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,32:48:99:729,0,279:10,6,14,18 chr2 119988565 . G A 1181.34 PASS AC=1;AF=0.65;AN=2;DP=5417;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:106,122:228:99:2609,0,2486:51,55,64,58 chr2 120003642 . C T 2091.06 PASS AC=2;AF=0.909;AN=2;DP=3746;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,82:82:99:2681,246,0:0,0,40,42 chr2 120003780 . A G 421.21 PASS AC=1;AF=0.575;AN=2;DP=928;MQ=60;set=variant-variant2-variant3-variant4-variant14-variant15-variant19-variant20-variant24-variant26-variant28-variant31-variant32-variant35-variant36-variant37-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,15:47:99:369,0,908:12,20,5,10 chr2 120005840 . TC T,TCC 655.13 PASS AC=1,0;AF=0.574,0.088;AN=2;DP=3631;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant42-variant44 GT:DP:GQ:SB 0/1:125:99:23,43,23,36 chr2 120012171 . G A 913.37 PASS AC=1;AF=0.55;AN=2;DP=1708;MQ=60;set=variant-variant2-variant3-variant4-variant14-variant15-variant19-variant20-variant24-variant26-variant28-variant31-variant32-variant35-variant36-variant37-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,40:87:99:930,0,1200:26,21,23,17 chr2 120014985 . A G 331.77 PASS AC=2;AF=1;AN=2;DP=998;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:748,66,0:0,0,16,6 chr2 120021319 . C T 1037.43 PASS AC=2;AF=0.652;AN=2;DP=3138;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,106:106:99:3530,318,0:0,0,46,60 chr2 120021785 . T C 1047.71 PASS AC=2;AF=0.943;AN=2;DP=2393;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:2435,237,0:0,0,39,40 chr2 120022385 . C T 457.31 PASS AC=2;AF=0.636;AN=2;DP=1497;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2258,208,0:0,0,36,34 chr2 120023188 . A G 5296.53 PASS AC=2;AF=0.943;AN=2;DP=7004;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,142:142:99:4306,423,0:0,0,77,65 chr2 120023260 . C T 1269.29 PASS AC=2;AF=0.586;AN=2;DP=3497;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 1/1:1,132:133:99:3868,388,0:1,0,54,78 chr2 120125029 . A G 4838.05 PASS AC=2;AF=0.841;AN=2;DP=6894;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,158:158:99:5070,473,0:0,0,93,65 chr2 120125936 . T C 1156.15 PASS AC=2;AF=0.83;AN=2;DP=3117;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:2317,236,0:0,0,35,44 chr2 120187344 . A G 77.3 PASS AC=1;AF=0.705;AN=2;DP=923;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,24:33:99:731,0,309:9,0,17,7 chr2 120189404 . A G 538.86 PASS AC=2;AF=0.864;AN=2;DP=643;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:653,57,0:0,0,13,6 chr2 120189433 . G C 787.34 PASS AC=2;AF=0.864;AN=2;DP=838;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:775,72,0:0,0,17,7 chr2 120194651 . A AGTGTGC 5059.99 PASS AC=2;AF=0.909;AN=2;DP=7932;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,188:188:99:8422,577,0:0,0,91,97 chr2 120195182 . C G 1424.6 PASS AC=2;AF=0.907;AN=2;DP=2282;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,74:74:99:2260,222,0:0,0,33,41 chr2 120195496 . AGGACT A 946.25 PASS AC=1;AF=0.688;AN=2;DP=2388;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,21:52:99:789,0,1567:15,16,8,13 chr2 120195699 . T TC 2469.1 PASS AC=2;AF=0.917;AN=2;DP=2740;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,82:82:99:3629,250,0:0,0,39,43 chr2 120195700 . G C,GC 2325.77 PASS AC=2,0;AF=0.9,0.1;AN=2;DP=2261;FS=0;MQ=60;set=variant14-variant16-variant17-variant18-variant19-variant2-variant20-variant21-variant3-variant22-variant4-variant23-variant5-variant24-variant25-variant6-variant26-variant27-variant7-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:DP:GQ:SB 1/1:82:99:0,0,39,43 chr2 120197670 . G A 1068.44 PASS AC=1;AF=0.675;AN=2;DP=4102;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,56:123:99:1358,0,1701:36,31,30,26 chr2 120199140 . A G 809.26 PASS AC=2;AF=0.907;AN=2;DP=3535;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,107:107:99:3084,319,0:0,0,48,59 chr2 120204514 . C T 360.02 PASS AC=1;AF=0.5;AN=2;DP=79;FractionInformativeReads=1;MQ=60;set=variant35-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,15:31:99:388,0,457:4,12,4,11 chr2 120209689 . A G 1841.72 PASS AC=2;AF=0.907;AN=2;DP=5171;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,144:144:99:4469,432,0:0,0,63,81 chr2 120219287 . CAAAAA CAA,CA,CAAAA,CAAA,C 217.24 PASS AC=0,1,0,0,0;AF=0.159,0.091,0.205,0.068,0.023;AN=2;DP=329;set=variant4-variant7-variant8-variant10-variant12-variant16-variant19-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant43 GT:DP:GQ:SB 0/2:19:99:8,5,5,1 chr2 120221585 . G A 132.17 PASS AC=1;AF=0.7;AN=2;DP=799;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,14:27:99:384,0,369:10,3,10,4 chr2 120221861 . G A 465.73 PASS AC=1;AF=0.529;AN=2;DP=1604;MQ=60;set=variant-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant15-variant19-variant31-variant32-variant35-variant36-variant37-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:47,64:111:99:1733,0,1147:16,31,26,38 chr2 120221984 . A C 463.53 PASS AC=2;AF=0.919;AN=2;DP=886;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:1025,72,0:0,0,7,17 chr2 120221992 . T C 79.69 PASS AC=1;AF=0.529;AN=2;DP=321;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant15-variant19-variant31-variant32-variant35-variant36-variant37-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:9,13:22:99:420,0,235:4,5,3,10 chr2 120222030 . GA G,GAA 245.67 PASS AC=1,0;AF=0.5,0.125;AN=2;DP=45;MQ=60;set=variant8-variant30-variant31-variant35 GT:DP:GQ:SB 0/1:9:72:2,2,0,5 chr2 120230998 . G A 1992.23 PASS AC=2;AF=0.905;AN=2;DP=4184;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,120:120:99:3624,359,0:0,0,71,49 chr2 120231165 . T C 5079.83 PASS AC=2;AF=0.857;AN=2;DP=7499;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,208:209:99:6205,615,0:1,0,94,114 chr2 120231303 . T C 1868.17 PASS AC=2;AF=0.907;AN=2;DP=2534;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,78:78:99:2558,234,0:0,0,30,48 chr2 120236332 . A C 118.66 PASS AC=1;AF=0.531;AN=2;DP=302;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant6-variant7-variant8-variant12-variant13-variant17-variant19-variant31-variant32-variant35-variant36-variant37-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:16,8:24:99:222,0,494:10,6,5,3 chr2 120317621 . CTT CT,CTTT,CTTTT,C 167.59 PASS AC=0,0,0,1;AF=0.273,0.136,0.03,0.091;AN=2;DP=3278;set=filterInvariant-variant3-variant4-variant5-variant7-filterInvariant9-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-filterInvariant27-filterInvariant28-variant29-variant30-variant32-variant34-variant35-variant38-variant39-filterInvariant40-variant41-variant42-variant44 GT:DP:GQ:SB 0/4:77:99:27,27,7,16 chr2 120362407 . C T 3828.3 PASS AC=2;AF=0.955;AN=2;DP=6083;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,133:133:99:3993,398,0:0,0,64,69 chr2 120362897 . T A 1126.92 PASS AC=2;AF=1;AN=2;DP=1842;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1123,104,0:0,0,10,25 chr2 120366057 . G GT,GTT 384.45 PASS AC=2,0;AF=0.875,0.045;AN=2;DP=1352;set=Intersection GT:DP:GQ:SB 1/1:24:71:0,0,17,7 chr2 120369300 . T C 3021.8 PASS AC=2;AF=1;AN=2;DP=4595;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,104:104:99:3057,312,0:0,0,51,53 chr2 120385094 . GATATATATAT GATAT,GAT,GATATAT,G,GATATATAT 341.69 PASS AC=1,1,0,0,0;AF=0.75,0.119,0.048,0.036,0.012;AN=2;DP=434;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 2/1:9:80:0,0,8,1 chr2 120387637 . G C 196.77 PASS AC=2;AF=1;AN=2;DP=281;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:238,24,0:0,0,3,5 chr2 120388412 . G A 6409.69 PASS AC=2;AF=1;AN=2;DP=9098;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,211:212:99:6688,623,0:0,1,110,101 chr2 120404629 . AT A 1418.21 PASS AC=2;AF=0.989;AN=2;DP=3871;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,77:78:99:1974,208,0:1,0,31,46 chr2 120409430 . A G 1281.35 PASS AC=2;AF=1;AN=2;DP=1187;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:835,69,0:0,0,19,4 chr2 120436681 . A G 909.24 PASS AC=2;AF=0.966;AN=2;DP=1216;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:875,69,0:0,0,17,6 chr2 120438523 . A G 639.4 PASS AC=2;AF=0.83;AN=2;DP=6262;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,127:127:99:3903,380,0:0,0,61,66 chr2 120438696 . A G 3178.22 PASS AC=2;AF=1;AN=2;DP=8952;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,221:221:99:7159,660,0:0,0,130,91 chr2 120439230 . C G 627.88 PASS AC=2;AF=0.83;AN=2;DP=5506;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,148:148:99:4355,442,0:0,0,69,79 chr2 120439459 . C A 327.41 PASS AC=2;AF=0.83;AN=2;DP=2499;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:2152,202,0:0,0,31,37 chr2 120439702 . G GTTT,GTT,GT 89.9 PASS AC=0,0,1;AF=0.154,0.481,0.212;AN=2;DP=268;set=variant2-variant3-variant4-variant6-variant8-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant24-variant25-variant26-variant28-variant31-variant33-variant34-variant35-variant37-variant40-variant41-variant42 GT:DP:GQ:SB 0/3:7:6:0,1,0,6 chr2 120443443 . A G 950.14 PASS AC=2;AF=0.795;AN=2;DP=3437;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,109:109:99:3089,326,0:0,0,48,61 chr2 120443665 . T C 621.83 PASS AC=2;AF=0.818;AN=2;DP=2310;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:1485,144,0:0,0,24,24 chr2 120443845 . TA T 162.73 PASS AC=2;AF=0.826;AN=2;DP=1173;MQ=60;set=variant-variant2-variant3-variant4-filterInvariant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:489,48,0:0,0,4,12 chr2 120517593 . C T 3242.44 PASS AC=2;AF=0.786;AN=2;DP=7015;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,171:172:99:4748,496,0:1,0,72,99 chr2 120689905 . A G 417.99 PASS AC=2;AF=0.762;AN=2;DP=710;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:740,63,0:0,0,17,4 chr2 120703842 . A G 357.65 PASS AC=2;AF=0.813;AN=2;DP=398;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:222,18,0:0,0,5,1 chr2 120704164 . A AT 7975.92 PASS AC=2;AF=0.762;AN=2;DP=7533;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,174:174:99:7793,530,0:0,0,86,88 chr2 120704166 . G T 7984.96 PASS AC=2;AF=0.762;AN=2;DP=7379;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,174:174:99:7793,530,0:0,0,85,89 chr2 120714401 . CT C,CTT 229.24 PASS AC=1,0;AF=0.488,0.013;AN=2;DP=2813;MQ=60;set=variant-filterInvariant2-variant3-variant4-filterInvariant5-filterInvariant6-variant7-filterInvariant8-filterInvariant9-filterInvariant10-variant11-filterInvariant12-variant13-filterInvariant14-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant18-variant19-variant20-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant27-variant28-filterInvariant29-variant31-filterInvariant32-filterInvariant33-variant34-variant35-variant36-filterInvariant37-variant38-filterInvariant39-filterInvariant40-filterInvariant43-filterInvariant44 GT:DP:GQ:SB 0/1:68:99:23,23,10,12 chr2 120718322 . A G 644.69 PASS AC=2;AF=0.762;AN=2;DP=890;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:924,84,0:0,0,20,8 chr2 120718672 . T G 737.45 PASS AC=2;AF=0.966;AN=2;DP=501;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:299,24,0:0,0,2,6 chr2 120725704 . A G 406.13 PASS AC=2;AF=0.989;AN=2;DP=433;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.406;ReadPosRankSum=0.406;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:753,51,0:0,0,0,17 chr2 120736007 . GT G 994.36 PASS AC=2;AF=0.966;AN=2;DP=1701;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:907,87,0:0,0,13,16 chr2 120738504 . G A 4090.52 PASS AC=2;AF=0.977;AN=2;DP=4816;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:2576,216,0:0,0,28,44 chr2 120739236 . T C 9108.99 PASS AC=2;AF=0.793;AN=2;DP=9352;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,206:206:99:6309,617,0:0,0,121,85 chr2 120740051 . C CTA 5160.65 PASS AC=2;AF=1;AN=2;DP=5392;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,126:127:99:5784,357,0:1,0,66,60 chr2 120741083 . T C 12659.3 PASS AC=2;AF=0.793;AN=2;DP=13575;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,326:326:99:9682,975,0:0,0,136,190 chr2 120770633 . T C 2008.38 PASS AC=2;AF=1;AN=2;DP=2798;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,63:63:99:2051,189,0:0,0,38,25 chr2 120770708 . A C 2202.53 PASS AC=2;AF=0.821;AN=2;DP=3227;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,84:84:99:2496,252,0:0,0,45,39 chr2 120776972 . TG T 1195.13 PASS AC=2;AF=0.833;AN=2;DP=980;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:1340,96,0:0,0,4,28 chr2 120830815 . A G 1029.62 PASS AC=2;AF=0.833;AN=2;DP=1519;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:860,84,0:0,0,13,15 chr2 120862453 . G T 2800.04 PASS AC=2;AF=0.798;AN=2;DP=3483;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,74:74:99:2635,221,0:0,0,53,21 chr2 120885310 . G A 4044.94 PASS AC=2;AF=0.798;AN=2;DP=5069;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,129:129:99:3708,386,0:0,0,72,57 chr2 120889173 . G C 2117.49 PASS AC=2;AF=0.798;AN=2;DP=4560;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,103:105:99:2554,256,0:1,1,66,37 chr2 120918585 . A C 1792.76 PASS AC=2;AF=0.798;AN=2;DP=2449;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,53:54:99:1684,120,0:0,1,16,37 chr2 120935419 . TGTTCTTGG T 2293.22 PASS AC=1;AF=0.5;AN=2;DP=125;FS=0;FractionInformativeReads=0.984;MQ=60;MQRankSum=-1.308;QD=18.35;ReadPosRankSum=1.667;SOR=0.762;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:63,60:123:99:2330,0,3703:41,22,40,20 chr2 120979322 . T C 1944.98 PASS AC=2;AF=0.814;AN=2;DP=3338;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,110:110:99:3396,330,0:0,0,63,47 chr2 120980428 . G C 5435.95 PASS AC=2;AF=0.744;AN=2;DP=8224;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,240:240:99:7421,718,0:0,0,112,128 chr2 120997868 . TA T 169.68 PASS AC=1;AF=0.5;AN=2;DP=361;set=variant4-variant10-filterInvariant13-variant17-variant20-variant28-variant32-filterInvariant35-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:13,5:18:76:76,0,278:3,10,2,3 chr2 120997869 . A T 175.94 PASS AC=1;AF=0.556;AN=2;DP=1178;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,12:18:99:239,0,116:3,3,2,10 chr2 121010443 . A T 2301.4 PASS AC=2;AF=0.89;AN=2;DP=3034;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:2100,215,0:0,0,37,35 chr2 121036385 . T G 728.03 PASS AC=2;AF=0.878;AN=2;DP=1708;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:2500,169,0:0,0,20,36 chr2 121036386 . T A 728.03 PASS AC=2;AF=0.878;AN=2;DP=1673;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:2500,169,0:0,0,20,35 chr2 121038290 . GA G 692.39 PASS AC=2;AF=0.85;AN=2;DP=1017;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:445,51,0:0,0,11,6 chr2 121043403 . G A 932.48 PASS AC=2;AF=0.89;AN=2;DP=931;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:525,36,0:0,0,12,0 chr2 121050989 . T A 4768.32 PASS AC=2;AF=0.89;AN=2;DP=5195;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,113:113:99:3748,339,0:0,0,66,47 chr2 121052268 . A T 915.9 PASS AC=2;AF=0.9;AN=2;DP=830;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:857,69,0:0,0,3,20 chr2 121103903 . T G 426.39 PASS AC=1;AF=0.5;AN=2;DP=491;MQ=60;set=variant5-variant10-variant14-variant23-variant26-variant31-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:32,20:52:99:501,0,863:19,13,14,6 chr2 121223274 . C T 2468.18 PASS AC=1;AF=0.5;AN=2;DP=929;FractionInformativeReads=1;MQ=60;set=variant14-variant16-variant31-variant35-variant41 GT:AD:DP:GQ:PL:SB 0/1:89,93:182:99:2310,0,2284:47,42,56,37 chr2 121549800 . A C 151.77 PASS AC=2;AF=1;AN=2;DP=212;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:274,21,0:0,0,4,3 chr2 121684663 . C G 1370.12 PASS AC=2;AF=0.953;AN=2;DP=1743;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:1713,171,0:0,0,34,23 chr2 121708663 . A G 1570.95 PASS AC=2;AF=0.898;AN=2;DP=1847;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:2244,168,0:0,0,52,4 chr2 121712727 . GC G 379.77 PASS AC=1;AF=0.611;AN=2;DP=140;set=variant2-variant5-variant18-filterInvariant23-variant28-variant34-variant35-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:2,14:16:17:382,0,17:0,2,13,1 chr2 121712757 . TG T 125.7 PASS AC=1;AF=0.5;AN=2;DP=30;FS=2.542;FractionInformativeReads=1;MQ=59.75;MQRankSum=0.389;QD=4.19;ReadPosRankSum=1.789;SOR=1.329;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:24,6:30:99:163,0,727:20,4,6,0 chr2 121713022 . C G 2520.55 PASS AC=2;AF=1;AN=2;DP=2861;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:3463,238,0:0,0,17,62 chr2 121713030 . G A 2385.95 PASS AC=2;AF=0.898;AN=2;DP=2385;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,73:73:99:3271,220,0:0,0,14,59 chr2 121713041 . T C 1605.81 PASS AC=2;AF=0.898;AN=2;DP=1878;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:2284,174,0:0,0,7,51 chr2 121726447 . G A 6330.34 PASS AC=2;AF=0.932;AN=2;DP=14278;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,385:385:99:10909,1145,0:0,0,166,219 chr2 121729323 . A G 966.63 PASS AC=2;AF=0.886;AN=2;DP=1222;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:1134,96,0:0,0,23,9 chr2 121729360 . T C 1356.63 PASS AC=2;AF=0.943;AN=2;DP=2305;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:1714,171,0:0,0,35,22 chr2 121729490 . C T 4378.78 PASS AC=2;AF=0.943;AN=2;DP=8641;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,193:193:99:5600,575,0:0,0,102,91 chr2 121729686 . T C 1174.85 PASS AC=2;AF=0.943;AN=2;DP=1770;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,52:52:99:1696,156,0:0,0,17,35 chr2 121730138 . C G 2176.28 PASS AC=2;AF=0.943;AN=2;DP=2805;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,87:87:99:2883,261,0:0,0,62,25 chr2 121740190 . C T 976.17 PASS AC=2;AF=1;AN=2;DP=1258;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1580,108,0:0,0,29,6 chr2 121740194 . T G 976.17 PASS AC=2;AF=1;AN=2;DP=1353;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1605,111,0:0,0,29,8 chr2 121740505 . C T 507.89 PASS AC=2;AF=0.898;AN=2;DP=3243;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,82:83:99:2381,238,0:0,1,32,50 chr2 121744225 . A G 395.28 PASS AC=2;AF=0.789;AN=2;DP=2295;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:1773,170,0:0,0,24,33 chr2 121746956 . G T 1305.04 PASS AC=2;AF=0.782;AN=2;DP=7926;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,192:192:99:5816,573,0:0,0,82,110 chr2 121747406 . G A 1715.75 PASS AC=2;AF=0.808;AN=2;DP=6464;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,174:174:99:5851,522,0:0,0,80,94 chr2 121747429 . A G 1659.54 PASS AC=2;AF=0.782;AN=2;DP=5869;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,172:172:99:5520,515,0:0,0,80,92 chr2 121749067 . G C 854.1 PASS AC=2;AF=0.782;AN=2;DP=2685;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,84:84:99:2752,252,0:0,0,35,49 chr2 121749583 . TACACACACACACACACACAC T,TACACACACACACACACACACACAC,TACACACACACACACACAC,TACACACACACACACACACACACACAC,TACACACACACACACACACACAC,TACACACACACACAC,TACACACACACACACACACACACACACAC,TACACACACAC 283.97 PASS AC=0,1,0,1,0,0,0,0;AF=0.013,0.256,0.051,0.256,0.103,0.013,0.026,0.013;AN=2;DP=1053;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 2/4:15:99:0,0,13,2 chr2 121976519 . G A 607.38 PASS AC=1;AF=0.645;AN=2;DP=3125;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant21-variant24-variant25-variant27-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:51,47:98:99:1111,0,1329:30,21,28,19 chr2 121976642 . G A 1158.49 PASS AC=1;AF=0.667;AN=2;DP=4402;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:70,76:146:99:1741,0,1713:36,34,37,39 chr2 121976715 . T C 1443.46 PASS AC=2;AF=0.977;AN=2;DP=4185;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,95:95:99:2992,284,0:0,0,43,52 chr2 121977438 . G A 67.66 PASS AC=1;AF=0.5;AN=2;DP=355;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant10-variant11-variant12-variant15-variant16-variant17-variant21-variant25-variant27-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,5:10:99:111,0,143:1,4,3,2 chr2 121977629 . T C 499.46 PASS AC=1;AF=0.5;AN=2;DP=33;FS=7.702;FractionInformativeReads=1;MQ=60;MQRankSum=0.633;QD=15.14;ReadPosRankSum=-0.163;SOR=1.371;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:15,18:33:99:528,0,496:6,9,12,6 chr2 121978976 . TA T 92.83 PASS AC=2;AF=0.875;AN=2;DP=1009;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:471,54,0:0,0,11,7 chr2 121979217 . G C 3673.47 PASS AC=2;AF=0.866;AN=2;DP=8068;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,180:180:99:8137,551,0:0,0,104,76 chr2 121979220 . T TACA 3703.38 PASS AC=2;AF=0.866;AN=2;DP=8065;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,183:183:99:8294,563,0:0,0,107,76 chr2 121979534 . TA T 1414.89 PASS AC=2;AF=0.854;AN=2;DP=5166;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,112:112:99:3132,336,0:0,0,49,63 chr2 121980405 . TC T 438.54 PASS AC=2;AF=0.854;AN=2;DP=2264;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:2021,163,0:0,0,25,29 chr2 121980465 . C T 537.89 PASS AC=2;AF=0.854;AN=2;DP=2283;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1721,159,0:0,0,23,30 chr2 121980857 . ATAGT A 316.68 PASS AC=1;AF=0.691;AN=2;DP=1333;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,17:39:99:640,0,1292:11,11,6,11 chr2 121981210 . G A 514.63 PASS AC=1;AF=0.521;AN=2;DP=857;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant10-variant11-variant12-variant15-variant16-variant17-variant21-variant25-variant27-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:29,16:45:99:413,0,880:18,11,5,11 chr2 121981608 . A G 858.16 PASS AC=1;AF=0.521;AN=2;DP=2040;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant10-variant11-variant12-variant15-variant16-variant17-variant21-variant25-variant27-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:34,47:81:99:1322,0,804:14,20,21,26 chr2 121981950 . A G 1084.24 PASS AC=1;AF=0.521;AN=2;DP=2380;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant10-variant11-variant12-variant15-variant16-variant17-variant21-variant25-variant27-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:67,52:119:99:1331,0,1648:37,30,25,27 chr2 121982011 . T A 691.27 PASS AC=1;AF=0.697;AN=2;DP=3181;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,67:113:99:1702,0,991:24,22,36,31 chr2 121989489 . G A 629.34 PASS AC=1;AF=0.697;AN=2;DP=4114;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,68:132:99:1533,0,1464:33,31,32,36 chr2 122004596 . C G 642.87 PASS AC=1;AF=0.7;AN=2;DP=1780;MQ=60;set=variant-variant2-variant3-variant8-variant10-variant11-variant12-variant13-variant16-variant17-variant21-variant25-variant27-variant29-variant31-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:28,41:69:99:1176,0,712:8,20,11,30 chr2 122005928 . C T 1655.42 PASS AC=1;AF=0.538;AN=2;DP=1668;MQ=60;set=variant10-variant11-variant12-variant16-variant17-variant21-variant27-variant31-variant33-variant35-variant37-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:57,52:109:99:1328,0,1402:25,32,17,35 chr2 122006851 . A C 731.01 PASS AC=1;AF=0.531;AN=2;DP=1088;MQ=60;set=variant9-variant10-variant11-variant12-variant16-variant17-variant21-variant23-variant27-variant31-variant33-variant35-variant37-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:40,31:71:99:741,0,1005:16,24,12,19 chr2 122007378 . A C 527.38 PASS AC=1;AF=0.708;AN=2;DP=1219;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,22:44:99:557,0,545:6,16,7,15 chr2 122042750 . A T 5085.39 PASS AC=1;AF=0.647;AN=2;DP=6337;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:111,91:202:99:2168,0,2542:45,66,37,54 chr2 122095400 . T TTTG 5227.45 PASS AC=1;AF=0.529;AN=2;DP=4334;set=variant6-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant23-variant25-variant32-variant33-variant35-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:138,135:273:99:5057,0,5919:65,73,58,77 chr2 122095519 . GCC GC,G 1667.15 PASS AC=1,1;AF=0.795,0.159;AN=2;DP=3348;MQ=60;set=Intersection GT:DP:GQ:SB 2/1:61:99:2,2,21,36 chr2 122095640 . C T 181.94 PASS AC=1;AF=0.5;AN=2;DP=389;FractionInformativeReads=1;MQ=60;set=variant10-variant11-variant12-variant15-variant17-variant18-variant23-variant25-variant35-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:22,12:34:99:265,0,555:10,12,5,7 chr2 122096707 . CCACACA CCACA,CCACACACACACACA,CCACACACA,C,CCACACACACACACACACACA,CCA,CCACACACACA 117.32 PASS AC=0,0,1,0,0,0,1;AF=0.175,0.05,0.175,0.05,0.05,0.025,0.075;AN=2;DP=356;set=variant4-variant9-variant11-variant12-variant14-variant17-variant19-variant21-variant22-variant26-variant29-variant31-variant32-variant33-variant35-variant36-variant40-variant41-variant43-variant44 GT:DP:GQ:SB 3/7:14:95:0,1,3,10 chr2 122122969 . G A 403.31 PASS AC=1;AF=0.5;AN=2;DP=151;MQ=60;set=variant11-variant12-variant13-variant15-variant18-variant25-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,8:14:99:256,0,139:2,4,2,6 chr2 122125104 . C T 1591.58 PASS AC=1;AF=0.5;AN=2;DP=628;MQ=60;set=variant11-variant12-variant15-variant18-variant25-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:42,41:83:99:1150,0,1247:30,12,31,10 chr2 122145157 . G A 178.64 PASS AC=1;AF=0.5;AN=2;DP=71;FractionInformativeReads=1;MQ=60;set=variant12-variant15-variant18-variant25-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,3:9:64:64,0,230:6,0,2,1 chr2 122161850 . C T 621.39 PASS AC=1;AF=0.5;AN=2;DP=451;FractionInformativeReads=1;MQ=60;set=variant11-variant12-variant13-variant15-variant18-variant25-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:43,25:68:99:609,0,1167:29,14,18,7 chr2 122187367 . C T 527.2 PASS AC=1;AF=0.538;AN=2;DP=226;FractionInformativeReads=1;MQ=60;set=variant6-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant25-variant32-variant33-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:7,6:13:99:179,0,235:6,1,4,2 chr2 122205778 . G A 935.12 PASS AC=1;AF=0.5;AN=2;DP=673;MQ=60;set=variant11-variant12-variant13-variant15-variant18-variant25-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:46,39:85:99:976,0,1292:32,14,24,15 chr2 122208886 . G A 44.97 PASS AC=1;AF=0.571;AN=2;DP=39;FS=0;FractionInformativeReads=1;MQ=60;set=variant11-variant12-variant15-variant18-variant25-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:79:79,0,108:0,3,1,2 chr2 122216419 . A G 1119.69 PASS AC=1;AF=0.5;AN=2;DP=713;FractionInformativeReads=1;MQ=60;set=variant11-variant12-variant13-variant15-variant18-variant25-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:40,51:91:99:1250,0,951:26,14,31,20 chr2 122227869 . CTTTTTTTTTTTT CT,C,CTTTTT,CTTTTTTTTTTTTTT 122.5 PASS AC=1,0,0,0;AF=0.188,0.188,0.063,0.188;AN=2;DP=100;MQ=60;set=variant11-variant13-variant19-variant20-variant22-variant25-variant35-variant43 GT:DP:GQ:SB 0/1:5:99:1,1,0,3 chr2 122273187 . C G 736.33 PASS AC=1;AF=0.536;AN=2;DP=351;MQ=60;set=variant6-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant25-variant32-variant33-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,18:30:99:661,0,455:12,0,18,0 chr2 122283313 . G T 440.1 PASS AC=1;AF=0.536;AN=2;DP=860;FractionInformativeReads=1;MQ=60;set=variant6-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant25-variant32-variant33-variant35-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:34,32:66:99:727,0,920:23,11,19,13 chr2 122286442 . A G 280.11 PASS AC=1;AF=0.5;AN=2;DP=324;FractionInformativeReads=1;MQ=60;set=variant11-variant12-variant13-variant15-variant18-variant25-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:19,14:33:99:344,0,540:5,14,5,9 chr2 122407039 . TA T,TAA 36.04 PASS AC=0,1;AF=0.25,0.25;AN=2;DP=22;MQ=60;SOR=1.609;set=variant24-variant35 GT:DP:GQ:SB 0/2:9:10:1,1,5,2 chr2 124782826 . C T 573.37 PASS AC=1;AF=0.5;AN=2;DP=564;MQ=60;set=variant6-variant7-variant11-variant12-variant15-variant18-variant19-variant20-variant21-variant22-variant29-variant31-variant32-variant35-variant36-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,20:35:99:554,0,470:13,2,14,6 chr2 124782932 . T C 1342.16 PASS AC=1;AF=0.5;AN=2;DP=2143;MQ=60;set=variant6-variant7-variant11-variant12-variant15-variant18-variant19-variant20-variant21-variant22-variant29-variant31-variant32-variant35-variant36-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,63:116:99:1547,0,1212:30,23,32,31 chr2 125192068 . T C 1123.38 PASS AC=2;AF=0.932;AN=2;DP=5498;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,118:118:99:3828,354,0:0,0,64,54 chr2 125204192 . A G 624.5 PASS AC=2;AF=0.567;AN=2;DP=601;FractionInformativeReads=1;MQ=60;set=variant7-variant16-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant34-variant35-variant37-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:911,84,0:0,0,21,7 chr2 125204769 . AT A 128.16 PASS AC=2;AF=0.563;AN=2;DP=564;MQ=60;set=variant-variant3-variant4-variant7-variant10-variant14-variant16-variant17-variant19-variant20-filterInvariant21-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant35-variant37-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:508,54,0:0,0,4,14 chr2 125232609 . G T 801.34 PASS AC=2;AF=0.875;AN=2;DP=3455;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,87:88:99:2743,222,0:1,0,26,61 chr2 125405302 . C T 1123.53 PASS AC=1;AF=0.686;AN=2;DP=5215;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:82,74:156:99:1778,0,2005:50,32,43,31 chr2 125669260 . A G 548.54 PASS AC=1;AF=0.682;AN=2;DP=536;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant24-variant26-variant27-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,11:15:82:393,0,82:1,3,1,10 chr2 125672772 . TAC T 630.52 PASS AC=1;AF=0.5;AN=2;DP=96;MQ=60;set=variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:17,23:40:99:668,0,475:11,6,15,8 chr2 127413616 . G A 667.41 PASS AC=1;AF=0.692;AN=2;DP=1683;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant27-filterInvariant28-variant29-variant30-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,21:26:54:481,0,54:3,2,15,6 chr2 127656664 . A G 2113.09 PASS AC=1;AF=0.5;AN=2;DP=1033;MQ=60;set=variant9-variant10-variant20-variant22-variant29-variant33-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:78,73:151:99:1967,0,2095:42,36,38,35 chr2 127656857 . G A 2185.62 PASS AC=1;AF=0.5;AN=2;DP=1629;MQ=60;set=variant2-variant9-variant10-variant20-variant22-variant29-variant33-variant34-variant35-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:110,102:212:99:3871,0,5784:47,63,45,57 chr2 127656861 . C T 2772.36 PASS AC=1;AF=0.5;AN=2;DP=1178;FractionInformativeReads=1;MQ=60;set=variant9-variant10-variant20-variant22-variant29-variant33-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:109,98:207:99:3817,0,5768:46,63,41,57 chr2 127657044 . C T 1007.39 PASS AC=1;AF=0.5;AN=2;DP=482;MQ=60;set=variant9-variant10-variant20-variant22-variant29-variant33-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:45,32:77:99:799,0,1254:29,16,19,13 chr2 127657208 . C T 518.92 PASS AC=1;AF=0.5;AN=2;DP=370;MQ=60;set=variant2-variant9-variant10-variant13-variant20-variant22-variant29-variant33-variant34-variant35-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:17,19:36:99:558,0,607:5,12,10,9 chr2 127657221 . C T 1009.57 PASS AC=1;AF=0.814;AN=2;DP=1351;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,16:35:99:560,0,581:11,8,6,10 chr2 127659409 . G A 1091.83 PASS AC=1;AF=0.5;AN=2;DP=617;FractionInformativeReads=1;MQ=60;set=variant9-variant10-variant20-variant22-variant29-variant33-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:21,39:60:99:1032,0,506:14,7,24,15 chr2 127659531 . G A 1703.74 PASS AC=1;AF=0.5;AN=2;DP=1151;MQ=60;set=variant9-variant10-variant20-variant22-variant29-variant33-variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:73,63:136:99:1428,0,1680:41,32,34,29 chr2 127808226 . A T 1095.09 PASS AC=2;AF=0.635;AN=2;DP=2343;MQ=60;set=variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,112:112:99:3755,336,0:0,0,37,75 chr2 127808532 . G A 1514.64 PASS AC=2;AF=0.652;AN=2;DP=1982;MQ=60;set=variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant31-variant32-variant33-variant34-variant35-variant38-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:2319,225,0:0,0,30,45 chr2 127808909 . G A 2564.79 PASS AC=2;AF=0.635;AN=2;DP=3725;MQ=60;set=variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,161:161:99:4562,481,0:0,0,74,87 chr2 127811712 . G GCA 466.36 PASS AC=2;AF=0.64;AN=2;DP=774;MQ=60;set=variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant31-variant32-variant33-variant35-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:1350,90,0:0,0,13,17 chr2 127814835 . T C 222.69 PASS AC=2;AF=0.656;AN=2;DP=136;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant7-variant9-variant13-variant22-variant23-variant24-variant25-variant26-variant31-variant32-variant33-variant35-variant38-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:258,21,0:0,0,6,1 chr2 127816632 . G A 1542.1 PASS AC=1;AF=0.588;AN=2;DP=2093;MQ=60;set=variant3-variant4-variant7-variant9-variant13-variant22-variant23-variant24-variant25-variant26-variant28-variant31-variant32-variant33-variant35-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:60,80:140:99:2059,0,1444:38,22,49,31 chr2 127816846 . CTGTG CTG,CTGTGTG,C 262.77 PASS AC=2,0,0;AF=0.672,0.016,0.016;AN=2;DP=950;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant35-variant36-variant38-variant39-variant41-variant43-variant44 GT:DP:GQ:SB 1/1:22:66:0,0,4,18 chr2 127821085 . C T 339.63 PASS AC=1;AF=0.625;AN=2;DP=935;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant31-variant32-variant33-variant35-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,19:49:99:471,0,789:19,11,13,6 chr2 127821452 . C T 1763.88 PASS AC=1;AF=0.563;AN=2;DP=2630;set=variant4-variant7-variant9-variant13-variant22-variant23-variant24-variant25-variant26-variant28-variant31-variant32-variant33-variant35-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:118,86:204:99:2200,0,3254:69,49,51,35 chr2 127821499 . T C 3460.29 PASS AC=1;AF=0.625;AN=2;DP=6272;set=variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant31-variant32-variant33-variant35-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:163,138:301:99:3237,0,4187:90,73,73,65 chr2 127826533 . A G 851.04 PASS AC=1;AF=0.604;AN=2;DP=2412;MQ=60;set=variant-variant4-variant7-variant9-variant13-variant15-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant28-variant31-variant32-variant33-variant35-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:66,53:119:99:1324,0,1719:30,36,26,27 chr2 127826632 . A G 571.04 PASS AC=1;AF=0.559;AN=2;DP=797;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant6-variant8-variant9-variant10-variant12-variant13-variant15-variant19-variant20-variant21-variant31-variant35-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,30:56:99:801,0,681:9,17,10,20 chr2 127839474 . G A 1974.51 PASS AC=1;AF=0.654;AN=2;DP=2823;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant12-variant13-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant28-variant31-variant33-variant34-variant35-variant36-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,52:103:99:1272,0,1301:23,28,21,31 chr2 127839534 . T C 693.24 PASS AC=1;AF=0.577;AN=2;DP=612;MQ=60;set=variant4-variant7-variant9-variant13-variant19-variant22-variant23-variant24-variant28-variant31-variant33-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:27,28:55:99:903,0,801:6,21,8,20 chr2 127864546 . G A 6605.91 PASS AC=1;AF=0.577;AN=2;DP=5742;MQ=60;set=variant4-variant9-variant13-variant19-variant22-variant23-variant24-variant28-variant31-variant33-variant35-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:253,303:556:99:6570,0,5250:126,127,150,153 chr2 127941798 . T C 4502.86 PASS AC=1;AF=0.688;AN=2;DP=8738;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:125,131:256:99:3294,0,2836:59,66,57,74 chr2 127942231 . G A 380.65 PASS AC=1;AF=0.607;AN=2;DP=705;FractionInformativeReads=1;set=variant-variant3-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant26-variant27-variant30-variant31-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:16,17:33:99:413,0,412:11,5,12,5 chr2 127942334 . C T 907.59 PASS AC=1;AF=0.688;AN=2;DP=1719;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:37,33:70:99:904,0,897:20,17,14,19 chr2 127944781 . A AC 2858.62 PASS AC=1;AF=0.738;AN=2;DP=3507;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:46,41:87:99:1391,0,1599:21,25,23,18 chr2 127950904 . A T 284.84 PASS AC=1;AF=0.611;AN=2;DP=1130;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant26-variant27-variant30-variant31-variant35-variant36-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:19,21:40:99:648,0,612:4,15,3,18 chr2 127951458 . G A 735.07 PASS AC=1;AF=0.611;AN=2;DP=2077;MQ=60;set=variant-variant3-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant26-variant27-variant30-variant31-variant35-variant36-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:44,39:83:99:1428,0,2291:22,22,20,19 chr2 127951459 . C T 735.07 PASS AC=1;AF=0.611;AN=2;DP=2057;MQ=60;set=variant-variant3-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant26-variant27-variant30-variant31-variant35-variant36-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:44,38:82:99:1428,0,2291:22,22,19,19 chr2 127963423 . TC T 111.13 PASS AC=1;AF=0.643;AN=2;DP=504;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant16-variant18-variant19-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant35-variant36-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,12:18:99:338,0,157:3,3,2,10 chr2 127977550 . G C,A 3539.37 PASS AC=1,0;AF=0.629,0.016;AN=2;DP=3841;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43 GT:DP:GQ:SB 0/1:136:99:45,30,33,28 chr2 128015367 . C T 557.97 PASS AC=2;AF=0.866;AN=2;DP=815;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-filterInvariant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:586,54,0:0,0,5,13 chr2 128028792 . T C 1841.95 PASS AC=2;AF=0.857;AN=2;DP=2959;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,74:74:99:2411,222,0:0,0,48,26 chr2 128029065 . GA G 481.39 PASS AC=1;AF=0.536;AN=2;DP=1035;MQ=60;set=variant2-variant3-filterInvariant5-variant7-variant8-variant9-variant11-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant25-variant27-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,20:32:99:462,0,241:4,8,6,14 chr2 128050134 . T C 1436.56 PASS AC=2;AF=0.857;AN=2;DP=2382;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:2374,227,0:0,0,51,25 chr2 128056520 . AT A 2329.04 PASS AC=1;AF=0.596;AN=2;DP=2190;MQ=60;set=variant-variant3-variant5-variant7-variant9-variant12-variant14-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant26-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:39,38:77:99:905,0,882:13,26,17,21 chr2 128057560 . C CAG 10013.1 PASS AC=2;AF=0.932;AN=2;DP=9486;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,212:212:99:9425,637,0:0,0,104,108 chr2 128060017 . CCA C 1937.9 PASS AC=2;AF=0.775;AN=2;DP=2449;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,55:57:99:1742,151,0:2,0,38,17 chr2 128060068 . C A 5332.11 PASS AC=1;AF=0.6;AN=2;DP=3348;MQ=60;set=variant-variant3-variant5-variant7-variant9-variant12-variant14-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant26-variant29-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:63,70:133:99:1993,0,2023:47,16,48,22 chr2 128060163 . C T 14319.3 PASS AC=1;AF=0.6;AN=2;DP=10331;set=variant-variant3-variant5-variant7-variant9-variant12-variant14-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant26-variant29-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:192,186:378:99:4512,0,4879:117,75,100,86 chr2 128061053 . A G 3699.62 PASS AC=1;AF=0.629;AN=2;DP=3274;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:71,45:116:99:1196,0,1847:43,28,30,15 chr2 128061283 . GAACA G 3063.36 PASS AC=1;AF=0.523;AN=2;DP=4291;MQ=60;set=variant2-variant3-variant6-variant7-variant8-variant9-variant11-variant13-variant15-variant18-variant20-variant21-variant25-variant27-variant28-variant29-variant33-variant34-variant35-variant36-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,100:164:99:3976,0,3342:28,36,46,54 chr2 128062048 . T C 5176.68 PASS AC=1;AF=0.704;AN=2;DP=4019;MQ=60;set=variant-variant3-variant5-variant7-variant9-variant12-variant14-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant26-variant28-variant29-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:77,80:157:99:1888,0,2082:40,37,40,40 chr2 128062224 . T TA 3025.76 PASS AC=1;AF=0.5;AN=2;DP=1407;MQ=60;set=variant-variant9-variant14-variant22-variant35-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:104,102:206:99:2610,0,2661:52,52,57,45 chr2 128063506 . CTT C,CT 2140.69 PASS AC=1,1;AF=0.25,0.5;AN=2;DP=7424;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-filterInvariant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-filterInvariant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/2:153:99:24,4,63,62 chr2 128063846 . C T 1192.68 PASS AC=1;AF=0.523;AN=2;DP=2206;MQ=60;set=variant2-variant3-variant6-variant7-variant8-variant9-variant11-variant13-variant15-variant18-variant20-variant21-variant25-variant27-variant28-variant29-variant33-variant34-variant35-variant36-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,58:115:99:1873,0,1596:16,41,16,42 chr2 128063945 . T C 1998.93 PASS AC=2;AF=0.869;AN=2;DP=2134;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:1575,144,0:0,0,28,20 chr2 128064423 . CGTGTGT C,CGT,CGTGT,CGTGTGTGTGTGT 7846.14 PASS AC=0,1,1,0;AF=0.239,0.284,0.307,0.011;AN=2;DP=9545;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-filterInvariant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 2/3:187:99:1,1,93,92 chr2 128076022 . T C 227.92 PASS AC=1;AF=0.625;AN=2;DP=205;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant7-variant9-variant12-variant14-variant16-variant18-variant19-variant22-variant23-variant24-variant29-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:1,9:10:12:253,0,12:0,1,3,6 chr2 128081682 . C A 874.71 PASS AC=1;AF=0.604;AN=2;DP=571;MQ=60;set=variant-variant3-variant5-variant7-variant9-variant12-variant14-variant16-variant18-variant19-variant22-variant23-variant24-variant26-variant29-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:15,13:28:99:315,0,368:9,6,7,6 chr2 128175862 . C T 2839.68 PASS AC=1;AF=0.563;AN=2;DP=2332;MQ=60;set=variant-variant3-variant5-variant7-variant9-variant12-variant14-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant26-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:45,63:108:99:1767,0,1315:33,12,43,20 chr2 128175875 . G A 3391.4 PASS AC=2;AF=0.705;AN=2;DP=4374;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,124:124:99:4126,371,0:0,0,87,37 chr2 128176195 . G A 261.53 PASS AC=2;AF=1;AN=2;DP=761;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:653,48,0:0,0,1,15 chr2 128177377 . C T 4533.43 PASS AC=2;AF=0.718;AN=2;DP=8138;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,180:182:99:5449,494,0:1,1,99,81 chr2 128180872 . G T 3825.58 PASS AC=1;AF=0.681;AN=2;DP=4030;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,67:125:99:1837,0,1518:33,25,43,24 chr2 128181028 . A G 5081.22 PASS AC=2;AF=1;AN=2;DP=7875;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,250:250:99:7834,750,0:0,0,134,116 chr2 128181234 . GC G 2537.49 PASS AC=1;AF=0.681;AN=2;DP=2747;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,50:110:99:1302,0,1622:28,32,19,31 chr2 128183914 . G T 363.79 PASS AC=1;AF=0.575;AN=2;DP=405;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant6-variant7-variant8-variant9-variant11-variant13-variant15-variant17-variant18-variant21-variant28-variant29-variant33-variant34-variant35-variant36-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,8:25:99:268,0,603:2,15,3,5 chr2 128249441 . C T 106.65 PASS AC=2;AF=0.932;AN=2;DP=565;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:488,39,0:0,0,11,2 chr2 128271958 . C T 1065.9 PASS AC=1;AF=0.645;AN=2;DP=3625;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant26-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:84,81:165:99:2060,0,2044:37,47,36,45 chr2 128281469 . C T 304.32 PASS AC=2;AF=0.718;AN=2;DP=1062;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:880,69,0:0,0,3,20 chr2 128321770 . G A 611.71 PASS AC=1;AF=0.632;AN=2;DP=2737;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,52:107:99:1076,0,1304:28,27,25,27 chr2 128338519 . T G 363.87 PASS AC=1;AF=0.581;AN=2;DP=1451;MQ=60;set=variant-variant3-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant35-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:30,34:64:99:932,0,842:11,19,13,21 chr2 128339456 . G T 99.15 PASS AC=1;AF=0.581;AN=2;DP=1853;MQ=60;set=variant-variant3-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant35-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:46,29:75:99:684,0,1138:28,18,20,9 chr2 128339758 . C G 808.37 PASS AC=1;AF=0.647;AN=2;DP=1017;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,16:35:99:464,0,513:8,11,5,11 chr2 128342547 . G A 424.5 PASS AC=2;AF=0.92;AN=2;DP=2916;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:1894,177,0:0,0,18,41 chr2 128345960 . T C 944.78 PASS AC=1;AF=0.578;AN=2;DP=2723;MQ=60;set=variant-variant3-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:35,44:79:99:1257,0,827:21,14,27,17 chr2 128346228 . A C 177.19 PASS AC=2;AF=0.92;AN=2;DP=888;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1256,99,0:0,0,3,30 chr2 128350551 . G A 4438.84 PASS AC=1;AF=0.647;AN=2;DP=6359;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:109,101:210:99:2582,0,2928:34,75,32,69 chr2 128350578 . T TG 2037.52 PASS AC=2;AF=0.989;AN=2;DP=4954;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,126:126:99:4459,379,0:0,0,26,100 chr2 128351346 . T C 72.46 PASS AC=1;AF=0.671;AN=2;DP=714;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,5:22:99:115,0,609:4,13,2,3 chr2 128363530 . G GC 1662.15 PASS AC=2;AF=1;AN=2;DP=1850;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1559,132,0:0,0,5,39 chr2 128364684 . G A 1473.82 PASS AC=1;AF=0.595;AN=2;DP=1025;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant14-variant17-variant18-variant21-variant25-variant28-variant29-variant33-variant34-variant35-variant36-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,21:60:99:468,0,1012:22,17,13,8 chr2 128367092 . G A 913.52 PASS AC=1;AF=0.645;AN=2;DP=4114;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant14-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:79,78:157:99:1743,0,1938:48,31,43,35 chr2 128369752 . A G 1263.07 PASS AC=1;AF=0.595;AN=2;DP=1078;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant14-variant17-variant18-variant21-variant25-variant28-variant29-variant33-variant34-variant35-variant36-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,21:43:99:523,0,462:12,10,12,9 chr2 128369896 . A G 576.67 PASS AC=1;AF=0.713;AN=2;DP=4281;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,55:99:99:2131,0,2228:23,21,34,21 chr2 128369917 . C T 3827.69 PASS AC=1;AF=0.595;AN=2;DP=2505;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant14-variant17-variant18-variant21-variant25-variant28-variant29-variant33-variant34-variant35-variant36-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,63:112:99:2303,0,2299:28,21,38,25 chr2 128370200 . G A 622.98 PASS AC=1;AF=0.595;AN=2;DP=601;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant14-variant17-variant18-variant21-variant25-variant28-variant29-variant33-variant34-variant35-variant36-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,16:29:99:392,0,298:5,8,5,11 chr2 128377833 . C G 1114.23 PASS AC=1;AF=0.713;AN=2;DP=3979;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:66,55:121:99:1508,0,1796:33,33,27,28 chr2 128378136 . A C 527.25 PASS AC=1;AF=0.613;AN=2;DP=784;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant14-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-filterInvariant33-variant34-variant35-variant36-variant37-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,12:40:99:291,0,770:12,16,5,7 chr2 128382859 . C T 157.25 PASS AC=1;AF=0.7;AN=2;DP=727;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,16:33:99:432,0,538:14,3,13,3 chr2 128385224 . C G 1665.37 PASS AC=1;AF=0.578;AN=2;DP=4648;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,83:151:99:2174,0,1887:35,33,45,38 chr2 128388790 . G A 3808.03 PASS AC=1;AF=0.571;AN=2;DP=2948;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant14-variant17-variant18-variant21-variant25-variant28-variant29-variant33-variant34-variant35-variant36-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,63:130:99:1528,0,1696:32,35,33,30 chr2 128388862 . G C 4183.21 PASS AC=1;AF=0.571;AN=2;DP=3011;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant14-variant17-variant18-variant21-variant25-variant28-variant29-variant33-variant34-variant35-variant36-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:74,79:153:99:1945,0,1841:38,36,41,38 chr2 128389343 . C T 3082.48 PASS AC=1;AF=0.621;AN=2;DP=3322;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,45:105:99:1166,0,1645:16,44,15,30 chr2 128389422 . G C 887.42 PASS AC=1;AF=0.621;AN=2;DP=931;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,21:26:99:631,0,108:1,4,6,15 chr2 128393261 . T C 1452.43 PASS AC=1;AF=0.737;AN=2;DP=1964;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,27:52:99:705,0,706:17,8,18,9 chr2 128393289 . T C 1977.48 PASS AC=1;AF=0.655;AN=2;DP=1965;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant17-variant18-variant20-variant21-variant23-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,38:70:99:1115,0,799:22,10,27,11 chr2 128393800 . T C 4286.45 PASS AC=1;AF=0.565;AN=2;DP=3720;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant14-variant17-variant18-variant20-variant21-variant25-variant28-variant29-variant33-variant34-variant35-variant36-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:87,114:201:99:2784,0,2002:48,39,61,53 chr2 128394758 . T C 3138.9 PASS AC=1;AF=0.662;AN=2;DP=3821;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,61:121:99:1733,0,1714:32,28,31,30 chr2 128394875 . C CA 7170.79 PASS AC=1;AF=0.655;AN=2;DP=5367;set=variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant17-variant18-variant20-variant21-variant23-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:97,71:168:99:2703,0,4487:48,49,34,37 chr2 128394877 . C CT,T 7926.36 PASS AC=0,1;AF=0.237,0.5;AN=2;DP=7260;MQ=60;set=variant5-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant3-variant4-variant33-variant2-variant13-variant34-variant35-variant6-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:170:99:48,48,37,37 chr2 128394955 . A G 6150.01 PASS AC=1;AF=0.568;AN=2;DP=4840;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant14-variant17-variant18-variant20-variant21-variant25-variant28-variant29-variant33-variant34-variant35-variant36-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:117,104:221:99:2592,0,2790:52,65,54,50 chr2 128396037 . CAACA CAACAAACA,C,CAACAAACAAACA 4777.35 PASS AC=1,0,0;AF=0.483,0.133,0.017;AN=2;DP=2630;set=variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant39-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:97:99:29,24,24,20 chr2 128396807 . A G 1482.56 PASS AC=1;AF=0.714;AN=2;DP=1634;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,32:59:99:814,0,733:20,7,18,14 chr2 128400608 . C T 2745.76 PASS AC=1;AF=0.621;AN=2;DP=3477;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant22-variant23-variant24-variant27-variant28-variant30-variant31-variant33-variant35-variant36-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:79,54:133:99:1232,0,2042:34,45,28,26 chr2 128400783 . G A 1371.51 PASS AC=1;AF=0.708;AN=2;DP=1780;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant14-variant15-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,27:58:99:742,0,775:14,17,11,16 chr2 128401091 . A G 2519.28 PASS AC=1;AF=0.731;AN=2;DP=2962;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,20:81:99:343,0,1491:29,32,9,11 chr2 128401912 . G A 287.99 PASS AC=1;AF=0.635;AN=2;DP=275;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant14-variant15-variant17-variant18-variant20-variant21-variant25-variant26-variant28-variant29-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,10:14:99:318,0,99:2,2,5,5 chr2 128405721 . T C 1279.99 PASS AC=1;AF=0.603;AN=2;DP=1889;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,22:52:99:579,0,780:18,12,10,12 chr2 128407499 . G A 1458.29 PASS AC=1;AF=0.727;AN=2;DP=1640;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,21:47:99:498,0,691:18,8,14,7 chr2 128407771 . C T 241.45 PASS AC=1;AF=0.568;AN=2;DP=322;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant15-variant17-variant18-variant21-variant25-variant26-variant28-variant29-variant30-variant33-variant34-variant35-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,3:8:70:70,0,175:1,4,1,2 chr2 128408121 . G GC 2585.67 PASS AC=2;AF=1;AN=2;DP=2766;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,84:84:99:3360,253,0:0,0,49,35 chr2 128409419 . A G 668.09 PASS AC=1;AF=0.559;AN=2;DP=1229;FractionInformativeReads=1;MQ=60;set=variant5-variant6-variant7-variant8-variant11-variant16-variant17-variant19-variant20-variant21-variant24-variant26-variant29-variant32-variant35-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:39,35:74:99:920,0,995:21,18,19,16 chr2 128409905 . A G 1319.31 PASS AC=1;AF=0.648;AN=2;DP=2569;MQ=60;set=variant-variant3-variant4-variant9-variant10-variant12-variant13-variant14-variant16-variant18-variant19-variant21-variant22-variant23-variant26-variant27-variant28-variant31-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,41:102:99:915,0,1490:27,34,23,18 chr2 128410244 . C T 35.64 PASS AC=1;AF=0.563;AN=2;DP=259;FractionInformativeReads=1;MQ=60;set=variant5-variant6-variant7-variant8-variant11-variant16-variant17-variant19-variant20-variant21-variant24-variant26-variant29-variant32-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:4,10:14:99:312,0,132:0,4,2,8 chr2 128411934 . A G 630.86 PASS AC=1;AF=0.919;AN=2;DP=1701;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,18:65:99:403,0,1183:29,18,12,6 chr2 128411950 . A G 842.22 PASS AC=2;AF=0.93;AN=2;DP=2123;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:2358,237,0:0,0,48,31 chr2 128421763 . C T 90.48 PASS AC=1;AF=0.867;AN=2;DP=101;FS=0;FractionInformativeReads=1;MQ=60;set=variant5-variant6-variant7-variant8-variant11-variant16-variant19-variant20-variant21-variant26-variant29-variant32-variant35-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:4,2:6:69:69,0,81:2,2,2,0 chr2 128421829 . G A 314.98 PASS AC=1;AF=0.674;AN=2;DP=351;MQ=60;set=variant3-variant4-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant18-variant19-variant21-variant22-variant23-variant26-variant28-variant31-variant34-variant35-variant36-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,15:20:99:328,0,125:4,1,9,6 chr2 128431188 . A G 116.93 PASS AC=1;AF=0.648;AN=2;DP=768;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant16-variant17-variant19-variant20-variant21-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant35-variant36-variant37-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:14,12:26:99:306,0,416:10,4,7,5 chr2 128431397 . A G 492.97 PASS AC=1;AF=0.568;AN=2;DP=1972;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant16-variant17-variant19-variant20-variant21-variant24-variant26-variant28-variant29-variant32-variant35-variant37-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:55,47:102:99:1129,0,1398:29,26,25,22 chr2 128431494 . A G 524.16 PASS AC=1;AF=0.568;AN=2;DP=1423;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant16-variant17-variant19-variant20-variant21-variant24-variant26-variant28-variant29-variant32-variant35-variant37-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:36,37:73:99:950,0,1069:14,22,16,21 chr2 128431609 . T TG 217.2 PASS AC=1;AF=0.568;AN=2;DP=1405;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant16-variant17-variant19-variant20-variant21-variant24-variant26-variant28-variant29-variant32-variant35-variant37-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:43,37:80:99:1002,0,1226:22,21,17,20 chr2 128432534 . A G 1174.79 PASS AC=1;AF=0.579;AN=2;DP=1730;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant6-variant7-variant8-variant11-variant16-variant17-variant19-variant20-variant21-variant24-variant26-variant28-variant29-variant32-variant35-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:58,57:115:99:1243,0,1278:31,27,32,25 chr2 128439411 . A G 93.48 PASS AC=1;AF=0.679;AN=2;DP=119;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant8-variant16-variant17-variant19-variant24-variant26-variant28-variant29-variant32-variant35-variant37-variant42 GT:AD:DP:GQ:PL:SB 0/1:3,2:5:75:75,0,76:1,2,0,2 chr2 128458958 . A G 2117.38 PASS AC=1;AF=0.548;AN=2;DP=3513;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant11-variant16-variant17-variant19-variant20-variant21-variant24-variant26-variant28-variant29-variant32-variant35-variant37-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:73,90:163:99:2277,0,1791:35,38,43,47 chr2 128459039 . A G 4828.73 PASS AC=1;AF=0.667;AN=2;DP=3720;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant16-variant17-variant19-variant20-variant21-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:76,81:157:99:1903,0,1651:35,41,40,41 chr2 128459214 . C G 1486.57 PASS AC=1;AF=0.667;AN=2;DP=1239;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant16-variant17-variant19-variant20-variant21-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:28,29:57:99:711,0,784:14,14,16,13 chr2 128460956 . G A 1938.8 PASS AC=2;AF=0.989;AN=2;DP=2154;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:1812,179,0:0,0,26,34 chr2 128474754 . G A 1813.76 PASS AC=1;AF=0.5;AN=2;DP=140;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.171;QD=12.96;ReadPosRankSum=-0.417;SOR=0.692;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:67,73:140:99:1842,0,1633:33,34,37,36 chr2 128495645 . G A 2943.93 PASS AC=1;AF=0.742;AN=2;DP=6479;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant13-variant16-variant17-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:114,117:231:99:2766,0,2846:41,73,43,74 chr2 128520547 . G A 7248.15 PASS AC=1;AF=0.615;AN=2;DP=7421;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant11-variant16-variant17-variant19-variant20-variant21-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:161,126:287:99:2672,0,3950:83,78,70,56 chr2 128526579 . TTAAA TTAAATAAATAAA,T,TTAAATAAA,TTAAATAAATAAATAAA 1479.08 PASS AC=0,1,1,0;AF=0.122,0.256,0.476,0.024;AN=2;DP=5250;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:DP:GQ:SB 2/3:52:99:0,0,16,36 chr2 128528508 . C T 754.41 PASS AC=1;AF=0.5;AN=2;DP=631;MQ=60;set=variant-variant9-variant10-variant14-variant22-variant27-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:39,25:64:99:587,0,1061:20,19,11,14 chr2 128604232 . A T 488.99 PASS AC=1;AF=0.688;AN=2;DP=815;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant37-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,5:17:99:133,0,324:5,7,2,3 chr2 128605207 . TA T 596.38 PASS AC=1;AF=0.5;AN=2;DP=3189;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-filterInvariant23-variant24-variant25-variant26-variant27-filterInvariant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,26:66:99:258,0,667:20,20,17,9 chr2 128608271 . GAA GA,G 888.45 PASS AC=1,0;AF=0.764,0.014;AN=2;DP=824;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:DP:GQ:SB 0/1:23:99:1,6,5,11 chr2 128608290 . T C 842.46 PASS AC=1;AF=0.786;AN=2;DP=673;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,12:19:99:499,0,401:1,6,5,7 chr2 128608384 . G T 73.47 PASS AC=1;AF=0.727;AN=2;DP=150;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant11-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant26-variant28-variant29-variant30-variant32-variant35-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,5:9:99:117,0,110:1,3,3,2 chr2 128610719 . T C 839.97 PASS AC=1;AF=0.625;AN=2;DP=2656;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant26-variant28-variant29-variant30-variant32-variant35-variant37-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,41:105:99:1046,0,1740:32,32,19,22 chr2 128615330 . C G 1225.05 PASS AC=1;AF=0.682;AN=2;DP=1557;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,23:54:99:664,0,898:22,9,17,6 chr2 128615390 . G T 1862.23 PASS AC=1;AF=0.682;AN=2;DP=2848;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,47:106:99:1135,0,1462:36,23,30,17 chr2 128620363 . A AT 174.97 PASS AC=1;AF=0.615;AN=2;DP=649;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant14-variant15-variant16-variant17-variant19-variant21-variant24-variant26-variant28-variant29-variant30-variant32-variant35-variant37-variant39-variant40-variant42-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:8,5:13:99:101,0,321:2,6,1,4 chr2 128620372 . T C 772.07 PASS AC=1;AF=0.625;AN=2;DP=521;MQ=60;set=variant-variant3-variant10-variant12-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant32-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,8:13:99:237,0,186:1,4,2,6 chr2 128621094 . A G 679.24 PASS AC=1;AF=0.676;AN=2;DP=2060;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,30:51:99:835,0,474:9,12,9,21 chr2 128622491 . G A 1078.15 PASS AC=1;AF=0.676;AN=2;DP=1887;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,30:49:99:848,0,547:9,10,15,15 chr2 128629065 . G A 456.24 PASS AC=1;AF=0.5;AN=2;DP=50;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.123;QD=9.12;ReadPosRankSum=2.58;SOR=0.85;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:33,17:50:99:484,0,826:15,18,7,10 chr2 128642367 . C G 265.64 PASS AC=1;AF=0.707;AN=2;DP=949;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,10:31:99:232,0,485:9,12,4,6 chr2 128699750 . G C 518.7 PASS AC=1;AF=0.625;AN=2;DP=1104;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant15-variant16-variant17-variant19-variant24-variant25-variant26-variant29-variant32-variant33-variant35-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:24,30:54:99:770,0,681:9,15,12,18 chr2 128699833 . C T 1431.88 PASS AC=1;AF=0.65;AN=2;DP=960;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant10-variant12-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant32-variant34-variant35-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,21:42:99:640,0,702:9,12,10,11 chr2 128708063 . T C 1578.42 PASS AC=2;AF=0.989;AN=2;DP=3197;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,91:91:99:2661,273,0:0,0,43,48 chr2 128744580 . A G 1010.24 PASS AC=2;AF=0.93;AN=2;DP=2974;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,78:78:99:2279,233,0:0,0,38,40 chr2 128753854 . T C 1070.58 PASS AC=2;AF=0.989;AN=2;DP=3077;MQ=60;MQRankSum=-1.667;ReadPosRankSum=-2.723;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,85:85:99:2617,255,0:0,0,54,31 chr2 128757804 . C T 2393.89 PASS AC=2;AF=0.829;AN=2;DP=2512;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,64:64:99:2110,192,0:0,0,32,32 chr2 128848683 . G T 211.88 PASS AC=2;AF=0.989;AN=2;DP=704;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:457,39,0:0,0,11,2 chr2 128849114 . T C 2024.75 PASS AC=2;AF=0.989;AN=2;DP=4229;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,121:121:99:3675,361,0:0,0,49,72 chr2 128854948 . CA C,CAA 56.47 PASS AC=1,0;AF=0.375,0.125;AN=2;DP=110;MQ=60;set=variant13-filterInvariant29-filterInvariant35-variant39 GT:DP:GQ:SB 0/1:26:77:16,4,5,1 chr2 128860835 . A G 1428.81 PASS AC=2;AF=1;AN=2;DP=1834;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.075;ReadPosRankSum=1.657;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:2125,165,0:0,0,8,47 chr2 128870808 . T C 1467.55 PASS AC=2;AF=0.989;AN=2;DP=1873;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.739;ReadPosRankSum=-0.512;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1318,132,0:0,0,16,28 chr2 128872595 . C T 512.42 PASS AC=1;AF=0.593;AN=2;DP=831;MQ=60;set=variant-variant3-variant5-variant8-variant10-variant11-variant14-variant15-variant16-variant17-variant19-variant22-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,15:41:99:382,0,651:16,10,11,4 chr2 128874061 . G A 765.23 PASS AC=2;AF=0.989;AN=2;DP=1182;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:854,78,0:0,0,6,20 chr2 128877837 . G C 335.14 PASS AC=2;AF=0.989;AN=2;DP=429;FS=0;MQ=60;MQRankSum=1.683;ReadPosRankSum=-0.573;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:308,24,0:0,0,7,1 chr2 128878014 . G A 2138.88 PASS AC=2;AF=0.989;AN=2;DP=3644;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,102:102:99:3078,305,0:0,0,55,47 chr2 128878667 . T C 879.88 PASS AC=2;AF=0.989;AN=2;DP=671;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:454,39,0:0,0,10,3 chr2 128878979 . C CT,CTT,CTTT 213.99 PASS AC=1,0,0;AF=0.318,0.242,0.045;AN=2;DP=957;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant29-variant31-variant32-variant33-variant35-filterInvariant36-variant37-filterInvariant40-variant41-variant42-variant44 GT:DP:GQ:SB 0/1:17:15:1,3,4,9 chr2 128879022 . G C 328.54 PASS AC=2;AF=1;AN=2;DP=339;FS=0;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:360,24,0:0,0,0,8 chr2 128880899 . T A 1307.4 PASS AC=2;AF=0.989;AN=2;DP=1906;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1283,117,0:0,0,13,26 chr2 128880993 . A G 106.77 PASS AC=2;AF=1;AN=2;DP=280;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:222,15,0:0,0,0,5 chr2 128890878 . T TG 2426.19 PASS AC=1;AF=0.705;AN=2;DP=5407;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:72,79:151:99:2452,0,2229:30,42,34,45 chr2 128913757 . G A 221.58 PASS AC=1;AF=0.597;AN=2;DP=1104;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,15:26:99:409,0,300:8,3,11,4 chr2 128934400 . T C 1550.41 PASS AC=1;AF=0.595;AN=2;DP=4423;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,50:103:99:1173,0,1280:27,26,26,24 chr2 128936000 . T C 888.86 PASS AC=1;AF=0.589;AN=2;DP=1390;MQ=60;set=variant-variant3-variant5-variant8-variant10-variant11-variant14-variant15-variant16-variant17-variant19-variant22-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,30:64:99:735,0,885:18,16,15,15 chr2 128936171 . TATG T 1042.5 PASS AC=1;AF=0.596;AN=2;DP=578;MQ=60;set=variant3-variant5-variant8-variant10-variant11-variant14-variant15-variant16-variant17-variant19-variant22-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,7:19:99:258,0,567:3,9,2,5 chr2 128939598 . G A 1237.18 PASS AC=1;AF=0.593;AN=2;DP=1277;MQ=60;set=variant-variant3-variant5-variant8-variant10-variant11-variant14-variant15-variant16-variant17-variant19-variant22-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,28:51:99:887,0,548:15,8,22,6 chr2 128939695 . A G 1968.98 PASS AC=1;AF=0.548;AN=2;DP=2333;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant8-variant10-variant11-variant14-variant15-variant16-variant19-variant22-variant24-variant27-variant29-variant32-variant33-variant35-variant37-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:50,82:132:99:2123,0,1354:32,18,51,31 chr2 128939817 . G A 2083.48 PASS AC=1;AF=0.589;AN=2;DP=4633;MQ=60;set=variant-variant3-variant5-variant8-variant10-variant11-variant14-variant15-variant16-variant17-variant19-variant22-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:107,82:189:99:1934,0,2608:53,54,32,50 chr2 128941511 . TGAGAGAGA TGTGTGTGTGTGTGAGAGAGAGA,TGTGTGTGTGTGAGAGAGAGAGA,TGTGTGTGTGAGAGAGAGA,T,TGAGAGAGAGA,TGTGTGTGTGTGTGTGAGAGAGAGA 32.57 PASS AC=1,0,0,0,0,0;AF=0.167,0.056,0.111,0.056,0.056,0.056;AN=2;DP=132;set=variant8-variant10-variant15-variant20-variant22-variant24-variant35-variant37-variant43 GT:DP:GQ:SB 0/1:15:99:0,6,1,8 chr2 128944424 . T C 582.76 PASS AC=1;AF=0.597;AN=2;DP=2434;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,22:59:99:488,0,1024:9,28,8,14 chr2 128947505 . G A 873.39 PASS AC=1;AF=0.589;AN=2;DP=2262;set=variant-variant3-variant5-variant8-variant10-variant11-variant14-variant15-variant16-variant17-variant19-variant22-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,50:98:99:1269,0,1213:29,19,24,26 chr2 128947895 . T C 865.43 PASS AC=1;AF=0.589;AN=2;DP=2029;MQ=60;set=variant-variant3-variant5-variant8-variant10-variant11-variant14-variant15-variant16-variant17-variant19-variant22-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,38:67:99:1210,0,922:11,18,14,24 chr2 128948226 . C T 971.17 PASS AC=1;AF=0.5;AN=2;DP=702;FractionInformativeReads=1;MQ=60;set=variant14-variant16-variant22-variant27-variant33-variant35-variant43 GT:AD:DP:GQ:PL:SB 0/1:64,55:119:99:1354,0,1623:26,38,26,29 chr2 128949079 . C CT 166.47 PASS AC=1;AF=0.589;AN=2;DP=1040;MQ=60;set=variant-variant3-variant5-variant8-variant10-variant11-variant14-variant15-variant16-variant17-variant19-variant22-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,19:41:99:510,0,608:6,16,3,16 chr2 128949840 . GTT GT,G 214.57 PASS AC=1,0;AF=0.5,0.023;AN=2;DP=6387;set=filterInvariant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-filterInvariant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:142:99:48,40,28,26 chr2 128949893 . A G 2561.91 PASS AC=1;AF=0.589;AN=2;DP=4276;MQ=60;set=variant-variant3-variant5-variant8-variant10-variant11-variant14-variant15-variant16-variant17-variant19-variant22-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:85,87:172:99:2383,0,2221:45,40,42,45 chr2 130681407 . G C 331.77 PASS AC=1;AF=0.756;AN=2;DP=971;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,13:32:99:367,0,592:6,13,1,12 chr2 130681447 . G A 151.77 PASS AC=1;AF=0.763;AN=2;DP=488;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,3:11:89:89,0,275:2,6,0,3 chr2 130737541 . C T 181.69 PASS AC=1;AF=0.697;AN=2;DP=1077;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,16:37:99:525,0,666:12,9,10,6 chr2 130737578 . G A 205.39 PASS AC=1;AF=0.513;AN=2;DP=1964;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,19:65:99:388,0,1157:31,15,12,7 chr2 130738163 . G A 2318.4 PASS AC=1;AF=0.697;AN=2;DP=7358;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:89,81:170:99:1800,0,2184:34,55,32,49 chr2 130750446 . C A 267.2 PASS AC=1;AF=0.5;AN=2;DP=2319;FractionInformativeReads=1;set=variant-variant2-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant8-variant9-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant13-filterInvariant14-variant15-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant19-variant20-variant21-filterInvariant22-variant24-variant25-variant26-filterInvariant27-variant28-variant29-filterInvariant30-variant31-variant32-variant33-filterInvariant34-filterInvariant35-variant36-variant37-variant38-variant39-variant40-filterInvariant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,17:60:99:281,0,1029:17,26,6,11 chr2 130807680 . A G 100.44 PASS AC=1;AF=0.958;AN=2;DP=80;FractionInformativeReads=1;MQRankSum=-3.595;ReadPosRankSum=1.241;set=filterInvariant2-filterInvariant3-variant4-filterInvariant19-variant21-filterInvariant25-variant32-filterInvariant33-variant35-filterInvariant39-filterInvariant41-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:19,6:25:85:85,0,431:9,10,2,4 chr2 130832185 . G A 215.45 DRAGENHardSNP AC=2;AF=0.989;AN=2;DP=2109;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:1623,185,0:0,0,39,23 chr2 130832292 . T A 378.42 PASS AC=1;AF=0.659;AN=2;DP=3655;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant13-filterInvariant14-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-filterInvariant34-filterInvariant35-filterInvariant36-filterInvariant37-filterInvariant38-filterInvariant39-filterInvariant40-filterInvariant41-variant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:34,92:126:99:1947,0,598:24,10,40,52 chr2 130832444 . C A 214.89 PASS AC=1;AF=0.689;AN=2;DP=4238;set=variant-variant2-variant3-variant4-filterInvariant6-filterInvariant7-filterInvariant8-variant10-variant11-variant12-variant13-variant14-filterInvariant16-variant17-filterInvariant18-filterInvariant19-filterInvariant20-variant21-filterInvariant23-variant24-variant25-variant26-variant28-variant29-filterInvariant30-variant31-variant32-variant33-filterInvariant35-filterInvariant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:133,22:155:99:315,0,3723:82,51,22,0 chr2 130832531 . A G 2050.54 PASS AC=1;AF=0.654;AN=2;DP=13535;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:269,162:431:99:3496,0,6714:141,128,103,59 chr2 130833159 . G A 295.71 PASS AC=1;AF=0.571;AN=2;DP=811;set=variant-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-filterInvariant14-filterInvariant15-variant16-filterInvariant20-variant22-variant24-filterInvariant26-variant27-variant29-variant30-variant31-variant34-variant35-variant36-variant37-variant38-variant40-filterInvariant42-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:10,12:22:99:316,0,286:1,9,2,10 chr2 130872658 . A T 649.82 DRAGENHardSNP AC=1;AF=0.679;AN=2;DP=2663;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:31,43:74:99:909,0,626:20,11,28,15 chr2 130877752 . T C 301.8 PASS AC=1;AF=0.692;AN=2;DP=5699;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-filterInvariant10-variant11-variant12-variant13-variant14-variant16-filterInvariant17-filterInvariant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-filterInvariant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:142,40:182:99:671,0,3929:75,67,30,10 chr2 130897055 . G A 631.14 PASS AC=2;AF=0.731;AN=2;DP=3732;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,95:95:99:3264,285,0:0,0,70,25 chr2 130897218 . T C 4787.35 PASS AC=2;AF=0.618;AN=2;DP=4827;set=variant3-variant4-variant5-variant13-variant16-variant18-variant19-variant23-variant25-variant26-variant30-variant31-variant35-variant36-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,355:355:99:10640,1062,0:0,0,174,181 chr2 130899642 . C T 1310.39 PASS AC=1;AF=0.5;AN=2;DP=249;FractionInformativeReads=1;set=variant18-variant35 GT:AD:DP:GQ:PL:SB 0/1:59,57:116:99:1234,0,1395:41,18,34,23 chr2 130899804 . T C 581.68 PASS AC=2;AF=1;AN=2;DP=432;FS=0;FractionInformativeReads=1;set=variant3-variant4-variant7-variant8-variant10-variant11-variant14-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant26-variant28-variant31-variant32-variant33-variant34-variant35-filterInvariant36-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:702,60,0:0,0,0,20 chr2 130941065 . T C 1317.48 PASS AC=2;AF=0.909;AN=2;DP=3170;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,115:115:99:3598,345,0:0,0,74,41 chr2 130948314 . G GT,GTT 1011.49 PASS AC=1,0;AF=0.595,0.024;AN=2;DP=1389;set=variant4-variant5-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant22-filterInvariant24-variant25-variant26-variant30-variant31-variant35-variant36-variant39-variant40-variant41-variant44 GT:DP:GQ:SB 0/1:47:99:3,6,12,26 chr2 130949411 . G T 1363.59 PASS AC=2;AF=0.919;AN=2;DP=5221;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,124:124:99:4001,372,0:0,0,76,48 chr2 130951548 . G A 2349.83 PASS AC=2;AF=0.898;AN=2;DP=6778;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,162:163:99:5423,475,0:1,0,70,92 chr2 130951566 . G A 2468.97 PASS AC=1;AF=0.83;AN=2;DP=6538;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:92,62:154:99:1697,0,2744:38,54,28,34 chr2 130988166 . A G 691.88 PASS AC=1;AF=0.5;AN=2;DP=4342;set=variant-variant2-variant3-variant6-variant9-variant10-filterInvariant12-filterInvariant14-variant15-filterInvariant17-variant18-variant20-filterInvariant24-filterInvariant25-variant26-variant31-filterInvariant32-variant35-filterInvariant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:151,63:214:99:1178,0,4142:71,80,37,26 chr2 130988203 . C T 753.16 PASS AC=1;AF=0.5;AN=2;DP=4189;set=variant-variant2-variant3-variant6-variant9-variant10-variant12-variant14-variant15-variant17-variant18-variant20-variant24-variant25-variant26-variant31-variant32-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:133,93:226:99:1805,0,3688:62,71,47,46 chr2 130988216 . C G 876.86 PASS AC=1;AF=0.5;AN=2;DP=4133;set=variant-variant2-variant3-variant6-variant9-variant10-variant12-variant14-variant15-variant17-variant18-variant20-variant24-variant25-variant26-variant31-variant32-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:117,99:216:99:2001,0,3298:54,63,50,49 chr2 130988276 . C T 474.82 PASS AC=1;AF=0.5;AN=2;DP=3849;set=variant-variant2-variant3-variant6-variant9-variant10-variant12-variant14-variant15-variant17-variant18-variant20-variant24-variant25-variant26-variant31-variant32-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:114,64:178:99:1356,0,2993:58,56,28,36 chr2 130988410 . G A 1200.75 PASS AC=1;AF=0.5;AN=2;DP=5350;FractionInformativeReads=1;set=variant-variant2-variant3-variant6-variant9-variant10-variant12-variant14-variant15-variant17-variant18-variant20-variant24-variant25-variant26-variant31-variant32-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:215,125:340:99:2313,0,5500:128,87,71,54 chr2 130988421 . C T 1327.45 PASS AC=1;AF=0.5;AN=2;DP=5753;set=variant-variant2-variant3-variant6-variant9-variant10-variant12-variant14-variant15-variant17-variant18-variant20-variant24-variant25-variant26-variant31-variant32-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:231,147:378:99:2664,0,5841:134,97,81,66 chr2 131097247 . G A 3020.67 PASS AC=1;AF=0.542;AN=2;DP=1949;MQ=60;set=variant4-variant9-variant11-variant14-variant15-variant18-variant22-variant23-variant26-variant31-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:72,86:158:99:3355,0,4172:29,43,36,50 chr2 131097253 . G C 2935.67 PASS AC=1;AF=0.542;AN=2;DP=1887;FractionInformativeReads=1;MQ=60;set=variant4-variant9-variant11-variant14-variant15-variant18-variant22-variant23-variant26-variant31-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:67,84:151:99:3348,0,3982:25,42,34,50 chr2 131100496 . G A 2241.22 PASS AC=1;AF=0.542;AN=2;DP=2326;MQ=60;set=variant4-variant9-variant11-variant14-variant15-variant18-variant22-variant23-variant26-variant31-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:96,73:169:99:1564,0,2543:39,57,33,40 chr2 131100734 . G A 1897.16 PASS AC=1;AF=0.542;AN=2;DP=1751;MQ=60;set=variant4-variant9-variant11-variant14-variant15-variant18-variant22-variant23-variant26-variant31-variant35-variant40 GT:AD:DP:GQ:PL:SB 0/1:81,71:152:99:1912,0,2134:50,31,42,29 chr2 131103635 . C T 4126.37 PASS AC=1;AF=0.5;AN=2;DP=1781;MQ=60;set=variant5-variant13-variant19-variant35-variant36-variant41 GT:AD:DP:GQ:PL:SB 0/1:174,155:329:99:4027,0,4470:81,93,73,82 chr2 131221102 . T C 794.89 DRAGENHardSNP AC=2;AF=0.989;AN=2;DP=1983;FS=0;MQRankSum=-2.896;ReadPosRankSum=0.055;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1326,135,0:0,0,37,8 chr2 131221170 . C T 2296.48 DRAGENHardSNP AC=2;AF=0.895;AN=2;DP=7370;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,182:182:99:4670,543,0:0,0,107,75 chr2 131221445 . G A 33.29 DRAGENHardSNP AC=2;AF=0.988;AN=2;DP=218;FS=0;FractionInformativeReads=1;MQRankSum=-0.55;ReadPosRankSum=0.937;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:243,24,0:0,0,0,8 chr2 131245713 . C G 90.79 DRAGENHardSNP AC=2;AF=1;AN=2;DP=16;FS=0;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:61,6,0:0,0,0,2 chr2 131266530 . C A 2870.96 PASS AC=2;AF=0.875;AN=2;DP=11532;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:2,262:264:99:7637,759,0:1,1,149,113 chr2 131407692 . T C 158.89 PASS AC=1;AF=0.512;AN=2;DP=426;FractionInformativeReads=1;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,9:15:99:318,0,211:6,0,8,1 chr2 131407943 . T G 116.99 PASS AC=1;AF=0.5;AN=2;DP=1368;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant5-variant7-filterInvariant9-filterInvariant10-variant12-filterInvariant13-filterInvariant14-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant18-variant20-variant21-filterInvariant22-variant23-filterInvariant24-variant25-variant26-filterInvariant27-filterInvariant28-filterInvariant29-filterInvariant30-variant31-variant32-filterInvariant33-filterInvariant34-variant35-filterInvariant36-filterInvariant37-filterInvariant38-filterInvariant39-variant40-filterInvariant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:18,18:36:99:407,0,482:4,14,6,12 chr2 131414061 . A G 59.59 PASS AC=1;AF=0.513;AN=2;DP=719;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-filterInvariant29-variant30-variant31-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,9:22:99:313,0,477:12,1,9,0 chr2 131414073 . T A 142.1 PASS AC=1;AF=0.511;AN=2;DP=1012;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:14,12:26:99:442,0,512:13,1,12,0 chr2 131414176 . C T 1123.66 PASS AC=1;AF=0.511;AN=2;DP=5871;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-filterInvariant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:81,60:141:99:1157,0,2003:50,31,36,24 chr2 131487673 . A C 3726.13 PASS AC=2;AF=0.86;AN=2;DP=7169;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,173:173:99:5532,518,0:0,0,87,86 chr2 131520663 . T C 6108.01 PASS AC=2;AF=0.943;AN=2;DP=9706;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,241:241:99:7171,722,0:0,0,107,134 chr2 131524230 . T C 210.74 PASS AC=2;AF=0.907;AN=2;DP=477;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:440,33,0:0,0,8,3 chr2 131524745 . G A 538.2 PASS AC=1;AF=0.5;AN=2;DP=204;MQ=60;set=variant2-variant8-variant35-variant38 GT:AD:DP:GQ:PL:SB 0/1:38,24:62:99:653,0,1009:20,18,14,10 chr2 131672101 . T C 2093 PASS AC=1;AF=0.722;AN=2;DP=2619;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:36,34:70:99:763,0,967:17,19,16,18 chr2 131672271 . T C 1445.56 PASS AC=2;AF=1;AN=2;DP=3020;FS=0;MQ=60;MQRankSum=1.319;ReadPosRankSum=1.474;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,63:63:99:2019,189,0:0,0,36,27 chr2 131672950 . A G 1734.45 PASS AC=1;AF=0.686;AN=2;DP=4064;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:69,51:120:99:1355,0,1693:37,32,30,21 chr2 131673249 . A T 1190.69 PASS AC=1;AF=0.5;AN=2;DP=975;MQ=60;set=variant2-variant6-variant17-variant32-variant35-variant36 GT:AD:DP:GQ:PL:SB 0/1:84,74:158:99:2020,0,2096:33,51,27,47 chr2 131673316 . C T 2647.56 PASS AC=1;AF=0.714;AN=2;DP=4378;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:62,62:124:99:1441,0,1465:31,31,30,32 chr2 131673702 . G A 1448.07 PASS AC=1;AF=0.545;AN=2;DP=2616;MQ=60;set=variant2-variant4-variant6-variant12-variant16-variant17-variant18-variant19-variant20-variant24-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:88,61:149:99:1523,0,2382:40,48,24,37 chr2 131674285 . A G 1600.1 PASS AC=1;AF=0.686;AN=2;DP=2895;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant32-variant33-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,62:103:99:1547,0,963:21,20,29,33 chr2 131769237 . G A 1172.17 PASS AC=2;AF=0.846;AN=2;DP=2247;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1655,159,0:0,0,34,19 chr2 131798509 . A AC 31.66 PASS AC=1;AF=0.6;AN=2;DP=84;MQ=60;set=variant23-variant29-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:12,4:16:99:132,0,676:7,5,3,1 chr2 131798517 . C A 102.01 PASS AC=1;AF=0.5;AN=2;DP=93;FractionInformativeReads=1;MQ=60;set=variant23-variant29-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:13,5:18:99:163,0,695:7,6,4,1 chr2 131798737 . C G 1022.92 PASS AC=1;AF=0.6;AN=2;DP=516;MQ=60;set=variant23-variant29-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:59,62:121:99:1653,0,1620:31,28,40,22 chr2 131799563 . C T 916.39 PASS AC=1;AF=0.6;AN=2;DP=483;MQ=60;set=variant23-variant29-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:80,41:121:99:906,0,1903:36,44,15,26 chr2 131800943 . G C 484.1 PASS AC=1;AF=0.571;AN=2;DP=255;FractionInformativeReads=1;MQ=60;set=variant14-variant23-variant29-variant35-variant37-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:24,27:51:99:707,0,756:21,3,17,10 chr2 131802045 . C T 1464.8 PASS AC=1;AF=0.5;AN=2;DP=1213;MQ=60;set=variant14-variant23-variant29-variant35-variant37-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:115,93:208:99:2025,0,2760:52,63,39,54 chr2 131805984 . G T 916.48 PASS AC=1;AF=0.5;AN=2;DP=550;MQ=60;set=variant14-variant23-variant29-variant35-variant37-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:48,41:89:99:891,0,1307:20,28,15,26 chr2 131807460 . C T 4159.93 PASS AC=1;AF=0.5;AN=2;DP=344;FS=0.393;FractionInformativeReads=1;MQ=60;MQRankSum=1.144;QD=12.09;ReadPosRankSum=3.965;SOR=0.662;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:177,167:344:99:4188,0,4386:101,76,94,73 chr2 131809056 . GA G,GAA 205.56 PASS AC=1,0;AF=0.5,0.036;AN=2;DP=2792;set=filterInvariant2-filterInvariant5-filterInvariant10-filterInvariant12-variant14-filterInvariant19-variant21-variant23-variant29-variant35-variant37-variant38-variant40-variant41 GT:DP:GQ:SB 0/1:186:99:38,54,47,47 chr2 131809197 . C T 1797.59 PASS AC=1;AF=0.571;AN=2;DP=1464;MQ=60;set=variant14-variant23-variant29-variant35-variant37-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:108,138:246:99:3683,0,2542:63,45,78,60 chr2 131810267 . T G 118.94 PASS AC=1;AF=0.5;AN=2;DP=111;FractionInformativeReads=1;MQ=60;set=variant14-variant23-variant29-variant35-variant37-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:10,9:19:99:307,0,345:8,2,8,1 chr2 131812738 . C T 1028.88 PASS AC=1;AF=0.5;AN=2;DP=528;FractionInformativeReads=1;MQ=60;set=variant14-variant23-variant29-variant35-variant37-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:30,36:66:99:1032,0,911:22,8,28,8 chr2 131813442 . A G 201.22 PASS AC=2;AF=1;AN=2;DP=372;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:416,39,0:0,0,3,10 chr2 131829560 . A ACACC 950.33 PASS AC=1;AF=0.5;AN=2;DP=502;MQ=60;set=variant14-variant23-variant29-variant35-variant37-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:36,38:74:99:1480,0,1986:17,19,16,22 chr2 131865064 . A G 885.08 PASS AC=1;AF=0.5;AN=2;DP=669;MQ=60;set=variant14-variant23-variant29-variant35-variant37-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:65,41:106:99:991,0,1885:41,24,29,12 chr2 131888424 . C G 240.19 PASS AC=1;AF=0.571;AN=2;DP=81;FractionInformativeReads=1;MQ=60;set=variant23-variant29-variant34-variant35-variant37-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:7,7:14:99:270,0,208:0,7,0,7 chr2 131901988 . C A 1178.59 PASS AC=1;AF=0.5;AN=2;DP=189;FractionInformativeReads=1;MQ=60;set=variant35-variant42 GT:AD:DP:GQ:PL:SB 0/1:42,53:95:99:1207,0,1093:22,20,30,23 chr2 131906250 . C G 2676.61 PASS AC=1;AF=0.5;AN=2;DP=1508;set=variant14-variant23-variant29-variant34-variant35-variant37-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:99,113:212:99:3006,0,2562:56,43,63,50 chr2 131976272 . G C 1515.06 PASS AC=2;AF=0.953;AN=2;DP=4762;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,118:118:99:3751,354,0:0,0,67,51 chr2 131988269 . T C 138.58 PASS AC=2;AF=0.963;AN=2;DP=82;FS=0;FractionInformativeReads=1;MQRankSum=-1.231;set=variant3-filterInvariant4-variant5-variant7-variant8-variant9-variant13-variant15-variant16-variant18-variant19-filterInvariant21-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:70,6,0:0,0,2,0 chr2 132021463 . C G 4733.56 PASS AC=1;AF=0.5;AN=2;DP=419;FS=6.899;FractionInformativeReads=1;MQ=44.28;MQRankSum=1.572;QD=11.3;ReadPosRankSum=-1.269;SOR=0.955;set=variant35 GT:AD:DP:GQ:PL:SB 0/1:210,209:419:99:4762,0,4739:101,109,119,90 chr2 132021926 . C T 155.02 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=49;FS=1.806;FractionInformativeReads=1;MQ=27.5;MQRankSum=-3.29;QD=3.16;ReadPosRankSum=1.128;SOR=1.223;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:37,12:49:99:183,0,953:7,30,1,11 chr2 132021946 . G A 395.19 PASS AC=1;AF=0.5;AN=2;DP=1088;set=filterInvariant2-variant3-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant13-filterInvariant14-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-filterInvariant35-filterInvariant38-filterInvariant39-filterInvariant40-filterInvariant41-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:25,7:32:99:106,0,667:1,24,1,6 chr2 132044730 . G A 229.2 PASS AC=1;AF=0.5;AN=2;DP=580;set=variant2-variant4-variant6-variant8-variant9-variant10-variant11-variant14-variant15-variant17-variant19-variant20-variant22-variant25-variant26-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,3:15:60:60,0,397:11,1,2,1 chr2 132044746 . C A 276.63 PASS AC=1;AF=0.5;AN=2;DP=851;set=variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-filterInvariant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant25-variant28-variant30-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:17,10:27:99:198,0,521:15,2,4,6 chr2 132044787 . G A 49.44 PASS AC=1;AF=0.5;AN=2;DP=2049;set=filterInvariant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,10:55:99:284,0,1818:31,14,3,7 chr2 132044797 . C A 49.44 PASS AC=1;AF=0.5;AN=2;DP=2221;FractionInformativeReads=1;set=filterInvariant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,10:60:99:270,0,1911:31,19,3,7 chr2 132044849 . T A 382.67 PASS AC=1;AF=0.5;AN=2;DP=2181;set=variant2-variant4-variant6-filterInvariant7-variant8-variant9-variant11-variant12-variant13-variant16-variant17-variant18-variant19-variant20-filterInvariant21-variant22-variant23-filterInvariant24-variant25-variant26-filterInvariant27-variant28-filterInvariant29-filterInvariant30-variant33-filterInvariant35-variant36-variant38-variant39-variant40-variant41-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:68,10:78:78:78,0,1583:35,33,3,7 chr2 132044876 . T C 32.14 PASS AC=1;AF=0.5;AN=2;DP=2024;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant4-variant6-filterInvariant7-variant9-variant10-filterInvariant11-filterInvariant12-filterInvariant13-filterInvariant16-variant18-variant19-variant20-filterInvariant21-variant22-variant23-filterInvariant24-variant25-filterInvariant26-filterInvariant27-variant28-filterInvariant29-variant30-filterInvariant35-variant36-variant38-variant39-variant40-filterInvariant41-filterInvariant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:63,9:72:99:141,0,2667:29,34,2,7 chr2 132044881 . A G 46.26 PASS AC=1;AF=0.5;AN=2;DP=1844;set=filterInvariant2-filterInvariant3-filterInvariant4-variant6-filterInvariant7-filterInvariant9-variant10-filterInvariant12-filterInvariant13-filterInvariant16-variant18-variant19-variant20-filterInvariant21-variant22-variant23-filterInvariant24-variant25-filterInvariant26-filterInvariant27-variant28-filterInvariant29-variant30-filterInvariant35-variant36-variant38-variant39-variant40-filterInvariant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:67,7:74:92:92,0,2699:31,36,1,6 chr2 132044992 . T C 203.04 PASS AC=2;AF=1;AN=2;DP=527;FS=0;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-filterInvariant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-filterInvariant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-filterInvariant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:509,51,0:0,0,5,12 chr2 132110463 . G C 1093.01 PASS AC=2;AF=0.953;AN=2;DP=1849;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:1966,171,0:0,0,29,28 chr2 132110828 . G T 61.02 PASS AC=2;AF=0.932;AN=2;DP=159;FS=0;FractionInformativeReads=1;set=filterInvariant3-variant4-variant5-variant7-variant8-variant10-filterInvariant11-variant12-variant13-variant16-variant19-variant24-filterInvariant25-variant26-variant28-variant33-variant34-variant35-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:111,9,0:0,0,0,3 chr2 132111121 . G A 973.5 PASS AC=2;AF=0.942;AN=2;DP=1401;set=variant-variant2-variant3-filterInvariant4-variant5-filterInvariant6-variant7-variant8-variant9-filterInvariant10-variant11-variant12-variant13-variant14-variant15-filterInvariant16-filterInvariant17-variant18-filterInvariant19-variant20-variant21-variant22-variant24-variant25-variant26-filterInvariant27-variant28-variant29-filterInvariant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:935,63,0:0,0,8,13 chr2 132111123 . T C 973.5 PASS AC=2;AF=0.942;AN=2;DP=1362;FractionInformativeReads=1;set=variant-variant2-variant3-filterInvariant4-variant5-filterInvariant6-variant7-variant8-variant9-filterInvariant10-variant11-variant12-variant13-variant14-variant15-filterInvariant16-filterInvariant17-variant18-filterInvariant19-variant20-variant21-variant22-variant24-variant25-variant26-filterInvariant27-variant28-variant29-filterInvariant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:63:935,63,0:0,0,8,12 chr2 132111127 . G T 889.52 PASS AC=2;AF=0.942;AN=2;DP=1318;FractionInformativeReads=1;set=variant-variant2-variant3-filterInvariant4-variant5-filterInvariant6-variant7-variant8-variant9-filterInvariant10-variant11-variant12-variant13-variant14-variant15-filterInvariant16-filterInvariant17-variant18-filterInvariant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-filterInvariant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:900,60,0:0,0,8,12 chr2 132111166 . G GCC 907.08 PASS AC=2;AF=0.942;AN=2;DP=1389;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1635,120,0:0,0,19,19 chr2 132111167 . G GCCGCCGCCGC,GCCGCCGCCGCCGC,GCCGCCGC,GCCGCCACCGC 907.21 PASS AC=2,0,0,0;AF=0.884,0.012,0.023,0.023;AN=2;DP=1352;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:37:99:0,0,18,19 chr2 132120501 . C CT 1308.74 PASS AC=2;AF=0.895;AN=2;DP=2369;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,52:52:99:1618,159,0:0,0,45,7 chr2 132121350 . G C 309.42 PASS AC=2;AF=0.857;AN=2;DP=1136;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant24-variant25-variant26-variant27-variant28-variant29-variant30-filterInvariant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:969,99,0:0,0,16,17 chr2 132200096 . A G 306.23 PASS AC=2;AF=0.632;AN=2;DP=294;FractionInformativeReads=1;set=variant-variant2-variant3-variant6-variant9-variant10-variant12-variant15-variant17-variant18-variant20-variant24-variant25-variant26-variant31-variant32-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:595,45,0:0,0,10,5 chr2 132200114 . T C 512.99 PASS AC=2;AF=0.625;AN=2;DP=404;set=variant-variant2-variant3-variant6-variant9-variant10-variant12-variant14-variant15-variant17-variant18-variant20-variant24-variant25-variant26-variant31-variant32-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:849,69,0:0,0,17,6 chr2 132200136 . C A 596.53 PASS AC=2;AF=0.625;AN=2;DP=563;set=variant-variant2-variant3-variant6-variant9-variant10-variant12-variant14-variant15-variant17-variant18-variant20-variant24-variant25-variant26-variant31-variant32-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1167,102,0:0,0,26,8 chr2 132200256 . T C 3041.08 PASS AC=2;AF=0.625;AN=2;DP=2780;set=variant-variant2-variant3-variant6-variant9-variant10-variant12-variant14-variant15-variant17-variant18-variant20-variant24-variant25-variant26-variant31-variant32-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,185:185:99:5560,555,0:0,0,104,81 chr2 132200307 . G A 4344.5 PASS AC=2;AF=0.625;AN=2;DP=4211;set=variant-variant2-variant3-variant6-variant9-variant10-variant12-variant14-variant15-variant17-variant18-variant20-variant24-variant25-variant26-variant31-variant32-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 1/1:1,268:269:99:7724,778,0:1,0,138,130 chr2 132200345 . C T 2051.15 PASS AC=1;AF=0.583;AN=2;DP=4126;set=variant-variant2-variant3-variant6-variant9-variant12-variant14-variant15-variant17-variant18-variant20-variant24-variant25-variant26-variant31-variant32-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:124,139:263:99:3313,0,2981:63,61,63,76 chr2 132200529 . A G 3979.86 PASS AC=2;AF=0.625;AN=2;DP=3834;set=variant-variant2-variant3-variant6-variant9-variant10-variant12-variant14-variant15-variant17-variant18-variant20-variant24-variant25-variant26-variant31-variant32-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,169:169:99:5472,506,0:0,0,96,73 chr2 132200935 . C T 1271.28 PASS AC=2;AF=0.632;AN=2;DP=2602;set=variant-filterInvariant2-filterInvariant3-variant6-variant9-variant10-filterInvariant12-filterInvariant14-variant15-variant17-variant18-variant20-filterInvariant24-filterInvariant25-filterInvariant31-variant32-variant35-filterInvariant37-filterInvariant41 GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:2195,170,0:0,0,0,57 chr2 132200984 . G A 519.48 PASS AC=2;AF=0.679;AN=2;DP=1167;set=variant-filterInvariant3-variant6-filterInvariant9-variant15-filterInvariant17-variant18-variant24-variant25-filterInvariant31-filterInvariant32-variant35-filterInvariant37-filterInvariant41 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:1044,84,0:0,0,0,28 chr2 132200995 . C T 564.58 PASS AC=2;AF=0.615;AN=2;DP=987;FractionInformativeReads=1;set=variant-filterInvariant3-variant6-filterInvariant9-variant15-variant18-variant24-variant25-filterInvariant31-filterInvariant32-variant35-filterInvariant37-filterInvariant41 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:794,66,0:0,0,0,22 chr2 132201189 . G C 74.38 PASS AC=2;AF=1;AN=2;DP=6;FS=0;FractionInformativeReads=1;SOR=2.833;set=variant6-variant35 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:114,9,0:0,0,3,0 chr2 132201202 . G A 248.83 PASS AC=2;AF=0.875;AN=2;DP=17;FS=0;FractionInformativeReads=1;MQRankSum=-0.727;ReadPosRankSum=-0.727;set=variant6-variant15-variant18-variant35 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:169,12,0:0,0,4,0 chr2 132201288 . A G 1528.34 PASS AC=2;AF=0.625;AN=2;DP=2918;set=variant-variant2-variant3-variant6-variant9-variant10-variant12-variant14-variant15-variant17-variant18-variant20-variant24-variant25-variant26-variant31-variant32-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,96:96:99:3282,288,0:0,0,76,20 chr2 132201468 . G A 1608.52 PASS AC=1;AF=0.583;AN=2;DP=6066;set=variant-variant2-variant3-variant6-variant9-variant12-variant14-variant15-variant17-variant18-variant20-variant24-variant25-variant26-variant31-variant32-variant35-variant37 GT:AD:DP:GQ:PL:SB 0/1:174,206:380:99:5063,0,4075:83,91,100,106 chr2 132201582 . A G 3752.45 PASS AC=2;AF=0.625;AN=2;DP=5553;set=variant-variant2-variant3-variant6-variant9-variant10-variant12-variant14-variant15-variant17-variant18-variant20-variant24-variant25-variant26-variant31-variant32-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 1/1:1,347:348:99:10669,997,0:1,0,170,177 chr2 132201663 . T C 3945.33 PASS AC=2;AF=0.63;AN=2;DP=6896;set=variant-variant2-variant3-variant6-variant9-variant10-variant12-variant14-variant15-variant17-variant18-variant20-variant24-variant25-variant26-variant31-variant32-variant34-variant35-variant37-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,346:346:99:10657,1038,0:0,0,171,175 chr2 132201718 . T C 4168.14 PASS AC=2;AF=0.625;AN=2;DP=6007;set=variant-variant2-variant3-variant6-variant9-variant10-variant12-variant14-variant15-variant17-variant18-variant20-variant24-variant25-variant26-variant31-variant32-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 1/1:1,335:336:99:14746,996,0:0,1,168,167 chr2 132201736 . C G 3713.19 PASS AC=2;AF=0.625;AN=2;DP=5852;set=variant-variant2-variant3-variant6-variant9-variant10-variant12-variant14-variant15-variant17-variant18-variant20-variant24-variant25-variant26-variant31-variant32-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 1/1:1,329:330:99:14298,966,0:0,1,159,170 chr2 132201862 . C G 1220.38 PASS AC=2;AF=0.625;AN=2;DP=3480;set=variant-variant2-variant3-variant6-variant9-variant10-variant12-variant14-variant15-variant17-variant18-variant20-variant24-variant25-variant26-variant31-variant32-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,163:163:99:5340,489,0:0,0,59,104 chr2 132201889 . C A 1045.27 PASS AC=2;AF=0.625;AN=2;DP=2980;set=variant-variant2-variant3-variant6-variant9-variant10-variant12-variant14-variant15-variant17-variant18-variant20-variant24-variant25-variant26-variant31-variant32-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,142:142:99:4560,425,0:0,0,55,87 chr2 132201930 . T C 881.48 PASS AC=2;AF=0.625;AN=2;DP=2297;FractionInformativeReads=1;set=variant-variant2-variant3-variant6-variant9-variant10-variant12-variant14-variant15-variant17-variant18-variant20-variant24-variant25-variant26-variant31-variant32-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,116:116:99:3638,348,0:0,0,46,70 chr2 132202050 . T C 488.39 PASS AC=2;AF=0.625;AN=2;DP=964;set=variant-variant2-variant3-variant6-variant9-variant10-variant12-variant14-variant15-variant17-variant18-variant20-variant24-variant25-variant26-variant31-variant32-variant35-variant37-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1350,132,0:0,0,18,26 chr2 132229720 . T C,G 1160.4 PASS AC=2,0;AF=0.478,0.152;AN=2;DP=2030;set=variant-variant2-variant3-variant6-variant9-variant10-variant12-variant14-variant15-variant17-variant18-variant20-variant24-variant26-variant31-variant32-variant33-variant34-variant35-variant37-variant40-variant42-variant43 GT:DP:GQ:SB 1/1:73:99:0,1,16,56 chr2 132237983 . A G 1116.26 PASS AC=2;AF=0.735;AN=2;DP=1439;set=variant-variant2-variant3-variant6-variant9-variant12-variant14-variant15-variant17-variant18-variant20-variant24-variant25-variant26-filterInvariant31-variant32-va